diff --git a/build/icn3d.js b/build/icn3d.js
index fd2d382e..91f1142d 100644
--- a/build/icn3d.js
+++ b/build/icn3d.js
@@ -6863,7 +6863,7 @@ var icn3d = (function (exports) {
});
me.myEventCls.onIds("#" + me.pre + "mn1_dsn6", "click", function(e) { me.icn3d; //e.preventDefault();
- me.htmlCls.dialogCls.openDlg('dl_dsn6', 'Please input the DSN6 file to display electron density map');
+ me.htmlCls.dialogCls.openDlg('dl_dsn6', 'Please input the map file to display electron density map');
});
@@ -6890,7 +6890,7 @@ var icn3d = (function (exports) {
me.myEventCls.onIds("#" + me.pre + "mn1_dsn6url", "click", function(e) { me.icn3d; //e.preventDefault();
- me.htmlCls.dialogCls.openDlg('dl_dsn6url', 'Please input the DSN6 file to display electron density map');
+ me.htmlCls.dialogCls.openDlg('dl_dsn6url', 'Please input the map file to display electron density map');
});
me.myEventCls.onIds("#" + me.pre + "mn1_exportState", "click", function(e) { let ic = me.icn3d; //e.preventDefault();
@@ -9451,7 +9451,7 @@ var icn3d = (function (exports) {
html += this.getMenuSep();
- html += this.getMenuText('mn1_dsn6wrap', 'Electron Density(DSN6)', undefined, undefined, 2);
+ html += this.getMenuText('mn1_dsn6wrap', 'Electron Density', undefined, undefined, 2);
html += "Option 2 , search with PDB ID and chain name:Option 3 , search with a PDB file:Foldseek web server.AlphaFold Uniprot ID: "+e.htmlCls.inputTextStr+"id='"+e.pre+"afid' value='"+o+"' size=10>Orientations of Proteins in Membranes(OPM) PDB ID: "+e.htmlCls.inputTextStr+"id='"+e.pre+"opmid' value='6JXR' size=8> ",s+=e.htmlCls.buttonStr+"reload_opm'>Load",s+="",s+=e.htmlCls.divStr+"dl_pdbfile' class='"+n+"'>",s+=this.addNotebookTitle("dl_pdbfile","Please input a PDB file"),s+='Note: Several PDB files could be concatenated into a single PDB file. Use the line "ENDMDL" to separate PDB files.The custom JSON file on residue colors has the following format for proteins("ALA" and "ARG") and nucleotides("G" and "A"):
The custom file for the structure has two columns separated by space or tab: ',s+='residue number, and score in the range of 0-100. If you click "Apply Custom Color" button, ',s+='the scores 0, 50 and 100 correspond to the three colors specified below. If you click "Apply Custom Tube", ',s+='the selected residues will be displayed in a style similar to "B-factor Tube".
Score to Color: 0: ",s+=e.htmlCls.optionStr+"'red'>Red",s+=e.htmlCls.optionStr+"'green'>Green",s+=e.htmlCls.optionStr+"'blue' selected>Blue",s+=" ",s+="50 : ",s+=e.htmlCls.optionStr+"'white' selected>White",s+=e.htmlCls.optionStr+"'black'>Black",s+=" ",s+="100 : ",s+=e.htmlCls.optionStr+"'red' selected>Red",s+=e.htmlCls.optionStr+"'green'>Green",s+=e.htmlCls.optionStr+"'blue'>Blue",s+=" You can define your own reference numbers in a custom file using Excel, and then export it as a CSV file. An example file is shown below with cells separated by commas.
',s+="
refnum,11,12,,21,22,,10C,11C,20C ",s+="1TUP_C,,,,,,,200,201,230",s+='The first row defines the reference residue numbers, which could be any strings. The 1st cell could be anything. The rest cells are reference residue numbers (e.g., 11, 21, 10C, etc.) or empty cells. Each chain has a separate row. The first cell of the second row is the chain ID "1TUP_A". The rest cells are the corresponding real residue numbers for reference residue numbers in the first row. For example, the reference numbers for residues 100, 101, and 132 in the chain 1TUP_A are 11, 12, and 22, respectively. The fourth row shows another set of reference numners for the chain "1TUP_C". It could be a chain from a different structure.
',s+='To select all residues corresponding to the reference numbers, you can simplay replace ":" with "%" in the
Specification . For example, "%12" selects the residue 101 in 1TUP_A and the residue 111 in 1TUP_B. ".A%12" has the chain "A" filter and selects the residue 101 in 1TUP_A.
',s+="
VAST+ based on VAST : "+e.htmlCls.buttonStr+"reload_align_ori'>All Matching Molecules Superposed"+e.htmlCls.space3+e.htmlCls.buttonStr+"reload_align_refined'>Invariant Substructure SuperposedVAST+ based on TM-align : "+e.htmlCls.buttonStr+"reload_align_tmalign'>All Matching Molecules SuperposedAlphaFold Uniprot IDs: ",s+="All chains will be aligned to the first chain in the comma-separated chain IDs. Each chain ID has the form of PDBID_chain (e.g., 1HHO_A, case sensitive) or UniprotID (e.g., P69905 for AlphaFold structures).Chain IDs : "+e.htmlCls.inputTextStr+"id='"+e.pre+"chainalignids' value='P69905,P01942,1HHO_A' size=50>Align with TM-align "+e.htmlCls.buttonStr+"reload_chainalign_asym' style='margin-left:30px'>Align with VAST
",s+=e.htmlCls.divStr+"dl_chainalign2' class='"+n+"'>",s+=this.addNotebookTitle("dl_chainalign2","Align chains"),s+="",s+="All chains will be aligned to the first chain in the comma-separated chain IDs. Each chain ID has the form of PDBID_chain (e.g., 1HHO_A, case sensitive) or UniprotID (e.g., P69905 for AlphaFold structures).Chain IDs : "+e.htmlCls.inputTextStr+"id='"+e.pre+"chainalignids2' value='P69905,P01942,1HHO_A' size=50>Align by Sequence Alignment
",s+=e.htmlCls.divStr+"dl_chainalign3' class='"+n+"'>",s+=this.addNotebookTitle("dl_chainalign3","Align chains"),s+="",s+=this.getHtmlAlignResidueByResidue("chainalignids3","predefinedres","reload_chainalign_asym3"),s+="
",s+=e.htmlCls.divStr+"dl_realignresbyres' class='"+n+"'>",s+=this.addNotebookTitle("dl_realignresbyres","Realign residue by residue"),s+="",s+="
Option 1 : "+e.htmlCls.buttonStr+"realignSelection'>
Realign Current Selection Residue by Residue ",s+="
Option 2 :
",s+="
"+this.getHtmlAlignResidueByResidue("chainalignids4","predefinedres2","reload_chainalign_asym4")+"
",s+="
",s+='Please specify the mutations with a comma separated mutation list. Each mutation can be specified as "[
uppercase PDB ID or AlphaFold UniProt ID]_[Chain Name]_[Residue Number]_[One Letter Mutant Residue]". E.g., the mutation of N501Y in the E chain of PDB 6M0J can be specified as "6M0J_E_501_Y". For AlphaFold structures, the "Chain ID" is "A".
If you load a custom structure without PDB or UniProt ID, you can open "Seq. & Annotations" window and find the chain ID such as "stru_A". The part before the underscore is the structure ID, which can be used to specify the mutation such as "stru_A_...". Remember to choose "Show Mutation in: Current Page".
',s+="
Mutations:
"+e.htmlCls.inputTextStr+"id='"+e.pre+"mutationids' value='6M0J_E_484_K,6M0J_E_501_Y,6M0J_E_417_N' size=50>
",s+="
ID Type : ",s+='
PDB ID',s+='
AlphaFold UniProt ID
',s+="
Show Mutation in : ",s+='
Current Page',s+='
New Page
',s+=e.htmlCls.buttonStr+"reload_mutation_3d' title='Show the mutations in 3D using the scap program'>3D with scap",s+=e.htmlCls.buttonStr+"reload_mutation_inter' style='margin-left:20px' title='Show the mutations in 3D and the change of interactions'>Interactions",s+=e.htmlCls.buttonStr+"reload_mutation_pdb' style='margin-left:20px' title='Show the mutations in 3D and export the PDB of the mutant within 10 angstrom'>PDB",s+="
",s+=e.htmlCls.optionStr+"'pdb' selected>PDB",s+=e.htmlCls.optionStr+"'mmcif'>mmCIF",s+=e.htmlCls.optionStr+"'mol2'>Mol2",s+=e.htmlCls.optionStr+"'sdf'>SDF",s+=e.htmlCls.optionStr+"'xyz'>XYZ",s+=e.htmlCls.optionStr+"'icn3dpng'>iCn3D PNG",s+=e.htmlCls.optionStr+"'pae'>AlphaFold PAE",s+=" Note : The "biological unit " is the biochemically active form of a biomolecule ,
',s+=e.htmlCls.divStr+"asu_bu' style='display:none;'>",s+='which can range from a monomer (single protein molecule) to an oligomer of 100+ protein molecules.asymmetric unit " is the raw 3D structure data resolved by X-ray crystallography, NMR, or Cryo-electron microscopy. The asymmetric unit is equivalent to the biological unit in approximately 60% of structure records. In the remaining 40% of the records, the asymmetric unit represents a portion of the biological unit that can be reconstructed using crystallographic symmetry, or it represents multiple copies of the biological unit.',s+="",s+=e.htmlCls.divStr+"dl_mmdbafid' class='"+n+"' style='max-width:600px'>",s+=this.addNotebookTitle("dl_mmdbafid","Please input a list of PDB/AlphaFold IDs"),s+="List of PDB, MMDB, or AlphaFold UniProt structures: "+e.htmlCls.inputTextStr+"id='"+e.pre+"mmdbafid' placeholder='e.g., 1HHO,4N7N,P69905,P01942' size=30>
"+e.htmlCls.buttonStr+"reload_mmdbaf' style='width:150px'>Load Biological Unit"+e.htmlCls.buttonStr+"reload_mmdbaf_asym' style='margin-left:30px; width:250px'>Load Asymmetric Unit (All Chains)or
"+e.htmlCls.buttonStr+"reload_mmdbaf_append' style='width:150px'>Append Biological Unit"+e.htmlCls.buttonStr+"reload_mmdbaf_asym_append' style='margin-left:30px; width:250px'>Append Asymmetric Unit (All Chains)Note : The "biological unit " is the biochemically active form of a biomolecule ,
',s+=e.htmlCls.divStr+"asu_bu2' style='display:none;'>",s+='which can range from a monomer (single protein molecule) to an oligomer of 100+ protein molecules.asymmetric unit " is the raw 3D structure data resolved by X-ray crystallography, NMR, or Cryo-electron microscopy. The asymmetric unit is equivalent to the biological unit in approximately 60% of structure records. In the remaining 40% of the records, the asymmetric unit represents a portion of the biological unit that can be reconstructed using crystallographic symmetry, or it represents multiple copies of the biological unit.',s+="",s+=e.htmlCls.divStr+"dl_blast_rep_id' style='max-width:600px;' class='"+n+"'>",s+=this.addNotebookTitle("dl_blast_rep_id","Align sequence to structure"),s+="Enter a Sequence ID (or FASTA sequence) and the aligned protein accession, which can be found using the BLAST search with the Sequence ID or FASTA sequence as input. If the protein accession is not a PDB chain, the corresponding AlphaFold UniProt structure is used.Sequence ID (NCBI protein accession of a sequence): "+e.htmlCls.inputTextStr+"id='"+e.pre+"query_id' value='NP_001108451.1' size=8>NCBI protein accession (or a chain of a PDB): "+e.htmlCls.inputTextStr+"id='"+e.pre+"blast_rep_id' value='1TSR_A' size=8>ESM Metagenomic Atlas . The sequence should be less than 400 characters. For any sequence longer than 400, please see the discussion here .Note : Always load a PDB file before loading DSN6 files. 2fofc contour at: ";let a=["0","0.5","1","1.5","2","3","4","5","6","7","8","9","10"];s+=e.htmlCls.setHtmlCls.getOptionHtml(a,3),s+=" σ fofc contour at: ",s+=e.htmlCls.setHtmlCls.getOptionHtml(a,5),s+=" σ Note : Always load a PDB file before loading DSN6 files. 2fofc contour at: ",s+=e.htmlCls.setHtmlCls.getOptionHtml(a,3),s+=" σ fofc contour at: ",s+=e.htmlCls.setHtmlCls.getOptionHtml(a,5),s+=" σ ",s+=" "+e.htmlCls.space3,s+=e.htmlCls.buttonStr+"applysymmetry'>Apply"+e.htmlCls.space3,s+=e.htmlCls.buttonStr+"clearsymmetry'>Clear",s+="",s+=e.htmlCls.divStr+"dl_symd' style='max-width:400px' class='"+n+"'>Distance: ",s+=e.htmlCls.setHtmlCls.getOptionHtml(["4","5","6","7","8","9","10"],4),s+=" ",s+="Contact Type: ",s+=e.htmlCls.optionStr+"'calpha' >between C-alpha Atoms",s+=e.htmlCls.optionStr+"'cbeta' selected>between C-beta Atoms",s+=e.htmlCls.optionStr+"'heavyatoms' >between Heavy Atoms",s+=" "+e.htmlCls.buttonStr+"applycontactmap'>Display ",s+=""+e.htmlCls.inputCheckStr+"id='"+e.pre+"analysis_hbond' checked>Hydrogen Bonds "+e.htmlCls.space3+" ",s+="",s+=e.htmlCls.divNowrapStr+" ";let d=["3.2","3.3","3.4","3.5","3.6","3.7","3.8","3.9","4.0","4.1","4.2"];s+=e.htmlCls.setHtmlCls.getOptionHtml(d,6),s+=" Å"+e.htmlCls.space3+" ",s+=""+e.htmlCls.inputCheckStr+"id='"+e.pre+"analysis_saltbridge' checked>Salt Bridge/Ionic "+e.htmlCls.space3+" ",s+="",s+=e.htmlCls.divNowrapStr+" ";let c=["3","4","5","6","7","8"];s+=e.htmlCls.setHtmlCls.getOptionHtml(c,3),s+=" Å"+e.htmlCls.space3+" ",s+=""+e.htmlCls.inputCheckStr+"id='"+e.pre+"analysis_contact' checked>Contacts/Interactions "+e.htmlCls.space3+" ",s+="",s+=e.htmlCls.divNowrapStr+" ",s+=e.htmlCls.setHtmlCls.getOptionHtml(c,1),s+=" Å"+e.htmlCls.space3+" ",s+=" ",s+="",s+=""+e.htmlCls.inputCheckStr+"id='"+e.pre+"analysis_halogen' checked>Halogen Bonds "+e.htmlCls.space3+" ",s+="",s+=e.htmlCls.divNowrapStr+" ",s+=e.htmlCls.setHtmlCls.getOptionHtml(d,6),s+=" Å"+e.htmlCls.space3+" ",s+=""+e.htmlCls.inputCheckStr+"id='"+e.pre+"analysis_pication' checked>π-Cation "+e.htmlCls.space3+" ",s+="",s+=e.htmlCls.divNowrapStr+" ",s+=e.htmlCls.setHtmlCls.getOptionHtml(c,3),s+=" Å"+e.htmlCls.space3+" ",s+=""+e.htmlCls.inputCheckStr+"id='"+e.pre+"analysis_pistacking' checked>π-Stacking "+e.htmlCls.space3+" ",s+="",s+=e.htmlCls.divNowrapStr+" ",s+=e.htmlCls.setHtmlCls.getOptionHtml(["3","4","5"],99),s+=e.htmlCls.optionStr+"'5.5' selected>5.5",s+=e.htmlCls.setHtmlCls.getOptionHtml(["6","7","8"],99),s+=" Å"+e.htmlCls.space3+" ",s+="
",s+=e.htmlCls.divNowrapStr+"2. Select the first set:",s+="",s+="
",s+=" ",s+=e.htmlCls.divNowrapStr+"3. Select the second set:",s+="",s+="
",s+="
",s+="4. "+e.htmlCls.buttonStr+"applyhbonds'>3D Display Interactions
"+e.htmlCls.buttonStr+"hbondWindow'>Highlight Interactions in TableSort Interactions on : "+e.htmlCls.buttonStr+"sortSet1'> Set 1"+e.htmlCls.buttonStr+"sortSet2' style='margin-left:12px'>Set 2
"+e.htmlCls.buttonStr+"hbondLineGraph'>2D Interaction Network "+e.htmlCls.buttonStr+"hbondLineGraph2' style='margin-left:12px'>2D Network with Reference Numbers to show two lines of residue nodes
"+e.htmlCls.buttonStr+"hbondScatterplot'>2D Interaction Map "+e.htmlCls.buttonStr+"hbondScatterplot2' style='margin-left:12px'>2D Map with Reference Numbers to show map
Helix or Sheet'+r+e.pre+'dist_ss" size="4" value="100"> ',s+="Coil or Nucleotide"+r+e.pre+'dist_coil" size="4" value="50"> ',s+="Disulfide Bonds"+r+e.pre+'dist_ssbond" size="4" value="50"> Hydrogen Bonds"+r+e.pre+'dist_hbond" size="4" value="50"> ',s+="Salt Bridge/Ionic"+r+e.pre+'dist_ionic" size="4" value="50"> ',s+="Contacts"+r+e.pre+'dist_inter" size="4" value="25"> Halogen Bonds"+r+e.pre+'dist_halogen" size="4" value="50"> ',s+="π-Cation"+r+e.pre+'dist_pication" size="4" value="50"> ',s+="π-Stacking"+r+e.pre+'dist_pistacking" size="4" value="50">
(Note: you can also adjust thresholds at #1 to add/remove interactions.)
"+e.htmlCls.buttonStr+"areaWindow'>Buried Surface Area
5. "+e.htmlCls.buttonStr+"hbondReset'>Reset and select new sets
",s+="",s+=e.htmlCls.divStr+"dl_realign' class='"+n+"'>",s+=this.addNotebookTitle("dl_realign","Realign by sequence"),s+=e.htmlCls.divNowrapStr+"1. Select sets below ",s+="
2. "+e.htmlCls.buttonStr+"applyRealign'>Realign by Sequence
1 . Select sets below or use your current selection.
",s+="
2 . "+e.htmlCls.buttonStr+"applyRealignByStruct_tmalign'>Realign with TM-align"+e.htmlCls.buttonStr+"applyRealignByStruct' style='margin-left:30px'>Realign with VAST
",s+="
3. "+e.htmlCls.buttonStr+"applyRealignByStruct_vastplus'>VAST+ Alignment based on TM-align
",s+="
",s+="2. "+e.htmlCls.buttonStr+"applyColorSpectrumAcrossSets'>Spectrum Color for Sets
",s+="
",s+="2. "+e.htmlCls.buttonStr+"applyColorSpectrumBySets'>Spectrum Color for Residues in Sets
",s+="
",s+="2. "+e.htmlCls.buttonStr+"applyColorRainbowAcrossSets'>Rainbow Color for Sets
",s+="
",s+="2. "+e.htmlCls.buttonStr+"applyColorRainbowBySets'>Rainbow Color for Residues in Sets
',s+=e.htmlCls.space2+"Hold Ctrl key to select multiple nodes/lines.",s+=e.htmlCls.divStr+"dl_linegraphcolor' style='display:block;'>",s+=e.htmlCls.setHtmlCls.setColorHints(),s+="Scale : ";let h=["0.1","0.2","0.4","0.6","0.8","1","2","4","6","8","10"];s+=e.htmlCls.setHtmlCls.getOptionHtml(h,5),s+="
',s+="",s+=e.htmlCls.divStr+"dl_scatterplot' style='background-color:white' class='"+n+"'>",s+=this.addNotebookTitle("dl_scatterplot","2D Interaction Map"),s+=e.htmlCls.divNowrapStr+"Hold Ctrl key to select multiple nodes."+e.htmlCls.space3,s+='
',s+=e.htmlCls.divStr+"dl_scatterplotcolor' style='display:none;'>",s+=e.htmlCls.setHtmlCls.setColorHints(),s+="",e.scatterplotid=e.pre+"scatterplot",s+=e.htmlCls.divNowrapStr+l+e.scatterplotid+'_svg">SVG'+e.htmlCls.space2,s+=l+e.scatterplotid+'_png">PNG'+e.htmlCls.space2,s+=l+e.scatterplotid+'_json">JSON'+e.htmlCls.space4,s+="Scale : ",s+=e.htmlCls.setHtmlCls.getOptionHtml(h,5),s+="
',s+="",s+=e.htmlCls.divStr+"dl_contactmap' style='background-color:white' class='"+n+"'>",s+=this.addNotebookTitle("dl_contactmap","Contact Map"),s+=e.htmlCls.divNowrapStr+"Hold Ctrl key to select multiple nodes."+e.htmlCls.space3+"",e.contactmapid=e.pre+"contactmap",s+=e.htmlCls.divNowrapStr+l+e.contactmapid+'_svg">SVG'+e.htmlCls.space2,s+=l+e.contactmapid+'_png">PNG'+e.htmlCls.space2,s+=l+e.contactmapid+'_json">JSON'+e.htmlCls.space4,s+="Scale : ";let p=["0.01","0.02","0.04","0.06","0.08","0.1","0.2","0.4","0.6","0.8","1"];s+=e.htmlCls.setHtmlCls.getOptionHtml(p,10),s+="
',s+="",s+=e.htmlCls.divStr+"dl_alignerrormap' style='background-color:white' class='"+n+"'>",s+=this.addNotebookTitle("dl_alignerrormap","PAE Map"),s+=e.htmlCls.divNowrapStr+"Hold Ctrl key to select multiple nodes."+e.htmlCls.space3+"",e.alignerrormapid=e.pre+"alignerrormap",s+=e.htmlCls.divNowrapStr+l+e.alignerrormapid+'_svg">SVG'+e.htmlCls.space2,s+=l+e.alignerrormapid+'_png">PNG (slow)'+e.htmlCls.space2,s+=l+e.alignerrormapid+'_json">JSON'+e.htmlCls.space4,s+='Scale : ',s+=e.htmlCls.setHtmlCls.getOptionHtml(p,2),s+="
",s+="
0 5 10 15 20 25 30 Expected position error (Angstroms)
',s+="",s+=e.htmlCls.divStr+"dl_elecmap2fofc' class='"+n+"'>",s+=this.addNotebookTitle("dl_elecmap2fofc","Electron Density 2F0-Fc Map"),s+="Contour at: ",s+=e.htmlCls.setHtmlCls.getOptionHtml(a,3),s+=" σ "+e.htmlCls.buttonStr+"applymap2fofc'>Display "+e.htmlCls.buttonStr+"elecmapNo2'>Remove Map ",s+="",s+=e.htmlCls.divStr+"dl_elecmapfofc' class='"+n+"'>",s+=this.addNotebookTitle("dl_elecmapfofc","Electron Density F0-Fc Map"),s+="Contour at: ",s+=e.htmlCls.setHtmlCls.getOptionHtml(a,5),s+=" σ "+e.htmlCls.buttonStr+"applymapfofc'>Display "+e.htmlCls.buttonStr+"elecmapNo3'>Remove Map ",s+="",s+=e.htmlCls.divStr+"dl_emmap' class='"+n+"'>",s+=this.addNotebookTitle("dl_emmap","EM Density Map"),s+="Contour at: ",s+=e.htmlCls.setHtmlCls.getOptionHtml(["0","10","20","30","40","50","60","70","80","90","100"],3),s+=" % of maximum EM values "+e.htmlCls.buttonStr+"applyemmap'>Display "+e.htmlCls.buttonStr+"emmapNo2'>Remove EM Map ",s+="",s+=e.htmlCls.divStr+"dl_aroundsphere' class='"+n+"'>",s+=this.addNotebookTitle("dl_aroundsphere","Select a sphere around a set of residues"),s+=e.htmlCls.divNowrapStr+"1. Select the first set:",s+="",s+="
",s+="
"+e.htmlCls.buttonStr+"sphereExport'>Save interacting/contacting residue pairs in a file
",s+="",s+=e.htmlCls.divStr+"dl_adjustmem' class='"+n+"'>",s+=this.addNotebookTitle("dl_adjustmem","Adjust membranes"),s+="Note : The membranes are parallel to the X-Y plane. The center of the membranes is at Z = 0. Note : The membranes are parallel to the X-Y plane. The center of the membranes is at Z = 0. ",s+=e.htmlCls.divNowrapStr+"First set:",s+="",s+="
",s+=" ",s+=e.htmlCls.divNowrapStr+"Second set:",s+="",s+="
",s+="
",s+=e.htmlCls.spanNowrapStr+"2. Color: "+e.htmlCls.inputTextStr+"id='"+e.pre+"distancecolor2' value='"+"#ffff00' size=4>",s+=e.htmlCls.divNowrapStr+"First set:",s+="",s+="
",s+=" ",s+=e.htmlCls.divNowrapStr+"Second set:",s+="",s+="
",s+="
",s+=e.htmlCls.divNowrapStr+"2. Line style: ",s+=e.htmlCls.setHtmlCls.getOptionHtml(["Solid","Dashed"],0),s+=" ",s+=e.htmlCls.setHtmlCls.getOptionHtml(["1.0","0.9","0.8","0.7","0.6","0.5","0.4","0.3","0.2","0.1"],7),s+=" ",s+="
",s+=e.htmlCls.setHtmlCls.getOptionHtml(["Sphere","Cube"],0),s+=" ",s+=e.htmlCls.setHtmlCls.getOptionHtml(["1.0","0.9","0.8","0.7","0.6","0.5","0.4","0.3","0.2","0.1"],7),s+=" ",s+=e.htmlCls.divNowrapStr+"First sets:",s+="",s+="
",s+=" ",s+=e.htmlCls.divNowrapStr+"Second sets:",s+="",s+="
",s+="
",s+=e.htmlCls.spanNowrapStr+"2. "+e.htmlCls.buttonStr+"applydisttable'>Distances in Table",s+="",s+=e.htmlCls.divStr+"dl_stabilizer_rm' class='"+n+"'>",s+=this.addNotebookTitle("dl_stabilizer_rm","Remove a stabilizer"),e.utilsCls.isMobile()?s+=e.htmlCls.spanNowrapStr+"1. Touch TWO atomsNote : The following parameters will be saved in cache. You just need to set them once. Note: The full protein sequences with gaps in MSA are listed one by one. The sequence of the structure is listed at the top. Each sequence has a title line starting with \">\".
Precalculated Multiple Sequence Alignment (MSA) :Position of the first residue in Sequences & Annotations window : "+e.htmlCls.inputTextStr+"id='"+e.pre+"fasta_startpos' value='1' size=2> ",s+=e.htmlCls.optionStr+"'identity' selected>Identity",s+=e.htmlCls.optionStr+"'conservation'>Conservation",s+=" Note: Show exons for all isoforms of the protein in the same gene as specified below.
NCBI Gene IDPosition of the first residue in Sequences & Annotations window : "+e.htmlCls.inputTextStr+"id='"+e.pre+"fasta_startpos2' value='1' size=2> Save Clear URLs Used in Browsers iCn3D GitHub )Commands Used in Jupyter Noteboook Show All Chains Zoom : mouse wheel; "+e.htmlCls.space3+" Move : left button; "+e.htmlCls.space3+" Select Multiple Nodes : Ctrl Key and drag an Area"+e.htmlCls.space3,s+='
',s+=e.htmlCls.divStr+"dl_svgcolor' style='display:none;'>",s+=e.htmlCls.divNowrapStr+'Click "View > H-Bonds & Interactions" to adjust parameters and relaunch the graph ',s+=e.htmlCls.divNowrapStr+'Green : H-Bonds; ',s+='Cyan : Salt Bridge/Ionic; ',s+='Grey : contacts; ',s+='Orange : disulfide bonds',s+=e.htmlCls.divNowrapStr+'Magenta : Halogen Bonds; ',s+='Red : π-Cation; ',s+='Blue : π-Stacking',s+="",s+=e.htmlCls.divNowrapStr+l+e.svgid+'_svg">SVG'+e.htmlCls.space2,s+=l+e.svgid+'_png">PNG'+e.htmlCls.space2,s+=l+e.svgid+'_json">JSON',s+=e.htmlCls.space3+"Force on Nodes : ",s+=e.htmlCls.optionStr+"'0'>No",s+=e.htmlCls.optionStr+"'1'>X-axis",s+=e.htmlCls.optionStr+"'2'>Y-axis",s+=e.htmlCls.optionStr+"'3'>Circle",s+=e.htmlCls.optionStr+"'4' selected>Random",s+="
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",s+="",s+='EDTSurf algorithm : Toal : "+e.htmlCls.inputTextStr+"id='"+e.pre+"areavalue' value='' size='10'> Å2
",s+="",s+=e.htmlCls.divStr+"dl_colorbyarea' class='"+n+"'>",s+=this.addNotebookTitle("dl_colorbyarea","Color by surface area"),s+="Color each residue based on the percentage of solvent accessilbe surface area. The color ranges from blue, to white, to red for a percentage of 0, 35(variable), and 100, respectively.
Middle Percentage(White) : "+e.htmlCls.inputTextStr+"id='"+e.pre+"midpercent' value='35' size='10'>% Color Select residue based on the percentage of solvent accessilbe surface area. The values are in the range of 0-100.
Min Percentage : "+e.htmlCls.inputTextStr+"id='"+e.pre+"minpercentout' value='0' size='10'>% Max Percentage : "+e.htmlCls.inputTextStr+"id='"+e.pre+"maxpercentout' value='100' size='10'>% Apply Select residue based on B-factor/pLDDT. The values are in the range of 0-100.
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'+C+" "+t+" "+t+" "}getMenuUrl(e,t,s,i,n){let l=this.icn3dui;return l.icn3d,l.htmlCls.allMenus[e]=s,n&&(l.htmlCls.allMenusSel[e]=n),i&&(l.htmlCls.simpleMenus[e]=1),""+s+" "+t+" "+t+" "}getRadio(e,t,s,i,n,l){let r=this.icn3dui;r.icn3d,r.htmlCls.allMenus[t]=s,l&&(r.htmlCls.allMenusSel[t]=l),n&&(r.htmlCls.simpleMenus[t]=1);let o=i?" checked":"";return""+r.htmlCls.inputRadioStr+"name='"+r.pre+e+"' class='"+r.pre+e+"' v='"+s+"'"+o+">"+s+" "+o.htmlCls.inputRadioStr+"name='"+o.pre+e+"'"+a+">"+o.htmlCls.space3+" "+s+" ",n+="Select: "+t.htmlCls.inputTextStr+"id='"+t.pre+"command"+s+"' placeholder='$[structures].[chains]:[residues]@[atoms]' size='60'> Name: "+t.htmlCls.inputTextStr+"id='"+t.pre+"command_name"+s+"' placeholder='my_selection' size='60'> "+t.htmlCls.space3+t.htmlCls.buttonStr+"command_apply"+s+"'>Save Selection to Defined Sets
",n+='Specification Tips:
Specification: In the selection "$1HHO,4N7N.A,B,C:5-10,LV,3AlaVal,chemicals@CA,C,C*":',n+='"$1HHO,4N7N" uses "$" to indicate structure selection. ".A,B,C" uses "." to indicate chain selection. ":5-10,LV,3LeuVal,chemicals" uses the colon ":" to indicate residue selection. Residue selection could be residue number(5-10), one-letter IUPAC residue name abbreviations(LV), three-letter residue names(AlaVal, "3" indicates each residue name has three letters), or predefined names: "proteins", "nucleotides", "chemicals", "ions", and "water". IUPAC abbreviations can be written either as a contiguous string(e.g., ":LV"), in order to find all instances of that sequence in the structure, or they can be separated by commas(e.g., ":L,V") to select all residues of a given type in the structure(in the latter case, select all Leucine and Valine in the structure). "@CA,C,C*" uses "@" to indicate atom name selection. "C*" selects any atom names starting with "C". Partial definition is allowed, e.g., ":1-10" selects all residue IDs 1-10 in all chains. Different selections can be unioned(with "or ", default), intersected(with "and "), or negated(with "not "). For example, ":1-10 or :K" selects all residues 1-10 and all Lys residues. ":1-10 and :K" selects all Lys residues in the range of residue number 1-10. ":1-10 or not :K" selects all residues 1-10, which are not Lys residues. The wild card character "X" or "x" can be used to represent any character.',n+=" Set Operation: ",n+='Users can select multiple sets in the menu "Select > Defined Sets". Different sets can be unioned(with "or ", default), intersected(with "and "), or negated(with "not "). For example, if the "Defined Sets" menu has four sets ":1-10", ":11-20", ":5-15", and ":7-8", the command "saved atoms :1-10 or :11-20 and :5-15 not :7-8" unions all residues 1-10 and 11-20 to get the residues 1-20, then intersects with the residues 5-15 to get the residues 5-15, then exclude the residues 7-8 to get the final residues 5-6 and 9-15. Full commands in url or command window: ",n+="Select without saving the set: select $1HHO,4N7N.A,B,C:5-10,LV,chemicals@CA,C,C* Select and save: select $1HHO,4N7N.A,B,C:5-10,LV,chemicals@CA,C,C* | name my_name
",n+="",n}getOptionHtml(e,t){let s=this.icn3dui;s.icn3d;let i="";for(let n=0,l=e.length;n"+l+"":s.htmlCls.optionStr+"'"+l+"'>"+l+""}return i}setColorHints(){let e=this.icn3dui;e.icn3d;let t="";return t+=e.htmlCls.divNowrapStr+'Green : H-Bonds; ',t+='Cyan : Salt Bridge/Ionic; ',t+='Grey : contacts',t+=e.htmlCls.divNowrapStr+'Magenta : Halogen Bonds; ',t+='Red : π-Cation; ',t+='Blue : π-Stacking',t}setThicknessHtml(e){let t=this.icn3dui,s=t.icn3d,i="",n="3dprint"==e?"1":"0.1",l="3dprint"==e?"1.2":"0.3",r="3dprint"==e?"0.8":"0.4",o="3dprint"==e?"0.8":"0.4",a="3dprint"==e?"1":"0.4",d="3dprint"==e?"0.6":"0.3",c="3dprint"==e?"1":"0.2",h="3dprint"==e?"2":"1.3",p="3dprint"==e?"1.4":"0.8",m=40,u=.8,g=.4,f=.2,b=0,C=1,y=0;if("style"==e){if(""!=this.getCookie("shininess")&&(m=parseFloat(this.getCookie("shininess"))),""!=this.getCookie("light1")&&(u=parseFloat(this.getCookie("light1")),g=parseFloat(this.getCookie("light2")),f=parseFloat(this.getCookie("light3"))),""!=this.getCookie("lineRadius")){n=parseFloat(this.getCookie("lineRadius")),l=parseFloat(this.getCookie("coilWidth")),r=parseFloat(this.getCookie("cylinderRadius"));let e=this.getCookie("crosslinkRadius");o=isNaN(e)?s.crosslinkRadius:parseFloat(e),a=parseFloat(this.getCookie("traceRadius")),d=parseFloat(this.getCookie("dotSphereScale")),c=parseFloat(this.getCookie("ribbonthickness")),h=parseFloat(this.getCookie("helixSheetWidth")),p=parseFloat(this.getCookie("nucleicAcidWidth"))}""!=this.getCookie("glycan")&&(b=parseFloat(this.getCookie("glycan"))),""!=this.getCookie("membrane")&&(C=parseFloat(this.getCookie("membrane"))),""!=this.getCookie("cmdwindow")&&(y=parseFloat(this.getCookie("cmdwindow"))),i+="Note : The following parameters will be saved in cache. You just need to set them once. 1. Shininess : "+t.htmlCls.inputTextStr+"id='"+t.pre+"shininess' value='"+m+"' size=4>"+t.htmlCls.space3+"(for the shininess of the 3D objects, default 40)2. Three directional lights : Key Light : "+t.htmlCls.inputTextStr+"id='"+t.pre+"light1' value='"+u+"' size=4>"+t.htmlCls.space3+"(for the light strength of the key light, default 0.8)Fill Light : "+t.htmlCls.inputTextStr+"id='"+t.pre+"light2' value='"+g+"' size=4>"+t.htmlCls.space3+"(for the light strength of the fill light, default 0.4)Back Light : "+t.htmlCls.inputTextStr+"id='"+t.pre+"light3' value='"+f+"' size=4>"+t.htmlCls.space3+"(for the light strength of the back light, default 0.2)3. Thickness : Line Radius : "+t.htmlCls.inputTextStr+"id='"+t.pre+"linerad_"+e+"' value='"+n+"' size=4>"+t.htmlCls.space3+"(for stabilizers, hydrogen bonds, distance lines, default 0.1)Coil Radius : "+t.htmlCls.inputTextStr+"id='"+t.pre+"coilrad_"+e+"' value='"+l+"' size=4>"+t.htmlCls.space3+"(for coils, default 0.3)Stick Radius : "+t.htmlCls.inputTextStr+"id='"+t.pre+"stickrad_"+e+"' value='"+r+"' size=4>"+t.htmlCls.space3+"(for sticks, default 0.4)Cross-Linkage Radius : "+t.htmlCls.inputTextStr+"id='"+t.pre+"crosslinkrad_"+e+"' value='"+o+"' size=4>"+t.htmlCls.space3+"(for cross-linkages, default 0.4)Trace Radius : "+t.htmlCls.inputTextStr+"id='"+t.pre+"tracerad_"+e+"' value='"+a+"' size=4>"+t.htmlCls.space3+"(for C alpha trace, O3' trace, default 0.4)Ribbon Thickness : "+t.htmlCls.inputTextStr+"id='"+t.pre+"ribbonthick_"+e+"' value='"+c+"' size=4>"+t.htmlCls.space3+"(for helix and sheet ribbons, nucleotide ribbons, default 0.2)Protein Ribbon Width : "+t.htmlCls.inputTextStr+"id='"+t.pre+"prtribbonwidth_"+e+"' value='"+h+"' size=4>"+t.htmlCls.space3+"(for helix and sheet ribbons, default 1.3)Nucleotide Ribbon Width : "+t.htmlCls.inputTextStr+"id='"+t.pre+"nucleotideribbonwidth_"+e+"' value='"+p+"' size=4>"+t.htmlCls.space3+"(for nucleotide ribbons, default 0.8)Ball Scale : "+t.htmlCls.inputTextStr+"id='"+t.pre+"ballscale_"+e+"' value='"+d+"' size=4>"+t.htmlCls.space3+"(for styles 'Ball and Stick' and 'Dot', default 0.3)4. Show Glycan Cartoon : "+t.htmlCls.inputTextStr+"id='"+t.pre+"glycan' value='"+b+"' size=4>"+t.htmlCls.space3+"(0: hide, 1: show, default 0)5. Show Membrane : "+t.htmlCls.inputTextStr+"id='"+t.pre+"membrane' value='"+C+"' size=4>"+t.htmlCls.space3+"(0: hide, 1: show, default 1)6. Enlarge Command Window : "+t.htmlCls.inputTextStr+"id='"+t.pre+"cmdwindow' value='"+y+"' size=4>"+t.htmlCls.space3+"(0: Regular, 1: Large, default 0)":(n+='
',n+="Selection: Name: "+s.htmlCls.inputTextStr+"id='"+s.pre+"seq_command_name"+e+"' value='seq_"+l+"' size='5'> "+s.htmlCls.space2+"Save Clear
Residue labeling: standard residue with coordinates: UPPER case letter; nonstandard residue with coordinates: the first UPPER case letter plus a period except that water residue uses the letter 'O'; residue missing coordinates: lower case letter."+(s.utilsCls.isMac()&&!s.utilsCls.isMobile()?"Turn on scroll bar: System preferences -> General -> show scroll bars -> check Always":"")+"
',n+="Selection: Name: "+s.htmlCls.inputTextStr+"id='"+s.pre+"alignseq_command_name' value='alseq_"+l+"' size='10'> "+s.htmlCls.space2+"Save Clear
Residue labeling: aligned residue with coordinates: UPPER case letter; non-aligned residue with coordinates: lower case letter which can be highlighted; residue missing coordinates: lower case letter which can NOT be highlighted."+(s.utilsCls.isMac()&&!s.utilsCls.isMobile()?"Turn on scroll bar: System preferences -> General -> show scroll bars -> check Always":"")+"Select Aligned Sequences: touch to select, touch again to deselect, multiple selection is allowed without Ctrl key, click "Save Selection" to save the current selection.Select on 1D sequences: drag to select, drag again to deselect, multiple selection is allowed without Ctrl key, click "Save Selection" to save the current selection.Select on 2D interaction diagram: click on the nodes or lines. The nodes are chains and can be united with the Ctrl key. The lines are interactions and can NOT be united. Each click on the lines selects half of the lines, i.e., select the interacting residues in one of the two chains.Select on 3D structures: "+(e.utilsCls.isMobile()?"use finger to pick":'hold "Alt" and use mouse to pick')+', click the second time to deselect, hold "Ctrl" to union selection, hold "Shift" to select a range, press the up/down arrow to switch among atom/residue/strand/chain/structure, click "Save Selection" to save the current selection.Save the current selection (either on 3D structure, 2D interactions, or 1D sequence): open the menu "Select -> Save Selection", specify the name and description for the selection, and click "Save".Grid Size: ";s+=this.getOptionHtml(["65","97","129"],0),s+=" ",s+="Salt Concentration: ";return s+=this.getOptionHtml(["0","0.15"],1),s+=" M ";return"delphi"==e?s.cfg.cid?i+="
Note : Partial charges(MMFF94) are from PubChem Compound SDF files.
":(i+="
Note : Only the selected residues are used for
DelPhi potential calculation by solving linear Poisson-Boltzmann equation.",i+='
',i+=s.htmlCls.divStr+t+"' style='display:none;'>",i+="
The hydrogens and partial charges of proteins and nucleotides are added using
DelPhiPKa with the Amber charge and size files. The hydrogens of ligands are added using
Open Babel . The partial charges of ligands are calculated using
Antechamber with the Gasteiger charge method. All partial charges are calculated at pH 7.
",i+='Lipids are treated as ligands. Please use "HETATM" instead of "ATOM " for each lipid atom in your PDB file. Each phosphate in lipids is assigned with a charge of -1. You can download PQR and modify it, or prepare your PQR file using other tools. Then load the PQR file at the menu "Analysis > Load PQR/Potential".
',i+="
Note : Always load a PDB file before loading a PQR or DelPhi potential file.",i+='
DelPhi Web Server and be exported as a Cube file. ',"url"==e&&(i+="The PQR or potential file can be accessed in a URL if it is located in the same host as iCn3D."),i+="Potential contour at: ";let d;a+=this.getOptionHtml(["0.5","1","2","3","4","5","6","7","8","9","10"],2),a+=" kT/e(25.6mV at 298K) "+s.htmlCls.buttonStr+n+"mapNo'>Remove Map ",a+=s.htmlCls.divStr+n+"tab1_"+i+"'>",a+=this.addGsizeSalt(i)+"PQR File : "+s.htmlCls.inputFileStr+"id='"+s.pre+i+"file'> Phi File : "+s.htmlCls.inputFileStr+"id='"+s.pre+n+"file'> Cube File : "+s.htmlCls.inputFileStr+"id='"+s.pre+l+"file'> "+s.htmlCls.buttonStr+n+"mapNo'>Remove Map ",a+=s.htmlCls.divStr+n+"tab1_"+i+"2'>",a+=this.addGsizeSalt(i)+"PQR URL in the same host: "+s.htmlCls.inputTextStr+"id='"+s.pre+i+"file'> Phi URL in the same host: "+s.htmlCls.inputTextStr+"id='"+s.pre+n+"file'> Cube URL in the same host: "+s.htmlCls.inputTextStr+"id='"+s.pre+l+"file'> Surface with max potential at: ";a+=this.getOptionHtml(["0.5","1","2","3","4","5","6","7","8","9","10"],2),a+=" kT/e(25.6mV at 298K) Surface : ",a+="Van der Waals ",a+="Molecular Surface ",a+="Solvent Accessible ",a+=" ",a+="Opacity : ";return a+=this.getOptionHtml(["1.0","0.9","0.8","0.7","0.6","0.5","0.4","0.3","0.2","0.1"],0),a+=" Wireframe : ",a+="Yes ",a+="No ",a+=" "+s.htmlCls.buttonStr+n+"mapNo2'>Remove Surface ",a+=s.htmlCls.divStr+n+"tab2_"+i+"'>",a+=this.addGsizeSalt(i+"2")+"PQR File : "+s.htmlCls.inputFileStr+"id='"+s.pre+i+"file2'> Phi File : "+s.htmlCls.inputFileStr+"id='"+s.pre+n+"file2'> Cube File : "+s.htmlCls.inputFileStr+"id='"+s.pre+l+"file2'> "+s.htmlCls.buttonStr+n+"mapNo2'>Remove Surface ",a+=s.htmlCls.divStr+n+"tab2_"+i+"2'>",a+=this.addGsizeSalt(i+"2")+"PQR URL in the same host: "+s.htmlCls.inputTextStr+"id='"+s.pre+i+"file2'> Phi URL in the same host: "+s.htmlCls.inputTextStr+"id='"+s.pre+n+"file2'> Cube URL in the same host: "+s.htmlCls.inputTextStr+"id='"+s.pre+l+"file2'> Save File > iCn3D PNG Image"...');else if(-1!=l){let t=e.substr(l+n.length);s.htmlCls.clickMenuCls.setLogCmd("load iCn3D PNG image "+$("#"+s.pre+"pngimage").val(),!1),window.open(t,"_self")}else if(-1!=o){let n="Start of data file======\n",l=e.indexOf(n);i.bInputfile=-1!=l,i.bInputPNGWithData=i.bInputfile;let a,d=t?t.replace(/;/g,"\n"):"";if(i.bInputfile){let t=e.indexOf("End of data file======\n"),s=e.substr(l+n.length,t-l-n.length);i.InputfileData=i.InputfileData?i.InputfileData+"\nENDMDL\n"+s:s;let c="Start of type file======\n",h=e.indexOf(c),p=e.indexOf("End of type file======\n"),m=e.substr(h+c.length,p-h-c.length-1);i.InputfileType=m;let u=e.indexOf("End of state file======\n");a=e.substr(o+r.length,u-o-r.length),a=decodeURIComponent(a+"\n"+d),"pdb"===m?(await i.pdbParserCls.loadPdbData(s),i.commands=[],i.optsHistory=[]):("mol2"===m?await i.mol2ParserCls.loadMol2Data(s):"sdf"===m?await i.sdfParserCls.loadSdfData(s):"xyz"===m?await i.xyzParserCls.loadXyzData(s):"mmcif"===m&&await i.mmcifParserCls.loadMmcifData(s),i.commands=[],i.optsHistory=[])}else{let t=e.indexOf("End of state file======\n");a=e.substr(o+r.length,t-o-r.length),a=decodeURIComponent(a+"\n"+d),i.commands=[],i.optsHistory=[]}await i.loadScriptCls.loadScript(a,!0),s.htmlCls.clickMenuCls.setLogCmd("load iCn3D PNG image "+$("#"+s.pre+"pngimage").val(),!1)}}fileSupport(){window.File&&window.FileReader&&window.FileList&&window.Blob||alert("The File APIs are not fully supported in this browser.")}getLinkColor(){let e="";return e+=", linkmap: {\n",e+='3: {"type": "peptidebond", "c":""},\n',e+='4: {"type": "ssbond", "c":"FFA500"},\n',e+='5: {"type": "ionic", "c":"0FF"},\n',e+='6: {"type": "ionicInside", "c":"FFF"},\n',e+='11: {"type": "contact", "c":"888"},\n',e+='12: {"type": "contactInside", "c":"FFF"},\n',e+='13: {"type": "hbond", "c":"0F0"},\n',e+='14: {"type": "hbondInside", "c":"FFF"},\n',e+='15: {"type": "clbond", "c":"006400"},\n',e+='17: {"type": "halogen", "c":"F0F"},\n',e+='18: {"type": "halogenInside", "c":"FFF"},\n',e+='19: {"type": "pication", "c":"F00"},\n',e+='20: {"type": "picationInside", "c":"FFF"},\n',e+='21: {"type": "pistacking", "c":"00F"},\n',e+='22: {"type": "pistackingInside", "c":"FFF"}\n',e+="}}\n",', linkmap: {\n3: {"type": "peptidebond", "c":""},\n4: {"type": "ssbond", "c":"FFA500"},\n5: {"type": "ionic", "c":"0FF"},\n6: {"type": "ionicInside", "c":"FFF"},\n11: {"type": "contact", "c":"888"},\n12: {"type": "contactInside", "c":"FFF"},\n13: {"type": "hbond", "c":"0F0"},\n14: {"type": "hbondInside", "c":"FFF"},\n15: {"type": "clbond", "c":"006400"},\n17: {"type": "halogen", "c":"F0F"},\n18: {"type": "halogenInside", "c":"FFF"},\n19: {"type": "pication", "c":"F00"},\n20: {"type": "picationInside", "c":"FFF"},\n21: {"type": "pistacking", "c":"00F"},\n22: {"type": "pistackingInside", "c":"FFF"}\n}}\n'}setCookieForThickness(){let e=this.icn3dui,t=e.icn3d;if(!e.bNode){let e=3650;this.setCookie("lineRadius",t.lineRadius,e),this.setCookie("coilWidth",t.coilWidth,e),this.setCookie("cylinderRadius",t.cylinderRadius,e),this.setCookie("crosslinkRadius",t.crosslinkRadius,e),this.setCookie("traceRadius",t.traceRadius,e),this.setCookie("dotSphereScale",t.dotSphereScale,e),this.setCookie("ribbonthickness",t.ribbonthickness,e),this.setCookie("helixSheetWidth",t.helixSheetWidth,e),this.setCookie("nucleicAcidWidth",t.nucleicAcidWidth,e)}}setLineThickness(e,t){let s=this.icn3dui,i=s.icn3d;if(i.bSetThickness=!0,"style"==e&&(t&&($("#"+s.pre+"shininess").val("40"),$("#"+s.pre+"light1").val("0.8"),$("#"+s.pre+"light2").val("0.4"),$("#"+s.pre+"light3").val("0.2"),$("#"+s.pre+"glycan").val("0"),$("#"+s.pre+"membrane").val("1"),$("#"+s.pre+"cmdwindow").val("0")),i.shininess=parseFloat($("#"+s.pre+"shininess").val()),i.light1=parseFloat($("#"+s.pre+"light1").val()),i.light2=parseFloat($("#"+s.pre+"light2").val()),i.light3=parseFloat($("#"+s.pre+"light3").val()),i.bGlycansCartoon=parseInt($("#"+s.pre+"glycan").val()),i.bMembrane=parseInt($("#"+s.pre+"membrane").val()),i.bCmdWindow=parseInt($("#"+s.pre+"cmdwindow").val())),t&&($("#"+s.pre+"linerad_"+e).val(.1),$("#"+s.pre+"coilrad_"+e).val(.3),$("#"+s.pre+"stickrad_"+e).val(.4),$("#"+s.pre+"crosslinkrad_"+e).val(.4),$("#"+s.pre+"tracerad_"+e).val(.4),$("#"+s.pre+"ballscale_"+e).val(.3),$("#"+s.pre+"ribbonthick_"+e).val(.2),$("#"+s.pre+"prtribbonwidth_"+e).val(1.3),$("#"+s.pre+"nucleotideribbonwidth_"+e).val(.8)),i.lineRadius=parseFloat($("#"+s.pre+"linerad_"+e).val()),i.coilWidth=parseFloat($("#"+s.pre+"coilrad_"+e).val()),i.cylinderRadius=parseFloat($("#"+s.pre+"stickrad_"+e).val()),i.crosslinkRadius=parseFloat($("#"+s.pre+"crosslinkrad_"+e).val()),i.traceRadius=parseFloat($("#"+s.pre+"tracerad_"+e).val()),i.dotSphereScale=parseFloat($("#"+s.pre+"ballscale_"+e).val()),i.ribbonthickness=parseFloat($("#"+s.pre+"ribbonthick_"+e).val()),i.helixSheetWidth=parseFloat($("#"+s.pre+"prtribbonwidth_"+e).val()),i.nucleicAcidWidth=parseFloat($("#"+s.pre+"nucleotideribbonwidth_"+e).val()),!s.bNode){let e=3650;this.setCookie("shininess",i.shininess,e),this.setCookie("light1",i.light1,e),this.setCookie("light2",i.light2,e),this.setCookie("light3",i.light3,e),this.setCookie("glycan",i.bGlycansCartoon,e),this.setCookie("membrane",i.bMembrane,e),this.setCookie("cmdwindow",i.bCmdWindow,e)}if(this.setCookieForThickness(),e=t){let e="reset thickness";s.htmlCls.clickMenuCls.setLogCmd(e,!0),i.bSetThickness=!1,i.threeDPrintCls.resetAfter3Dprint()}else s.htmlCls.clickMenuCls.setLogCmd("set thickness | linerad "+i.lineRadius+" | coilrad "+i.coilWidth+" | stickrad "+i.cylinderRadius+" | crosslinkrad "+i.crosslinkRadius+" | tracerad "+i.traceRadius+" | ribbonthick "+i.ribbonthickness+" | proteinwidth "+i.helixSheetWidth+" | nucleotidewidth "+i.nucleicAcidWidth+" | ballscale "+i.dotSphereScale,!0),s.htmlCls.clickMenuCls.setLogCmd("set glycan "+i.bGlycansCartoon,!0),s.htmlCls.clickMenuCls.setLogCmd("set membrane "+i.bMembrane,!0),s.htmlCls.clickMenuCls.setLogCmd("set cmdwindow "+i.bCmdWindow,!0);i.drawCls.draw()}setCookie(e,t,s){let i=new Date;i.setTime(i.getTime()+24*s*60*60*1e3);let n="expires="+i.toUTCString();document.cookie=e+"="+t+";"+n+";path=/"}updateSurfPara(e){let t=this.icn3dui,s=t.icn3d;s.phisurftype=$("#"+t.pre+e+"surftype").val(),s.phisurfop=$("#"+t.pre+e+"surfop").val(),s.phisurfwf=$("#"+t.pre+e+"surfwf").val()}exportPdb(){let e=this.icn3dui,t=e.icn3d,s="",i=e.hashUtilsCls.intHash(t.dAtoms,t.hAtoms);if(s+=t.saveFileCls.getAtomPDB(i),!e.bNode){let i=Object.keys(e.utilsCls.getHlStructures()).join(",");t.saveFileCls.saveFile(i+"_icn3d.pdb","text",[s])}return s}exportSecondary(){let e=this.icn3dui,t=e.icn3d,s="",i=e.hashUtilsCls.intHash(t.dAtoms,t.hAtoms);if(s+=t.saveFileCls.getSecondary(i),!e.bNode){let i=Object.keys(e.utilsCls.getHlStructures()).join(",");t.saveFileCls.saveFile(i+"_icn3d_ss.txt","text",[s])}return s}}class g{constructor(e){let t=e;this.icn3dui=e,this.cfg=this.icn3dui.cfg,this.opts={},this.opts.background="black",this.allMenus={},this.allMenusSel={},this.simpleMenus={},this.shownMenus={},this.WIDTH=400,this.HEIGHT=400,this.RESIDUE_WIDTH=10,t.utilsCls.isMobile()||this.cfg.mobilemenu?this.MENU_HEIGHT=0:this.MENU_HEIGHT=40,this.LOG_HEIGHT=65,this.MENU_WIDTH=750,this.LESSWIDTH=20,this.LESSWIDTH_RESIZE=20,this.LESSHEIGHT=20,this.width2d=200,this.CMD_HEIGHT=.8*this.LOG_HEIGHT,this.EXTRAHEIGHT=this.MENU_HEIGHT+this.CMD_HEIGHT,null!=this.cfg.showmenu&&0==this.cfg.showmenu&&(this.EXTRAHEIGHT-=this.MENU_HEIGHT),null!=this.cfg.showcommand&&0==this.cfg.showcommand&&(this.EXTRAHEIGHT-=this.CMD_HEIGHT),this.GREY8="#AAAAAA",this.GREYB="#CCCCCC",this.GREYC="#DDDDDD",this.GREYD="#EEEEEE",this.ORANGE="#FFA500",this.themecolor="blue",this.defaultValue=1,this.ssValue=3,this.coilValue=3,this.contactValue=11,this.contactInsideValue=12,this.hbondValue=13,this.hbondInsideValue=14,this.ssbondValue=4,this.ionicValue=5,this.ionicInsideValue=6,this.clbondValue=15,this.halogenValue=17,this.halogenInsideValue=18,this.picationValue=19,this.picationInsideValue=20,this.pistackingValue=21,this.pistackingInsideValue=22,this.contactColor="888",this.contactInsideColor="FFF",this.hbondColor="0F0",this.hbondInsideColor="FFF",this.ssbondColor="FFA500",this.ionicColor="0FF",this.ionicInsideColor="FFF",this.clbondColor="006400",this.halogenColor="F0F",this.halogenInsideColor="FFF",this.picationColor="F00",this.picationInsideColor="FFF",this.pistackingColor="00F",this.pistackingInsideColor="FFF",this.hideedges=1,this.force=4,this.simulation=void 0,this.baseUrl=window&&window.location&&"structure.ncbi.nlm.nih.gov"==window.location.hostname?"https://structure.ncbi.nlm.nih.gov/Structure/":"https://www.ncbi.nlm.nih.gov/Structure/",this.divStr="",this.spanNowrapStr="
",this.inputTextStr="=0&&void 0===r[t]&&console.warn('THREE.GLTFLoader: Unknown extension "'+t+'".')}}a.setExtensions(l),a.setPlugins(r),a.parse(s,i)}parseAsync(e,t){const s=this;return new Promise((function(i,n){s.parse(e,t,i,n)}))}}function b(){let e={};return{get:function(t){return e[t]},add:function(t,s){e[t]=s},remove:function(t){delete e[t]},removeAll:function(){e={}}}}const C={KHR_BINARY_GLTF:"KHR_binary_glTF",KHR_DRACO_MESH_COMPRESSION:"KHR_draco_mesh_compression",KHR_LIGHTS_PUNCTUAL:"KHR_lights_punctual",KHR_MATERIALS_CLEARCOAT:"KHR_materials_clearcoat",KHR_MATERIALS_IOR:"KHR_materials_ior",KHR_MATERIALS_PBR_SPECULAR_GLOSSINESS:"KHR_materials_pbrSpecularGlossiness",KHR_MATERIALS_SHEEN:"KHR_materials_sheen",KHR_MATERIALS_SPECULAR:"KHR_materials_specular",KHR_MATERIALS_TRANSMISSION:"KHR_materials_transmission",KHR_MATERIALS_UNLIT:"KHR_materials_unlit",KHR_MATERIALS_VOLUME:"KHR_materials_volume",KHR_TEXTURE_BASISU:"KHR_texture_basisu",KHR_TEXTURE_TRANSFORM:"KHR_texture_transform",KHR_MESH_QUANTIZATION:"KHR_mesh_quantization",EXT_TEXTURE_WEBP:"EXT_texture_webp",EXT_MESHOPT_COMPRESSION:"EXT_meshopt_compression"};class y{constructor(e){this.parser=e,this.name=C.KHR_LIGHTS_PUNCTUAL,this.cache={refs:{},uses:{}}}_markDefs(){const e=this.parser,t=this.parser.json.nodes||[];for(let s=0,i=t.length;s=0)throw new Error("THREE.GLTFLoader: setKTX2Loader must be called before loading KTX2 textures");return null}return t.loadTextureImage(e,n.source,l)}}class R{constructor(e){this.parser=e,this.name=C.EXT_TEXTURE_WEBP,this.isSupported=null}loadTexture(e){const t=this.name,s=this.parser,i=s.json,n=i.textures[e];if(!n.extensions||!n.extensions[t])return null;const l=n.extensions[t],r=i.images[l.source];let o=s.textureLoader;if(r.uri){const e=s.options.manager.getHandler(r.uri);null!==e&&(o=e)}return this.detectSupport().then((function(n){if(n)return s.loadTextureImage(e,l.source,o);if(i.extensionsRequired&&i.extensionsRequired.indexOf(t)>=0)throw new Error("THREE.GLTFLoader: WebP required by asset but unsupported.");return s.loadTexture(e)}))}detectSupport(){return this.isSupported||(this.isSupported=new Promise((function(e){const t=new Image;t.src="data:image/webp;base64,UklGRiIAAABXRUJQVlA4IBYAAAAwAQCdASoBAAEADsD+JaQAA3AAAAAA",t.onload=t.onerror=function(){e(1===t.height)}}))),this.isSupported}}class I{constructor(e){this.name=C.EXT_MESHOPT_COMPRESSION,this.parser=e}loadBufferView(e){const t=this.parser.json,s=t.bufferViews[e];if(s.extensions&&s.extensions[this.name]){const e=s.extensions[this.name],i=this.parser.getDependency("buffer",e.buffer),n=this.parser.options.meshoptDecoder;if(!n||!n.supported){if(t.extensionsRequired&&t.extensionsRequired.indexOf(this.name)>=0)throw new Error("THREE.GLTFLoader: setMeshoptDecoder must be called before loading compressed files");return null}return Promise.all([i,n.ready]).then((function(t){const s=e.byteOffset||0,i=e.byteLength||0,l=e.count,r=e.byteStride,o=new ArrayBuffer(l*r),a=new Uint8Array(t[0],s,i);return n.decodeGltfBuffer(new Uint8Array(o),l,r,a,e.mode,e.filter),o}))}return null}}const T="glTF",E=1313821514,P=5130562;class M{constructor(e){this.name=C.KHR_BINARY_GLTF,this.content=null,this.body=null;const t=new DataView(e,0,12);if(this.header={magic:THREE.LoaderUtils.decodeText(new Uint8Array(e.slice(0,4))),version:t.getUint32(4,!0),length:t.getUint32(8,!0)},this.header.magic!==T)throw new Error("THREE.GLTFLoader: Unsupported glTF-Binary header.");if(this.header.version<2)throw new Error("THREE.GLTFLoader: Legacy binary file detected.");const s=this.header.length-12,i=new DataView(e,12);let n=0;for(;n",t).replace("#include ",s).replace("#include ",i).replace("#include ",n).replace("#include ",l)},Object.defineProperties(this,{specular:{get:function(){return r.specular.value},set:function(e){r.specular.value=e}},specularMap:{get:function(){return r.specularMap.value},set:function(e){r.specularMap.value=e,e?this.defines.USE_SPECULARMAP="":delete this.defines.USE_SPECULARMAP}},glossiness:{get:function(){return r.glossiness.value},set:function(e){r.glossiness.value=e}},glossinessMap:{get:function(){return r.glossinessMap.value},set:function(e){r.glossinessMap.value=e,e?(this.defines.USE_GLOSSINESSMAP="",this.defines.USE_UV=""):(delete this.defines.USE_GLOSSINESSMAP,delete this.defines.USE_UV)}}}),delete this.metalness,delete this.roughness,delete this.metalnessMap,delete this.roughnessMap,this.setValues(e)}copy(e){return super.copy(e),this.specularMap=e.specularMap,this.specular.copy(e.specular),this.glossinessMap=e.glossinessMap,this.glossiness=e.glossiness,delete this.metalness,delete this.roughness,delete this.metalnessMap,delete this.roughnessMap,this}}class L{constructor(){this.name=C.KHR_MATERIALS_PBR_SPECULAR_GLOSSINESS,this.specularGlossinessParams=["color","map","lightMap","lightMapIntensity","aoMap","aoMapIntensity","emissive","emissiveIntensity","emissiveMap","bumpMap","bumpScale","normalMap","normalMapType","displacementMap","displacementScale","displacementBias","specularMap","specular","glossinessMap","glossiness","alphaMap","envMap","envMapIntensity"]}getMaterialType(){return F}extendParams(e,t,s){const i=t.extensions[this.name];e.color=new Color(1,1,1),e.opacity=1;const n=[];if(Array.isArray(i.diffuseFactor)){const t=i.diffuseFactor;e.color.fromArray(t),e.opacity=t[3]}if(void 0!==i.diffuseTexture&&n.push(s.assignTexture(e,"map",i.diffuseTexture,sRGBEncoding)),e.emissive=new Color(0,0,0),e.glossiness=void 0!==i.glossinessFactor?i.glossinessFactor:1,e.specular=new Color(1,1,1),Array.isArray(i.specularFactor)&&e.specular.fromArray(i.specularFactor),void 0!==i.specularGlossinessTexture){const t=i.specularGlossinessTexture;n.push(s.assignTexture(e,"glossinessMap",t)),n.push(s.assignTexture(e,"specularMap",t,sRGBEncoding))}return Promise.all(n)}createMaterial(e){const t=new F(e);return t.fog=!0,t.color=e.color,t.map=void 0===e.map?null:e.map,t.lightMap=null,t.lightMapIntensity=1,t.aoMap=void 0===e.aoMap?null:e.aoMap,t.aoMapIntensity=1,t.emissive=e.emissive,t.emissiveIntensity=1,t.emissiveMap=void 0===e.emissiveMap?null:e.emissiveMap,t.bumpMap=void 0===e.bumpMap?null:e.bumpMap,t.bumpScale=1,t.normalMap=void 0===e.normalMap?null:e.normalMap,t.normalMapType=TangentSpaceNormalMap,e.normalScale&&(t.normalScale=e.normalScale),t.displacementMap=null,t.displacementScale=1,t.displacementBias=0,t.specularMap=void 0===e.specularMap?null:e.specularMap,t.specular=e.specular,t.glossinessMap=void 0===e.glossinessMap?null:e.glossinessMap,t.glossiness=e.glossiness,t.alphaMap=null,t.envMap=void 0===e.envMap?null:e.envMap,t.envMapIntensity=1,t}}class N{constructor(){this.name=C.KHR_MESH_QUANTIZATION}}class q extends THREE.Interpolant{constructor(e,t,s,i){super(e,t,s,i)}copySampleValue_(e){const t=this.resultBuffer,s=this.sampleValues,i=this.valueSize,n=e*i*3+i;for(let e=0;e!==i;e++)t[e]=s[n+e];return t}}q.prototype.beforeStart_=q.prototype.copySampleValue_,q.prototype.afterEnd_=q.prototype.copySampleValue_,q.prototype.interpolate_=function(e,t,s,i){const n=this.resultBuffer,l=this.sampleValues,r=this.valueSize,o=2*r,a=3*r,d=i-t,c=(s-t)/d,h=c*c,p=h*c,m=e*a,u=m-a,g=-2*p+3*h,f=p-h,b=1-g,C=f-h+c;for(let e=0;e!==r;e++){const t=l[u+e+r],s=l[u+e+o]*d,i=l[m+e+r],a=l[m+e]*d;n[e]=b*t+C*s+g*i+f*a}return n};const U=new THREE.Quaternion;class j extends q{interpolate_(e,t,s,i){const n=super.interpolate_(e,t,s,i);return U.fromArray(n).normalize().toArray(n),n}}const B=0,z=1,G=2,V=3,W=4,Y=5,X=6,K={5120:Int8Array,5121:Uint8Array,5122:Int16Array,5123:Uint16Array,5125:Uint32Array,5126:Float32Array},J={9728:THREE.NearestFilter,9729:THREE.LinearFilter,9984:THREE.NearestMipmapNearestFilter,9985:THREE.LinearMipmapNearestFilter,9986:THREE.NearestMipmapLinearFilter,9987:THREE.LinearMipmapLinearFilter},Q={33071:THREE.ClampToEdgeWrapping,33648:THREE.MirroredRepeatWrapping,10497:THREE.RepeatWrapping},Z={SCALAR:1,VEC2:2,VEC3:3,VEC4:4,MAT2:4,MAT3:9,MAT4:16},ee={POSITION:"position",NORMAL:"normal",TANGENT:"tangent",TEXCOORD_0:"uv",TEXCOORD_1:"uv2",COLOR_0:"color",WEIGHTS_0:"skinWeight",JOINTS_0:"skinIndex"},te={scale:"scale",translation:"position",rotation:"quaternion",weights:"morphTargetInfluences"},se={CUBICSPLINE:void 0,LINEAR:THREE.InterpolateLinear,STEP:THREE.InterpolateDiscrete},ie="OPAQUE",ne="MASK",le="BLEND";function re(e,t,s){for(const i in s.extensions)void 0===e[i]&&(t.userData.gltfExtensions=t.userData.gltfExtensions||{},t.userData.gltfExtensions[i]=s.extensions[i])}function oe(e,t){void 0!==t.extras&&("object"==typeof t.extras?Object.assign(e.userData,t.extras):console.warn("THREE.GLTFLoader: Ignoring primitive type .extras, "+t.extras))}function ae(e,t){if(e.updateMorphTargets(),void 0!==t.weights)for(let s=0,i=t.weights.length;s{const s=this.associations.get(e);null!=s&&this.associations.set(t,s);for(const[s,i]of e.children.entries())n(i,t.children[s])};return n(s,i),i.name+="_instance_"+e.uses[t]++,i}_invokeOne(e){const t=Object.values(this.plugins);t.push(this);for(let s=0;s=2&&m.setY(t,c[e*l+1]),l>=3&&m.setZ(t,c[e*l+2]),l>=4&&m.setW(t,c[e*l+3]),l>=5)throw new Error("THREE.GLTFLoader: Unsupported itemSize in sparse BufferAttribute.")}}return m}))}loadTexture(e){const t=this.json,s=this.options,i=t.textures[e].source,n=t.images[i];let l=this.textureLoader;if(n.uri){const e=s.manager.getHandler(n.uri);null!==e&&(l=e)}return this.loadTextureImage(e,i,l)}loadTextureImage(e,t,s){const i=this,n=this.json,l=n.textures[e],r=n.images[t],o=(r.uri||r.bufferView)+":"+l.sampler;if(this.textureCache[o])return this.textureCache[o];const a=this.loadImageSource(t,s).then((function(t){t.flipY=!1,l.name&&(t.name=l.name);const s=(n.samplers||{})[l.sampler]||{};return t.magFilter=J[s.magFilter]||LinearFilter,t.minFilter=J[s.minFilter]||LinearMipmapLinearFilter,t.wrapS=Q[s.wrapS]||RepeatWrapping,t.wrapT=Q[s.wrapT]||RepeatWrapping,i.associations.set(t,{textures:e}),t})).catch((function(){return null}));return this.textureCache[o]=a,a}loadImageSource(e,t){const s=this,i=this.json,n=this.options;if(void 0!==this.sourceCache[e])return this.sourceCache[e].then((e=>e.clone()));const l=i.images[e],r=self.URL||self.webkitURL;let o=l.uri||"",a=!1;if(void 0!==l.bufferView)o=s.getDependency("bufferView",l.bufferView).then((function(e){a=!0;const t=new Blob([e],{type:l.mimeType});return o=r.createObjectURL(t),o}));else if(void 0===l.uri)throw new Error("THREE.GLTFLoader: Image "+e+" is missing URI and bufferView");const d=Promise.resolve(o).then((function(e){return new Promise((function(s,i){let l=s;!0===t.isImageBitmapLoader&&(l=function(e){const t=new Texture(e);t.needsUpdate=!0,s(t)}),t.load(THREE.LoaderUtils.resolveURL(e,n.path),l,void 0,i)}))})).then((function(e){var t;return!0===a&&r.revokeObjectURL(o),e.userData.mimeType=l.mimeType||((t=l.uri).search(/\.jpe?g($|\?)/i)>0||0===t.search(/^data\:image\/jpeg/)?"image/jpeg":t.search(/\.webp($|\?)/i)>0||0===t.search(/^data\:image\/webp/)?"image/webp":"image/png"),e})).catch((function(e){throw console.error("THREE.GLTFLoader: Couldn't load texture",o),e}));return this.sourceCache[e]=d,d}assignTexture(e,t,s,i){const n=this;return this.getDependency("texture",s.index).then((function(l){if(void 0===s.texCoord||0==s.texCoord||"aoMap"===t&&1==s.texCoord||console.warn("THREE.GLTFLoader: Custom UV set "+s.texCoord+" for texture "+t+" not yet supported."),n.extensions[C.KHR_TEXTURE_TRANSFORM]){const e=void 0!==s.extensions?s.extensions[C.KHR_TEXTURE_TRANSFORM]:void 0;if(e){const t=n.associations.get(l);l=n.extensions[C.KHR_TEXTURE_TRANSFORM].extendTexture(l,e),n.associations.set(l,t)}}return void 0!==i&&(l.encoding=i),e[t]=l,l}))}assignFinalMaterial(e){const t=e.geometry;let s=e.material;const i=void 0===t.attributes.tangent,n=void 0!==t.attributes.color,l=void 0===t.attributes.normal;if(e.isPoints){const e="PointsMaterial:"+s.uuid;let t=this.cache.get(e);t||(t=new PointsMaterial,Material.prototype.copy.call(t,s),t.color.copy(s.color),t.map=s.map,t.sizeAttenuation=!1,this.cache.add(e,t)),s=t}else if(e.isLine){const e="LineBasicMaterial:"+s.uuid;let t=this.cache.get(e);t||(t=new LineBasicMaterial,Material.prototype.copy.call(t,s),t.color.copy(s.color),this.cache.add(e,t)),s=t}if(i||n||l){let e="ClonedMaterial:"+s.uuid+":";s.isGLTFSpecularGlossinessMaterial&&(e+="specular-glossiness:"),i&&(e+="derivative-tangents:"),n&&(e+="vertex-colors:"),l&&(e+="flat-shading:");let t=this.cache.get(e);t||(t=s.clone(),n&&(t.vertexColors=!0),l&&(t.flatShading=!0),i&&(t.normalScale&&(t.normalScale.y*=-1),t.clearcoatNormalScale&&(t.clearcoatNormalScale.y*=-1)),this.cache.add(e,t),this.associations.set(t,this.associations.get(s))),s=t}s.aoMap&&void 0===t.attributes.uv2&&void 0!==t.attributes.uv&&t.setAttribute("uv2",t.attributes.uv),e.material=s}getMaterialType(){return MeshStandardMaterial}loadMaterial(e){const t=this,s=this.json,i=this.extensions,n=s.materials[e];let l;const r={},o=n.extensions||{},a=[];if(o[C.KHR_MATERIALS_PBR_SPECULAR_GLOSSINESS]){const e=i[C.KHR_MATERIALS_PBR_SPECULAR_GLOSSINESS];l=e.getMaterialType(),a.push(e.extendParams(r,n,t))}else if(o[C.KHR_MATERIALS_UNLIT]){const e=i[C.KHR_MATERIALS_UNLIT];l=e.getMaterialType(),a.push(e.extendParams(r,n,t))}else{const s=n.pbrMetallicRoughness||{};if(r.color=new Color(1,1,1),r.opacity=1,Array.isArray(s.baseColorFactor)){const e=s.baseColorFactor;r.color.fromArray(e),r.opacity=e[3]}void 0!==s.baseColorTexture&&a.push(t.assignTexture(r,"map",s.baseColorTexture,sRGBEncoding)),r.metalness=void 0!==s.metallicFactor?s.metallicFactor:1,r.roughness=void 0!==s.roughnessFactor?s.roughnessFactor:1,void 0!==s.metallicRoughnessTexture&&(a.push(t.assignTexture(r,"metalnessMap",s.metallicRoughnessTexture)),a.push(t.assignTexture(r,"roughnessMap",s.metallicRoughnessTexture))),l=this._invokeOne((function(t){return t.getMaterialType&&t.getMaterialType(e)})),a.push(Promise.all(this._invokeAll((function(t){return t.extendMaterialParams&&t.extendMaterialParams(e,r)}))))}!0===n.doubleSided&&(r.side=DoubleSide);const d=n.alphaMode||ie;if(d===le?(r.transparent=!0,r.depthWrite=!1):(r.transparent=!1,d===ne&&(r.alphaTest=void 0!==n.alphaCutoff?n.alphaCutoff:.5)),void 0!==n.normalTexture&&l!==MeshBasicMaterial&&(a.push(t.assignTexture(r,"normalMap",n.normalTexture)),r.normalScale=new Vector2(1,1),void 0!==n.normalTexture.scale)){const e=n.normalTexture.scale;r.normalScale.set(e,e)}return void 0!==n.occlusionTexture&&l!==MeshBasicMaterial&&(a.push(t.assignTexture(r,"aoMap",n.occlusionTexture)),void 0!==n.occlusionTexture.strength&&(r.aoMapIntensity=n.occlusionTexture.strength)),void 0!==n.emissiveFactor&&l!==MeshBasicMaterial&&(r.emissive=(new Color).fromArray(n.emissiveFactor)),void 0!==n.emissiveTexture&&l!==MeshBasicMaterial&&a.push(t.assignTexture(r,"emissiveMap",n.emissiveTexture,sRGBEncoding)),Promise.all(a).then((function(){let s;return s=l===F?i[C.KHR_MATERIALS_PBR_SPECULAR_GLOSSINESS].createMaterial(r):new l(r),n.name&&(s.name=n.name),oe(s,n),t.associations.set(s,{materials:e}),n.extensions&&re(i,s,n),s}))}createUniqueName(e){const t=PropertyBinding.sanitizeNodeName(e||"");let s=t;for(let e=1;this.nodeNamesUsed[s];++e)s=t+"_"+e;return this.nodeNamesUsed[s]=!0,s}loadGeometries(e){const t=this,s=this.extensions,i=this.primitiveCache;function n(e){return s[C.KHR_DRACO_MESH_COMPRESSION].decodePrimitive(e,t).then((function(s){return ue(s,e,t)}))}const l=[];for(let s=0,r=e.length;s0&&ae(h,n),h.name=t.createUniqueName(n.name||"mesh_"+e),oe(h,n),c.extensions&&re(i,h,c),t.assignFinalMaterial(h),a.push(h)}for(let s=0,i=a.length;s1?new Group:1===t.length?t[0]:new Object3D,r!==t[0])for(let e=0,s=t.length;e{const t=new Map;for(const[e,s]of n.associations)(e instanceof Material||e instanceof Texture)&&t.set(e,s);return e.traverse((e=>{const s=n.associations.get(e);null!=s&&t.set(e,s)})),t})(l),l}))}}function me(e,t,s,i){const n=s.nodes[e];return i.getDependency("node",e).then((function(e){if(void 0===n.skin)return e;let t;return i.getDependency("skin",n.skin).then((function(e){t=e;const s=[];for(let e=0,n=t.joints.length;e{const s=n[e];return s&&(l={profileId:e,profilePath:`${t}/${s.path}`,deprecated:!!s.deprecated}),!!l})),!l){if(!s)throw new Error("No matching profile name found");const e=n[s];if(!e)throw new Error(`No matching profile name found and default profile "${s}" missing.`);l={profileId:s,profilePath:`${t}/${e.path}`,deprecated:!!e.deprecated}}const r=await be(l.profilePath);let o;if(i){let t;if(t="any"===e.handedness?r.layouts[Object.keys(r.layouts)[0]]:r.layouts[e.handedness],!t)throw new Error(`No matching handedness, ${e.handedness}, in profile ${l.profileId}`);t.assetPath&&(o=l.profilePath.replace("profile.json",t.assetPath))}return{profile:r,assetPath:o}}const ye={xAxis:0,yAxis:0,button:0,state:fe.ComponentState.DEFAULT};class ve{constructor(e){this.componentProperty=e.componentProperty,this.states=e.states,this.valueNodeName=e.valueNodeName,this.valueNodeProperty=e.valueNodeProperty,this.valueNodeProperty===fe.VisualResponseProperty.TRANSFORM&&(this.minNodeName=e.minNodeName,this.maxNodeName=e.maxNodeName),this.value=0,this.updateFromComponent(ye)}updateFromComponent({xAxis:e,yAxis:t,button:s,state:i}){const{normalizedXAxis:n,normalizedYAxis:l}=function(e=0,t=0){let s=e,i=t;if(Math.sqrt(e*e+t*t)>1){const n=Math.atan2(t,e);s=Math.cos(n),i=Math.sin(n)}return{normalizedXAxis:.5*s+.5,normalizedYAxis:.5*i+.5}}(e,t);switch(this.componentProperty){case fe.ComponentProperty.X_AXIS:this.value=this.states.includes(i)?n:.5;break;case fe.ComponentProperty.Y_AXIS:this.value=this.states.includes(i)?l:.5;break;case fe.ComponentProperty.BUTTON:this.value=this.states.includes(i)?s:0;break;case fe.ComponentProperty.STATE:this.valueNodeProperty===fe.VisualResponseProperty.VISIBILITY?this.value=this.states.includes(i):this.value=this.states.includes(i)?1:0;break;default:throw new Error(`Unexpected visualResponse componentProperty ${this.componentProperty}`)}}}class _e{constructor(e,t){if(!(e&&t&&t.visualResponses&&t.gamepadIndices&&0!==Object.keys(t.gamepadIndices).length))throw new Error("Invalid arguments supplied");this.id=e,this.type=t.type,this.rootNodeName=t.rootNodeName,this.touchPointNodeName=t.touchPointNodeName,this.visualResponses={},Object.keys(t.visualResponses).forEach((e=>{const s=new ve(t.visualResponses[e]);this.visualResponses[e]=s})),this.gamepadIndices=Object.assign({},t.gamepadIndices),this.values={state:fe.ComponentState.DEFAULT,button:void 0!==this.gamepadIndices.button?0:void 0,xAxis:void 0!==this.gamepadIndices.xAxis?0:void 0,yAxis:void 0!==this.gamepadIndices.yAxis?0:void 0}}get data(){return{id:this.id,...this.values}}updateFromGamepad(e){if(this.values.state=fe.ComponentState.DEFAULT,void 0!==this.gamepadIndices.button&&e.buttons.length>this.gamepadIndices.button){const t=e.buttons[this.gamepadIndices.button];this.values.button=t.value,this.values.button=this.values.button<0?0:this.values.button,this.values.button=this.values.button>1?1:this.values.button,t.pressed||1===this.values.button?this.values.state=fe.ComponentState.PRESSED:(t.touched||this.values.button>fe.ButtonTouchThreshold)&&(this.values.state=fe.ComponentState.TOUCHED)}void 0!==this.gamepadIndices.xAxis&&e.axes.length>this.gamepadIndices.xAxis&&(this.values.xAxis=e.axes[this.gamepadIndices.xAxis],this.values.xAxis=this.values.xAxis<-1?-1:this.values.xAxis,this.values.xAxis=this.values.xAxis>1?1:this.values.xAxis,this.values.state===fe.ComponentState.DEFAULT&&Math.abs(this.values.xAxis)>fe.AxisTouchThreshold&&(this.values.state=fe.ComponentState.TOUCHED)),void 0!==this.gamepadIndices.yAxis&&e.axes.length>this.gamepadIndices.yAxis&&(this.values.yAxis=e.axes[this.gamepadIndices.yAxis],this.values.yAxis=this.values.yAxis<-1?-1:this.values.yAxis,this.values.yAxis=this.values.yAxis>1?1:this.values.yAxis,this.values.state===fe.ComponentState.DEFAULT&&Math.abs(this.values.yAxis)>fe.AxisTouchThreshold&&(this.values.state=fe.ComponentState.TOUCHED)),Object.values(this.visualResponses).forEach((e=>{e.updateFromComponent(this.values)}))}}class we{constructor(e,t,s){if(!e)throw new Error("No xrInputSource supplied");if(!t)throw new Error("No profile supplied");this.xrInputSource=e,this.assetUrl=s,this.id=t.profileId,this.layoutDescription=t.layouts[e.handedness],this.components={},Object.keys(this.layoutDescription.components).forEach((e=>{const t=this.layoutDescription.components[e];this.components[e]=new _e(e,t)})),this.updateFromGamepad()}get gripSpace(){return this.xrInputSource.gripSpace}get targetRaySpace(){return this.xrInputSource.targetRaySpace}get data(){const e=[];return Object.values(this.components).forEach((t=>{e.push(t.data)})),e}updateFromGamepad(){Object.values(this.components).forEach((e=>{e.updateFromGamepad(this.xrInputSource.gamepad)}))}}class Se extends THREE.Object3D{constructor(){super(),this.motionController=null,this.envMap=null}setEnvironmentMap(e){return this.envMap==e||(this.envMap=e,this.traverse((e=>{e.isMesh&&(e.material.envMap=this.envMap,e.material.needsUpdate=!0)}))),this}updateMatrixWorld(e){super.updateMatrixWorld(e),this.motionController&&(this.motionController.updateFromGamepad(),Object.values(this.motionController.components).forEach((e=>{Object.values(e.visualResponses).forEach((e=>{const{valueNode:t,minNode:s,maxNode:i,value:n,valueNodeProperty:l}=e;t&&(l===fe.VisualResponseProperty.VISIBILITY?t.visible=n:l===fe.VisualResponseProperty.TRANSFORM&&(t.quaternion.slerpQuaternions(s.quaternion,i.quaternion,n),t.position.lerpVectors(s.position,i.position,n)))}))})))}}function Ae(e,t){!function(e,t){Object.values(e.components).forEach((e=>{const{type:s,touchPointNodeName:i,visualResponses:n}=e;if(s===fe.ComponentType.TOUCHPAD)if(e.touchPointNode=t.getObjectByName(i),e.touchPointNode){const t=new SphereGeometry(.001),s=new MeshBasicMaterial({color:255}),i=new Mesh(t,s);e.touchPointNode.add(i)}else console.warn(`Could not find touch dot, ${e.touchPointNodeName}, in touchpad component ${e.id}`);Object.values(n).forEach((e=>{const{valueNodeName:s,minNodeName:i,maxNodeName:n,valueNodeProperty:l}=e;if(l===fe.VisualResponseProperty.TRANSFORM){if(e.minNode=t.getObjectByName(i),e.maxNode=t.getObjectByName(n),!e.minNode)return void console.warn(`Could not find ${i} in the model`);if(!e.maxNode)return void console.warn(`Could not find ${n} in the model`)}e.valueNode=t.getObjectByName(s),e.valueNode||console.warn(`Could not find ${s} in the model`)}))}))}(e.motionController,t),e.envMap&&t.traverse((t=>{t.isMesh&&(t.material.envMap=e.envMap,t.material.needsUpdate=!0)})),e.add(t)}class xe{constructor(e=null){this.gltfLoader=e,this.path="https://cdn.jsdelivr.net/npm/@webxr-input-profiles/assets@1.0/dist/profiles",this._assetCache={},this.gltfLoader||(this.gltfLoader=new f)}createControllerModel(e){const t=new Se;let s=null;return e.addEventListener("connected",(e=>{const i=e.data;"tracked-pointer"===i.targetRayMode&&i.gamepad&&Ce(i,this.path,"generic-trigger").then((({profile:e,assetPath:n})=>{t.motionController=new we(i,e,n);const l=this._assetCache[t.motionController.assetUrl];if(l)s=l.scene.clone(),Ae(t,s);else{if(!this.gltfLoader)throw new Error("GLTFLoader not set.");this.gltfLoader.setPath(""),this.gltfLoader.load(t.motionController.assetUrl,(e=>{this._assetCache[t.motionController.assetUrl]=e,s=e.scene.clone(),Ae(t,s)}),null,(()=>{throw new Error(`Asset ${t.motionController.assetUrl} missing or malformed.`)}))}})).catch((e=>{console.warn(e)}))})),e.addEventListener("disconnected",(()=>{t.motionController=null,t.remove(s),s=null})),t}}class ke extends THREE.EventDispatcher{constructor(e){if(super(),void 0===e)return void console.error("ControllerGestures must be passed a renderer");const t=new THREE.Clock;this.controller1=e.xr.getController(0),this.controller1.userData.gestures={index:0},this.controller1.userData.selectPressed=!1,this.controller1.addEventListener("selectstart",i),this.controller1.addEventListener("selectend",n),this.controller2=e.xr.getController(1),this.controller2.userData.gestures={index:1},this.controller2.userData.selectPressed=!1,this.controller2.addEventListener("selectstart",i),this.controller2.addEventListener("selectend",n),this.doubleClickLimit=.2,this.pressMinimum=.4,this.right=new THREE.Vector3(1,0,0),this.up=new THREE.Vector3(0,1,0),this.type="unknown",this.prevTap="none",this.clock=t;const s=this;function i(){const e=this.userData.gestures;e.startPosition=void 0,e.startTime=t.getElapsedTime(),-1==s.type.indexOf("tap")&&(e.taps=0),s.type="unknown",this.userData.selectPressed=!0}function n(){const e=this.userData.gestures;e.endTime=t.getElapsedTime();e.endTime-e.startTime.05&&(e.startPosition=this.controller1.position.clone())),this.controller2.userData.selectPressed&&void 0===t.startPosition&&(i=s-t.startTime,i>.05&&(t.startPosition=this.controller2.position.clone())),!this.controller1.userData.selectPressed&&"tap"===this.type&&(i=this.clock.getElapsedTime()-e.endTime,i>this.doubleClickLimit)){switch(e.taps){case 1:self.prevTap="tap";break;case 2:this.dispatchEvent({type:"doubletap",position:this.controller1.position,matrixWorld:this.controller1.matrixWorld}),self.prevTap="doubletap"}this.type="unknown",e.taps=0}if("unknown"===this.type&&this.touch)"doubletap"==self.prevTap?(this.type="pinch",this.startDistance=this.controller1.position.distanceTo(this.controller2.position),this.dispatchEvent({type:"pinch",delta:new THREE.Vector3(0,0,0),scale:1,initialise:!0})):(this.type="pan",this.startPosition=this.controller1.position.clone(),this.dispatchEvent({type:"pan",delta:new THREE.Vector3(0,0,0),initialise:!0}));else if(("pinch"===this.type||"pan"===this.type)&&"doubletap"==self.prevTap&&this.controller2.position){const e=this.controller1.position.distanceTo(this.controller2.position)/this.startDistance,t=this.controller1.position.clone().sub(this.startPosition);this.dispatchEvent({type:"pinch",delta:t,scale:e})}}}class Oe{constructor(e,t){this.config=void 0===t?{panelSize:{width:1,height:1},width:512,height:512,opacity:.7,body:{fontFamily:"Arial",fontSize:30,padding:2,backgroundColor:"#000",fontColor:"#fff",borderRadius:6}}:t,void 0===this.config.width&&(this.config.width=512),void 0===this.config.height&&(this.config.height=512),void 0===this.config.body&&(this.config.body={fontFamily:"Arial",size:30,padding:2,backgroundColor:"#000",fontColor:"#fff",borderRadius:6});const s=this.config.body;void 0===s.borderRadius&&(s.borderRadius=6),void 0===s.fontFamily&&(s.fontFamily="Arial"),void 0===s.padding&&(s.padding=2),void 0===s.fontSize&&(s.fontSize=30),void 0===s.backgroundColor&&(s.backgroundColor="#000"),void 0===s.fontColor&&(s.fontColor="#fff"),Object.entries(this.config).forEach((([e,t])=>{if(!("object"!=typeof t||"panelSize"===e||t instanceof THREE.WebGLRenderer||t instanceof THREE.Scene)){const e=void 0!==t.position?t.position:{x:0,y:0};void 0!==e.left&&void 0===e.x&&(e.x=e.left),void 0!==e.top&&void 0===e.y&&(e.y=e.top);const s=void 0!==t.width?t.width:this.config.width,i=void 0!==t.height?t.height:this.config.height;void 0!==e.right&&void 0===e.x&&(e.x=this.config.width-e.right-s),void 0!==e.bottom&&void 0===e.y&&(e.y=this.config.height-e.bottom-i),void 0===e.x&&(e.x=0),void 0===e.y&&(e.y=0),t.position=e,void 0===t.type&&(t.type="text")}}));const i=this.createOffscreenCanvas(this.config.width,this.config.height);this.context=i.getContext("2d"),this.context.save();const n=void 0!==this.config.opacity?this.config.opacity:.7,l=new THREE.MeshBasicMaterial({transparent:!0,opacity:n});this.panelSize=void 0!==this.config.panelSize?this.config.panelSize:{width:1,height:1};const r=new THREE.PlaneGeometry(this.panelSize.width,this.panelSize.height);this.mesh=new THREE.Mesh(r,l),this.texture=new THREE.CanvasTexture(i),this.mesh.material.map=this.texture,this.scene=this.config.scene;if(Object.values(this.config).filter((e=>"input-text"===e.type)).length>0){this.keyboard=new Re(this.panelSize.width,this.config.renderer);this.keyboard.mesh.position.set(0,-.3,.2),this.mesh.add(this.keyboard.mesh)}if(void 0===e)this.content={body:""},this.config.body.type="text";else{this.content=e;Object.values(t).filter((e=>"button"===e.type||"scroll"===e.overflow||"input-text"===e.type)).length>0&&(void 0===t||void 0===t.renderer?console.warn("CanvasUI: button, scroll or input-text in the config but no renderer"):(this.renderer=t.renderer,this.initControllers()))}this.selectedElements=[void 0,void 0],this.selectPressed=[!1,!1],this.scrollData=[void 0,void 0],this.intersects=[void 0,void 0],this.needsUpdate=!0,this.update()}getIntersectY(e){const t=this.config.height||512,s=this.intersects[e];return void 0===s||void 0===s.uv?0:(1-s.uv.y)*t}initControllers(){this.vec3=new THREE.Vector3,this.mat4=new THREE.Matrix4,this.raycaster=new THREE.Raycaster;const e=this;function t(t){const s=t.target===e.controller?0:1,i=e.selectedElements[s];if(void 0!==i)if("button"==i.type)e.select(s);else if("input-text"==i.type&&e.keyboard)if(e.keyboard.visible)e.keyboard.linkedUI=void 0,e.keyboard.linkedText=void 0,e.keyboard.linkedElement=void 0,e.keyboard.visible=!1;else{let t;e.keyboard.linkedUI=e,Object.entries(e.config).forEach((([e,s])=>{s==i&&(t=e)}));const s=(.5-(i.position.y+i.height+e.config.body.padding)/e.config.height)*e.panelSize.height,n=Math.max(e.panelSize.width,e.panelSize.height)/2;e.keyboard.position.set(0,-n/1.5-s,.1),e.keyboard.linkedText=e.content[t],e.keyboard.linkedName=t,e.keyboard.linkedElement=i,e.keyboard.visible=!0}}function s(t){const s=t.target===e.controller?0:1;if(e.selectPressed[s]=!0,void 0!==e.selectedElements[s]&&"scroll"==e.selectedElements[s].overflow){const t=e.selectedElements[s];e.scrollData[s]={scrollY:t.scrollY,rayY:e.getIntersectY(s)}}}function i(t){const s=t.target===e.controller?0:1;e.selectPressed[s]=!1,void 0!==e.selectedElements[s]&&"scroll"==e.selectedElements[s].overflow&&(e.scrollData[s]=void 0)}if(this.controller=this.renderer.xr.getController(0),this.controller.addEventListener("select",t),this.controller.addEventListener("selectstart",s),this.controller.addEventListener("selectend",i),this.controller1=this.renderer.xr.getController(1),this.controller1.addEventListener("select",t),this.controller1.addEventListener("selectstart",s),this.controller1.addEventListener("selectend",i),this.scene){const e=.015,t=new THREE.IcosahedronBufferGeometry(e),s=new THREE.MeshBasicMaterial({color:170}),i=new THREE.Mesh(t,s);i.visible=!1,this.scene.add(i);const n=new THREE.Mesh(t,s);n.visible=!1,this.scene.add(n),this.intersectMesh=[i,n]}}setClip(e){const t=this.context;if(t.restore(),t.save(),void 0!==e.clipPath){const s=new Path2D(e.clipPath);t.clip(s)}else{const s=void 0!==e.position?e.position:{x:0,y:0},i=e.borderRadius||0,n=e.width||this.config.width,l=e.height||this.config.height;if(t.beginPath(),0!==i){const e=Math.PI/2;t.moveTo(s.x+i,s.y),t.arc(s.x+i,s.y+i,i,e,2*e,!0),t.lineTo(s.x,s.y+l-i),t.arc(s.x+i,s.y+l-i,i,0,e,!0),t.lineTo(s.x+n-i,s.y+l),t.arc(s.x+n-i,s.y+l-i,i,3*e,4*e,!0),t.lineTo(s.x+n,s.y+i),t.arc(s.x+n-i,s.y+i,i,2*e,3*e,!0),t.closePath(),t.clip()}else t.rect(s.x,s.y,n,l),t.clip()}}setPosition(e,t,s){void 0!==this.mesh&&this.mesh.position.set(e,t,s)}setRotation(e,t,s){void 0!==this.mesh&&this.mesh.rotation.set(e,t,s)}updateElement(e,t){let s=this.content[e];void 0!==s?("object"==typeof s?s.content=t:s=t,this.content[e]=s,this.needsUpdate=!0):console.warn(`CanvasGUI.updateElement: No ${e} found`)}get panel(){return this.mesh}getElementAtLocation(e,t){const s=this,i=Object.entries(this.config).filter((([i,n])=>{if(!("object"!=typeof n||"panelSize"===i||"body"===i||n instanceof THREE.WebGLRenderer||n instanceof THREE.Scene)){const i=n.position,l=void 0!==n.width?n.width:s.config.width,r=void 0!==n.height?n.height:s.config.height;return e>=i.x&&e=i.y&&t0?(this.hover(t,s[0].uv),this.intersects[t]=s[0],this.scroll(t)):(this.hover(t),this.intersects[t]=void 0,this.scroll(t))}update(){if(void 0===this.mesh)return;if(this.controller&&this.handleController(this.controller,0),this.controller1&&this.handleController(this.controller1,1),this.keyboard&&this.keyboard.visible&&this.keyboard.update(),!this.needsUpdate)return;let e=this.context;e.clearRect(0,0,this.config.width,this.config.height);const t=this.config.body.backgroundColor?this.config.body.backgroundColor:"#000";!this.config.body.fontFamily||this.config.body.fontFamily;const s=this.config.body.fontColor?this.config.body.fontColor:"#fff";!this.config.body.fontSize||this.config.body.fontSize,this.setClip(this.config.body),e.fillStyle=t,e.fillRect(0,0,this.config.width,this.config.height);const i=this;Object.entries(this.content).forEach((([t,n])=>{const l=void 0!==i.config[t]?i.config[t]:i.config.body;if("none"!==(void 0!==l.display?l.display:"block")){const r=void 0!==l.position?l.position:{x:0,y:0},o=void 0!==l.width?l.width:i.config.width,a=void 0!==l.height?l.height:i.config.height;"button"!=l.type||n.toLowerCase().startsWith("")||(void 0===l.borderRadius&&(l.borderRadius=6),void 0===l.textAlign&&(l.textAlign="center")),i.setClip(l);const d=n.toLowerCase().startsWith(""),c=void 0!==i.selectedElements[0]&&this.selectedElements[0]===l||void 0!==i.selectedElements[1]&&this.selectedElements[1]===l;if(void 0!==l.backgroundColor&&(c&&"button"==l.type&&void 0!==l.hover?e.fillStyle=l.hover:e.fillStyle=l.backgroundColor,e.fillRect(r.x,r.y,o,a)),"text"==l.type||"button"==l.type||"input-text"==l.type){let h=!1;if(c?(d||"button"!=l.type?e.fillStyle=void 0!==l.hover?l.hover:void 0!==l.fontColor?l.fontColor:s:e.fillStyle=void 0!==l.fontColor?l.fontColor:s,h=void 0===l.hover):e.fillStyle=void 0!==l.fontColor?l.fontColor:s,d){const t=n.toUpperCase().substring(6,n.length-7);e.save(),e.translate(r.x,r.y);const s=new Path2D(t);e.fill(s),e.restore()}else i.wrapText(t,n);h&&(e.beginPath(),e.strokeStyle="#fff",e.lineWidth=2,e.rect(r.x,r.y,o,a),e.stroke())}else if("img"==l.type)if(void 0===l.img)this.loadImage(n).then((e=>{console.log(`w: ${e.width} | h: ${e.height}`),l.img=e,i.needsUpdate=!0,i.update()})).catch((e=>console.error(e)));else{const t=o/(l.img.width/l.img.height);e.drawImage(l.img,r.x,r.y,o,t)}}})),this.needsUpdate=!1,this.texture.needsUpdate=!0}loadImage(e){return new Promise(((t,s)=>{const i=new THREE.Image;i.addEventListener("load",(()=>t(i))),i.addEventListener("error",(e=>s(e))),i.src=e}))}createOffscreenCanvas(e,t){const s=document.createElement("canvas");return s.width=e,s.height=t,s}fillRoundedRect(e,t,s,i,n){const l=this.context;l.beginPath(),l.moveTo(e+n,t),l.lineTo(e+s-n,t),l.quadraticCurveTo(e+s,t,e+s,t+n),l.lineTo(e+s,t+i-n),l.quadraticCurveTo(e+s,t+i,e+s-n,t+i),l.lineTo(e+n,t+i),l.quadraticCurveTo(e,t+i,e,t+i-n),l.lineTo(e,t+n),l.quadraticCurveTo(e,t,e+n,t),l.closePath(),l.fill()}lookAt(e){void 0!==this.mesh&&(e instanceof Vector3?this.mesh.lookAt(e):console.error("CanvasUI lookAt called parameter not a THREE.Vector3"))}get visible(){return void 0!==this.mesh&&this.mesh.visible}set visible(e){this.mesh&&(this.mesh.visible=e)}get position(){if(void 0!==this.mesh)return this.mesh.position}set position(e){void 0!==this.mesh&&(e instanceof Vector3?this.mesh.position.copy(e):console.error("CanvasUI trying to set the mesh position using a parameter that is not a THREE.Vector3"))}get quaternion(){if(void 0!==this.mesh)return this.mesh.quaternion}set quaternion(e){void 0!==this.mesh&&(e instanceof QUaternion?this.mesh.quaternion.copy(e):console.error("CanvasUI trying to set the mesh quaternion using a parameter that is not a THREE.Quaternion"))}wrapText(e,t){const s=t.split(" ");let i="";const n=[],l=void 0!==this.config[e]?this.config[e]:this.config.body,r=void 0!==l.width?l.width:this.config.width,o=void 0!==l.height?l.height:this.config.height,a=void 0!==l.position?l.position:{x:0,y:0},d=void 0!==l.padding?l.padding:void 0!==this.config.body.padding?this.config.body.padding:10,c=void 0!==l.paddingTop?l.paddingTop:d,h=void 0!==l.paddingLeft?l.paddingLeft:d,p=void 0!==l.paddingBottom?l.paddingBottom:d,m=void 0!==l.paddingRight?l.paddingRight:d,u={x:a.x+h,y:a.y+c,width:r-h-m,height:o-c-p},g=void 0!==l.textAlign?l.textAlign:void 0!==this.config.body.textAlign?this.config.body.textAlign:"left",f=void 0!==l.fontSize?l.fontSize:void 0!==this.config.body.fontSize?this.config.body.fontSize:30,b=void 0!==l.fontFamily?l.fontFamily:void 0!==this.config.body.fontFamily?this.config.body.fontFamily:"Arial",C=f+(void 0!==l.leading?l.leading:void 0!==this.config.body.leading?this.config.body.leading:8),y=this.context;y.textAlign=g,y.font=`${f}px '${b}'`,s.forEach((function(e){let t=s.length>1?`${i}${e} `:e,l=y.measureText(t);if(l.width>u.width&&e.length>1)if(0==i.length&&l.width>u.width){for(;l.width>u.width;){let s=0;do{s++,t=e.substr(0,s),l=y.measureText(t)}while(l.widthu.height&&"scroll"===l.overflow){void 0===l.scrollY&&(l.scrollY=0);const e=void 0!==l.fontColor?l.fontColor:this.config.body.fontColor;y.fillStyle="#aaa",this.fillRoundedRect(a.x+r-12,a.y,12,o,6),y.fillStyle="#666";const t=u.height/v,s=t*o,i=-l.scrollY*t;this.fillRoundedRect(a.x+r-12,a.y+i,12,s,6),y.fillStyle=e,_=l.scrollY,l.minScrollY=u.height-v}let w,S=_+u.y+f/2;switch(g){case"center":w=u.x+u.width/2;break;case"right":w=u.x+u.width;break;default:w=u.x}n.forEach((e=>{S+C>0&&y.fillText(e,w,S),S+=C}))}}class Re{constructor(e,t,s="EN"){const i=this.getConfig(s);i.panelSize={width:e,height:.5*e},i.height=256,i.body={backgroundColor:"#555"},i.renderer=t;const n=this.getContent(s);this.keyboard=new Oe(n,i),this.keyboard.mesh.visible=!1,this.shift=!1}get mesh(){return this.keyboard.mesh}getConfig(e){const t={};let s=10;const i=39.2,n=49,l="#333",r="#000";let o=s,a=s;for(let e=0;e<10;e++){const d={type:"button",position:{x:a,y:o},width:i,height:n,padding:s,paddingTop:20,backgroundColor:r,borderRadius:6,hover:l,onSelect:this.onSelect.bind(this,e)};t[`btn${e}`]=d,a+=49.2}o+=59,a=s;for(let e=0;e<10;e++){const d={type:"button",position:{x:a,y:o},width:i,height:n,padding:s,paddingTop:20,backgroundColor:r,borderRadius:6,hover:l,onSelect:this.onSelect.bind(this,e+10)};t[`btn${e+10}`]=d,a+=49.2}o+=59,a=s;for(let e=0;e<9;e++){const d=0==e||8==e?1.5*i+5:i,c={type:"button",position:{x:a,y:o},width:d,height:n,padding:s,paddingTop:20,backgroundColor:r,borderRadius:6,hover:l,onSelect:this.onSelect.bind(this,e+20)};t[`btn${e+20}`]=c,a+=d+s}o+=59,a=s;for(let e=0;e<5;e++){const d=0==e||4==e?88.4:2==e?186.8:i,c={type:"button",position:{x:a,y:o},width:d,height:n,padding:s,paddingTop:20,backgroundColor:r,borderRadius:6,hover:l,onSelect:this.onSelect.bind(this,e+30)};0==e&&(c.fontSize=20),t[`btn${e+30}`]=c,a+=d+s}return t}getContent(e,t=0){let s,i={};switch(this.language=e,this.keyboardIndex=t,t){case 0:s=["q","w","e","r","t","y","u","i","o","p","a","s","d","f","g","h","j","k","l","@","⇧","z","x","c","v","b","n","m","⇦","","?123",","," ",".","↲"];for(let e=0;e","_","`","~",":",";","⇦","","abc",","," ",".","↲"];for(let e=0;e=0;e--){let s=t.scene.children[e];t.scene.remove(s)}else t.scene=new THREE.Scene;if(void 0!==t.scene_ghost)for(let e=t.scene_ghost.children.length-1;e>=0;e--){let s=t.scene_ghost.children[e];t.scene_ghost.remove(s)}else t.scene_ghost=new THREE.Scene;if(""!=s.htmlCls.setHtmlCls.getCookie("shininess")){let e=parseFloat(s.htmlCls.setHtmlCls.getCookie("shininess"));t.shininess!=e&&s.htmlCls.clickMenuCls.setLogCmd("set shininess "+e,!0),t.shininess=e}if(!s.bNode&&""!=s.htmlCls.setHtmlCls.getCookie("light1")){let e=parseFloat(s.htmlCls.setHtmlCls.getCookie("light1")),i=parseFloat(s.htmlCls.setHtmlCls.getCookie("light2")),n=parseFloat(s.htmlCls.setHtmlCls.getCookie("light3"));t.light1==e&&t.light2==i&&t.light3==n||s.htmlCls.clickMenuCls.setLogCmd("set light | light1 "+e+" | light2 "+i+" | light3 "+n,!0),t.light1=e,t.light2=i,t.light3=n}t.directionalLight=new THREE.DirectionalLight(16777215,t.light1),t.directionalLight2=new THREE.DirectionalLight(16777215,t.light2),t.directionalLight3=new THREE.DirectionalLight(16777215,t.light3),t.cam_z>0?(t.directionalLight.position.set(-1,1,1),t.directionalLight2.position.set(1,1,1),t.directionalLight3.position.set(1,1,-1),t.lightPos=new THREE.Vector3(-1,1,1),t.lightPos2=new THREE.Vector3(1,1,1),t.lightPos3=new THREE.Vector3(1,1,-1)):(t.directionalLight.position.set(-1,1,-1),t.directionalLight2.position.set(1,1,-1),t.directionalLight3.position.set(1,1,1),t.lightPos=new THREE.Vector3(-1,1,-1),t.lightPos2=new THREE.Vector3(1,1,-1),t.lightPos3=new THREE.Vector3(1,1,1));let i=new THREE.AmbientLight(4210752);if(t.scene.add(t.directionalLight),t.scene.add(i),void 0!==t.mdl)for(let e=t.mdl.children.length-1;e>=0;e--){let s=t.mdl.children[e];s.geometry&&s.geometry.dispose(),s.material&&s.material.dispose(),t.mdl.remove(s)}if(void 0!==t.mdlImpostor){for(let e=t.mdlImpostor.children.length-1;e>=0;e--){let s=t.mdlImpostor.children[e];s.geometry&&s.geometry.dispose(),s.material&&s.material.dispose(),t.mdlImpostor.remove(s)}t.mdlImpostor.children.length=0}s.bNode||t.renderer.renderLists.dispose(),t.mdl=new THREE.Object3D,t.mdlImpostor=new THREE.Object3D,t.scene.add(t.mdl),t.scene.add(t.mdlImpostor),t.mdl_ghost=new THREE.Object3D,t.scene_ghost.add(t.mdl_ghost),t.objects=[],t.objects_ghost=[],t.raycaster=new THREE.Raycaster,t.projector=new THREE.Projector,t.mouse=new THREE.Vector2;let n=s.parasCls.backgroundColors[t.opts.background.toLowerCase()];s.bNode||("transparent"===t.opts.background.toLowerCase()?t.renderer.setClearColor(n,0):t.renderer.setClearColor(n,1)),t.perspectiveCamera=new THREE.PerspectiveCamera(20,t.container.whratio,.1,1e4),t.perspectiveCamera.position.set(0,0,t.cam_z),t.perspectiveCamera.lookAt(new THREE.Vector3(0,0,0)),t.orthographicCamera=new THREE.OrthographicCamera,t.orthographicCamera.position.set(0,0,t.cam_z),t.orthographicCamera.lookAt(new THREE.Vector3(0,0,0)),t.cams={perspective:t.perspectiveCamera,orthographic:t.orthographicCamera}}setVrAr(){let e=this.icn3d;e.icn3dui;let t=this;e.bSetVrAr=!0,e.bVr?(e.canvasUI=this.createUI(),e.raycasterVR=new THREE.Raycaster,e.workingMatrix=new THREE.Matrix4,e.workingVector=new THREE.Vector3,e.origin=new THREE.Vector3,e.dolly=new THREE.Object3D,e.dolly.position.z=5,e.dolly.add(e.cam),e.scene.add(e.dolly),e.dollyId=e.dolly.id,e.dummyCam=new THREE.Object3D,e.cam.add(e.dummyCam),e.clock=new THREE.Clock,e.controllers=this.getControllers(),e.controllers.forEach((s=>{s.addEventListener("connected",(function(e){try{const s={},i="https://cdn.jsdelivr.net/npm/@webxr-input-profiles/assets@1.0/dist/profiles",n="generic-trigger";Ce(e.data,i,n).then((({profile:i,assetPath:n})=>{s.name=i.profileId,s.targetRayMode=e.data.targetRayMode,Object.entries(i.layouts).forEach((([e,t])=>{const i={};Object.values(t.components).forEach((e=>{i[e.rootNodeName]=e.gamepadIndices})),s[e]=i})),t.updateControllers(s)}))}catch(e){}})),s.addEventListener("disconnected",(function(){this.remove(this.children[0]),e.controllers.forEach((e=>{}))}))}))):e.bAr&&(e.gestures=new ke(e.renderer),e.scene.add(e.gestures.controller1),e.scene.add(e.gestures.controller2),e.gestures.addEventListener("doubletap",(e=>{t.positionCenter()})),e.gestures.addEventListener("pinch",(s=>{if(void 0!==s.initialise)t.startPosition=e.mdl.position.clone(),t.startScale=e.mdl.scale.clone();else{let i=1;const n=t.startScale.clone().multiplyScalar(s.scale*i);e.mdl.scale.copy(n)}})))}positionCenter(){let e=this.icn3d;e.icn3dui;const t=e.gestures.controller1;e.mdl.position.set(-.06,0,-.6).applyMatrix4(t.matrixWorld),e.mdl.scale.copy(new THREE.Vector3(.005,.005,.005))}setVrArButtons(){let e=this.icn3d,t=e.icn3dui;e.bSetVrArButtons=!0,t.bNode||($("#"+t.pre+"VRButton").remove(),$("#"+t.pre+"viewer").get(0).appendChild(e.VRButtonCls.createButton(e.renderer)),$("#"+t.pre+"ARButton").remove(),$("#"+t.pre+"viewer").get(0).appendChild(e.ARButtonCls.createButton(e.renderer)))}updateControllers(e){this.icn3d.icn3dui,this.addEventForController(e,"right"),this.addEventForController(e,"left")}addEventForController(e,t){let s=this.icn3d;s.icn3dui;const i="right"==t?s.renderer.xr.getController(0):s.renderer.xr.getController(1),n="right"==t?e.right:e.left;if(i&&void 0!==n){let e=!1,t=!1;Object.keys(n).forEach((i=>{-1!=i.indexOf("trigger")&&(e=!0),-1!=i.indexOf("squeeze")&&(t=!0),-1==i.indexOf("thumbstick")&&-1==i.indexOf("touchpad")||(s.xAxisIndex=n[i].xAxis,s.yAxisIndex=n[i].yAxis)})),e&&(i.addEventListener("selectstart",(function(){this.userData.selectPressed=!0})),i.addEventListener("selectend",(function(){this.userData.selectPressed=!1,this.userData.selected=void 0}))),t&&(i.addEventListener("squeezestart",(function(){this.userData.squeezePressed=!0,s.cam.add(s.canvasUI.mesh)})),i.addEventListener("squeezeend",(function(){this.userData.squeezePressed=!1,s.cam.remove(s.canvasUI.mesh)})))}}createUI(){let e=this.icn3d,t=e.icn3dui,s=94,i=50,n=94,l=34,r=12,o="#1c94c4",a="#ccc",d="#fbcb09",c=20;const h={panelSize:{width:2,height:1.6},height:400,select:{type:"button",paddingTop:c,position:{top:6,left:6},width:s,height:i,fontColor:"#000",fontSize:14,backgroundColor:a},residue:{type:"button",paddingTop:c,position:{top:62,left:6},width:s,height:i,fontColor:o,fontSize:r,backgroundColor:a,hover:d,onSelect:function(){e.pk=2,e.pAtomNum||(e.pAtomNum=0),e.cam.remove(e.canvasUI.mesh)}},secondarySelect:{type:"button",paddingTop:12,position:{top:118,left:6},width:s,height:i,fontColor:o,fontSize:r,backgroundColor:a,hover:d,onSelect:function(){e.pk=3,e.pAtomNum||(e.pAtomNum=0),e.cam.remove(e.canvasUI.mesh)}},chainSelect:{type:"button",paddingTop:c,position:{top:174,left:6},width:s,height:i,fontColor:o,fontSize:r,backgroundColor:a,hover:d,onSelect:function(){e.pk=5,e.pAtomNum||(e.pAtomNum=0),e.cam.remove(e.canvasUI.mesh)}},atom:{type:"button",paddingTop:c,position:{top:230,left:6},width:s,height:i,fontColor:o,fontSize:r,backgroundColor:a,hover:d,onSelect:function(){e.pk=1,e.pAtomNum||(e.pAtomNum=0),e.cam.remove(e.canvasUI.mesh)}},reset:{type:"button",paddingTop:c,position:{top:286,left:6},width:s,height:i,fontColor:o,fontSize:r,backgroundColor:a,hover:d,onSelect:function(){e.viewInterPairsCls.resetInteractionPairs(),e.selectionCls.resetAll(),e.cam.remove(e.canvasUI.mesh)}},togglehl:{type:"button",paddingTop:12,position:{top:342,left:6},width:s,height:i,fontColor:o,fontSize:r,backgroundColor:a,hover:d,onSelect:function(){e.hlUpdateCls.toggleHighlight(),e.cam.remove(e.canvasUI.mesh)}},style:{type:"button",paddingTop:c,position:{top:6,left:106},width:s,height:i,fontColor:"#000",fontSize:14,backgroundColor:a},ribbon:{type:"button",paddingTop:c,position:{top:62,left:106},width:s,height:i,fontColor:o,fontSize:r,backgroundColor:a,hover:d,onSelect:function(){e.setOptionCls.setStyle("proteins","ribbon"),e.setOptionCls.setStyle("nucleotides","nucleotide cartoon"),e.cam.remove(e.canvasUI.mesh)}},schematic:{type:"button",paddingTop:c,position:{top:118,left:106},width:s,height:i,fontColor:o,fontSize:r,backgroundColor:a,hover:d,onSelect:function(){e.setOptionCls.setStyle("proteins","schematic"),e.setOptionCls.setStyle("nucleotides","schematic"),e.cam.remove(e.canvasUI.mesh)}},stick:{type:"button",paddingTop:c,position:{top:174,left:106},width:s,height:i,fontColor:o,fontSize:r,backgroundColor:a,hover:d,onSelect:function(){e.setOptionCls.setStyle("proteins","stick"),e.setOptionCls.setStyle("nucleotides","stick"),e.cam.remove(e.canvasUI.mesh)}},sphere:{type:"button",paddingTop:c,position:{top:230,left:106},width:s,height:i,fontColor:o,fontSize:r,backgroundColor:a,hover:d,onSelect:function(){e.setOptionCls.setStyle("proteins","sphere"),e.setOptionCls.setStyle("nucleotides","sphere"),e.cam.remove(e.canvasUI.mesh)}},surface:{type:"button",paddingTop:c,position:{top:286,left:106},width:s,height:i,fontColor:o,fontSize:r,backgroundColor:a,hover:d,onSelect:function(){e.opts.surface="molecular surface",e.applyMapCls.applySurfaceOptions(),e.cam.remove(e.canvasUI.mesh)}},surfaceTrn:{type:"button",paddingTop:12,position:{top:342,left:106},width:s,height:i,fontColor:o,fontSize:r,backgroundColor:a,hover:d,onSelect:function(){e.opts.surface="molecular surface",e.opts.opacity="0.2",e.applyMapCls.applySurfaceOptions(),e.cam.remove(e.canvasUI.mesh)}},color:{type:"button",paddingTop:c,position:{top:6,left:206},width:s,height:i,fontColor:"#000",fontSize:14,backgroundColor:a},rainbow:{type:"button",paddingTop:c,position:{top:62,left:206},width:s,height:i,fontColor:o,fontSize:r,backgroundColor:a,hover:d,onSelect:function(){e.setOptionCls.setOption("color","rainbow for chains"),e.cam.remove(e.canvasUI.mesh)}},atomColor:{type:"button",paddingTop:c,position:{top:118,left:206},width:s,height:i,fontColor:o,fontSize:r,backgroundColor:a,hover:d,onSelect:function(){e.setOptionCls.setOption("color","atom"),e.cam.remove(e.canvasUI.mesh)}},chainColor:{type:"button",paddingTop:c,position:{top:174,left:206},width:s,height:i,fontColor:o,fontSize:r,backgroundColor:a,hover:d,onSelect:function(){e.setOptionCls.setOption("color","chain"),e.cam.remove(e.canvasUI.mesh)}},secondaryColor:{type:"button",paddingTop:12,position:{top:230,left:206},width:s,height:i,fontColor:o,fontSize:r,backgroundColor:a,hover:d,onSelect:function(){e.setOptionCls.setOption("color","secondary structure green"),e.cam.remove(e.canvasUI.mesh)}},charge:{type:"button",paddingTop:c,position:{top:342,left:206},width:s,height:i,fontColor:o,fontSize:r,backgroundColor:a,hover:d,onSelect:function(){e.setOptionCls.setOption("color","charge"),e.cam.remove(e.canvasUI.mesh)}},AlphaFold:{type:"button",paddingTop:c,position:{top:286,left:206},width:s,height:i,fontColor:o,fontSize:r,backgroundColor:a,hover:d,onSelect:function(){e.setOptionCls.setOption("color","confidence"),e.cam.remove(e.canvasUI.mesh)}},unicolor:{type:"button",paddingTop:c,position:{top:6,left:306},width:s,height:i,fontColor:"#000",fontSize:14,backgroundColor:a},red:{type:"button",position:{top:i,left:300},width:n,height:l,fontColor:"red",hover:d,onSelect:function(){e.setOptionCls.setOption("color","red"),e.cam.remove(e.canvasUI.mesh)}},green:{type:"button",position:{top:78,left:300},width:n,height:l,fontColor:"green",hover:d,onSelect:function(){e.setOptionCls.setOption("color","green"),e.cam.remove(e.canvasUI.mesh)}},blue:{type:"button",position:{top:106,left:300},width:n,height:l,fontColor:"blue",hover:d,onSelect:function(){e.setOptionCls.setOption("color","blue"),e.cam.remove(e.canvasUI.mesh)}},blueviolet:{type:"button",position:{top:134,left:300},width:n,height:l,fontColor:"#8A2BE2",hover:d,onSelect:function(){e.setOptionCls.setOption("color","8A2BE2"),e.cam.remove(e.canvasUI.mesh)}},magenta:{type:"button",position:{top:162,left:300},width:n,height:l,fontColor:"magenta",hover:d,onSelect:function(){e.setOptionCls.setOption("color","magenta"),e.cam.remove(e.canvasUI.mesh)}},yellow:{type:"button",position:{top:190,left:300},width:n,height:l,fontColor:"yellow",hover:d,onSelect:function(){e.setOptionCls.setOption("color","yellow"),e.cam.remove(e.canvasUI.mesh)}},orange:{type:"button",position:{top:218,left:300},width:n,height:l,fontColor:"orange",hover:d,onSelect:function(){e.setOptionCls.setOption("color","FFA500"),e.cam.remove(e.canvasUI.mesh)}},cyan:{type:"button",position:{top:246,left:300},width:n,height:l,fontColor:"cyan",hover:d,onSelect:function(){e.setOptionCls.setOption("color","cyan"),e.cam.remove(e.canvasUI.mesh)}},gray:{type:"button",position:{top:274,left:300},width:n,height:l,fontColor:"gray",hover:d,onSelect:function(){e.setOptionCls.setOption("color","888888"),e.cam.remove(e.canvasUI.mesh)}},white:{type:"button",position:{top:302,left:300},width:n,height:l,fontColor:"white",hover:d,onSelect:function(){e.setOptionCls.setOption("color","white"),e.cam.remove(e.canvasUI.mesh)}},analysis:{type:"button",paddingTop:c,position:{top:6,left:406},width:s,height:i,fontColor:"#000",fontSize:14,backgroundColor:a},distance:{type:"button",paddingTop:c,position:{top:62,left:406},width:s,height:i,fontColor:o,fontSize:r,backgroundColor:a,hover:d,onSelect:function(){try{e.bMeasureDistance=!0;let s=e.pickingCls.getPickedAtomList(e.pk,e.pAtom),i=e.pickingCls.getPickedAtomList(e.pk,e.pAtom2),n=e.applyCenterCls.centerAtoms(t.hashUtilsCls.hash2Atoms(s,e.atoms)).center,l=e.applyCenterCls.centerAtoms(t.hashUtilsCls.hash2Atoms(i,e.atoms)).center,r=0,o=0,a="#FFFF00",d=(n.x+l.x)/2,c=(n.y+l.y)/2,h=(n.z+l.z)/2,p=!0;e.analysisCls.addLine(n.x,n.y,n.z,l.x,l.y,l.z,a,p,"distance");let m=(parseInt(10*n.distanceTo(l))/10).toString()+" A";e.analysisCls.addLabel(m,d,c,h,r,a,o,"distance"),e.drawCls.draw(),e.cam.remove(e.canvasUI.mesh)}catch(e){}}},interaction:{type:"button",paddingTop:c,position:{top:118,left:406},width:s,height:i,fontColor:o,fontSize:r,backgroundColor:a,hover:d,onSelect:function(){try{e.viewInterPairsCls.viewInteractionPairs(["selected"],["non-selected"],!1,"3d",1,1,1,1,1,1),e.cam.remove(e.canvasUI.mesh)}catch(e){}}},delphi:{type:"button",paddingTop:c,position:{top:174,left:406},width:s,height:i,fontColor:o,fontSize:r,backgroundColor:a,hover:d,onSelect:async function(){e.phisurftype=22,e.phisurfop=1,e.phisurfwf="no",await e.delphiCls.CalcPhi(65,.15,2,!0),e.cam.remove(e.canvasUI.mesh)}},removeLabel:{type:"button",paddingTop:c,position:{top:230,left:406},width:s,height:i,fontColor:o,fontSize:r,backgroundColor:a,hover:d,onSelect:function(){for(let t in e.labels)e.labels[t]=[];e.drawCls.draw(),e.cam.remove(e.canvasUI.mesh)}},renderer:e.renderer},p=new Oe({select:"Select",residue:"Residue",secondarySelect:"Secondary Structure",chainSelect:"Chain",atom:"Atom",reset:"Reset",togglehl:"Toggle Highlight",style:"Style",ribbon:"Ribbon",schematic:"Schematic",stick:"Stick",sphere:"Sphere",surface:"Surface",surfaceTrn:"Transparent Surface",color:"Color",rainbow:"Rainbow",atomColor:"Atom",chainColor:"Chain",secondaryColor:"Secondary Structure",AlphaFold:"AlphaFold",charge:"Charge",unicolor:"UniColor",red:"M 100 15 L 15 15 L 15 100 L 100 100 Z",green:"M 100 15 L 15 15 L 15 100 L 100 100 Z",blue:"M 100 15 L 15 15 L 15 100 L 100 100 Z",blueviolet:"M 100 15 L 15 15 L 15 100 L 100 100 Z",magenta:"M 100 15 L 15 15 L 15 100 L 100 100 Z",yellow:"M 100 15 L 15 15 L 15 100 L 100 100 Z",orange:"M 100 15 L 15 15 L 15 100 L 100 100 Z",cyan:"M 100 15 L 15 15 L 15 100 L 100 100 Z",gray:"M 100 15 L 15 15 L 15 100 L 100 100 Z",white:"M 100 15 L 15 15 L 15 100 L 100 100 Z",analysis:"Analysis",distance:"Distance",interaction:"Interaction",delphi:"DelPhi Potential",removeLabel:"Remove Label"},h);return p.mesh.position.set(0,0,-3),p}createUILog(){let e=this.icn3d;e.icn3dui;const t={panelSize:{width:2,height:2},height:512,info:{type:"text",overflow:"scroll",position:{top:6,left:6},width:506,height:506,backgroundColor:"#aaa",fontColor:"#000"},renderer:e.renderer},s=new Oe({info:"Debug info"},t);return s.mesh.position.set(0,-1,-2),s}getControllers(){let e=this.icn3d;e.icn3dui;const t=new xe,s=(new THREE.BufferGeometry).setFromPoints([new THREE.Vector3(0,0,0),new THREE.Vector3(0,0,-1)]),i=new THREE.Line(s);i.name="line",i.scale.z=50;const n=[];for(let s=0;s<=1;s++){const l=e.renderer.xr.getController(s);if(!l)continue;e.dolly.add(l),l.add(i.clone()),l.userData.selectPressed=!1,e.cam.add(l),n.push(l);const r=e.renderer.xr.getControllerGrip(s);r.add(t.createControllerModel(r)),e.scene.add(r)}return n}}class Te{constructor(e){this.icn3d=e}setCamera(){let e=this.icn3d,t=e.icn3dui;if(e.bControlGl&&!t.bNode){window.cam=e.cams[e.opts.camera.toLowerCase()];let s=e.maxD;if(window.cam===e.perspectiveCamera){let i=void 0!==e.biomtMatrices&&e.biomtMatrices.length*e.cnt>e.maxatomcnt;i?window.camMaxDFactor=1:void 0!==window.camMaxDFactorFog?window.camMaxDFactor=window.camMaxDFactorFog:window.camMaxDFactor=3,window.cam_z>0?window.cam.position.z=s*window.camMaxDFactor:window.cam.position.z=-s*window.camMaxDFactor,"yes"===e.opts.slab?i?window.cam.near=.1:void 0!==window.camMaxDFactorFog?window.cam.near=s*window.camMaxDFactorFog-10:window.cam.near=s*window.camMaxDFactor:window.cam.near=.1,window.cam.far=1e4,e.bControlGl&&!t.bNode?window.controls=new THREE.TrackballControls(window.cam,void 0,e):t.bNode?e.controls=new THREE.TrackballControls(e.cam,document,e):e.controls=new THREE.TrackballControls(e.cam,document.getElementById(e.id),e)}else window.cam===e.orthographicCamera&&(void 0!==e.biomtMatrices&&e.biomtMatrices.length*e.cnt>10*e.maxatomcnt?window.cam.right=e.maxD/2*1.5:window.cam.right=e.maxD/2*2.5,window.cam.left=-window.cam.right,window.cam.top=window.cam.right/e.container.whratio,window.cam.bottom=-window.cam.right/e.container.whratio,"yes"===e.opts.slab?window.cam.near=2*e.maxD:window.cam.near=0,window.cam.far=1e4,e.bControlGl&&!t.bNode?window.controls=new THREE.OrthographicTrackballControls(window.cam,void 0,e):t.bNode?e.controls=new THREE.OrthographicTrackballControls(e.cam,document,e):e.controls=new THREE.OrthographicTrackballControls(e.cam,document.getElementById(e.id),e));window.cam.updateProjectionMatrix()}e.cam=e.cams[e.opts.camera.toLowerCase()];let s=e.maxD;if(e.cam===e.perspectiveCamera){let i=void 0!==e.biomtMatrices&&e.biomtMatrices.length*e.cnt>e.maxatomcnt;i?e.camMaxDFactor=1:void 0!==e.camMaxDFactorFog?e.camMaxDFactor=e.camMaxDFactorFog:e.camMaxDFactor=3,e.cam_z>0?e.cam.position.z=s*e.camMaxDFactor:e.cam.position.z=-s*e.camMaxDFactor,"yes"===e.opts.slab?i?e.cam.near=.1:void 0!==e.camMaxDFactorFog?e.cam.near=s*e.camMaxDFactorFog-10:e.cam.near=s*e.camMaxDFactor:e.cam.near=.1,e.cam.far=1e4,e.bControlGl&&!t.bNode?window.controls=new THREE.TrackballControls(e.cam,void 0,e):t.bNode?e.controls=new THREE.TrackballControls(e.cam,document,e):e.controls=new THREE.TrackballControls(e.cam,document.getElementById(e.id),e)}else e.cam===e.orthographicCamera&&(void 0!==e.biomtMatrices&&e.biomtMatrices.length*e.cnt>10*e.maxatomcnt?e.cam.right=e.maxD/2*1.5:e.cam.right=e.maxD/2*2.5,e.cam.left=-e.cam.right,e.cam.top=e.cam.right/e.container.whratio,e.cam.bottom=-e.cam.right/e.container.whratio,"yes"===e.opts.slab?e.cam.near=2*e.maxD:e.cam.near=0,e.cam.far=1e4,e.bControlGl&&!t.bNode?window.controls=new THREE.OrthographicTrackballControls(e.cam,void 0,e):t.bNode?e.controls=new THREE.OrthographicTrackballControls(e.cam,document,e):e.controls=new THREE.OrthographicTrackballControls(e.cam,document.getElementById(e.id),e));e.cam.updateProjectionMatrix()}}class Ee{constructor(e){this.icn3d=e}setFog(e){let t=this.icn3d,s=t.icn3dui.parasCls.backgroundColors[t.opts.background.toLowerCase()];if(e){let e=t.applyCenterCls.centerAtoms(t.hAtoms);t.maxD=e.maxD,t.maxD<25&&(t.maxD=25)}let i=void 0!==t.biomtMatrices&&t.biomtMatrices.length*t.cnt>t.maxatomcnt;if("yes"===t.opts.fog)if("perspective"===t.opts.camera)if(i)t.scene.fog=void 0,t.bSetFog=!1;else{let e=t._zoomFactor>1?1*t._zoomFactor:t._zoomFactor;t.scene.fog=new THREE.Fog(s,2.5*t.maxD*e,4*t.maxD*e),t.bSetFog=!0,t.camMaxDFactorFog=3}else"orthographic"===t.opts.camera&&(t.scene.fog=void 0,t.bSetFog=!1);else t.scene.fog=void 0,t.bSetFog=!1}}class Pe{constructor(e){this.icn3d=e}createBox(e,t,s,i,n,l){let r=this.icn3d,o=r.icn3dui;if(o.bNode)return;void 0===t&&(t=.8),void 0===s&&(s=!1),void 0===i&&(i=.8),l?void 0===n&&(n=r.hColor):void 0===n&&(n=e.color);let a=s?t:(o.parasCls.vdwRadii[e.elem.toUpperCase()]||t)*(i||1);this.createBox_base(e.coord,a,n,l)}createBox_base(e,t,s,i,n,l,r){let o,a=this.icn3d;a.icn3dui.bNode||(void 0===r&&(r=l?.5:1),new THREE.BoxGeometry(1,1,1),o=new THREE.Mesh(a.boxGeometry,new THREE.MeshPhongMaterial({transparent:!0,opacity:r,specular:a.frac,shininess:a.shininess,emissive:a.emissive,color:s})),o.scale.x=o.scale.y=o.scale.z=t,o.position.copy(e),a.mdl.add(o),i?a.prevHighlightObjects.push(o):n?a.prevOtherMesh.push(o):a.objects.push(o))}createBoxRepresentation_P_CA(e,t,s){let i=this.icn3d;if(i.icn3dui.bNode)return;let n=this;i.reprSubCls.createRepresentationSub(e,(function(e){"CA"!==e.name&&"O3'"!==e.name&&"O3*"!==e.name||n.createBox(e,void 0,void 0,t,void 0,s)}))}}class Me{constructor(e){this.icn3d=e}createBrick(e,t,s,i){let n=this.icn3d;if(n.icn3dui.bNode)return;let l=new THREE.CylinderGeometry(1,1,1,4,1),r=new THREE.Mesh(l,new THREE.MeshPhongMaterial({specular:n.frac,shininess:n.shininess,emissive:n.emissive,color:i}));r.position.copy(e).add(t).multiplyScalar(.5),r.matrixAutoUpdate=!1,r.lookAt(t.clone().sub(e)),r.updateMatrix(),r.matrix.multiply((new THREE.Matrix4).makeScale(s,s,e.distanceTo(t))).multiply((new THREE.Matrix4).makeRotationX(.5*Math.PI)),n.mdl.add(r)}}class De{constructor(e){this.icn3d=e}createCurveSubArrow(e,t,s,i,n,l,r,o,a,d,c,h,p,m,u){if(this.icn3d.icn3dui.bNode)return;let g=[],f=[];g.push(e),f.push(o),this.prepareStrand(g,f,t,s,i,void 0,n,l,r,a,d,!1,c,h,p,m,u),g=[],f=[]}createStripArrow(e,t,s,i,n,l,r,o,a,d,c,h,p,m,u,g){if(this.icn3d.icn3dui.bNode)return;let f=[],b=[];f.push(e),f.push(t),b.push(o),b.push(a),this.prepareStrand(f,b,void 0,s,i,n,l,void 0,r,d,c,!0,h,p,m,u,g),f=[],b=[]}prepareStrand(e,t,s,i,n,l,r,o,a,d,c,h,p,m,u,g,f){let b=this.icn3d,C=b.icn3dui;if(1===d.length)return;let y=i,v=!u,_=[];_.push(i[i.length-2]),_.push(i[i.length-1]),n=n||b.axisDIV;let w,S,A,x,k=2/(a-1),O={};for(let e=0,s=t.length;e1)if(void 0!==d){let i,n,l=[];for(let r=0,o=p.length;r0&&i.tubeCls.createTube(a,"CA",i.coilWidth,s),Object.keys(d).length>0&&i.strandCls.createStrand(d,void 0,void 0,!0,0,i.helixSheetWidth,!1,2*i.ribbonthickness,s)):(Object.keys(a).length>0&&i.tubeCls.createTube(a,"CA",i.coilWidth),Object.keys(d).length>0&&i.strandCls.createStrand(d,void 0,void 0,!0,0,i.helixSheetWidth,!1,2*i.ribbonthickness))}createCylinderCurve(e,t,s,i,n){let l=this.icn3d;if(l.icn3dui.bNode)return;let r,o,a,d,c,h,p=null;for(a in e)if(d=e[a],!d.het&&(c=d.structure+"_"+d.chain,h=d.structure+"_"+r,-1!=t.indexOf(d.name))){if(null!==p&&r===d.chain&&l.ParserUtilsCls.getResiNCBI(h,o)+1===l.ParserUtilsCls.getResiNCBI(c,d.resi)&&Math.abs(p.coord.x-d.coord.x)<8&&Math.abs(p.coord.y-d.coord.y)<8&&Math.abs(p.coord.z-d.coord.z)<8){let e=p.coord.clone().add(d.coord).multiplyScalar(.5);if(n)1===n&&(this.createCylinder(p.coord,e,s,p.color,n),this.createCylinder(e,d.coord,s,d.color,n),l.sphereCls.createSphere(d,s,!0,1,n));else if(i){let t=l.lineCls.createSingleLine(p.coord,e,p.color,!1);l.mdl.add(t),l.objects.push(t),t=l.lineCls.createSingleLine(e,d.coord,d.color,!1),l.mdl.add(t),l.objects.push(t)}else this.createCylinder(p.coord,e,s,p.color),this.createCylinder(e,d.coord,s,d.color),l.sphereCls.createSphere(d,s,!0,1,n)}p=d,r=d.chain,o=d.resi,l.sphereCls.createSphere(d,s,!0,1,n),2===n&&l.boxCls.createBox(d,void 0,void 0,void 0,void 0,n)}if(null!==p&&r===d.chain&&l.ParserUtilsCls.getResiNCBI(h,o)+1===l.ParserUtilsCls.getResiNCBI(c,d.resi)&&Math.abs(p.coord.x-d.coord.x)<8&&Math.abs(p.coord.y-d.coord.y)<8&&Math.abs(p.coord.z-d.coord.z)<8){let e=p.coord.add(d.coord).multiplyScalar(.5);if(n)1===n&&(this.createCylinder(p.coord,e,s,p.color,n),this.createCylinder(e,d.coord,s,d.color,n),l.sphereCls.createSphere(d,s,!0,1,n));else if(i){let t=l.lineCls.createSingleLine(p.coord,e,p.color,!1);l.mdl.add(t),l.objects.push(t),t=l.lineCls.createSingleLine(e,d.coord,d.color,!1),l.mdl.add(t),l.objects.push(t)}else this.createCylinder(p.coord,e,s,p.color),this.createCylinder(e,d.coord,s,d.color)}}}class Le{constructor(e){this.icn3d=e}createLineRepresentation(e,t){let s=this.icn3d;if(s.icn3dui.bNode)return;let i=new THREE.BufferGeometry,n=[],l=[],r=0,o=0;s.reprSubCls.createRepresentationSub(e,void 0,(function(e,t){if(e.color===t.color)n[r++]=e.coord.x,n[r++]=e.coord.y,n[r++]=e.coord.z,n[r++]=t.coord.x,n[r++]=t.coord.y,n[r++]=t.coord.z,l[o++]=e.color.r,l[o++]=e.color.g,l[o++]=e.color.b,l[o++]=t.color.r,l[o++]=t.color.g,l[o++]=t.color.b;else{let s=e.coord.clone().add(t.coord).multiplyScalar(.5);n[r++]=e.coord.x,n[r++]=e.coord.y,n[r++]=e.coord.z,n[r++]=s.x,n[r++]=s.y,n[r++]=s.z,n[r++]=t.coord.x,n[r++]=t.coord.y,n[r++]=t.coord.z,n[r++]=s.x,n[r++]=s.y,n[r++]=s.z,l[o++]=e.color.r,l[o++]=e.color.g,l[o++]=e.color.b,l[o++]=e.color.r,l[o++]=e.color.g,l[o++]=e.color.b,l[o++]=t.color.r,l[o++]=t.color.g,l[o++]=t.color.b,l[o++]=t.color.r,l[o++]=t.color.g,l[o++]=t.color.b}}));if(i.setAttribute("position",new THREE.BufferAttribute(new Float32Array(n),3)),i.setAttribute("color",new THREE.BufferAttribute(new Float32Array(l),3)),2!==t){let e;1===t||(e=new THREE.LineSegments(i,new THREE.LineBasicMaterial({linewidth:s.linewidth,vertexColors:!0})),s.mdl.add(e)),1===t?s.prevHighlightObjects.push(e):s.objects.push(e)}else 2===t&&s.boxCls.createBoxRepresentation_P_CA(e,.8,t)}createConnCalphSidechain(e,t){let s=this.icn3d;if(s.icn3dui.bNode)return;let i={};for(let s in e){let n=e[s];if(!n.het&&n.style2===t){i[n.structure+"_"+n.chain+"_"+n.resi]=1}}let n=[],l=[];for(let e in i){let t=s.firstAtomObjCls.getFirstAtomObjByName(s.residues[e],"CA");if(void 0!==t)for(let e=0,i=t.bonds.length;e=t.bonds.length&&e.bonds.length>1)s=e.serial,l=e.bonds[0],d=e.bonds[1];else{if(!(t.bonds.length>=e.bonds.length&&t.bonds.length>1))return void console.log("Double bond was not drawn due to the undefined cross plane");s=t.serial,l=t.bonds[0],d=t.bonds[1]}let i=r.atoms[s].coord.clone();i.sub(r.atoms[l].coord);let n=r.atoms[s].coord.clone();n.sub(r.atoms[d].coord),i.cross(n),0==parseInt(1e4*i.length())&&(i=new THREE.Vector3(.2,.3,.5)),c=t.coord.clone(),c.sub(e.coord),c.cross(i).normalize().multiplyScalar(.2*o),0==parseInt(1e4*c.length())&&(i=new THREE.Vector3(.5,.3,.2),c.cross(i).normalize().multiplyScalar(.2*o))}e.color===t.color?r.dAtoms.hasOwnProperty(e.serial)&&r.dAtoms.hasOwnProperty(t.serial)&&(r.cylinderCls.createCylinder(e.coord.clone().add(c),t.coord.clone().add(c),a,e.color,n),r.cylinderCls.createCylinder(e.coord.clone().sub(c),t.coord.clone().sub(c),a,e.color,n)):r.bImpo?r.dAtoms.hasOwnProperty(e.serial)&&r.dAtoms.hasOwnProperty(t.serial)&&(r.cylinderCls.createCylinder(e.coord.clone().add(c),t.coord.clone().add(c),a,e.color,n,t.color),r.cylinderCls.createCylinder(e.coord.clone().sub(c),t.coord.clone().sub(c),a,e.color,n,t.color)):r.dAtoms.hasOwnProperty(e.serial)&&r.dAtoms.hasOwnProperty(t.serial)&&(r.cylinderCls.createCylinder(e.coord.clone().add(c),i.clone().add(c),a,e.color,n),r.cylinderCls.createCylinder(t.coord.clone().add(c),i.clone().add(c),a,t.color,n),r.cylinderCls.createCylinder(e.coord.clone().sub(c),i.clone().sub(c),a,e.color,n),r.cylinderCls.createCylinder(t.coord.clone().sub(c),i.clone().sub(c),a,t.color,n))}else if(r.aromaticbonds.hasOwnProperty(l)){let s,l,d;if(e.bonds.length>t.bonds.length&&e.bonds.length>1)s=e.serial,l=e.bonds[0],d=e.bonds[1];else{if(!(t.bonds.length>1))return;s=t.serial,l=t.bonds[0],d=t.bonds[1]}let c=r.atoms[s].coord.clone();c.sub(r.atoms[l].coord);let h=r.atoms[s].coord.clone();h.sub(r.atoms[d].coord),c.cross(h);let p=t.coord.clone();p.sub(e.coord),p.cross(c).normalize().multiplyScalar(.2*o);let m=0;for(let s=0,i=e.bondOrder.length;so+1?(s=k.clone(),i=d.atoms[G[G.length-1-o-1]].coord.clone(),i.sub(s)):s=new THREE.Vector3(Math.random(),Math.random(),Math.random()))):d.bCalphaOnly&&"CA"===b.name&&(G.length>o+1?(s=k.clone(),i=d.atoms[G[G.length-1-o-1]].coord.clone(),i.sub(s)):s=new THREE.Vector3(Math.random(),Math.random(),Math.random())),s.normalize(),s.multiplyScalar(f),null!==I&&s.dot(I)<0&&s.negate(),I=s;for(let e=0,s=2/(t-1);e6||c&&Math.abs(S.y-c.y)>6||c&&Math.abs(S.z-c.z)>6;if((u!==b.chain||b.ssbegin||b.ssend||B===j-1||p)&&m[0].length>0){let c="CA",u=[],g=[];if(isNaN(d.atoms[M].resi))u=[];else{let e=d.atoms[M].structure+"_"+d.atoms[M].chain+"_"+(parseInt(d.atoms[M].resi)-1).toString(),t=d.firstAtomObjCls.getAtomCoordFromResi(e,c);u=void 0!==t?[t]:[]}if(!isNaN(d.atoms[M].resi)){let e=d.atoms[M].structure+"_"+d.atoms[M].chain+"_"+(parseInt(d.atoms[M].resi)+1).toString(),t=d.firstAtomObjCls.getAtomCoordFromResi(e,c);void 0!==t&&g.push(t);let s=d.atoms[M].structure+"_"+d.atoms[M].chain+"_"+(parseInt(d.atoms[M].resi)+2).toString(),i=d.firstAtomObjCls.getAtomCoordFromResi(s,c);void 0!==i&&g.push(i)}if(!p){1===a||2===a?w.push(d.hColor):w.push(R),f=b.ssend&&"sheet"===b.ss?0:"coil"===T&&b.ssbegin||E&&b.ssbegin||"coil"===b.ss?n:l;let s,i,o=4;"O"===b.name?(s=A.clone(),s.sub(S)):d.bCalphaOnly&&"CA"===b.name&&(G.length>o?(s=S.clone(),i=d.atoms[G[G.length-1-o]].coord.clone(),i.sub(s)):s=new THREE.Vector3(Math.random(),Math.random(),Math.random())),s.normalize(),s.multiplyScalar(f),null!==I&&s.dot(I)<0&&s.negate(),I=s;for(let e=0,s=2/(t-1);e0){let e="CA",n=[],l=[];if(isNaN(d.atoms[M].resi))n=[];else{let t=d.atoms[M].structure+"_"+d.atoms[M].chain+"_"+(parseInt(d.atoms[M].resi)-1).toString();d.firstAtomObjCls.getAtomCoordFromResi(t,e)}for(let e=0;!i&&e0;--e){let t=a.structure+"_"+a.chain+"_"+e;if(!c.residues.hasOwnProperty(t))break;let s=c.firstAtomObjCls.getFirstCalphaAtomObj(c.residues[t]);if(s.ss===a.ss&&s.ssbegin){g=s.resi;break}}for(let e=g;e0&&(o!==c.chain||Math.abs(c.coord.x-h.coord.x)>6||Math.abs(c.coord.y-h.coord.y)>6||Math.abs(c.coord.z-h.coord.z)>6||r.ParserUtilsCls.getResiNCBI(c.structure+"_"+o,a)+13||Math.abs(c.coord.y-h.coord.y)>3||Math.abs(c.coord.z-h.coord.z)>3))){if(2!==i){if(!isNaN(d.resi)&&!isNaN(h.resi)){let e=d.structure+"_"+d.chain+"_"+(parseInt(d.resi)-1).toString(),i=r.firstAtomObjCls.getAtomCoordFromResi(e,t);g=void 0!==i?[i]:[];let l=h.structure+"_"+h.chain+"_"+(parseInt(h.resi)+1).toString(),o=h.structure+"_"+h.chain+"_"+(parseInt(h.resi)+2).toString(),a=h.structure+"_"+h.chain+"_"+(parseInt(h.resi)+3).toString();if(r.residues.hasOwnProperty(l)){let e=r.firstAtomObjCls.getAtomFromResi(l,t);void 0!==e&&e.ssbegin&&(l=h.structure+"_"+h.chain+"_"+(parseInt(h.resi)+2).toString(),o=h.structure+"_"+h.chain+"_"+(parseInt(h.resi)+3).toString(),p.push(e.coord),n?u.push(this.getCustomtubesize(l)):u.push(this.getRadius(s,e)),m.push(e.color))}if(1==p.length&&r.residues.hasOwnProperty(l)){let e=r.firstAtomObjCls.getAtomFromResi(l,t);if(e){p.push(e.coord),m.push(e.color);let t=this.getRadius(s,c);u.push(t),l=o,o=a}}let b=r.firstAtomObjCls.getAtomCoordFromResi(l,t);void 0!==b&&f.push(b);let C=r.firstAtomObjCls.getAtomCoordFromResi(o,t);void 0!==C&&f.push(C)}C.push({pnts:p,colors:m,radii:u,prevone:g,nexttwo:f})}p=[],m=[],u=[],g=[],f=[],d=c,b=0}if(0==p.length&&!isNaN(c.resi)){let e=c.structure+"_"+c.chain+"_"+(parseInt(c.resi)-1).toString();r.residues.hasOwnProperty(e)&&(h=r.firstAtomObjCls.getAtomFromResi(e,t),void 0!==h&&h.ssend&&(p.push(h.coord),n?u.push(this.getCustomtubesize(e)):u.push(this.getRadius(s,h)),m.push(h.color)))}let e;p.push(c.coord),e=n?this.getCustomtubesize(c.structure+"_"+c.chain+"_"+c.resi):this.getRadius(s,c),u.push(e),m.push(c.color),1===b&&(m[m.length-2]=c.color),o=c.chain,a=c.resi;let l=1.2;2!==i||c.ssbegin||r.boxCls.createBox(c,void 0,void 0,l,void 0,i),++b,h=c}if(2!==i){if(g=[],void 0!==d&&!isNaN(d.resi)){let e=d.structure+"_"+d.chain+"_"+(parseInt(d.resi)-1).toString(),s=r.firstAtomObjCls.getAtomCoordFromResi(e,t);g=void 0!==s?[s]:[]}if(f=[],void 0!==c&&!isNaN(c.resi)){let e=c.structure+"_"+c.chain+"_"+(parseInt(c.resi)+1).toString(),i=c.structure+"_"+c.chain+"_"+(parseInt(c.resi)+2).toString(),n=c.structure+"_"+c.chain+"_"+(parseInt(c.resi)+3).toString();if(1==p.length&&r.residues.hasOwnProperty(e)){let l=r.firstAtomObjCls.getAtomFromResi(e,t);if(l){p.push(l.coord),m.push(l.color);let t=this.getRadius(s,c);u.push(t),e=i,i=n}}let l=r.firstAtomObjCls.getAtomCoordFromResi(e,t);void 0!==l&&f.push(l);let o=r.firstAtomObjCls.getAtomCoordFromResi(i,t);void 0!==o&&f.push(o)}C.push({pnts:p,colors:m,radii:u,prevone:g,nexttwo:f})}for(let e=0,t=C.length;e1?a.parasCls.thr(t[t.length-2]):a.parasCls.thr(t[e]),f[y++]=d.r,f[y++]=d.g,f[y++]=d.b}}let x,k=0;for(let e=0,t=w.length-1;er&&(l=r,e=1);for(let t=0;t0&&t.b<=100?.01*t.b:t.b>100?1:s.coilWidth),i}}class ze{constructor(e){this.icn3d=e}drawCartoonNucleicAcid(e,t,s,i){this.drawStrandNucleicAcid(e,2,t,!0,void 0,s,i)}drawStrandNucleicAcid(e,t,s,i,n,l,r){let o,a,d,c=this.icn3d;if(c.icn3dui.bNode)return;2===r&&(t=void 0,l=void 0),n=n||c.nucleicAcidWidth,s=s||c.axisDIV,t=t||c.nucleicAcidStrandDIV;let h=[];for(d=0;dy?y=C:C=y);let v=.8*b/y;if(g.width=C,g.height=y,f.clearRect(0,0,C,y),h)if(f.fillStyle="rgba("+n.r+","+n.g+","+n.b+","+n.a+")",f.strokeStyle="rgba("+l.r+","+l.g+","+l.b+","+l.a+")",f.lineWidth=r,p){let e=.4*C;this.circle(f,0,0,C,y,e)}else{let e=0;this.roundRect(f,0,0,C,y,e)}f.font="Bold "+a+"px "+o,f.textAlign="center",f.textBaseline="middle",f.fillStyle="rgba("+u.r+", "+u.g+", "+u.b+", 1.0)",f.strokeStyle="rgba("+u.r+", "+u.g+", "+u.b+", 1.0)",f.fillText(e,.5*C,.5*y);let _=new THREE.Texture(g);_.needsUpdate=!0;let w=new THREE.SpriteMaterial({map:_,depthTest:!1,depthWrite:!1});w.map.minFilter=THREE.LinearFilter;let S=new THREE.Sprite(w);return p?S.scale.set(.3*d,.3*d,1):S.scale.set(v*d,d,1),S.renderOrder=1,S}roundRect(e,t,s,i,n,l){e.beginPath(),e.moveTo(t+l,s),e.lineTo(t+i-l,s),e.quadraticCurveTo(t+i,s,t+i,s+l),e.lineTo(t+i,s+n-l),e.quadraticCurveTo(t+i,s+n,t+i-l,s+n),e.lineTo(t+l,s+n),e.quadraticCurveTo(t,s+n,t,s+n-l),e.lineTo(t,s+l),e.quadraticCurveTo(t,s,t+l,s),e.closePath(),e.fill(),e.stroke()}circle(e,t,s,i,n,l){e.beginPath(),e.arc(t+i/2,.9*(s+n/2),l,0,2*Math.PI,!0),e.closePath(),e.fill(),e.stroke()}}class Ve{constructor(e){this.icn3d=e,this.textSpriteCls=new Ge(e)}createLabelRepresentation(e){let t=this.icn3d;t.icn3dui;let s=t.oriMaxD/100;s<.4&&(s=.4);let i=3*s*t.labelScale;for(let s in e){let n=void 0!==e[s]?e[s]:[],l="black"!=t.opts.background?t.colorWhitebkgd:t.colorBlackbkgd;for(let e=0,r=n.length;e.99999)h.set(0,0,0,1);else if(e.y<-.99999)h.set(1,0,0,0);else{let t=new THREE.Vector3;t.set(e.z,0,-e.x).normalize();let s=Math.acos(e.y);h.setFromAxisAngle(t,s)}return c.applyQuaternion(h),c.scale.set(l,n,l),c.position.copy(t),c}setPc1Axes(){let e=this.icn3d,t=e.icn3dui;if(t.bNode)return;let s=t.hashUtilsCls.intHash(e.hAtoms,e.dAtoms),i=[],n=Object.keys(s).length<100;for(let t in s){let s=e.atoms[t],l=s.structure+"_"+s.chain+"_"+s.resi;(n||""!=l)&&i.push(s.coord.clone())}let l=t.rmsdSuprCls.getEigenForSelection(i,i.length),r=new THREE.Vector3(l.h1[0],l.h1[1],l.h1[2]);if(0==l.k&&e.bRender)return void alert("Can't determine the first principal component. Please select a subset and try it again.");let o=e.applyCenterCls.centerAtoms(s),a=o.maxD,d=o.center,c=d.clone().add(r.normalize().multiplyScalar(.4*a)),h=new THREE.Vector3(l.h2[0],l.h2[1],l.h2[2]),p=d.clone().add(h.normalize().multiplyScalar(.3*a)),m=new THREE.Vector3(l.h3[0],l.h3[1],l.h3[2]),u=d.clone().add(m.normalize().multiplyScalar(.3*a));this.buildAxes(void 0,d,c,p,u,!0);let g=[d,c,p,u];return e.axes.push(g),e.drawCls.draw(),g}}class Ye{constructor(e){this.icn3d=e}showGlycans(){let e=this.icn3d,t=e.icn3dui;if(t.bNode)return;let s={},i=e.dAtoms;for(let n in i){let i=e.atoms[n];i.het&&-1!=t.parasCls.glycanHash.hasOwnProperty(i.resn)&&(void 0===s[i.resn]&&(s[i.resn]={}),"Misc"!=i.chain&&(s[i.resn][i.structure+"_"+i.chain+"_"+i.resi]=1))}let n=Object.keys(s);for(let i=0,l=n.length;i>2))+i+((2&t)>>1))*c+n+(1&t)]&this.ISDONE)<=3&&(t.push(t[i]),i=t.length-1,t.push(t[n]),n=t.length-1,t.push(t[l]),l=t.length-1),s.push(i),s.push(n),s.push(l)}}},Xe.prototype.laplacianSmooth=function(e,t,s){let i,n,l,r,o,a=new Array(t.length);for(i=0,n=t.length;ithis.origextent[1][0])&&(!(tthis.origextent[1][1])&&!(sthis.origextent[1][2]))},Ke.prototype.getFacesAndVertices=function(){let e,t,s=this.verts;for(e=0,t=s.length;eh&&(h=this.pmaxy-this.pminy),this.pmaxz-this.pminz>h&&(h=this.pmaxz-this.pminz),this.scaleFactor=(c-1)/h,this.scaleFactor=this.defaultScaleFactor,this.defaultScaleFactor*h>this.threshbox&&(c=Math.floor(this.threshbox),this.scaleFactor=(this.threshbox-1)/h),this.bCalcArea&&(this.scaleFactor=this.defaultScaleFactor),this.pLength=Math.ceil(this.scaleFactor*(this.pmaxx-this.pminx))+1,this.pWidth=Math.ceil(this.scaleFactor*(this.pmaxy-this.pminy))+1,this.pHeight=Math.ceil(this.scaleFactor*(this.pmaxz-this.pminz))+1,this.boundingatom(t),this.cutRadius=this.probeRadius*this.scaleFactor,this.vpBits=new Uint8Array(this.pLength*this.pWidth*this.pHeight),this.vpDistance=new Float64Array(this.pLength*this.pWidth*this.pHeight),this.vpAtomID=new Int32Array(this.pLength*this.pWidth*this.pHeight),this.vpColor=[],this.vpPot=[]},Ke.prototype.boundingatom=function(e){let t,s,i,n,l=[];for(let r in this.vdwRadii){if(!this.vdwRadii.hasOwnProperty(r))continue;let o=this.vdwRadii[r];l[r]=e?(o+this.probeRadius)*this.scaleFactor+.5:o*this.scaleFactor+.5,i=l[r]*l[r],this.widxz[r]=Math.floor(l[r])+1,this.depty[r]=new Int32Array(this.widxz[r]*this.widxz[r]),n=0;for(let e=0;ei?this.depty[r][n]=-1:(s=Math.sqrt(i-t),this.depty[r][n]=Math.floor(s)),n++}},Ke.prototype.fillvoxels=function(e,t){let s,i,n,l;for(s=0,l=this.vpBits.length;sc&&(a=c),C>h&&(C=h),v>p&&(v=p);let _,w=g[o*m+d*u+y],S=g[a*m+d*u+y],A=g[o*m+C*u+y],x=g[o*m+d*u+v],k=g[a*m+C*u+y],O=g[o*m+C*u+v],R=g[a*m+d*u+v],I=g[a*m+C*u+v],T=r.x-o,E=r.y-d,P=r.z-y,M=((w*(1-T)+S*T)*(1-E)+(A*(1-T)+k*T)*E)*(1-P)+((x*(1-T)+R*T)*(1-E)+(O*(1-T)+I*T)*E)*P,D=s*f+i*b+n;this.vpPot[D]=M,M>this.isovalue&&(M=this.isovalue),M<-this.isovalue&&(M=-this.isovalue),M>0?(M/=1*this.isovalue,_=new THREE.Color(1-M,1-M,1)):(M/=-1*this.isovalue,_=new THREE.Color(1,1-M,1-M)),this.vpColor[D]=_}}for(s=0,l=this.vpBits.length;s=this.pLength||g>=this.pWidth||f>=this.pHeight)continue;let h=u*S+g*this.pHeight+f;if(this.vpBits[h]&this.INOUT){let p=t[this.vpAtomID[h]];p.serial!=e.serial&&(l=s+a-Math.floor(.5+this.scaleFactor*(p.x+this.ptranx)),r=i+d-Math.floor(.5+this.scaleFactor*(p.y+this.ptrany)),o=n+c-Math.floor(.5+this.scaleFactor*(p.z+this.ptranz)),a*a+d*d+c*c=this.pLength||p>=this.pWidth||m>=this.pHeight)continue;let u=h*S+p*this.pHeight+m;if(this.vpBits[u]&this.ISDONE){let h=t[this.vpAtomID[u]];h.serial!=e.serial&&(l=s+a-Math.floor(.5+this.scaleFactor*(h.x+this.ptranx)),r=i+d-Math.floor(.5+this.scaleFactor*(h.y+this.ptrany)),o=n+c-Math.floor(.5+this.scaleFactor*(h.z+this.ptranz)),a*a+d*d+c*c-1&&r-1&&a-1&&o=h)||(this.vpBits[n]|=this.ISBOUND))},Ke.prototype.fastoneshell=function(e,t){let s,i,n,l,r,o,a,d,c,h,p,m,u=[];if(0===e.length)return u;let g={ix:-1,iy:-1,iz:-1},f=this.pWidth*this.pHeight;for(a=0,c=e.length;a-1&&g.iy-1&&g.iz-1&&(m=g.ix*f+this.pHeight*g.iy+g.iz,this.vpBits[m]&this.INOUT&&!(this.vpBits[m]&this.ISDONE)?(t.set(g.ix,g.iy,n+this.nb[d][2],p),l=g.ix-p.ix,r=g.iy-p.iy,o=g.iz-p.iz,h=l*l+r*r+o*o,this.vpDistance[m]=h,this.vpBits[m]|=this.ISDONE,this.vpBits[m]|=this.ISBOUND,u.push({ix:g.ix,iy:g.iy,iz:g.iz})):this.vpBits[m]&this.INOUT&&this.vpBits[m]&this.ISDONE&&(l=g.ix-p.ix,r=g.iy-p.iy,o=g.iz-p.iz,h=l*l+r*r+o*o,h-1&&g.iy-1&&g.iz-1&&(m=g.ix*f+this.pHeight*g.iy+g.iz,this.vpBits[m]&this.INOUT&&!(this.vpBits[m]&this.ISDONE)?(t.set(g.ix,g.iy,n+this.nb[d][2],p),l=g.ix-p.ix,r=g.iy-p.iy,o=g.iz-p.iz,h=l*l+r*r+o*o,this.vpDistance[m]=h,this.vpBits[m]|=this.ISDONE,this.vpBits[m]|=this.ISBOUND,u.push({ix:g.ix,iy:g.iy,iz:g.iz})):this.vpBits[m]&this.INOUT&&this.vpBits[m]&this.ISDONE&&(l=g.ix-p.ix,r=g.iy-p.iy,o=g.iz-p.iz,h=l*l+r*r+o*o,h-1&&g.iy-1&&g.iz-1&&(m=g.ix*f+this.pHeight*g.iy+g.iz,this.vpBits[m]&this.INOUT&&!(this.vpBits[m]&this.ISDONE)?(t.set(g.ix,g.iy,n+this.nb[d][2],p),l=g.ix-p.ix,r=g.iy-p.iy,o=g.iz-p.iz,h=l*l+r*r+o*o,this.vpDistance[m]=h,this.vpBits[m]|=this.ISDONE,this.vpBits[m]|=this.ISBOUND,u.push({ix:g.ix,iy:g.iy,iz:g.iz})):this.vpBits[m]&this.INOUT&&this.vpBits[m]&this.ISDONE&&(l=g.ix-p.ix,r=g.iy-p.iy,o=g.iz-p.iz,h=l*l+r*r+o*o,hm&&(m=this.pmaxy-this.pminy),this.pmaxz-this.pminz>m&&(m=this.pmaxz-this.pminz),this.scaleFactor=1,this.pLength=Math.floor(.5+this.scaleFactor*(this.pmaxx-this.pminx))+1,this.pWidth=Math.floor(.5+this.scaleFactor*(this.pmaxy-this.pminy))+1,this.pHeight=Math.floor(.5+this.scaleFactor*(this.pmaxz-this.pminz))+1,this.cutRadius=this.probeRadius*this.scaleFactor,this.vpBits=new Uint8Array(this.pLength*this.pWidth*this.pHeight),this.vpAtomID=new Uint8Array(this.pLength*this.pWidth*this.pHeight)},Je.prototype.transformMemPro=function(e,t,s,i){let n=e.clone();n.sub(s);let l=n.x*t[0]+n.y*t[1]+n.z*t[2]+i.x,r=n.x*t[3]+n.y*t[4]+n.z*t[5]+i.y,o=n.x*t[6]+n.y*t[7]+n.z*t[8]+i.z;return n.x=l,n.y=r,n.z=o,n},Je.prototype.fillvoxels=function(e,t){let s,i,n,l,r,o;for(s=0,l=this.vpBits.length;sthis.pLength&&(o=this.pLength),p>this.pWidth&&(p=this.pWidth),b>this.pHeight&&(b=this.pHeight);let C,y=l[r*a+h*d+f],v=l[o*a+h*d+f],_=l[r*a+p*d+f],w=l[r*a+h*d+b],S=l[o*a+p*d+f],A=l[r*a+p*d+b],x=l[o*a+h*d+b],k=l[o*a+p*d+b],O=n.x-r,R=n.y-h,I=n.z-f,T=((y*(1-O)+v*O)*(1-R)+(_*(1-O)+S*O)*R)*(1-I)+((w*(1-O)+x*O)*(1-R)+(A*(1-O)+k*O)*R)*I;T>this.isovalue&&(T=this.isovalue),T<-this.isovalue&&(T=-this.isovalue),T>0?(T/=1*this.isovalue,C=new THREE.Color(1-T,1-T,1)):(T/=-1*this.isovalue,C=new THREE.Color(1,1-T,1-T)),this.icn3d.atoms[t[s]].color=C,this.icn3d.atomPrevColors[t[s]]=C}}else{for(let p in t){let f,b=e[t[p]];if("DUM"!==b.resn){if(void 0!==this.rmsd_supr&&void 0!==this.rmsd_supr.rot){f=this.transformMemPro(b.coord,g,u,m).applyMatrix4(c)}else f=b.coord.clone().applyMatrix4(c);for(s=Math.floor(f.x)-this.maxdist,l=Math.ceil(f.x)+this.maxdist;s<=l;++s)if(!(s<0||s>this.header.xExtent*this.scaleFactor-1))for(i=Math.floor(f.y)-this.maxdist,r=Math.ceil(f.y)+this.maxdist;i<=r;++i)if(!(i<0||i>this.header.yExtent*this.scaleFactor-1))for(n=Math.floor(f.z)-this.maxdist,o=Math.ceil(f.z)+this.maxdist;n<=o;++n){if(n<0||n>this.header.zExtent*this.scaleFactor-1)continue;let e=s*a+i*d+n;h.push(e)}}}for(s=0,l=h.length;s=this.isovalue?1:0:"fofc"==this.type?(this.vpBits[e]=this.dataArray[e]>=this.isovalue||this.dataArray[e]<=-this.isovalue?1:0,this.vpAtomID[e]=this.dataArray[e]>=0?1:0):"em"==this.type&&(this.vpBits[e]=this.dataArray[e]>=this.isovalue?1:0)}}}else for(s=0;s=this.isovalue||this.dataArray[e]<=-this.isovalue?1:0,this.vpAtomID[t]=this.dataArray[e]>=0?1:0)}for(s=0,l=this.vpBits.length;s-1&&r-1&&a-1&&o1?"Structure ":"",a=Object.keys(i).length>1?"Chain ":"";n+=""+o+a+"Residue Number SASA (Å2 ) Percent Out In/Out ";for(let e in l.resid2area){let d=e.lastIndexOf("_"),c=e.substr(d+1),h=r.utilsCls.getIdArray(e.substr(0,d));o=Object.keys(s).length>1?""+h[0]+" ":"",a=Object.keys(i).length>1?""+h[1]+" ":"";let p="",m="";l.resid2area[e]=(l.resid2area[e]/t).toFixed(2),r.parasCls.residueArea.hasOwnProperty(c)&&(m=parseInt(l.resid2area[e]/r.parasCls.residueArea[c]*100),m>100&&(m=100),m>=50&&(p="out"),m<20&&(p="in")),n+=''+o+a+""+c+' '+h[2]+' '+l.resid2area[e]+' '+m+"% "+p+" "}return n+="",void(l.areahtml=n)}let p,m,u,g=c.vertices,f=c.faces,b=r.parasCls.thr("#00FFFF"),C=r.parasCls.thr("#00FF00"),y=r.parasCls.thr("#ff0000"),v=r.parasCls.thr("#00FFFF"),_=r.parasCls.thr("#0000FF"),w=r.parasCls.thr("#FF0000");11!=t&&12!=t&&13!=t&&14!=t||void 0===l.rmsd_supr||void 0===l.rmsd_supr.rot||(p=l.rmsd_supr.rot,m=l.rmsd_supr.trans1,u=l.rmsd_supr.trans2);let S=(11==t||12==t||13==t||14==t&&"delphi"!=l.loadPhiFrom)&&void 0!==l.rmsd_supr&&void 0!==l.rmsd_supr.rot;n=new THREE.BufferGeometry;let A,x=[],k=[],O=[],R=0;for(let e=0,s=g.length;e0?-parseInt(C.z):parseInt(C.z),y.onBeforeRender=function(e,t,s,i,n,o){let a,d=new THREE.Vector3(0,0,0),c=i.getAttribute("position").array;for(let e=0,t=c.length;e0?-parseInt(a.z):parseInt(a.z)},l.mdl.add(y),11==t||12==t?l.prevMaps.push(y):13==t?l.prevEmmaps.push(y):14==t?l.prevPhimaps.push(y):l.prevSurfaces.push(y)}}else{let e=new THREE.Mesh(n,new THREE.MeshPhongMaterial({specular:l.frac,shininess:20,emissive:l.emissive,vertexColors:!0,wireframe:s,opacity:i,transparent:!0,depthWrite:10==parseInt(10*i),side:THREE.DoubleSide}));e.renderOrder=-2,l.mdl.add(e),11==t||12==t?l.prevMaps.push(e):13==t?l.prevEmmaps.push(e):14==t?l.prevPhimaps.push(e):l.prevSurfaces.push(e)}c=null,g=null,f=null,n=null}transformMemPro(e,t,s,i,n){this.icn3d.icn3dui;let l=e.clone();l.sub(s),n&&console.log("sub coord: "+JSON.stringify(l));let r=l.x*t[0]+l.y*t[1]+l.z*t[2]+i.x,o=l.x*t[3]+l.y*t[4]+l.z*t[5]+i.y,a=l.x*t[6]+l.y*t[7]+l.z*t[8]+i.z;return l.x=r,l.y=o,l.z=a,n&&console.log("out coord: "+JSON.stringify(l)),l}SetupSurface(e){let t=this.icn3d;t.icn3dui;let s=e.threshbox,i=new Ke(t,s);i.initparm(e.extent,1!==e.type,e.bCalcArea,e.atomsToShow,e.header,e.data,e.matrix,e.isovalue,e.loadPhiFrom),i.fillvoxels(e.allatoms,e.extendedAtoms),i.buildboundary(),2===e.type&&(i.fastdistancemap(),i.boundingatom(!1),i.fillvoxelswaals(e.allatoms,e.extendedAtoms));let n=i.marchingcube();i.vpBits=null,i.vpDistance=null,i.vpAtomID=null;let l=i.getFacesAndVertices(e.atomsToShow);return l.area=n.area,l.serial2area=n.serial2area,l.scaleFactor=n.scaleFactor,i.faces=null,i.verts=null,l}SetupMap(e){let t=this.icn3d;t.icn3dui;let s,i=new Je(t);return i.initparm(e.header,e.data,e.matrix,e.isovalue,e.center,e.maxdist,e.pmin,e.pmax,e.water,e.type,e.rmsd_supr,e.loadPhiFrom,e.icn3d),i.fillvoxels(e.allatoms,e.extendedAtoms),e.header.bSurface||i.buildboundary(),e.header.bSurface||i.marchingcube(),i.vpBits=null,i.vpAtomID=null,e.header.bSurface||(s=i.getFacesAndVertices(e.allatoms,e.atomsToShow)),i.faces=null,i.verts=null,s}}class Ze{constructor(e){this.icn3d=e}applyCenterOptions(e){let t,s=this.icn3d;switch(s.icn3dui,void 0===e&&(e=s.opts),e.rotationcenter.toLowerCase()){case"molecule center":void 0!==s.center&&this.setRotationCenter(s.center);break;case"pick center":void 0!==s.pAtom&&this.setRotationCenter(s.pAtom.coord);break;case"display center":t=this.centerAtoms(s.dAtoms).center,this.setRotationCenter(t);break;case"highlight center":t=this.centerAtoms(s.hAtoms).center,this.setRotationCenter(t)}}setRotationCenter(e){this.icn3d.icn3dui,this.setCenter(e)}setCenter(e){let t=this.icn3d;t.icn3dui,t.mdl.position.set(0,0,0),t.mdlImpostor.position.set(0,0,0),t.mdl_ghost.position.set(0,0,0),t.mdl.position.sub(e),t.mdlImpostor.position.sub(e),t.mdl_ghost.position.sub(e)}centerSelection(e,t){let s=this.icn3d,i=s.icn3dui;if(s.opts.rotationcenter="highlight center",void 0===e&&(e=i.hashUtilsCls.hash2Atoms(s.hAtoms,s.atoms)),t||(s._zoomFactor=1,s.mouseChange=new THREE.Vector2(0,0),s.quaternion=new THREE.Quaternion(0,0,0,1)),Object.keys(e).length>1){let t=this.centerAtoms(e);s.center=t.center,this.setCenter(s.center),s.cameraCls.setCamera()}}centerAtoms(e){let t=this.icn3d;t.icn3dui;let s=new THREE.Vector3(9999,9999,9999),i=new THREE.Vector3(-9999,-9999,-9999),n=new THREE.Vector3;for(let l in e){let e=t.atoms[l].coord;n.add(e),s.min(e),i.max(e)}let l=t.ParserUtilsCls.getGeoCenter(s,i);return{center:l,maxD:t.ParserUtilsCls.getStructureSize(e,s,i,l),pmin:s,pmax:i}}setWidthHeight(e,t){let s=this.icn3d;s.icn3dui,void 0===s.scaleFactor&&(s.scaleFactor=1),s.renderer.setSize(e*s.scaleFactor,t*s.scaleFactor),s.renderer.domElement.style.width=e*s.scaleFactor+"px",s.renderer.domElement.style.height=t*s.scaleFactor+"px",s.renderer.domElement.width=e*s.scaleFactor,s.renderer.domElement.height=t*s.scaleFactor,s.container.whratio=e/t}}class et{constructor(e){this.icn3d=e}applyClbondsOptions(e){let t=this.icn3d,s=t.icn3dui;if(void 0===e&&(e=t.opts),t.bCalcCrossLink||(t.clbondpnts={},t.clbondResid2serial={},this.applyClbondsOptions_base("chemical"),this.applyClbondsOptions_base("all"),t.bCalcCrossLink=!0),"yes"===e.clbonds.toLowerCase()&&"nothing"!==e.chemicals){let e="#006400";if(s.parasCls.thr(25600),t.lines.clbond=[],t.residuesHashClbonds={},t.structures){let i=Object.keys(t.structures);for(let n=0,l=i.length;n1&&"sphere"!==a[Object.keys(a)[0]].style&&"dot"!==a[Object.keys(a)[0]].style){if(void 0===i.bCid||!i.bCid)for(let e in a){let t=a[e],n=1;i.boxCls.createBox(t,void 0,void 0,n,void 0,s)}}else for(let e in o){let l=i.firstAtomObjCls.getFirstCalphaAtomObj(i.residues[e]),r=l,o=r.structure+"_"+r.chain+"_"+(parseInt(r.resi)-1).toString(),a=r.structure+"_"+r.chain+"_"+(parseInt(r.resi)+1).toString();if("cylinder and plate"===r.style&&"helix"===r.ss)for(let t in i.residues[e]){let e=i.atoms[t],n=1;i.boxCls.createBox(e,void 0,void 0,n,void 0,s)}else if("ribbon"===r.style&&"coil"===r.ss||"strand"===r.style&&"coil"===r.ss||"o3 trace"===r.style||"schematic"===r.style||"c alpha trace"===r.style||"b factor tube"===r.style||"cylinder and plate"===r.style&&"helix"!==r.ss){if(void 0!==l&&void 0!==l.style2&&"nothing"!==l.style2)continue;let e=!1;if(!isNaN(r.resi)&&!e&&i.residues.hasOwnProperty(a)){let s=Object.keys(i.residues[a])[0],l=n.hashUtilsCls.hash2Atoms(i.residues[a],i.atoms)[s];if(r.style===l.style&&!l.ssbegin||l.ssbegin){let s=i.residues[a];if(t=n.hashUtilsCls.unionHash(t,s),e=!0,l.ssbegin)for(let e in s)i.atoms[e].notshow=!0}}if(!isNaN(r.resi)&&!e&&i.residues.hasOwnProperty(o)){let s=Object.keys(i.residues[o])[0],l=n.hashUtilsCls.hash2Atoms(i.residues[o],i.atoms)[s];r.style===l.style&&(t=n.hashUtilsCls.unionHash(t,i.residues[o]),e=!0)}}else if("ribbon"===r.style&&"coil"!==r.ss&&r.ssend||"strand"===r.style&&"coil"!==r.ss&&r.ssend){if(void 0!==l&&void 0!==l.style2&&"nothing"!==l.style2)continue;let e=!1;if(!isNaN(r.resi)&&!e&&i.residues.hasOwnProperty(a)){let s=Object.keys(i.residues[a])[0];n.hashUtilsCls.hash2Atoms(i.residues[a],i.atoms)[s],t=n.hashUtilsCls.unionHash(t,i.residues[a]),e=!0}}}a={}}if(i.bInitial){if(""!=n.htmlCls.setHtmlCls.getCookie("membrane")){let e=parseInt(n.htmlCls.setHtmlCls.getCookie("membrane"));i.bMembrane!=e&&n.htmlCls.clickMenuCls.setLogCmd("set membrane "+e,!0),i.bMembrane=isNaN(e)?0:parseInt(e)}i.bMembrane?i.selectionCls.toggleMembrane(!0):i.selectionCls.toggleMembrane(!1)}i.setStyleCls.setStyle2Atoms(t);let d=.5*i.cylinderRadius;void 0!==i.labels&&delete i.labels.schematic;for(let e in i.style2atoms){let t=i.style2atoms[e],l=n.hashUtilsCls.intHash(t,i.nucleotides),r=n.utilsCls.isCalphaPhosOnly(n.hashUtilsCls.hash2Atoms(l,i.atoms));if("ribbon"===e)i.strandCls.createStrand(n.hashUtilsCls.hash2Atoms(t,i.atoms),2,void 0,!0,void 0,void 0,!1,i.ribbonthickness,s);else if("strand"===e)i.strandCls.createStrand(n.hashUtilsCls.hash2Atoms(t,i.atoms),null,null,null,null,null,!1,void 0,s);else if("cylinder and plate"===e)i.cylinderCls.createCylinderHelix(n.hashUtilsCls.hash2Atoms(t,i.atoms),i.cylinderHelixRadius,s);else if("nucleotide cartoon"===e)r?i.cylinderCls.createCylinderCurve(n.hashUtilsCls.hash2Atoms(t,i.atoms),["P"],i.traceRadius,!1,s):(i.cartoonNuclCls.drawCartoonNucleicAcid(n.hashUtilsCls.hash2Atoms(t,i.atoms),null,i.ribbonthickness,s),2!==s&&i.cartoonNuclCls.drawNucleicAcidStick(n.hashUtilsCls.hash2Atoms(t,i.atoms),s));else if("o3 trace"===e)r?i.cylinderCls.createCylinderCurve(n.hashUtilsCls.hash2Atoms(t,i.atoms),["P"],i.traceRadius,!1,s):i.cylinderCls.createCylinderCurve(n.hashUtilsCls.hash2Atoms(t,i.atoms),["O3'","O3*"],i.traceRadius,!1,s);else if("schematic"===e){let e=i.firstAtomObjCls.getFirstAtomObj(t);if(i.chemicals.hasOwnProperty(e.serial)){i.residueLabelsCls.addNonCarbonAtomLabels(n.hashUtilsCls.hash2Atoms(t,i.atoms));let e=!0;i.stickCls.createStickRepresentation(n.hashUtilsCls.hash2Atoms(t,i.atoms),d,d,void 0,s,e)}else i.residueLabelsCls.addResidueLabels(n.hashUtilsCls.hash2Atoms(t,i.atoms),!0),r?i.cylinderCls.createCylinderCurve(n.hashUtilsCls.hash2Atoms(t,i.atoms),["P"],i.traceRadius,!1,s):i.cylinderCls.createCylinderCurve(n.hashUtilsCls.hash2Atoms(t,i.atoms),["O3'","O3*"],i.traceRadius,!1,s),i.cylinderCls.createCylinderCurve(n.hashUtilsCls.hash2Atoms(t,i.atoms),["CA"],i.traceRadius,!1,s)}else"c alpha trace"===e?i.cylinderCls.createCylinderCurve(n.hashUtilsCls.hash2Atoms(t,i.atoms),["CA"],i.traceRadius,!1,s):"b factor tube"===e?i.tubeCls.createTube(n.hashUtilsCls.hash2Atoms(t,i.atoms),"CA",null,s,!1,!0):"custom tube"===e?i.tubeCls.createTube(n.hashUtilsCls.hash2Atoms(t,i.atoms),"CA",null,s,!0,!0):"lines"===e||"lines2"===e?(1===s?i.stickCls.createStickRepresentation(n.hashUtilsCls.hash2Atoms(t,i.atoms),i.hlLineRadius,i.hlLineRadius,void 0,s):i.lineCls.createLineRepresentation(n.hashUtilsCls.hash2Atoms(t,i.atoms),s),i.lineCls.createConnCalphSidechain(n.hashUtilsCls.hash2Atoms(t,i.atoms),e)):"stick"===e||"stick2"===e?(i.stickCls.createStickRepresentation(n.hashUtilsCls.hash2Atoms(t,i.atoms),i.cylinderRadius,i.cylinderRadius,void 0,s,void 0),i.lineCls.createConnCalphSidechain(n.hashUtilsCls.hash2Atoms(t,i.atoms),e)):"backbone"===e?(t=this.selectMainChainSubset(t),i.stickCls.createStickRepresentation(n.hashUtilsCls.hash2Atoms(t,i.atoms),i.cylinderRadius,i.cylinderRadius,void 0,s,void 0)):"ball and stick"===e||"ball and stick2"===e?(i.stickCls.createStickRepresentation(n.hashUtilsCls.hash2Atoms(t,i.atoms),i.cylinderRadius,.5*i.cylinderRadius,i.dotSphereScale,s,void 0),i.lineCls.createConnCalphSidechain(n.hashUtilsCls.hash2Atoms(t,i.atoms),e)):"sphere"===e||"sphere2"===e?i.sphereCls.createSphereRepresentation(n.hashUtilsCls.hash2Atoms(t,i.atoms),i.sphereRadius,void 0,void 0,s):"dot"===e&&i.sphereCls.createSphereRepresentation(n.hashUtilsCls.hash2Atoms(t,i.atoms),i.sphereRadius,!1,i.dotSphereScale,s)}if(i.cnt>i.maxmaxatomcnt&&i.init_base(),void 0!==i.labels&&Object.keys(i.labels).length>0){i.labelCls.hideLabels();for(let e in i.labels)"schematic"!=e&&this.changeLabelColor(i.labels[e]);i.labelCls.createLabelRepresentation(i.labels)}}changeLabelColor(e){let t=this.icn3d;if(t.icn3dui,e)for(let s=0,i=e.length;s0){this.updateStabilizer();let e="#FFFFFF",s=t.stabilizerpnts;t.lines.stabilizer=[];for(let i=0,n=Math.floor(s.length/2);i0)for(let e=0,s=t.distPnts.length;e0&&t.applySymdCls.applySymd(),void 0!==t.prevOtherMesh)for(let e=0,s=t.prevOtherMesh.length;e0&&(e=s.hashUtilsCls.hash2Atoms(t.chemicals,t.atoms));let i=4;if(void 0!==e){let n=t.contactCls.getAtomsWithinAtom(t.atoms,e,i),l=3.5;t.opts.hbonds="yes",Object.keys(n).length>0&&t.hBondCls.calculateChemicalHbonds(e,n,parseFloat(l)),t.bSetFog||t.transformCls.zoominSelection(s.hashUtilsCls.unionHash(e,n))}}else"hide"===e.chemicalbinding&&(t.hBondCls.hideHbonds(),t.showInterCls.hideExtraBonds(),t.bSetFog||t.transformCls.zoominSelection(t.atoms))}updateStabilizer(){let e=this.icn3d;if(e.icn3dui,e.stabilizerpnts=[],void 0!==e.pairArray)for(let t=0,s=e.pairArray.length;t=0;i--){let r=t.ssbondpnts[e][2*i],o=t.ssbondpnts[e][2*i+1],a={};a.color=n,a.dashed=!1;let d=[],c=[],h=[],p=[],m=!1,u=!1;for(let e in t.residues[r])"SG"===t.atoms[e].name&&(h.push(t.atoms[e].coord),d.push(t.atoms[e].serial),m=!0);if(!m)for(let e in t.residues[r])if("CA"===t.atoms[e].name){h.push(t.atoms[e].coord),d.push(t.atoms[e].serial),m=!0,u=!0;break}m=!1;for(let e in t.residues[o])"SG"===t.atoms[e].name&&(p.push(t.atoms[e].coord),c.push(t.atoms[e].serial),m=!0);if(!m)for(let e in t.residues[o])if("CA"===t.atoms[e].name){p.push(t.atoms[e].coord),c.push(t.atoms[e].serial),m=!0,u=!0;break}let g=u?7:3,f=!1;for(let e=0,t=h.length;e1&&(l=!0)}if(t)if(l){let t=Object.keys(r)[0];e=i.chains[t]}else{0==Object.keys(i.hAtoms).length&&(i.hAtoms=n.hashUtilsCls.cloneHash(i.dAtoms));let t,s=parseInt(Object.keys(i.hAtoms).length/u),l=0;for(let n in i.hAtoms)if(e[n]=1,t=n,++l,l>s)break;let r=i.atoms[t].structure+"_"+i.atoms[t].chain+"_"+i.atoms[t].resi;e=n.hashUtilsCls.unionHash(e,i.residues[r])}else{let t=Object.keys(i.structures)[0]+"_"+g;if(i.chains.hasOwnProperty(t)||(t=Object.keys(i.structures)[0]+"_"+g.toLowerCase()),!i.chains.hasOwnProperty(t)){t=Object.keys(i.chains)[0];for(let e in i.chains){let s=Object.keys(i.chains[e])[0];if(i.proteins.hasOwnProperty(s)){t=e;break}}}e=i.chains[t]}let a=s.clone().add(h).multiplyScalar(.5),c=new THREE.Vector3,p=0,f=h.clone().sub(s).normalize(),b=new THREE.Vector3(0,0,1),C=new THREE.Quaternion;C.setFromUnitVectors(f,b);let y=-9999;for(let t in e){let e=i.atoms[t].coord.clone();c.add(e),e.sub(a).applyQuaternion(C);let s=e.x*e.x+e.y*e.y;s>y&&(y=s),++p}let v=i.ParserUtilsCls.getMassCenter(c,p),_=new THREE.Line3(s,h),w=new THREE.Vector3;_.closestPointToPoint(v,!0,w);let S,A,x,k,O=Math.sqrt(y),R=v.clone().sub(w).normalize().multiplyScalar(O),I=a.clone().add(s.clone().sub(a).multiplyScalar(.83)).add(R),T=a.clone().add(h.clone().sub(a).multiplyScalar(.83)).add(R),E=2*Math.PI/o;for(let e=0;et&&(i.sphereCls.createSphereBase(r,colorPolygon,d,1,0),i.cylinderCls.createCylinder(e,r,d,colorPolygon,0),i.cylinderCls.createCylinder(s,r,d,colorPolygon,0),void 0!==n&&i.cylinderCls.createCylinder(c[n],r,d,colorPolygon,0),n=l)}}else if("O"==r)for(let e=0,t=c.length;e0&&(e.mdl.remove(e.prevSurfaces[e.prevSurfaces.length-1]),e.prevSurfaces.slice(e.prevSurfaces.length-1,1))}removeMaps(){let e=this.icn3d;e.icn3dui;for(let t=0,s=e.prevMaps.length;t0&&(e.mdl.remove(e.prevMaps[e.prevMaps.length-1]),e.prevMaps.slice(e.prevMaps.length-1,1))}removeLastEmmap(){let e=this.icn3d;e.icn3dui,e.prevEmmaps.length>0&&(e.mdl.remove(e.prevEmmaps[e.prevEmmaps.length-1]),e.prevEmmaps.slice(e.prevEmmaps.length-1,1))}removeLastPhimap(){let e=this.icn3d;e.icn3dui,e.prevPhimaps.length>0&&(e.mdl.remove(e.prevPhimaps[e.prevPhimaps.length-1]),e.prevPhimaps.slice(e.prevPhimaps.length-1,1))}}class ot{constructor(e){this.icn3d=e}addResidueLabels(e,t,s,i,n){let l=this.icn3d,r=l.icn3dui;if(r.bNode)return;let o=r.hashUtilsCls.intHash(l.hAtoms,e);t?void 0===l.labels.schematic&&(l.labels.schematic=[]):void 0===l.labels.residue&&(l.labels.residue=[]);let a="";for(let e in o){let s=l.atoms[e],o={},d=s.structure+"_"+s.chain+"_"+s.resi;if(!s.het&&("CA"===s.name||"O3'"===s.name||"O3*"===s.name)||l.water.hasOwnProperty(s.serial)||l.ions.hasOwnProperty(s.serial)||l.chemicals.hasOwnProperty(s.serial)&&d!==a){if(o.position=s.coord,o.bSchematic=0,t&&(o.bSchematic=1),o.text=r.utilsCls.residueName2Abbr(s.resn),i)o.text+=s.resi;else if(n){let e=s.structure+"_"+s.chain+"_"+s.resi,t="";l.resid2refnum[e]&&(t=" "==l.resid2refnum[e].substr(0,1)?"":l.resid2refnum[e]),o.text=t}o.size=18,o.factor=.3;let e=s.color.getHexString().toUpperCase();o.color=i?"black"!=l.opts.background?l.colorWhitebkgd:l.colorBlackbkgd:n?"#00FFFF":"CCCCCC"===e||"C8C8C8"===e?"#888888":"#"+e,o.background="#FFFFFF",t?l.labels.schematic.push(o):l.labels.residue.push(o)}a=d}l.hlObjectsCls.removeHlObjects()}addNonCarbonAtomLabels(e){let t=this.icn3d,s=t.icn3dui;if(s.bNode)return;let i=s.hashUtilsCls.intHash(t.hAtoms,e);void 0===t.labels.schematic&&(t.labels.schematic=[]);for(let e in i){let s=t.atoms[e];if(!t.residues.hasOwnProperty(s.structure+"_"+s.chain+"_"+s.resi))continue;if("C"===s.elem)continue;let i={};i.position=s.coord,i.bSchematic=1,i.text=s.elem,i.size=18,i.color="black"!=t.opts.background?t.colorWhitebkgd:s.color.getHexString(),i.background="#FFFFFF",t.labels.schematic.push(i)}t.hlObjectsCls.removeHlObjects()}addAtomLabels(e,t){let s=this.icn3d,i=s.icn3dui;if(i.bNode)return;let n=i.hashUtilsCls.intHash(s.hAtoms,e);n=i.hashUtilsCls.intHash(s.dAtoms,n),void 0===s.labels.residue&&(s.labels.residue=[]);for(let e in n){let i=s.atoms[e],n={};n.position=i.coord,n.bSchematic=0,n.text=t?i.elem:i.name.padEnd(2," "),n.size=18,t&&(n.bSchematic=!0);let l=i.color.getHexString().toUpperCase();n.color="black"!=s.opts.background?s.colorWhitebkgd:s.colorBlackbkgd,t&&(n.color="CCCCCC"===l||"C8C8C8"===l?"#888888":"#"+l),n.background="#FFFFFF",s.labels.residue.push(n)}s.hlObjectsCls.removeHlObjects()}}class at{constructor(e){this.icn3d=e}onBeforeRender(e,t,s,i,n,l){let r=n.uniforms,o=[];if(r.objectId&&(r.objectId.value=SupportsReadPixelsFloat?this.id:this.id/255,o.push("objectId")),(r.modelViewMatrixInverse||r.modelViewMatrixInverseTranspose||r.modelViewProjectionMatrix||r.modelViewProjectionMatrixInverse)&&this.modelViewMatrix.multiplyMatrices(s.matrixWorldInverse,this.matrixWorld),r.modelViewMatrixInverse&&(r.modelViewMatrixInverse.value.copy(this.modelViewMatrix).invert(),o.push("modelViewMatrixInverse")),r.modelViewMatrixInverseTranspose&&(r.modelViewMatrixInverse?r.modelViewMatrixInverseTranspose.value.copy(r.modelViewMatrixInverse.value).transpose():r.modelViewMatrixInverseTranspose.value.copy(this.modelViewMatrix).invert().transpose(),o.push("modelViewMatrixInverseTranspose")),r.modelViewProjectionMatrix&&(s.updateProjectionMatrix(),r.modelViewProjectionMatrix.value.multiplyMatrices(s.projectionMatrix,this.modelViewMatrix),o.push("modelViewProjectionMatrix")),r.modelViewProjectionMatrixInverse){let e=new THREE.Matrix4;r.modelViewProjectionMatrix?(e.copy(r.modelViewProjectionMatrix.value),r.modelViewProjectionMatrixInverse.value.copy(e).invert()):(s.updateProjectionMatrix(),e.multiplyMatrices(s.projectionMatrix,this.modelViewMatrix),r.modelViewProjectionMatrixInverse.value.copy(e).invert()),o.push("modelViewProjectionMatrixInverse")}if(r.projectionMatrix&&(s.updateProjectionMatrix(),r.projectionMatrix.value.copy(s.projectionMatrix),o.push("projectionMatrix")),r.projectionMatrixInverse&&(s.updateProjectionMatrix(),r.projectionMatrixInverse.value.copy(s.projectionMatrix).invert(),o.push("projectionMatrixInverse")),o.length){let t=e.properties.get(n);if(t.program){let s=e.getContext(),i=t.program;s.useProgram(i.program);let n=i.getUniforms();o.forEach((function(e){n.setValue(s,e,r[e].value)}))}}}setParametersForShader(e){let t,s=this.icn3d,i=s.icn3dui.parasCls.backgroundColors[s.opts.background.toLowerCase()],n=2.5*s.maxD,l=4*s.maxD,r=void 0!==s.biomtMatrices&&s.biomtMatrices.length*s.cnt>s.maxatomcnt;"yes"===s.opts.slab?r?t=.1:void 0!==s.camMaxDFactorFog?(t=s.maxD*s.camMaxDFactorFog-10,n=2.5*s.maxD-t<0?0:2.5*s.maxD-t,l=4*s.maxD-t):t=s.maxD*s.camMaxDFactor:t=.1;let o=void 0!==e?e:1,a=s.shininess/100*.5;s.uniforms=THREE.UniformsUtils.merge([THREE.UniformsLib.common,{modelViewMatrix:{value:new THREE.Matrix4},modelViewMatrixInverse:{value:new THREE.Matrix4},modelViewMatrixInverseTranspose:{value:new THREE.Matrix4},modelViewProjectionMatrix:{value:new THREE.Matrix4},modelViewProjectionMatrixInverse:{value:new THREE.Matrix4},projectionMatrix:{value:new THREE.Matrix4},projectionMatrixInverse:{value:new THREE.Matrix4},diffuse:{type:"v3",value:[1,1,1]},emissive:{type:"v3",value:[.06,.06,.06]},roughness:{type:"f",value:.5},metalness:{type:"f",value:a},opacity:{type:"f",value:o},nearClip:{type:"f",value:t},ortho:{type:"f",value:0},shrink:{type:"f",value:.13},fogColor:{type:"v3",value:[i.r,i.g,i.b]},fogNear:{type:"f",value:n},fogFar:{type:"f",value:l},fogDensity:{type:"f",value:2}},THREE.UniformsLib.ambient,THREE.UniformsLib.lights]),s.defines={USE_COLOR:1,NEAR_CLIP:1,CAP:1},"yes"!==s.opts.fog||r||(s.defines.USE_FOG=1,"orthographic"===s.opts.camera&&(s.defines.FOG_EXP2=1)),s.bExtFragDepth&&(s.defines.USE_LOGDEPTHBUF_EXT=1)}drawImpostorShader(){this.icn3d.icn3dui.bNode||(this.setParametersForShader(),this.createImpostorShaderSphere("SphereImpostor"),this.createImpostorShaderCylinder("CylinderImpostor"))}getShader(e){this.icn3d.icn3dui;let t=$NGL_shaderTextHash[e];return t=t.replace(/#include\s+(\S+)/gim,(function(e,t){let s;return THREE.ShaderChunk.hasOwnProperty(t)&&(s=THREE.ShaderChunk[t]),s||""})),t}createImpostorShaderBase(e,t,s,i,n,l,r,o,a){let d=this.icn3d;d.icn3dui;let c=new THREE.ShaderMaterial({defines:d.defines,uniforms:d.uniforms,vertexShader:this.getShader(e+".vert"),fragmentShader:this.getShader(e+".frag"),depthTest:!0,depthWrite:!0,lights:!0});c.extensions.fragDepth=!0,"CylinderImpostor"==e?d.CylinderImpostorMaterial=c:"SphereImpostor"==e&&(d.SphereImpostorMaterial=c);let h,p,m=l*r,u=l*o,g=new(m>65535?Uint32Array:Uint16Array)(u);for(let e=0;e=0;t--){let s=a.children[t];s.onBeforeRender=e.impostorCls.onBeforeRender,s.frustumCulled=!1}l.add(a)}void 0!==e.mdl_ghost&&(a=e.mdl_ghost.clone(),this.applyMat(a,d),r.add(a));let c=e.center.clone();this.applyMat(c,d,!0),s.add(c),++t}e.mdl.add(n),e.mdlImpostor.add(l),e.mdl_ghost.add(r),void 0!==e.bSetInstancing&&e.bSetInstancing?(e.maxD=e.maxDAssembly,e.center=e.centerAssembly.clone(),e.applyCenterCls.setCenter(e.center),e.cameraCls.setCamera()):(e.maxD*=Math.sqrt(t),e.center=e.ParserUtilsCls.getMassCenter(s,t),e.maxDAssembly=e.maxD,e.centerAssembly=e.center.clone(),e.applyCenterCls.setCenter(e.center),e.cameraCls.setCamera()),e.bSetInstancing=!0}createInstancedGeometry(e){let t=this.icn3d,s=t.icn3dui,i=e.geometry,n=new THREE.InstancedBufferGeometry,l=[],r=[],o=[],a=[],d=[],c=[],h=[],p=[];if(t.bImpo&&"Cylinder"==e.type){t.instancedMaterial=this.getInstancedMaterial("CylinderInstancing");let e=s.hashUtilsCls.hashvalue2array(i.attributes.position1.array),r=s.hashUtilsCls.hashvalue2array(i.attributes.color.array),m=s.hashUtilsCls.hashvalue2array(i.attributes.position2.array),u=s.hashUtilsCls.hashvalue2array(i.attributes.color2.array),g=s.hashUtilsCls.hashvalue2array(i.index.array),f=s.hashUtilsCls.hashvalue2array(i.attributes.radius.array),b=s.hashUtilsCls.hashvalue2array(i.attributes.mapping.array);l=l.concat(e),o=o.concat(r),h=h.concat(m),p=p.concat(u),a=a.concat(g),d=d.concat(f),c=c.concat(b),n.setAttribute("position1",new THREE.BufferAttribute(new Float32Array(l),3)),n.setAttribute("color",new THREE.BufferAttribute(new Float32Array(o),3)),n.setAttribute("position2",new THREE.BufferAttribute(new Float32Array(h),3)),n.setAttribute("color2",new THREE.BufferAttribute(new Float32Array(p),3)),n.setAttribute("radius",new THREE.BufferAttribute(new Float32Array(d),1)),n.setAttribute("mapping",new THREE.BufferAttribute(new Float32Array(c),3)),n.setIndex(new THREE.BufferAttribute(new Uint32Array(a),1)),e=null,r=null,m=null,u=null,g=null,f=null,b=null}else if(t.bImpo&&"Sphere"==e.type){t.instancedMaterial=this.getInstancedMaterial("SphereInstancing");let e=s.hashUtilsCls.hashvalue2array(i.attributes.position.array),r=s.hashUtilsCls.hashvalue2array(i.attributes.color.array),h=s.hashUtilsCls.hashvalue2array(i.index.array),p=s.hashUtilsCls.hashvalue2array(i.attributes.radius.array),m=s.hashUtilsCls.hashvalue2array(i.attributes.mapping.array);l=l.concat(e),o=o.concat(r),a=a.concat(h),d=d.concat(p),c=c.concat(m),n.setAttribute("position",new THREE.BufferAttribute(new Float32Array(l),3)),n.setAttribute("color",new THREE.BufferAttribute(new Float32Array(o),3)),n.setAttribute("radius",new THREE.BufferAttribute(new Float32Array(d),1)),n.setAttribute("mapping",new THREE.BufferAttribute(new Float32Array(c),2)),n.setIndex(new THREE.BufferAttribute(new Uint32Array(a),1)),e=null,r=null,h=null,p=null,m=null}else{t.instancedMaterial=this.getInstancedMaterial("Instancing");let e=i.attributes.position?s.hashUtilsCls.hashvalue2array(i.attributes.position.array):[],d=i.attributes.normal?s.hashUtilsCls.hashvalue2array(i.attributes.normal.array):[],c=i.attributes.color?s.hashUtilsCls.hashvalue2array(i.attributes.color.array):[],h=i.index?s.hashUtilsCls.hashvalue2array(i.index.array):[];l=l.concat(e),r=r.concat(d),o=o.concat(c),a=a.concat(h);let p=[],m="CylinderGeometry"==i.type?1:0;for(let e=0,t=l.length/3;e0&&(e.dAtoms=t.hashUtilsCls.cloneHash(s)),e.bShowHighlight=!1}e.applyMapCls.removeSurfaces(),e.applyMapCls.applySurfaceOptions(),e.applyMapCls.removeMaps(),e.applyMapCls.applyMapOptions(),e.applyMapCls.removeEmmaps(),e.applyMapCls.applyEmmapOptions(),e.applyMapCls.removePhimaps(),e.applyMapCls.applyPhimapOptions(),e.applyMapCls.removeSurfaces(),e.applyMapCls.applyphisurfaceOptions(),e.axes=[],e.pc1&&e.axesCls.setPc1Axes(),e.opts.rotationcenter="highlight center",e.drawCls.draw(),e.bShowHighlight=!0}async alternateWrapper(){let e=this.icn3d;e.icn3dui,e.bAlternate=!0,await this.alternateStructures(),e.bAlternate=!1}}class ht{constructor(e){this.icn3d=e}draw(e){let t=this.icn3d,s=t.icn3dui;if(t.impostorCls.clearImpostors(),!t.bRender||t.hAtoms&&0!=Object.keys(t.hAtoms)||(t.hAtoms=s.hashUtilsCls.cloneHash(t.atoms)),t.sceneCls.rebuildScene(),t.bImpo&&t.impostorCls.drawImpostorShader(),t.setColorCls.applyPrevColor(),void 0!==t.biomtMatrices&&t.biomtMatrices.length>1)if(t.bAssembly&&1==Object.keys(t.structures).length&&(void 0===s.cfg.mmdbid&&1==s.cfg.bu||void 0!==s.cfg.mmdbid&&1==s.cfg.bu&&Object.keys(t.atoms).length*t.biomtMatrices.length>t.maxatomcnt))t.instancingCls.drawSymmetryMates();else{let e=!0;t.applyCenterCls.centerSelection(void 0,e)}let i=void 0!==t.hAtoms?Object.keys(t.hAtoms).length:0;if(i>0&&i0){e.children[0].scale.z=t[0].distance,t[0].point.sub(r.mdl.position);let s=r.rayThreshold,i=r.rayCls.getAtomsFromPosition(t[0].point,s);for(;!i&&s<10;)s+=.5,i=r.rayCls.getAtomsFromPosition(t[0].point,s);i&&(r.pAtomNum%2==0?r.pAtom=i:r.pAtom2=i,++r.pAtomNum,this.showPickingVr(r.pk,i))}}}}catch(e){}}showPickingVr(e,t){let s=this.icn3d;s.icn3dui,e||(e=2),s.hAtoms=s.pickingCls.getPickedAtomList(e,t),2===e?s.residueLabelsCls.addResidueLabels(s.hAtoms,void 0,void 0,!0):1===e&&s.residueLabelsCls.addAtomLabels(s.hAtoms),s.setOptionCls.setStyle("proteins",t.style)}render_base(){let e=this.icn3d,t=e.icn3dui,s=this;if(t.bNode)return;let i=e.bControlGl&&!t.bNode?window.cam:e.cam;if(e.directionalLight){let t=new THREE.Quaternion;t.setFromUnitVectors(new THREE.Vector3(0,0,e.cam_z).normalize(),i.position.clone().normalize()),e.directionalLight.position.copy(e.lightPos.clone().applyQuaternion(t).normalize()),e.directionalLight2.position.copy(e.lightPos2.clone().applyQuaternion(t).normalize()),e.directionalLight3.position.copy(e.lightPos3.clone().applyQuaternion(t).normalize())}if(e.bVr||e.renderer.setPixelRatio(window.devicePixelRatio),e.bVr){let t=.04;if(e.controllers){let i=this.updateGamepadState();for(let n=0,l=e.controllers.length;n{const i=e.gamepad.axes;let r=parseInt(1e3*i[t]),o=parseInt(-1e3*i[s]);n.push(r),l.push(o)})),{xArray:n,yArray:l}}return{xArray:[0,0],yArray:[0,0]}}}class pt{constructor(e){this.icn3d=e}getAtomsWithinAtom(e,t,s,i,n,l,r){let o=this.icn3d;o.icn3dui;let a=this.getNeighboringAtoms(e,t,s,r);i&&(o.resid2Residhash={});let d={};for(let e in t){let c,h,p=o.atoms[e],m=p.structure+"_"+p.chain+"_"+p.resi;for(let e in o.residues[m])if(o.atoms[e]&&("CA"===o.atoms[e].name&&"C"===o.atoms[e].elem||"O3'"===o.atoms[e].name||"O3*"===o.atoms[e].name)){c=o.atoms[e];break}void 0===c&&(c=p),i&&(h=p.resn+" $"+p.structure+"."+p.chain+":"+p.resi,void 0===o.resid2Residhash[h]&&(o.resid2Residhash[h]={}));let u=p.structure+"_"+p.chain+"_"+p.resi;for(let e in a){let m=a[e];if(!o.crossstrucinter&&p.structure!=m.structure)continue;if(!r&&m.serial in t)continue;if(o.bOpm&&"DUM"===m.resn)continue;let g=m.coord.distanceTo(p.coord);if(go?r:o,d=Math.sqrt(a),c=(d+s)*(d+s),h={};for(let r in e){let e=n.atoms[r];!i&&t.hasOwnProperty(e.serial)||(this.bOpm&&"DUM"===e.resn||e.coord.xl[1][0]+s||e.coord.yl[1][1]+s||e.coord.zl[1][2]+s||(e.coord.x-l[2][0])*(e.coord.x-l[2][0])+(e.coord.y-l[2][1])*(e.coord.y-l[2][1])+(e.coord.z-l[2][2])*(e.coord.z-l[2][2])e.coord.x?n:e.coord.x,l=l>e.coord.y?l:e.coord.y,r=r>e.coord.z?r:e.coord.z}return[[t,s,i],[n,l,r],[o/c,a/c,d/c]]}hideContact(){let e=this.icn3d;e.icn3dui,e.opts.contact="no",void 0===e.lines&&(e.lines={}),e.lines.contact=[],e.contactpnts=[]}}class mt{constructor(e){this.icn3d=e}isHbondDonorAcceptor(e){let t=this.icn3d;if(t.icn3dui,"N"==e.name&&!e.het||"N"==e.elem&&"Arg"==e.resn||"N"==e.elem&&"Asn"==e.resn||"N"==e.elem&&"Gln"==e.resn||"N"==e.elem&&"Lys"==e.resn||"N"==e.elem&&"Trp"==e.resn)return"donor";if("O"==e.name&&!e.het||"S"==e.elem&&"Met"==e.resn||"O"==e.elem&&"Asn"==e.resn||"O"==e.elem&&"Asp"==e.resn||"O"==e.elem&&"Gln"==e.resn||"O"==e.elem&&"Glu"==e.resn)return"acceptor";if("S"==e.elem&&"Cys"==e.resn||"N"==e.elem&&"His"==e.resn||"O"==e.elem&&"Ser"==e.resn||"O"==e.elem&&"Thr"==e.resn||"O"==e.elem&&"Tyr"==e.resn)return"both";if("Pro"==e.resn)return"none";if("N"==e.elem){if("Asn"==e.resn||"Gln"==e.resn)return"both";let s=0,i=0;for(let i=0,n=e.bonds.length;i1?"ring":"donor":"none"}if("O"==e.elem&&1==e.bonds.length){if("Asn"==e.resn||"Gln"==e.resn)return"both";for(let s=0,i=e.bonds.length;s=2?"acceptor":"both"}if("O"==e.elem&&2==e.bonds.length){for(let s=0,i=e.bonds.length;s1);++t)"H"!=s.atoms[e.bonds[t]].elem&&(i=s.atoms[e.bonds[t]],l[r++].subVectors(s.atoms[e.bonds[t]].coord,e.coord));if(1===r)for(let t=0,n=i.bonds.length;t1);++t)"H"!=s.atoms[i.bonds[t]].elem&&s.atoms[i.bonds[t]].serial!=e.serial&&l[r++].subVectors(s.atoms[i.bonds[t]].coord,e.coord);if(2!==r)return;let o=l[0].cross(l[1]);return Math.abs(Math.PI/2-o.angleTo(n))}isValidHbond(e,t,s){let i=this.icn3d;i.icn3dui;let n,l,r=this.isHbondDonorAcceptor(e),o=this.isHbondDonorAcceptor(t),a=50*Math.PI/180,d=50*Math.PI/180,c=90*Math.PI/180,h=30*Math.PI/180;if("donor"==r&&("acceptor"==o||"both"==o||"ring"==o)||"acceptor"==o&&("donor"==r||"both"==r||"ring"==r))n=e,l=t;else if("acceptor"==r&&("donor"==o||"both"==o||"ring"==o)||"donor"==o&&("acceptor"==r||"both"==r||"ring"==r))l=e,n=t;else{if("both"!=r&&"ring"!=r||"both"!=o&&"ring"!=o)return!1;n=e,l=t,i.nucleotides.hasOwnProperty(e.serial)&&i.nucleotides.hasOwnProperty(t.serial)&&("ring"==r||"ring"==o)||(e.het||t.het)&&"ring"==r&&"ring"==o||(h=90*Math.PI/180)}let p=this.calcAngles(n,l),m=90*Math.PI/180;for(let e=0,t=p.length;ed)return!1;let u=this.calcPlaneAngle(n,l);if(void 0!==u&&u>h)return!1;let g=this.calcAngles(l,n),f=90*Math.PI/180;for(let e=0,t=g.length;ea)return!1;let b=this.calcPlaneAngle(l,n);return!(void 0!==b&&b>c)}calculateChemicalHbonds(e,t,s,i,n,l){let r=this.icn3d,o=r.icn3dui;if(0===Object.keys(e).length||0===Object.keys(t).length)return;r.resid2Residhash={};let a,d,c={},h=s*s;for(let t in e){let s=e[t],n=i?"LYS"===s.resn&&"N"===s.elem&&"N"!==s.name||"ARG"===s.resn&&("NH1"===s.name||"NH2"===s.name)||("GLU"===s.resn||"ASP"===s.resn)&&"O"===s.elem&&"O"!==s.name||s.het&&("N"===s.elem||"O"===s.elem||"S"===s.elem):"N"===s.elem||"O"===s.elem||"S"===s.elem&&(s.het||"Cys"===s.resn||"Met"===s.resn);n=r.bOpm?n&&"DUM"!==s.resn:n,n&&(a=s.structure+"_"+s.chain+"_"+s.resi,d=a+"_"+s.name,c[d]=s)}let p={},m={},u=.5,g=-27.888,f={};for(let e in t){let b=t[e],C=i?"LYS"===b.resn&&"N"===b.elem&&"N"!==b.name||"ARG"===b.resn&&("NH1"===b.name||"NH2"===b.name)||("GLU"===b.resn||"ASP"===b.resn)&&"O"===b.elem&&"O"!==b.name||b.het&&("N"===b.elem||"O"===b.elem||"S"===b.elem):"N"===b.elem||"O"===b.elem||"S"===b.elem&&(b.het||"Cys"===b.resn||"Met"===b.resn);if(C=r.bOpm?C&&"DUM"!==b.resn:C,C){a=b.structure+"_"+b.chain+"_"+b.resi,d=a+"_"+b.name;let e=b.resn+" $"+b.structure+"."+b.chain+":"+b.resi+"@"+b.name;void 0===r.resid2Residhash[e]&&(r.resid2Residhash[e]={});for(let t in c){if(i&&!(("LYS"!==b.resn&&"ARG"!==b.resn||"LYS"!==c[t].resn&&"ARG"!==c[t].resn)&&("GLU"!==b.resn&&"ASP"!==b.resn||"GLU"!==c[t].resn&&"ASP"!==c[t].resn)))continue;if(!r.crossstrucinter&&b.structure!=c[t].structure)continue;if(a==t.substr(0,t.lastIndexOf("_")))continue;let d=Math.abs(b.coord.x-c[t].coord.x);if(d>s)continue;let C=Math.abs(b.coord.y-c[t].coord.y);if(C>s)continue;let y=Math.abs(b.coord.z-c[t].coord.z);if(y>s)continue;let v=d*d+C*C+y*y;if(v>h)continue;if(!r.proteins.hasOwnProperty(b.serial)||!r.proteins.hasOwnProperty(c[t].serial)||"N"!==b.name&&"O"!==b.name||"O"!==c[t].name&&"N"!==c[t].name){if(!this.isValidHbond(b,c[t],s))continue}else{if(b.name===c[t].name)continue;if(b.structure==c[t].structure&&b.chain==c[t].chain&&Math.abs(b.resi-c[t].resi)<=1)continue;let e,i="N"===b.name?b:c[t],n="O"===b.name?b:c[t];if("Pro"===i.resn)continue;if(void 0===i.hcoord){if(!this.isValidHbond(b,c[t],s))continue}else{let s,l=i.hcoord,o=i.coord,a=n.structure+"_"+n.chain+"_"+n.resi;for(let e in r.residues[a])if("C"===r.atoms[e].name){s=r.atoms[e];break}if(!s)continue;let d=s.coord,h=n.coord,p=l.distanceTo(h),m=l.distanceTo(d),f=o.distanceTo(d),C=o.distanceTo(h);e=p2||f[c[t].serial]>2)continue;void 0===f[b.serial]?f[b.serial]=1:++f[b.serial],void 0===f[c[t].serial]?f[c[t].serial]=1:++f[c[t].serial],"graph"!==n&&(i?(r.saltbridgepnts.push({serial:b.serial,coord:b.coord}),r.saltbridgepnts.push({serial:c[t].serial,coord:c[t].coord})):(r.hbondpnts.push({serial:b.serial,coord:b.coord}),r.hbondpnts.push({serial:c[t].serial,coord:c[t].coord})));let _=c[t].structure+"_"+c[t].chain+"_"+c[t].resi;p=o.hashUtilsCls.unionHash(p,r.residues[a]),p=o.hashUtilsCls.unionHash(p,r.residues[_]),m[a]=1,m[_]=1;let w=c[t].resn+" $"+c[t].structure+"."+c[t].chain+":"+c[t].resi+"@"+c[t].name,S=a+"_"+b.resn+","+_+"_"+c[t].resn;void 0!==r.resids2interAll[S]&&void 0!==r.resids2interAll[S].ionic&&r.resids2interAll[S].ionic.hasOwnProperty(e+","+w)||(r.resid2Residhash[e][w]=v.toFixed(1),l||(void 0===r.resids2inter[S]&&(r.resids2inter[S]={}),void 0===r.resids2inter[S].hbond&&(r.resids2inter[S].hbond={}),r.resids2inter[S].hbond[e+","+w]=v.toFixed(1)),void 0===r.resids2interAll[S]&&(r.resids2interAll[S]={}),void 0===r.resids2interAll[S].hbond&&(r.resids2interAll[S].hbond={}),r.resids2interAll[S].hbond[e+","+w]=v.toFixed(1))}}}let b=Object.keys(m);if("graph"!==n)for(let e=0,t=b.length;en)return!1;let c=Math.abs(e.coord.y-t.coord.y);if(c>n)return!1;let h=Math.abs(e.coord.z-t.coord.z);if(h>n)return!1;let p=d*d+c*c+h*h;if(p>l)return!1;"graph"!==s&&("halogen"==i?(a.halogenpnts.push({serial:e.serial,coord:e.coord}),a.halogenpnts.push({serial:t.serial,coord:t.coord})):"pi-cation"==i?(a.picationpnts.push({serial:e.serial,coord:e.coord}),a.picationpnts.push({serial:t.serial,coord:t.coord})):"pi-stacking"==i&&(a.pistackingpnts.push({serial:e.serial,coord:e.coord}),a.pistackingpnts.push({serial:t.serial,coord:t.coord})));let m=t.resn+" $"+t.structure+"."+t.chain+":"+t.resi+"@"+t.name;a.resid2Residhash[r][m]=p.toFixed(1);let u=e.structure+"_"+e.chain+"_"+e.resi+"_"+e.resn+","+t.structure+"_"+t.chain+"_"+t.resi+"_"+t.resn;return o||(void 0===a.resids2inter[u]&&(a.resids2inter[u]={}),void 0===a.resids2inter[u][i]&&(a.resids2inter[u][i]={}),a.resids2inter[u][i][r+","+m]=p.toFixed(1)),void 0===a.resids2interAll[u]&&(a.resids2interAll[u]={}),void 0===a.resids2interAll[u][i]&&(a.resids2interAll[u][i]={}),a.resids2interAll[u][i][r+","+m]=p.toFixed(1),!0}getRingNormal(e){if(this.icn3d.icn3dui,e.length<3)return;let t=e[0].clone().sub(e[1]),s=e[1].clone().sub(e[2]);return t.cross(s).normalize()}getAromaticRings(e,t,s){let i=this.icn3d;i.icn3dui;let n=[],l=[],r=[],o=[];if("nucleotide"==s){let s=new THREE.Vector3,a=new THREE.Vector3;if("A"==e.trim().toUpperCase()||"DA"==e.trim().toUpperCase()||"G"==e.trim().toUpperCase()||"DG"==e.trim().toUpperCase()){for(let e in i.residues[t]){let t=i.atoms[e];"N1"==t.name||"C2"==t.name||"N3"==t.name||"C6"==t.name?(s.add(t.coord),r.push(t.coord)):"C4"==t.name||"C5"==t.name?(s.add(t.coord),a.add(t.coord),r.push(t.coord),o.push(t.coord)):"N7"!=t.name&&"C8"!=t.name&&"N9"!=t.name||(a.add(t.coord),o.push(t.coord))}6==r.length&&(s.multiplyScalar(1/6),n.push(s),l.push(this.getRingNormal(r))),5==o.length&&(a.multiplyScalar(.2),n.push(a),l.push(this.getRingNormal(o)))}else if("C"==e.trim().toUpperCase()||"DC"==e.trim().toUpperCase()||"T"==e.trim().toUpperCase()||"DT"==e.trim().toUpperCase()||"U"==e.trim().toUpperCase()||"DU"==e.trim().toUpperCase()){for(let e in i.residues[t]){let t=i.atoms[e];"N1"==t.name||"C2"==t.name||"N3"==t.name||"C6"==t.name?(s.add(t.coord),r.push(t.coord)):"C4"!=t.name&&"C5"!=t.name||(s.add(t.coord),r.push(t.coord))}6==r.length&&(s.multiplyScalar(1/6),n.push(s),l.push(this.getRingNormal(r)))}}else if("protein"==s){let s=new THREE.Vector3,a=new THREE.Vector3;if("PHE"==e.toUpperCase()||"TYR"==e.toUpperCase()){for(let e in i.residues[t]){let t=i.atoms[e];"CG"!=t.name&&"CD1"!=t.name&&"CE1"!=t.name&&"CZ"!=t.name&&"CE2"!=t.name&&"CD2"!=t.name||(s.add(t.coord),r.push(t.coord))}6==r.length&&(s.multiplyScalar(1/6),n.push(s),l.push(this.getRingNormal(r)))}else if("HIS"==e.toUpperCase()){for(let e in i.residues[t]){let t=i.atoms[e];"CG"!=t.name&&"ND1"!=t.name&&"CE1"!=t.name&&"NE2"!=t.name&&"CD2"!=t.name||(s.add(t.coord),r.push(t.coord))}5==r.length&&(s.multiplyScalar(.2),n.push(s),l.push(this.getRingNormal(r)))}else if("TRP"==e.toUpperCase()){for(let e in i.residues[t]){let t=i.atoms[e];"CZ2"==t.name||"CH2"==t.name||"CZ3"==t.name||"CE3"==t.name?(s.add(t.coord),r.push(t.coord)):"CD2"==t.name||"CE2"==t.name?(s.add(t.coord),a.add(t.coord),r.push(t.coord),o.push(t.coord)):"CG"!=t.name&&"CD1"!=t.name&&"NE1"!=t.name||(a.add(t.coord),o.push(t.coord))}6==r.length&&(s.multiplyScalar(1/6),n.push(s),l.push(this.getRingNormal(r))),5==o.length&&(a.multiplyScalar(.2),n.push(a),l.push(this.getRingNormal(o)))}}return{piPosArray:n,normalArray:l}}dfs_cycle(e,t,s){let i=this.icn3d;if(i.icn3dui,2==i.ring_color[e])return s;if(1==i.ring_color[e]){s++;let n=t;for(i.ring_mark[n]=s;n!=e;)n=i.ring_par[n],i.ring_mark[n]=s;return s}if(i.ring_par[e]=t,i.ring_color[e]=1,void 0!==i.atoms[e])for(let t=0,n=i.atoms[e].bonds.length;t=3&&o<=6&&a[0]&&a[1]&&a[2]&&a[3]){let i=a[0].clone().sub(a[1]).normalize(),r=a[1].clone().sub(a[2]).normalize(),d=a[2].clone().sub(a[3]).normalize(),c=i.cross(r).normalize(),h=c.dot(d);if(Math.abs(h)<.052){l.multiplyScalar(1/o);let i=t.atoms[n];s[e+"_pi"+n]={resn:i.resn,name:"pi"+n,coord:l,serial:i.serial,structure:i.structure,chain:i.chain,resi:i.resi,normal:c}}}}return s}hideHalogenPi(){let e=this.icn3d;e.icn3dui,e.opts.halogen="no",e.opts["pi-cation"]="no",e.opts["pi-stacking"]="no",void 0===e.lines&&(e.lines={}),e.lines.halogen=[],e.lines["pi-cation"]=[],e.lines["pi-stacking"]=[],e.halogenpnts=[],e.picationpnts=[],e.pistackingpnts=[]}}class gt{constructor(e){this.icn3d=e}calculateIonicInteractions(e,t,s,i,n,l){let r=this.icn3d,o=r.icn3dui;if(0===Object.keys(e).length||0===Object.keys(t).length)return;r.resid2Residhash={};let a,d,c={},h={},p=s*s;for(let t in e){let s=e[t];if("ARG"===s.resn&&"NH2"===s.name||"GLU"===s.resn&&"OE2"===s.name||"ASP"===s.resn&&"OD2"===s.name)continue;let i=("LYS"===s.resn||"HIS"===s.resn)&&"N"===s.elem&&"N"!==s.name||"ARG"===s.resn&&("NH1"===s.name||"NH2"===s.name)||s.het&&-1!==o.parasCls.cationsTrimArray.indexOf(s.elem)||s.het&&"N"===s.elem&&1==s.bonds.length,n=this.isAnion(s);i=r.bOpm?i&&"DUM"!==s.resn:i,n=r.bOpm?n&&"DUM"!==s.resn:n,(i||n)&&(a=s.structure+"_"+s.chain+"_"+s.resi,d=a+"_"+s.name,i&&(c[d]=s),n&&(h[d]=s))}let m={},u={};for(let e in t){let i=t[e];if("ARG"===i.resn&&"NH2"===i.name||"GLU"===i.resn&&"OE2"===i.name||"ASP"===i.resn&&"OD2"===i.name)continue;let g=("LYS"===i.resn||"HIS"===i.resn)&&"N"===i.elem&&"N"!==i.name||"ARG"===i.resn&&("NH1"===i.name||"NH2"===i.name)||i.het&&-1!==o.parasCls.cationsTrimArray.indexOf(i.elem),f=this.isAnion(i);if(g=r.bOpm?g&&"DUM"!==i.resn:g,f=r.bOpm?f&&"DUM"!==i.resn:f,g||f){a=i.structure+"_"+i.chain+"_"+i.resi,d=a+"_"+i.name;let e=i.resn+" $"+i.structure+"."+i.chain+":"+i.resi+"@"+i.name;void 0===r.resid2Residhash[e]&&(r.resid2Residhash[e]={});let t={};g?t=h:f&&(t=c);let b,C=i.structure+"_"+i.chain+"_"+i.resi;g&&"ARG"===i.resn&&"NH1"===i.name?b=r.firstAtomObjCls.getFirstAtomObjByName(r.residues[C],"NH2"):f&&"GLU"===i.resn&&"OE1"===i.name?b=r.firstAtomObjCls.getFirstAtomObjByName(r.residues[C],"OE2"):f&&"ASP"===i.resn&&"OD1"===i.name&&(b=r.firstAtomObjCls.getFirstAtomObjByName(r.residues[C],"OD2"));let y=void 0===b?i.coord:i.coord.clone().add(b.coord).multiplyScalar(.5);for(let d in t){if(a==d.substr(0,d.lastIndexOf("_")))continue;if(!r.crossstrucinter&&i.structure!=t[d].structure)continue;let c,h=t[d].structure+"_"+t[d].chain+"_"+t[d].resi;f&&"ARG"===t[d].resn&&"NH1"===t[d].name?c=r.firstAtomObjCls.getFirstAtomObjByName(r.residues[h],"NH2"):g&&"GLU"===t[d].resn&&"OE1"===t[d].name?c=r.firstAtomObjCls.getFirstAtomObjByName(r.residues[h],"OE2"):g&&"ASP"===t[d].resn&&"OD1"===t[d].name&&(c=r.firstAtomObjCls.getFirstAtomObjByName(r.residues[h],"OD2"));let b=void 0===c?t[d].coord:t[d].coord.clone().add(c.coord).multiplyScalar(.5),C=Math.abs(y.x-b.x);if(C>s)continue;let v=Math.abs(y.y-b.y);if(v>s)continue;let _=Math.abs(y.z-b.z);if(_>s)continue;let w=C*C+v*v+_*_;if(w>p)continue;"graph"!==n&&(r.saltbridgepnts.push({serial:i.serial,coord:y}),r.saltbridgepnts.push({serial:t[d].serial,coord:b}));let S=t[d].structure+"_"+t[d].chain+"_"+t[d].resi;m=o.hashUtilsCls.unionHash(m,r.residues[a]),m=o.hashUtilsCls.unionHash(m,r.residues[S]),u[a]=1,u[S]=1;let A=t[d].resn+" $"+t[d].structure+"."+t[d].chain+":"+t[d].resi+"@"+t[d].name;r.resid2Residhash[e][A]=w.toFixed(1);let x=a+"_"+i.resn+","+S+"_"+t[d].resn;l||(void 0===r.resids2inter[x]&&(r.resids2inter[x]={}),void 0===r.resids2inter[x].ionic&&(r.resids2inter[x].ionic={}),r.resids2inter[x].ionic[e+","+A]=w.toFixed(1)),void 0===r.resids2interAll[x]&&(r.resids2interAll[x]={}),void 0===r.resids2interAll[x].ionic&&(r.resids2interAll[x].ionic={}),r.resids2interAll[x].ionic[e+","+A]=w.toFixed(1)}}}let g=Object.keys(u);if("graph"!==n)for(let e=0,t=g.length;e1?1/(n-1):1;for(let n in e){let e=t.atoms[n];e.color=e.het?s.parasCls.atomColors[e.elem]||s.parasCls.defaultAtomColor:s.parasCls.thr().setHSL(3/4*(1-i++*l),1,.45),t.atomPrevColors[n]=e.color}}colorRainbow(e){let t=this.icn3d,s=t.icn3dui,i=0,n=0;e=s.hashUtilsCls.intHash(e,t.hAtoms);for(let s in e){t.atoms[s].het||++n}let l=n>1?1/(n-1):1;for(let n in e){let e=t.atoms[n];e.color=e.het?s.parasCls.atomColors[e.elem]||s.parasCls.defaultAtomColor:s.parasCls.thr().setHSL(3/4*i++*l,1,.45),t.atomPrevColors[n]=e.color}}setColorAcrossSets(e,t){let s=this.icn3d,i=s.icn3dui,n=0,l=e.length,r=l>1?1/(l-1):1;for(let l=0,o=e.length;l0)this.setMmdbChainColor();else{let e=-1,s="",l=n.parasCls.stdChainColors.length;for(let r in t){let t=i.atoms[r];t.chain!=s&&(++e,e%=l),t.het?(t.color=n.parasCls.atomColors[t.elem],i.atomPrevColors[r]=t.color):(t.color=n.parasCls.stdChainColors[e],Object.keys(i.chainsColor).length>0&&this.updateChainsColor(t),i.atomPrevColors[r]=t.color),s=t.chain}}break;case"domain":s=0,l=0;let m=Object.keys(i.tddomains);l=m.length,r=l>1?1/(l-1):1;for(let e=0,t=m.length;e1?1/(l-1):1;for(let e=0;e Defined Sets", and try it again.');break;case"secondary structure green":i.sheetcolor="green";for(let e in t){let t=i.atoms[e];t.color=t.het?n.parasCls.atomColors[t.elem]||n.parasCls.defaultAtomColor:n.parasCls.ssColors[t.ss]||n.parasCls.thr(16711935),i.atomPrevColors[e]=t.color}break;case"secondary structure yellow":case"secondary structure":i.sheetcolor="yellow";for(let e in t){let t=i.atoms[e];t.color=t.het?n.parasCls.atomColors[t.elem]||n.parasCls.defaultAtomColor:n.parasCls.ssColors2[t.ss]||n.parasCls.thr(16711935),i.atomPrevColors[e]=t.color}break;case"secondary structure spectrum":s=0,l=0;let u,g,f=[],b=-9999;for(let e in t){if(!i.proteins.hasOwnProperty(e))continue;let t=i.atoms[e];-9999==b&&(u=parseInt(e)),-9999!=b&&(t.ss!=g.ss||Math.abs(t.resi-g.resi)>1||t.ssbegin&&g.ssend)&&("coil"==g.ss||f.push([u,b]),u=e),b=parseInt(e),g=t}"coil"==g.ss||f.push([u,b]),l=f.length,r=l>1?1/(l-1):1;for(let e=0,t=f.length;e100&&(e=100);let r=(i.middB-e)*i.spanBinv1,o=(e-i.middB)*i.spanBinv2;e=90?t.color=n.parasCls.thr().setRGB(0,.325,.839):e>=70&&e<90?t.color=n.parasCls.thr().setRGB(.396,.572,.953):e>=50&&e<70?t.color=n.parasCls.thr().setRGB(1,.859,.075):e<50&&(t.color=n.parasCls.thr().setRGB(1,.49,.271))}i.atomPrevColors[e]=t.color}break;case"b factor":i.middB=50,i.spanBinv1=.02,i.spanBinv2=.02;for(let e in t){let t=i.atoms[e];if(void 0===t.b||isNaN(t.b)||0==parseInt(1e3*t.b))t.color=n.parasCls.thr().setRGB(0,1,0);else{let e=t.b;e>100&&(e=100),e=t.structure.substr(0,4)!=i.defaultPdbId&&t.structure.length>5?100-e:e;let s=(i.middB-e)*i.spanBinv1,l=(e-i.middB)*i.spanBinv2;t.color=et.b&&(o=t.b),a5?100-t.b:t.b,s=i.bfactorArray.indexOf(e)/C;t.color=s<.5?n.parasCls.thr().setRGB(2*s,2*s,1):n.parasCls.thr().setRGB(1,2*(1-s),2*(1-s))}i.atomPrevColors[e]=t.color}break;case"area":if(void 0===i.resid2area){let e=n.hashUtilsCls.cloneHash(i.hAtoms);i.hAtoms=n.hashUtilsCls.cloneHash(i.atoms),i.bCalcArea=!0,i.opts.surface="solvent accessible surface",i.applyMapCls.applySurfaceOptions(),i.bCalcArea=!1,i.hAtoms=n.hashUtilsCls.cloneHash(e)}let y=void 0!==i.midpercent?i.midpercent:35;i.spanBinv1=.02,i.spanBinv2=.02;for(let e in t){let t=i.atoms[e],s=t.structure+"_"+t.chain+"_"+t.resi+"_"+t.resn,l=n.parasCls.residueArea.hasOwnProperty(t.resn)?i.resid2area[s]/n.parasCls.residueArea[t.resn]*100:y;l>100&&(l=100);let r=(y-l)*i.spanBinv1,o=(l-y)*i.spanBinv2;t.color=l[e,s.parasCls.hydrophobicValues[e]]));l.sort(((e,t)=>parseFloat(e[1])-parseFloat(t[1])));var r=l.map((e=>[e[0],Object.keys(o[e[0]])[0]]));n+="","normalized hydrophobic"==e?(n+="Dark green (W, F, L, I, Y, M, V, C): Hydrophobic
",n+="Light green (P, T, S, A, Q, N, G): Polar
",n+="Grey: Charged, not hydrophobic
"):(n+="Green (W, F, L, I, Y, M, V, C): Hydrophobic
",n+="Yellow (P, T, S, A, Q, N, G): Polar
",n+="Red: Negatively Charged
",n+="Blue: Positively Charged
");let a=0;for(let e of r)s.parasCls.residueAbbrev[e[0]]&&(n+="
",n+="
",n+=s.parasCls.residueAbbrev[e[0]]+"
",a%4==3&&(n+="
"),++a);n+="
B factor quantitates the uncertainty for each atom. A high B factor reflects that the position is less certain.
"+e+" ";for(let e in l[s])n+="
";n+=i.parasCls.atomnames[s.toUpperCase()]+" "}n+="
"}return n}getRes2color(e,t){let s=this.icn3d,i=s.icn3dui,n={},l=s.firstAtomObjCls.getResiduesFromAtoms(e);for(let e in l){let l=s.residues[e],r=s.firstAtomObjCls.getFirstAtomObj(l),o=t?r.resn:i.parasCls.residueAbbrev[r.resn],a=void 0===r||void 0===r.color||"FFFFFF"===r.color.getHexString().toUpperCase()?"DDDDDD":r.color.getHexString();null!=o&&(void 0===n[o]&&(n[o]={}),n[o][a]=1)}return n}getColorLegendForResidue(e){this.icn3d.icn3dui;let t="",s=this.getRes2color(e);if(Object.keys(s).length>0){t+="
";let e=Object.keys(s).sort(),i="",n=0;for(let l=0,r=e.length;l
";for(let e in s[o])r+="
";r+=o+" ",n%4==3&&(r+="
"),-1!=o.indexOf("(")?(t+=r,++n):i+=r}i&&(t+="
"+i),t+="
";for(let e=0,t=r.length;e
",s+="
",s+=t,s+=" ";for(let e in s){t+="
",t+="
",t+=e,t+=" "}return t+="
Protodomain 1 ":"","A Strand":"0000FF","B Strand":"006400","C Strand":"F7DC6F","C' Strand":"FFA500","Linker ":"","C'' Strand":"FF0000","Protodomain 2 ":"","D Strand":"0000FF","E Strand":"006400","F Strand":"F7DC6F","G Strand":"FFA500","":"",Loop:"CCCCCC"};t+="A protodomain is a supersecondary structure
that by its duplication, symmetry operations
can generate a structural domain.
";for(let e in s){let i=s[e];t+="
",i&&(t+="
"),t+=e,t+=" "}return t+="
',p=h,m=h,u=d.doms;n.bNode&&!i.resid2cdd[c]&&(i.resid2cdd[c]=[]);let g=l.setDomainFeature(u,c,!0,h,p,m);i.chainid2pssmid[c]={pssmid2name:g.pssmid2name,pssmid2fromArray:g.pssmid2fromArray,pssmid2toArray:g.pssmid2toArray};let f=g.acc2domain;h=g.html+"",p=g.html2+"",m=g.html3+"",$("#"+i.pre+"dt_cdd_"+c).html(h),$("#"+i.pre+"ov_cdd_"+c).html(p),$("#"+i.pre+"tt_cdd_"+c).html(m),h='',p=h,m=h;let b=d.motifs;n.bNode&&!i.resid2site[c]&&(i.resid2site[c]=[]),g=l.setDomainFeature(b,c,!1,h,p,m,f),h=g.html,p=g.html2,m=g.html3;let C=a.data[e].sites,y=void 0!==C?C.length:0;for(let e=0;e17&&(s=s.substr(0,17)+"...");let l,r=C[e].title,o=[];for(let t=0,s=C[e].locs.length;t'+s+"
",u=''+t.toString()+" Res ",g='';m+=d+u+"1&&(l=s[0]+"..");let r=i.ParserUtilsCls.getResi(c,t);if(h+=''+s+" ",n.bNode){let t={};t[c+"_"+r]="site: "+C[e].title,i.resid2site[c].push(t)}p+=i.showSeqCls.insertGapOverview(c,t);let o=n.cfg.blast_rep_id==c?Math.round(i.seqAnnWidth*t/(i.maxAnnoLength+i.nTotalGap)-b-y):Math.round(i.seqAnnWidth*t/i.maxAnnoLength-b-y);o>=0&&(p+='
',p+='
',b+=o,y+=v)}else h+="- ";i.seqStartLen&&i.seqStartLen[c]&&(h+=i.showSeqCls.insertMulGap(i.seqEndLen[c],"-")),g=' '+t.toString()+" Residues ",g+=" ",g+="m&&(v=v.substr(0,m)+"...");let _=b+": "+C;s&&(o[p]=C);let w=e[g].locs;if(w)for(let e=0,r=w.length;e'+v+" ",I=''+S.toString()+" Res ";l+=R+I+"';i+=R+I+T,s&&(n+='
'),n+=''+v+"
",n+=I+T;let E=b+g.toString();c.seqStartLen&&c.seqStartLen[t]&&(i+=c.showSeqCls.insertMulGap(c.seqStartLen[t],"-"));for(let e=0,n=c.giSeq[t].length;e1&&(l=n[0]+"..");let r=c.ParserUtilsCls.getResi(t,e);if(i+=''+n+" ",h.bNode){let e={};e[t+"_"+r]=_,s?c.resid2cdd[t].push(e):c.resid2site[t].push(e)}}else i+="- ";c.seqStartLen&&c.seqStartLen[t]&&(i+=c.showSeqCls.insertMulGap(c.seqEndLen[t],"-"));let P=c.firstAtomObjCls.getFirstCalphaAtomObj(c.chains[t]),M=void 0===P.color||"FFFFFF"===P.color.getHexString()?"DDDDDD":P.color.getHexString(),D=void 0!==P.color?M:"CCCCCC";if(c.seqStartLen&&c.seqStartLen[t]&&(n+=c.showSeqCls.insertMulGapOverview(t,c.seqStartLen[t])),h.cfg.blast_rep_id!=t)for(let s=0,i=r.length;s ',n+=''+C+"
"}else{let s=[],i=[];for(let e=0,t=r.length;e ',n+=''+C+"
"}}T=' '+S.toString()+" Residues ",T+=" ",T+="',d=a,c=a;if(0==n.length)return $("#"+r.pre+"dt_"+s+"_"+e).html(""),$("#"+r.pre+"ov_"+s+"_"+e).html(""),void $("#"+r.pre+"tt_"+s+"_"+e).html("");let h=i;i.length>17&&(i=i.substr(0,17)+"...");let p=[];for(let e=0,t=n.length;e'+i+"
",f=''+m.toString()+" Res ";c+=g+f+"';a+=g+f+b,d+=g+f+b;let C=s,y=0,v=0;r.seqStartLen&&r.seqStartLen[e]&&(d+=r.showSeqCls.insertMulGapOverview(e,r.seqStartLen[e])),r.seqStartLen&&r.seqStartLen[e]&&(a+=r.showSeqCls.insertMulGap(r.seqStartLen[e],"-"));for(let t=0,i=r.giSeq[e].length;t1&&(c=n[0]+"..");let h=i,p=e+"_"+i,m=n+i;if("ssbond"==s){m="Residue "+p+" has disulfide bond with";let t="";if(void 0!==l[p])for(let e=0,s=l[p].length;e'+c+" ",d+=r.showSeqCls.insertGapOverview(e,t);let u=o.cfg.blast_rep_id==e?Math.round(r.seqAnnWidth*t/(r.maxAnnoLength+r.nTotalGap)-y-v):Math.round(r.seqAnnWidth*t/r.maxAnnoLength-y-v);u>=0&&(d+='
',d+='
',y+=u,v+=1)}else a+="- "}r.seqStartLen&&r.seqStartLen[e]&&(a+=r.showSeqCls.insertMulGap(r.seqEndLen[e],"-")),b=' '+m.toString()+" Residues ",b+="",b+="4)continue;let o,a=s.firstAtomObjCls.getFirstCalphaAtomObj(s.chains[t]);s.chemicals.hasOwnProperty(a.serial)?o="chemical":s.nucleotides.hasOwnProperty(a.serial)?o="nucleotide":s.ions.hasOwnProperty(a.serial)?o="ion":s.proteins.hasOwnProperty(a.serial)?o="protein":s.water.hasOwnProperty(a.serial)&&(o="water");let d=s.contactCls.getAtomsWithinAtom(i.hashUtilsCls.hash2Atoms(s.chains[l],s.atoms),i.hashUtilsCls.hash2Atoms(s.chains[t],s.atoms),4);if(0==Object.keys(d).length)continue;let c={};for(let e in d){let t=s.atoms[e];c[t.structure+"_"+t.chain+"_"+t.resi]=1}let h=t.substr(t.indexOf("_")+1)+"("+o+")";s.chainname2residues[l][h]=Object.keys(c)}}let o='',a=o,d=o,c=0;for(let t in s.chainname2residues[e]){let n=s.chainname2residues[e][t];if(!n)continue;let l="Interact ."+t;l.length>17&&(l=l.substr(0,17)+"...");let r="Interact ."+t,h=[];for(let e=0,t=n.length;e'+l+"
",g=''+p.toString()+" Res ";d+=u+g+"';o+=u+g+f,a+=u+g+f;let b="inter"+c.toString(),C=0,y=0,v=1;s.seqStartLen&&s.seqStartLen[e]&&(a+=s.showSeqCls.insertMulGapOverview(e,s.seqStartLen[e])),s.seqStartLen&&s.seqStartLen[e]&&(o+=s.showSeqCls.insertMulGap(s.seqStartLen[e],"-"));for(let t=0,n=s.giSeq[e].length;t1&&(d=l[0]+"..");let c=n;if(o+=''+d+" ",i.bNode){let t={};t[e+"_"+c]=r,s.resid2contact[e].push(t)}a+=s.showSeqCls.insertGapOverview(e,t);let h=i.cfg.blast_rep_id==e?Math.round(s.seqAnnWidth*t/(s.maxAnnoLength+s.nTotalGap)-C-y):Math.round(s.seqAnnWidth*t/s.maxAnnoLength-C-y);h>=0&&(a+='
',a+='
',C+=h,y+=v)}else o+="- "}s.seqStartLen&&s.seqStartLen[e]&&(o+=s.showSeqCls.insertMulGap(s.seqEndLen[e],"-")),f=' '+p.toString()+" Residues ",f+=" ",f+="',o+=r,a+=r;let d=s.substr(0,s.indexOf("_"));for(let c in t){let h=t[c],p=[],m=!1;for(let e=0,t=h.length;e5?p.push(e-1):i.UPResi2ResiPosPerChain&&i.UPResi2ResiPosPerChain[s][e]&&p.push(i.UPResi2ResiPosPerChain[s][e]),!m&&i.residues.hasOwnProperty(s+"_"+e)&&(m=!0)}if(0==p.length)continue;let u=p.length,g="ptm"==e?"PTM: "+c:"Transmembrane";g.length>17&&(g=g.substr(0,17)+"...");let f=c,b=''+g+"
",C=''+u.toString()+" Res ",y='';a+=b+C+"1&&(l=t[0]+"..");let a=i.ParserUtilsCls.getResi(s,e);if(r+=''+t+" ",n.bNode){let e={};e[s+"_"+a]=g,i.resid2ptm[s].push(e)}o+=i.showSeqCls.insertGapOverview(s,e);let d=n.cfg.blast_rep_id==s?Math.round(i.seqAnnWidth*e/(i.maxAnnoLength+i.nTotalGap)-_-w):Math.round(i.seqAnnWidth*e/i.maxAnnoLength-_-w);d>=0&&(o+='
',o+='
',_+=d,w+=S)}else r+="- ";i.seqStartLen&&i.seqStartLen[s]&&(r+=i.showSeqCls.insertMulGap(i.seqEndLen[s],"-")),y=' '+u.toString()+" Residues ",y+=" ",y+="',a=o,d=o,c=e.indexOf("_"),h=e.substr(c+1);if(s)n=e,i=t.domains[e]?t.domains[e].domains:[];else{let e,s=t.moleculeInfor;for(let t in s)if(s[t].chain===h){e=t,n=s[t].name;break}void 0!==e&&void 0!==t.domains[e]&&(i=t.domains[e].domains),void 0===i&&(i=[])}for(let t=0,s=i.length;t17?s.substr(0,17)+"...":s,h=i[t].intervals,p={},m={},u=[],g=[],f={},b=0;for(let e=0,t=h.length;e'+c+" ",y=''+b.toString()+" Res ";d+=C+y+"';o+=C+y+v,a+=C+y+v;let _="domain3d"+t.toString();l.seqStartLen&&l.seqStartLen[e]&&(o+=l.showSeqCls.insertMulGap(l.seqStartLen[e],"-"));for(let t=0,s=l.giSeq[e].length;t1&&(n=i[0]+"..");let r=s;o+=''+i+" "}else o+="- "}l.seqStartLen&&l.seqStartLen[e]&&(o+=l.showSeqCls.insertMulGap(l.seqEndLen[e],"-"));let w=l.firstAtomObjCls.getFirstCalphaAtomObj(l.chains[e]),S=void 0===w.color||"FFFFFF"===w.color.getHexString()?"DDDDDD":w.color.getHexString(),A=void 0!==w.color?S:"CCCCCC";if(l.seqStartLen&&l.seqStartLen[e]&&(a+=l.showSeqCls.insertMulGapOverview(e,l.seqStartLen[e])),r.cfg.blast_rep_id!=e)for(let i=0,n=u.length;i ',a+='3D domain '+(t+1).toString()+"
"}else{let i=[],n=[];for(let e=0,t=u.length;e ',a+='3D domain '+(t+1).toString()+"
"}}v=' '+b.toString()+" Residues ",v+=" ",v+="0?o[0]:"N/A");let a=i.applyCenterCls.centerAtoms(n.hashUtilsCls.hash2Atoms(i.residues[s],i.atoms));r.length>30&&(r=r.substr(0,30)+"..."),i.selectionCls.removeSelection(),null==i.labels&&(i.labels={}),i.labels.clinvar=[];let d=i.LABELSIZE,c="black"!=i.opts.background?i.colorWhitebkgd:i.colorBlackbkgd;i.analysisCls.addLabel(r,a.center.x+1,a.center.y+1,a.center.z+1,d,c,void 0,"clinvar"),i.hAtoms={};for(let e in i.residues[s])i.hAtoms[e]=1;$("#clinvar_"+i.pre+s).addClass("icn3d-highlightSeq"),void 0===$("#"+i.pre+"modeswitch")[0]||$("#"+i.pre+"modeswitch")[0].checked||i.definedSetsCls.setMode("selection"),i.drawCls.draw()}getSnpLine(e,t,s,i,n,l,r,o,a,d,c,h,p,m,u,g){let f=this.icn3d,b=f.icn3dui,C="",y=m?"clinvar":"snp",v=!1;for(let e in i){for(let t=0,s=i[e].length;t(from human)",i=" (based on human sequences and mapped to this structure by sequence similarity) "),C+=m?''+e+s+"
":''+t+s+"
"}else if(2==e&&m){let e=b.utilsCls.isMobile()?"none":"button";C+='< ClinVar
',C+='ClinVar >
'}else C+='
';let _=y,w=0,S=0,A={},x={};for(let t=1,i=f.giSeq[h].length;t<=i;++t)if(void 0!==r[t]){++w;let i="";for(let n=0,r=s[t].length;n'+k+" Res":'';let O="",R=0,I=0;p?f.seqStartLen&&f.seqStartLen[h]&&(C+=f.showSeqCls.insertMulGapOverview(h,f.seqStartLen[h])):f.seqStartLen&&f.seqStartLen[h]&&(C+=f.showSeqCls.insertMulGap(f.seqStartLen[h],"-"));for(let t=1,a=f.giSeq[h].length;t<=a;++t)if(p){if(void 0!==r[t]){let e=f.giSeq[h][t-1],i=e;e.length>1&&(i=e[0]+"..");let n=f.ParserUtilsCls.getResi(h,t-1)+i+">";for(let e=0,i=s[t].length;e=0&&(C+='
',C+='
',R+=r,I+=1):r>0&&(C+='
',C+='
',R+=r,I+=1)}}else if(C+=f.showSeqCls.insertGap(h,t-1,"-"),void 0!==r[t])if(m||1!=e){let r=f.giSeq[h][t-1],a=r;r.length>1&&(a=r[0]+"..");let d,c=f.ParserUtilsCls.getResi(h,t-1),p="",u="",y=s[t].length,v=0,w=0;if(2==e&&(v=0,w=y),m){d=1;let r=0;for(let e=v;e
0?w+="; ":0!==e&&1!==e||(O='disease="'+v[t]+'"'),w+=v[t]+"("+_[t]+")",++S;""!=w&&(r"+s[t][e],u+=": "+w,C&&!b.cfg.hidelicense&&(u+="ClinVar , dbSNP(rs"+i[t][e]+") ",e"+s[t][e],g)C&&!b.cfg.hidelicense&&(u+="dbSNP(rs"+i[t][e]+") "),e0?d+="; ":0!==e&&1!==e||(O='disease="'+s[t]+'"'),d+=s[t]+"("+a[t]+")",++c;""!=d?(u+=": "+d,C&&!b.cfg.hidelicense&&(u+="ClinVar , dbSNP(rs"+i[t][e]+") "):(C&&!b.cfg.hidelicense&&(u+="dbSNP(rs"+i[t][e]+") "),e ⇓ ":""==p||" "==p?"- ":''+p+" ":C+="- ":C+=""==p||" "==p?"- ":g?''+p+" ":''+p+" "}else C+="⇓ ";else C+="- ";return p||f.seqStartLen&&f.seqStartLen[h]&&(C+=f.showSeqCls.insertMulGap(f.seqEndLen[h],"-")),C+=1==e?' '+k+" Residues ":' ",C+="',a=o,d=o,c='
',h=c,p=c,m=!i||n?e.data:e.split("\n"),u={},g={},f={};void 0===l.resi2disease_nonempty[t]&&(l.resi2disease_nonempty[t]={});let b={},C={},y={},v={},_={},w="";r.bNode&&(i?(l.resid2snp||(l.resid2snp={}),l.resid2snp[t]||(l.resid2snp[t]=[])):(l.resid2clinvar||(l.resid2clinvar={}),l.resid2clinvar[t]||(l.resid2clinvar[t]=[])));for(let e=0,s=m.length;e")+1),h=s[4],p=i?"":s[5],S=i?"":s[6],A=i?"":s[7],x=l.ParserUtilsCls.getResi(t,d-1);v[x]=1,""!=S&&(_[x]=1),g[d]=e+1,void 0===u[d]&&(u[d]=[]),u[d].push(c),void 0===C[d]&&(C[d]=[]),C[d].push(h),void 0===y[d]&&(y[d]=[]),y[d].push(p),void 0===f[d]&&(f[d]=[]),f[d].push(S),""!=S&&(void 0===l.resi2disease_nonempty[t][d]&&(l.resi2disease_nonempty[t][d]=[]),l.resi2disease_nonempty[t][d].push(S)),void 0===b[d]&&(b[d]=[]),b[d].push(A)}let S=Object.keys(v),A=Object.keys(_);if(i){let e=!1;o+=this.getSnpLine(1,2,u,C,y,f,g,b,S,A,1,t,!1,e,void 0,i),o+=this.getSnpLine(2,2,u,C,y,f,g,b,S,A,0,t,!1,e,void 0,i),d+=this.getSnpLine(1,2,u,C,y,f,g,b,S,A,1,t,!1,e,!0,i),d+=this.getSnpLine(2,2,u,C,y,f,g,b,S,A,0,t,!1,e,!0,i),a+=this.getSnpLine(1,2,u,C,y,f,g,b,S,A,1,t,!0,e,void 0,i),o+="
",a+="
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r=this.getFullText(s);return s=r.text,this.showNewTrack(e,t,s,void 0,void 0,i,n,l),!1}setTimeout((function(){a.checkGiSeq(e,t,s,i,n,l,r+1)}),100)}getFullText(e){this.icn3d.icn3dui;let t="",s=[],i=[],n=e.split(","),l=-1;for(let e=0,r=n.length;ep?t+=c.substr(0,p):t+=c;for(let e=0;ed&&(d=t.length,c=h),++h}o=n.htmlCls.baseUrl+"pwaln/pwaln.fcgi?from=msa";let p=e.split(","),m={};m[t]=0;for(let e=0,t=p.length;e0&&(g+=","+p.join(","));let f={targets:u,queries:g},b=await n.getAjaxPostPromise(o,f);if(!b.data)return void console.log("The protein accessions "+u+","+g+" can not be aligned...");let C=[];i.qt_start_end={};let y=[],v=[],_=Object.keys(b.targets)[0],w=b.targets[_].seqdata;p.splice(0,0,t);for(let e=0,s=p.length;eA&&(A=e)}let x=S,k=w.length-(A+1),O=[],R=[];for(let e=0,t=p.length;ea&&(a=t.length,d=c),++c}s.qt_start_end={};let m="genomeRes",u={};for(let e=0,i=h.length;ef&&(f=e)}for(let 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s=e.firstAtomObjCls.getFirstCalphaAtomObj(e.chains[i]);if(void 0!==s.resn){let i=t.utilsCls.residueName2Abbr(s.resn.substr(0,3));$("#"+e.pre+"anno_"+i).show()}}}showAnnoAllChains(){let e=this.icn3d;e.icn3dui,$("#"+e.pre+"dl_annotations > .icn3d-annotation").show()}setAnnoView(e){let t=this.icn3d;t.icn3dui.bNode||("detailed view"===e?(t.view="detailed view",$("#"+t.pre+"dl_anno_view_tabs").tabs("option","active",1)):(t.view="overview",$("#"+t.pre+"dl_anno_view_tabs").tabs("option","active",0)))}setAnnoDisplay(e,t){let s=this.icn3d;s.icn3dui;let i=["giseq","custom","site","ptm","snp","clinvar","cdd","domain","interaction","ssbond","crosslink","transmem"];for(let n in i){let l=i[n];$("[id^="+s.pre+t+"_"+l+"]").attr("style",e)}}showFixedTitle(){this.icn3d.icn3dui;this.setAnnoDisplay("display:block;","tt")}hideFixedTitle(){this.icn3d.icn3dui;this.setAnnoDisplay("display:none!important;","tt")}setAnnoViewAndDisplay(e){let t=this.icn3d;if(t.icn3dui,"detailed view"===e){this.setAnnoView("detailed view");let e="display:block;";this.setAnnoDisplay(e,"dt"),$("#"+t.pre+"seqguide_wrapper").attr("style",e),e="display:none;",this.setAnnoDisplay(e,"ov")}else{this.setAnnoView("overview"),this.hideFixedTitle();let e="display:none;";this.setAnnoDisplay(e,"dt"),$("#"+t.pre+"seqguide_wrapper").attr("style",e),e="display:block;",this.setAnnoDisplay(e,"ov")}}async updateClinvar(){let e=this.icn3d;if(e.icn3dui,void 0===e.bClinvarShown||!e.bClinvarShown)for(let t in e.protein_chainid){let s=e.protein_chainid[t];await e.annoSnpClinVarCls.showClinvar(t,s)}e.bClinvarShown=!0}async updateSnp(){let e=this.icn3d;if(e.icn3dui,void 0===e.bSnpShown||!e.bSnpShown)for(let t in e.protein_chainid){let s=e.protein_chainid[t];await e.annoSnpClinVarCls.showSnp(t,s)}e.bSnpShown=!0}updateDomain(){let e=this.icn3d;e.icn3dui,void 0!==e.bDomainShown&&e.bDomainShown||e.annoDomainCls.showDomainAll(),e.bDomainShown=!0}updateInteraction(){let e=this.icn3d;if(e.icn3dui,void 0===e.bInteractionShown||!e.bInteractionShown)for(let t in e.interactChainbase){let s=e.interactChainbase[t];e.annoContactCls.showInteraction(t,s)}e.bInteractionShown=!0}async updatePTM(){let e=this.icn3d;if(e.icn3dui,void 0===e.bPTMShown||!e.bPTMShown)for(let t in e.PTMChainbase){let s=e.PTMChainbase[t];await e.annoPTMCls.showPTM(t,s,"ptm")}e.bPTMShown=!0}updateSsbond(){let e=this.icn3d;if(e.icn3dui,void 0===e.bSSbondShown||!e.bSSbondShown)for(let t in e.ssbondChainbase){let s=e.ssbondChainbase[t];e.annoSsbondCls.showSsbond(t,s)}e.bSSbondShown=!0}updateCrosslink(){let e=this.icn3d;if(e.icn3dui,void 0===e.bCrosslinkShown||!e.bCrosslinkShown)for(let t in e.crosslinkChainbase){let s=e.crosslinkChainbase[t];e.annoCrossLinkCls.showCrosslink(t,s)}e.bCrosslinkShown=!0}async updateTransmem(){let e=this.icn3d,t=e.icn3dui;if(void 0===e.bTranememShown||!e.bTranememShown)for(let s in e.protein_chainid){let i=e.protein_chainid[s];if(void 0!==t.cfg.opmid)e.annoTransMemCls.showTransmem(s,i);else if(e.bAfMem&&e.afmem_start_end){let t=e.afmem_start_end[0],n=e.afmem_start_end[1];await e.annoPTMCls.showPTM(s,i,"afmem",t,n)}else await e.annoPTMCls.showPTM(s,i,"transmem")}e.bTranememShown=!0}}class Et{constructor(e){this.icn3d=e}showAnnotations_part1(){let e=this.icn3d,t=e.icn3dui;if(t.htmlCls.dialogCls.openDlg("dl_selectannotations","Sequences and Annotations"),(void 0===e.bAssemblyNote||!e.bAssemblyNote)&&void 0!==e.asuCnt){let t=" Assembly Tips: Only the asymmetric unit is shown in the sequence window."+e.asuCnt+" asymmetric unit).
";$("#"+e.pre+"dl_annotations_tabs").append(t),e.bAssemblyNote=!0}e.bResetAnno&&(e.giSeq={},e.currClin={},e.resi2disease_nonempty={},e.baseResi={},e.matchedPos={},$("#"+t.pre+"dl_annotations").empty(),e.annotationCls.setAnnoView("overview"));let s={},i={},n={};if(void 0===e.bAnnoShown||!e.bAnnoShown||e.bResetAnno){e.protein_chainid={};let l,r=Object.keys(e.chains);void 0===e.giSeq&&(e.giSeq={}),void 0===e.currClin&&(e.currClin={}),void 0===e.resi2disease_nonempty&&(e.resi2disease_nonempty={}),void 0===e.baseResi&&(e.baseResi={}),void 0===e.matchedPos&&(e.matchedPos={}),l=t.bNode?500:t.cfg.notebook?t.htmlCls.WIDTH/2:$("#"+e.pre+"dl_selectannotations").dialog("option","width"),e.seqAnnWidth=l-120-60-50;for(let l=0,o=r.length;l1)e.protein_chainid[r[l]]=a;else if(e.nucleotides.hasOwnProperty(o.serial)&&e.chainsSeq[r[l]].length>1)s[r[l]]=a;else if(e.chainsSeq[r[l]].length>1)i[r[l]]=a;else{let t=e.chainsSeq[r[l]][0].name,s=r[l]+"_"+e.chainsSeq[r[l]][0].resi;void 0===n[t]&&(n[t]=[]),n[t].push(s)}if((void 0!==t.cfg.pdbid||void 0!==t.cfg.opmid||void 0!==t.cfg.mmcifid||void 0!==t.cfg.mmtfid)&&(e.proteins.hasOwnProperty(o.serial)||e.nucleotides.hasOwnProperty(o.serial)))for(let t=0,s=e.chainsSeq[r[l]].length;te.maxAnnoLengthOri&&(e.protein_chainid.hasOwnProperty(t)||s.hasOwnProperty(t))&&(e.maxAnnoLengthOri=e.chainsSeq[t].length);e.maxAnnoLength=e.maxAnnoLengthOri}return{nucleotide_chainid:s,chemical_chainid:i,chemical_set:n}}async showAnnotations(){let e=this.icn3d,t=e.icn3dui,s=this,i=this.showAnnotations_part1(),n=i.nucleotide_chainid,l=i.chemical_chainid,r=i.chemical_set;if(!e.bAnnoShown||e.bResetAnno)if(e.bAnnoShown=!0,void 0===t.cfg.blast_rep_id){if(e.bFullUi){if(void 0!==t.cfg.mmtfid){let t=Object.keys(e.structures)[0];await e.mmcifParserCls.downloadMmcifSymmetry(t,"mmtfid")}await this.showAnnoSeqData(n,l,r)}}else if(void 0===t.cfg.blast_rep_id||e.bSmithwm||e.bLocalSmithwm){if(void 0!==t.cfg.blast_rep_id&&(e.bSmithwm||e.bLocalSmithwm)){let i,o,a=[t.cfg.blast_rep_id];if(-1!=t.cfg.query_id.indexOf(">")?o=t.cfg.query_id.substr(t.cfg.query_id.indexOf("\n")+1):!/\d/.test(t.cfg.query_id)||t.cfg.query_id.length>50?o=t.cfg.query_id:a.push(t.cfg.query_id),e.blastAcxn){let s=t.cfg.afid+"_A",n="";for(let t=0,i=e.chainsSeq[s].length;t5){let n;e.uniprot2acc&&e.uniprot2acc[i]?e.uniprot2acc[i]:e.uniprot2acc={},n="https://rest.uniprot.org/uniprotkb/search?format=json&fields=xref_geneid,gene_names&query="+i;let l=await t.getAjaxPromise(n,"json"),r=l.results[0]&&l.results[0].uniProtKBCrossReferences&&l.results[0].uniProtKBCrossReferences[0]?l.results[0].uniProtKBCrossReferences[0].id:void 0,o=l.results[0]&&l.results[0].genes&&l.results[0].genes[0]&&l.results[0].genes[0].geneName?l.results[0].genes[0].geneName.value:"ID "+r;e.chainsGene[s]={geneId:r,geneSymbol:o}}}for(let s in e.protein_chainid){let i=t.utilsCls.isMobile()?"none":"button",l=e.showSeqCls.getProteinName(s),r=l,o=0==n?"Proteins : "+e.chainsGene[s].geneSymbol+" )":"",d=s.substr(0,s.indexOf("_")),c=d.length>5?''+s+" ":s,h=""+o+"
Annotations of "+c+" :
"+r+" "+a+" "+this.addButton(s,"icn3d-addtrack","Add Track","Add a custom track",60,i)+" ";h+=this.addButton(s,"icn3d-customcolor","Custom Color/Tube","Use a custom file to define the colors or tubes in 3D structure",110,i)+" ",h+=this.addButton(s,"icn3d-helixsets","Helix Sets",'Define sets for each helix in this chain and add them to the menu of "Defined Sets"',60,i)+" "+this.addButton(s,"icn3d-sheetsets","Sheet Sets",'Define sets for each sheet in this chain and add them to the menu of "Defined Sets"',60,i)+" "+this.addButton(s,"icn3d-coilsets","Coil Sets",'Define sets for each coil in this chain and add them to the menu of "Defined Sets"',60,i),e.bShowRefnum&&e.chainid2refpdbname.hasOwnProperty(s)&&e.chainid2refpdbname[s].length>0&&(h+=" "+this.addButton(s,"icn3d-igstrandsets","Ig Strand Sets",'Define sets for each Ig strand in this chain and add them to the menu of "Defined Sets"',80,i)+" "+this.addButton(s,"icn3d-igloopsets","Ig Loop Sets",'Define sets for each Ig loop in this chain and add them to the menu of "Defined Sets"',80,i)),$("#"+e.pre+"dl_annotations").append(h);let p=["giseq","cdd","clinvar","snp","site","ptm","ssbond","crosslink","transmem","domain","custom","interaction"];for(let t in p){let i=p[t];$("#"+e.pre+"anno_"+s).append(this.getAnDiv(s,i))}$("#"+e.pre+"anno_"+s).append("
"),++n}if(t.bNode||e.annoCddSiteCls.setToolTip(),void 0!==e.chainid_seq)await this.processSeqData(e.chainid_seq);else try{let n=[],l=[];for(let e=0,t=i.length;e
=6?l.push(i[e]):n.push(i[e])}if(n.length>0){let s=t.htmlCls.baseUrl+"/vastdyn/vastdyn.cgi?chainlist="+n;e.chainid_seq=await t.getAjaxPromise(s,"jsonp")}else e.chainid_seq={};for(let t=0,s=l.length;t40&&(r=r.substr(0,40)+"...");let o="";0==i&&("protein"==s?o="Proteins : Nucleotides : Chemicals/Ions/Water : "+o+""+e+" : "+r+"
"),$("#"+n.pre+"anno_"+e).append(this.getAnDiv(e,"giseq")),$("#"+n.pre+"anno_"+e).append(this.getAnDiv(e,"interaction")),$("#"+n.pre+"anno_"+e).append("Chemicals/Ions/Water : "+e+" ":""+e+" ",$("#"+n.pre+"dl_annotations").append(""+r+i+"
"),$("#"+n.pre+"anno_"+e).append(""),$("#"+n.pre+"anno_"+e).append("';c+='
Chem. '+e+"
",c+='
Count: '+t.length+" ",c+='
';let h=c,p=c;for(let s=0,i=t.length;s3&&(l=i.substr(0,3)),s'+l+" "}let m=l.htmlCls.GREY8,u=Math.round(n.seqAnnWidth*t.length/n.maxAnnoLength);u<1&&(u=1),p+='
',c="",c+="
",c+="
14?"Query: "+o.substr(0,6)+"...":isNaN(s.cfg.query_id)?"Query: "+o:"Query: gi "+o;let a="cannot be aligned";t.queryStart="",t.queryEnd="",t.bRender&&alert("The sequence can NOT be aligned to the structure"),t.showSeqCls.showSeq(i,n,void 0,e,l,a,r)}else if(s.cfg.blast_rep_id==i&&(void 0!==t.seqStructAlignData||void 0!==t.seqStructAlignDataSmithwm)){let e,l,r,o,a,d=s.cfg.oriQuery_id?s.cfg.oriQuery_id:s.cfg.query_id;if(e=d.length>14?"Query: "+d.substr(0,6)+"...":isNaN(s.cfg.query_id)?"Query: "+d:"Query: gi "+d,void 0!==t.seqStructAlignData){let e,s,i=t.seqStructAlignData;if(void 0!==i.data){e=i.data[0].query;let t=Object.keys(i.data[0].targets);s=i.data[0].targets[t[0]],s=void 0!==s&&s.hsps.length>0?s.hsps[0]:void 0}if(void 0!==e&&void 0!==s){l=s.scores.e_value.toPrecision(2),l>1e-200&&(l=parseFloat(l).toExponential()),s.scores.bit_score;let t=Object.keys(i.targets);r=i.targets[t[0]].seqdata,o=e.seqdata,a=s.segs}}else{let e=t.seqStructAlignDataSmithwm;l=e.score,r=e.target.replace(/-/g,""),o=e.query.replace(/-/g,""),a=[];let s=-1,i=-1,n=!1,d={};for(let t=0,l=e.target.length;t0)if(i.orifrom-ni.from-l)for(let t=n+1;t
"+i+"
"+i+"
"+s+"
"}addSnpButton(e,t,s,i,n,l){let r=this.icn3d;return r.icn3dui,""+s+"
"}conservativeReplacement(e,t){let s=this.icn3d.icn3dui,i=-1!==s.parasCls.b62ResArray.indexOf(e)?s.parasCls.b62ResArray.indexOf(e):s.parasCls.b62ResArray.length-1,n=-1!==s.parasCls.b62ResArray.indexOf(t)?s.parasCls.b62ResArray.indexOf(t):s.parasCls.b62ResArray.length-1;return s.parasCls.b62Matrix[i][n]>0}getColorhexFromBlosum62(e,t){let s=this.icn3d.icn3dui,i="333333";if(!e||!t)return i;e=e.toUpperCase(),t=t.toUpperCase();let n=-1!==s.parasCls.b62ResArray.indexOf(e)?s.parasCls.b62ResArray.indexOf(e):s.parasCls.b62ResArray.length-1,l=-1!==s.parasCls.b62ResArray.indexOf(t)?s.parasCls.b62ResArray.indexOf(t):s.parasCls.b62ResArray.length-1,r=s.parasCls.b62Matrix[n][l];if(void 0===r)return"333333";if(r>0){let e=221-parseInt(r/11*221),t=e<10?"0"+e.toString(16):e.toString(16);i="DD"+t+t}else{let e=221-parseInt(-1*r/4*221),t=e<10?"0"+e.toString(16):e.toString(16);i=t+t+"DD"}return i}}class Pt{constructor(e){this.icn3d=e}showSeq(e,t,s,i,n,l,r){let o,a=this.icn3d,d=a.icn3dui,c=!1;if(void 0===d.cfg.mmdbid&&void 0===d.cfg.gi&&void 0===d.cfg.blast_rep_id&&void 0===d.cfg.align&&void 0===d.cfg.chainalign&&void 0===d.cfg.mmdbafid){c=!0,o=[];for(let t=0;t10){u='';let t=a.firstAtomObjCls.getFirstCalphaAtomObj(a.chains[e]);void 0===d.cfg.mmdbid&&void 0===d.cfg.gi&&void 0===d.cfg.blast_rep_id&&void 0===d.cfg.align&&void 0===d.cfg.chainalign&&void 0===d.cfg.mmdbafid||void 0===t.resi_ori||t.resi_ori==t.resi||-1!=e.indexOf("Misc")?u+='
':u+='
NCBI Residue Numbers
',u+='
',b+=u+"
",g+=u+'
';let s=0,i=0,n="";a.seqStartLen&&a.seqStartLen[e]&&(g+=this.insertMulGap(a.seqStartLen[e]," "));for(let t=0,l=o.length;t",l%10==0&&(g+=l);let r=e+"_"+l,o=l%10!=0&&l%10!=1&&l%10!=9;if(a.residues.hasOwnProperty(r)){let e=a.firstAtomObjCls.getFirstCalphaAtomObj(a.residues[r]);"H"==a.secondaries[r]&&e.ssbegin?(++s,n='H'+s+" ",o&&(g+=n,n="")):"E"==a.secondaries[r]&&e.ssbegin?(++i,"green"==a.sheetcolor?n='S'+i+" ":"yellow"==a.sheetcolor&&(n='S'+i+" "),o&&(g+=n,n="")):e.ssend&&(n=""),""!=n&&o&&(g+=n,n="")}g+=" "}a.seqStartLen&&a.seqStartLen[e]&&(g+=this.insertMulGap(a.seqEndLen[e]," ")),g+='
',g+="",g+="
",g+="
',u+='
',u+='
',b+=u+"
",g+=u+'
',a.seqStartLen&&a.seqStartLen[e]&&(g+=this.insertMulGap(a.seqStartLen[e],"-"));for(let t=0,s=o.length;t':'',g+=" ";else if("E"==a.secondaries[s]){a.firstAtomObjCls.getFirstCalphaAtomObj(a.residues[s]).ssend?"green"==a.sheetcolor?g+='':"yellow"==a.sheetcolor&&(g+=''):"green"==a.sheetcolor?g+='':"yellow"==a.sheetcolor&&(g+=''),g+=" "}else"c"==a.secondaries[s]?g+=' ':"o"==a.secondaries[s]&&(g+=' ');else g+="- "}a.seqStartLen&&a.seqStartLen[e]&&(g+=this.insertMulGap(a.seqEndLen[e],"-")),g+=' ",g+=" ':'
';let C="Protein",y="Protein";void 0!==s&&("nucleotide"==s?(C="Nucl.",y="Nucleotide"):"chemical"==s&&(C="Chem.",y="Chemical")),u+='
'+C+" "+e+"
",u+='
'+(a.baseResi[e]+1).toString()+" ",b+=u+"
";let v='
';g+=u+v,f+=u+v;let _,w=0;a.seqStartLen&&a.seqStartLen[e]&&(g+=this.insertMulGap(a.seqStartLen[e],"-"));for(let t=0,s=o.length;t1&&(i=s[0]+".."),_=a.ParserUtilsCls.getResi(e,t),a.residues.hasOwnProperty(e+"_"+_)){let n="333333";if(d.cfg.blast_rep_id==e&&void 0!==a.fullpos2ConsTargetpos&&void 0!==a.fullpos2ConsTargetpos[t+w])n=a.fullpos2ConsTargetpos[t+w].color;else{let t=a.firstAtomObjCls.getFirstCalphaAtomObj(a.residues[e+"_"+_]),s=void 0===t.color||"FFFFFF"===t.color.getHexString().toUpperCase()||"FFF"===t.color.getHexString().toUpperCase()?"DDDDDD":t.color.getHexString();n=void 0!==t.color?s:"CCCCCC"}g+=''+i+" "}else i=i.toLowerCase(),g+=''+i+" "}a.seqStartLen&&a.seqStartLen[e]&&(g+=this.insertMulGap(a.seqEndLen[e],"-")),d.cfg.blast_rep_id==e&&(a.opts.color=a.blastAcxn?"confidence":"conservation",a.setColorCls.setColorByOptions(a.opts,a.atoms));let S=a.firstAtomObjCls.getFirstCalphaAtomObj(a.chains[e]),A=S.color?S.color.getHexString():"CCCCCC",x=Math.round(a.seqAnnWidth*o.length/(a.maxAnnoLength+a.nTotalGap));if(x<1&&(x=1),a.seqStartLen&&a.seqStartLen[e]&&(f+=this.insertMulGapOverview(e,a.seqStartLen[e])),d.cfg.blast_rep_id!=e)f+=''+e+"
";else{let t=[],s=[];t.push(0);for(let e=0,i=o.length;e';for(let i=0,n=t.length;i'+e+" ";f+="
'+_+" ",u+="",u+="'+n+"
",u+='';g+=u+t,f+=u+t;let s=0,i=0,l=1;a.queryStart;for(let t=0,n=r.length;t- ";else if(" "==n)g+=" ";else{let r=a.fullpos2ConsTargetpos[t].pos;if(a.residues.hasOwnProperty(e+"_"+r)){let s=a.fullpos2ConsTargetpos[t].color;g+=''+n+" "}else n=n.toLowerCase(),g+=''+n+" ";f+=this.insertGapOverview(e,t);let o=Math.round(a.seqAnnWidth*t/(a.maxAnnoLength+a.nTotalGap)-s-i);o>=0&&(f+='
',f+='
',s+=o,i+=l)}}u=''+i+"
",u+=''+a.queryStart+" ",b+=u+"';g+=u+t,f+=u+t;let s=a.queryStart;for(let t=0,i=l.length;t- ":(void 0===a.fullpos2ConsTargetpos||void 0===a.fullpos2ConsTargetpos[t]||a.residues.hasOwnProperty(e+"_"+a.fullpos2ConsTargetpos[t].pos)||(i=i.toLowerCase()),g+=''+i+" ",++s)}let o=a.firstAtomObjCls.getFirstCalphaAtomObj(a.chains[e]),d=void 0===o.color||"FFFFFF"===o.color.getHexString()?"DDDDDD":o.color.getHexString(),c=void 0!==o.color?d:"CCCCCC",h=[],p=[],m="-";for(let e=0,t=l.length;e ',f+=''+i+"
"}u=''+a.queryEnd+" ",u+="",u+="',u+='
',u+='
PDB Residue Numbers
',u+='
',b+=u+"
",g+=u+'
',a.seqStartLen&&a.seqStartLen[e]&&(g+=this.insertMulGap(a.seqStartLen[e],"-"));for(let t=0,s=o.length;t",e%10==0&&(g+=e+" "),g+=" "}else g+="
"}a.seqStartLen&&a.seqStartLen[e]&&(g+=this.insertMulGap(a.seqEndLen[e],"-")),g+='
',g+="",g+="
",g+="
",g+="
';c+='
',c+=i?'
Custom Ref. No.
':1==s?'
Kabat Ref. No.
':2==s?'
IMGT Ref. No.
':'
IgStRAnD Ref. No.
',c+='
',o+=c+"
",r+=c+'
';let h=!1;for(let s=0,l=e.length;s0){h=!0;break}}if(1==s&&!h)return{html:"",html3:""};let p=!1;for(let s=0,l=e.length;s0){p=!0;break}}if(2==s&&!p)return{html:"",html3:""};let m,u,g,f,b,C,y,v=!1,_="",w="",S=1,A=!1;if(!i&&!s&&!l.bNode){let e=l.hashUtilsCls.intHash(n.chains[t],n.hAtoms),s=n.firstAtomObjCls.getResiduesFromAtoms(e);for(let e in s)delete n.residIgLoop[e]}let x,k=[],O={},R=0,I=0,T=0,E=0;if(!i&&!s){for(let s=0,i=e.length;s=0;--t)"G"!=k[t].strand.substr(0,1)&&k[t].endRefnum-k[t].startRefnum+1<3&&(t!=e-1&&(k[t+1].loopResCnt+=k[t].loopResCnt+parseInt(k[t].endResi)-parseInt(k[t].startResi)+1),k.splice(t,1));R=0;let s,i,l=0,r=!0,o=!0,a=0;A=!1;let d=0;if(k.length>0)for(let c=0,h=e.length;ck[R].endResi:parseInt(e)>parseInt(k[R].endResi),c=!t&&!p,t)if(n.residIgLoop[h]=1,r)A?(i=k[R].startRefnum-k[R].loopResCnt+l,s=k[R].strand+i,m=s+k[R].strandPostfix):(s=void 0,m=void 0);else if(a>=0&&"G"==k[a].strand.substr(0,1))o?A&&n.resid2refnum[h]?(o=!0,i=k[a].endRefnum+l,s=k[a].strand+i,m=s+k[a].strandPostfix):(A=!1,r=!0,o=!1,s=void 0,m=void 0):(s=void 0,m=void 0);else{o=!0;let e=k[R].loopResCnt;l<=parseInt(e/2+.5)?(i=k[a].endRefnum+l,s=k[a].strand+i,m=s+k[a].strandPostfix):(i=k[R].startRefnum-e+l-1,s=k[R].strand+i,m=s+k[R].strandPostfix)}else c?(r=!1,k[R].anchorRefnum&&(e==k[R].startResi?(d=k[R].anchorRefnum-k[R].resCntBfAnchor,k[R].startRefnum=d):e==k[R].endResi&&(k[R].endRefnum=d),s=k[R].strand+d,m=s+k[R].strandPostfix),e==k[R].endResi&&(++R,l=0,k[R]||--R)):p&&(n.residIgLoop[h]=1,o?n.resid2refnum[h]?(o=!0,i=k[R].endRefnum+l,s=k[R].strand+i,m=s+k[R].strandPostfix):(o=!1,s=void 0,m=void 0):(s=void 0,m=void 0))}else m=void 0;w=_,a=R-1,n.resid2refnum[h]=m,g=n.refnumCls.rmStrandFromRefnumlabel(m),n.refnum2residArray.hasOwnProperty(g)?n.refnum2residArray[g].push(h):n.refnum2residArray[g]=[h],n.chainsMapping.hasOwnProperty(t)||(n.chainsMapping[t]={}),n.chainsMapping[t][h]=s}}for(let l=0,o=e.length;l'+g+" ":'
'}else r+="
";else if(1==s||2==s)if(g){let e=parseInt(g).toString(),t='style="color:'+this.getRefnumColor(_,!0)+'"';r+=parseInt(e.substr(e.length-2,2))%2==0?"
'+g+" ":"
'}else r+="
";else" "!=_?(v=n.residIgLoop[e],r+=this.getRefnumHtml(e,g,u,m,_,v,a)):r+="
";else r+="
";w=x}return r+='
',r+="",r+="
",r+="
",r+="
'+p+" "):u+=" ':(o.hAtomsRefnum=a.hashUtilsCls.unionHash(o.hAtomsRefnum,o.residues[e]),u+="'+i.substr(0,1)+" "+i.substr(1)+""+t+"";return i}insertGapOverview(e,t){let s=this.icn3d;s.icn3dui;let i="";return void 0!==s.targetGapHash&&s.targetGapHash.hasOwnProperty(t)&&(i+=this.insertMulGapOverview(e,s.targetGapHash[t].to-s.targetGapHash[t].from+1)),i}insertMulGapOverview(e,t){let s=this.icn3d;s.icn3dui;let i="",n=s.seqAnnWidth*t/(s.maxAnnoLength+s.nTotalGap);return n=parseInt(n),i+='
',i}setAlternativeSeq(e,t){let s=this.icn3d;s.icn3dui;let i=s.chainsSeq[e];s.giSeq[e]=[];for(let t=0,n=i.length;t1&&s.htmlCls.clickMenuCls.setLogCmd("select sets "+e,!0)}else{let o={};if(void 0!==$(e).attr("domain")||void 0!==$(e).attr("feat")||void 0!==$(e).attr("3ddomain")||void 0!==$(e).attr("custom")){t.hlUpdateCls.hlSummaryDomain3ddomain(e);let a,d,c,h=$(e).attr("from").split(","),p=$(e).attr("to").split(",");r.substr(0,r.indexOf("_"));for(let s=0,i=h.length;s1&&s.htmlCls.clickMenuCls.setLogCmd("select sets "+c,!0)}}else{t.bCtrl||t.bShift?(t.currSelectedSets.push(i),t.selectionCls.selectAChain(r,i,!0,!0)):(t.currSelectedSets=[i],t.selectionCls.selectAChain(r,i,t.bAlignSeq)),t.bAlignSeq?s.htmlCls.clickMenuCls.setLogCmd("select alignChain "+r,!0):s.htmlCls.clickMenuCls.setLogCmd("select chain "+r,!0);let e=t.currSelectedSets.join(" or ");t.currSelectedSets.length>1&&s.htmlCls.clickMenuCls.setLogCmd("select sets "+e,!0)}else t.hlObjectsCls.removeHlObjects(),t.hlUpdateCls.removeHl2D(),$("#"+t.pre+"atomsCustom").val("")}}selectResidues(e,t){let s=this.icn3d,i=s.icn3dui;if(!i.bNode&&(!1!==s.bSelectResidue||s.bShift||s.bCtrl||s.selectionCls.removeSelection(),void 0!==e&&""!==e)){e=e.substr(e.indexOf("_")+1),s.bSelectResidue=!0,$(t).toggleClass("icn3d-highlightSeq");let n=e.substr(e.indexOf("_")+1);if(s.residues.hasOwnProperty(n))if($(t).hasClass("icn3d-highlightSeq")){for(let e in s.residues[n])s.hAtoms[e]=1;if(s.selectedResidues[n]=1,s.bAnnotations&&void 0!==$(t).attr("disease")){let e=$(t).attr("disease"),l=s.applyCenterCls.centerAtoms(i.hashUtilsCls.hash2Atoms(s.residues[n],s.atoms)),r=15;e.length>r&&(e=e.substr(0,r)+"...");let o=s.LABELSIZE,a=i.htmlCls.GREYD;s.analysisCls.addLabel(e,l.center.x,l.center.y,l.center.z,o,a,void 0,"custom")}}else{for(let e in s.residues[n])delete s.hAtoms[e];delete s.selectedResidues[n],s.hlObjectsCls.removeHlObjects()}}}}class Dt{constructor(e){this.icn3d=e}update2DdgmContent(){let e=this.icn3d,t=e.icn3dui,s="";void 0!==t.cfg.mmdbid||void 0!==t.cfg.gi?(s+=e.diagram2dCls.draw2Ddgm(e.interactionData,e.inputid,void 0,!0),s+=e.diagram2dCls.set2DdgmNote(),$("#"+e.pre+"dl_2ddgm_html").html(s)):e.mmdbidArray&&(void 0!==t.cfg.align||void 0!==t.cfg.chainalign||e.bRealign)&&(s+=e.diagram2dCls.draw2Ddgm(e.interactionData1,e.mmdbidArray[0].toUpperCase(),0,!0),void 0!==e.mmdbid_q&&e.mmdbid_q===e.mmdbid_t?s+=e.diagram2dCls.draw2Ddgm(e.interactionData2,e.mmdbidArray[0].toUpperCase(),1,!0):s+=e.diagram2dCls.draw2Ddgm(e.interactionData2,e.mmdbidArray[1].toUpperCase(),1,!0),s+=e.diagram2dCls.set2DdgmNote(!0),$("#"+e.pre+"dl_2ddgm_html").html(s))}changeSeqColor(e){let t=this.icn3d,s=t.icn3dui;for(let i=0,n=e.length;i0&&($("#"+e.pre+"dl_2ddgm svg line").attr("stroke","#000000"),$("#"+e.pre+"dl_2ddgm line").attr("stroke-width",1))}removeHlMenus(){let e=this.icn3d;e.icn3dui,$("#"+e.pre+"atomsCustom").val(""),$("#"+e.pre+"atomsCustom")[0].blur()}updateHlAll(e,t,s,i){let n=this.icn3d,l=n.icn3dui;n.prevHighlightAtoms=l.hashUtilsCls.cloneHash(n.hAtoms),this.updateHlObjects(i),void 0!==e?this.updateHlSeqInChain(e,s):this.updateHlSeq(void 0,void 0,s),this.updateHl2D(),(void 0===t||t)&&this.updateHlMenus(e)}updateHlObjects(e){let t=this.icn3d;t.icn3dui,t.hlObjectsCls.removeHlObjects(),(t.hAtoms&&t.atoms&&Object.keys(t.hAtoms).length0&&(e=s.defNames2Residues[i]);let t={};if(void 0!==s.defNames2Atoms[i]&&s.defNames2Atoms[i].length>0){for(let e=0,n=s.defNames2Atoms[i].length;e0&&(r=t.firstAtomObjCls.getFirstCalphaAtomObj(l))}let o=void 0!==r&&void 0!==r.color?"#"+r.color.getHexString():"#FFFFFF",a=$("#"+t.pre+"dl_2ddgm g[chainid="+e[i]+"] rect[class='icn3d-hlnode']"),d=$("#"+t.pre+"dl_2ddgm g[chainid="+e[i]+"] rect[class='icn3d-basenode']");void 0!==a&&(t.diagram2dCls.highlightNode("rect",a,d,l),$(a).attr("fill",o)),a=$("#"+t.pre+"dl_2ddgm g[chainid="+e[i]+"] circle[class='icn3d-hlnode']"),d=$("#"+t.pre+"dl_2ddgm g[chainid="+e[i]+"] circle[class='icn3d-basenode']"),void 0!==a&&(t.diagram2dCls.highlightNode("circle",a,d,l),$(a).attr("fill",o)),a=$("#"+t.pre+"dl_2ddgm g[chainid="+e[i]+"] ellipse[class='icn3d-hlnode']"),void 0!==a&&t.diagram2dCls.highlightNode("ellipse",a,void 0,l),a=$("#"+t.pre+"dl_2ddgm g[chainid="+e[i]+"] polygon[class='icn3d-hlnode']"),d=$("#"+t.pre+"dl_2ddgm g[chainid="+e[i]+"] polygon[class='icn3d-basenode']"),void 0!==a&&(t.diagram2dCls.highlightNode("polygon",a,d,l),$(a).attr("fill",o))}if(void 0!==t.lineArray2d)for(let e=0,i=t.lineArray2d.length;e1){let e={},l=[],o=[],a=[],c=[],h=[],m=[],u=[],g=[],f=[],b=[],C=[],y=[],v={},_={};for(let t=0,s=p.length;t0&&(T=1,t=i.getGraphCls.getNodeTopBottom(c[e],d,void 0,T,g[e]),h[e]=t.nodeArray1,m[e]=t.nodeArray2,d=n.hashUtilsCls.unionHash(d,t.name2node),T=2,t=i.getGraphCls.getNodeTopBottom(c[e],d,void 0,T,y[e]),f[e]=t.nodeArray1,b[e]=t.nodeArray2,d=n.hashUtilsCls.unionHash(d,t.name2node)),k[e]=l[e].length,O[e]=o[e].length,R=Math.max(R,O[e]),I.push(p[e])}let E,P,M,D,H,F=1,L=3*F,N=7*F,q=10,U=10,$=30,j=20;t?(M=(n.utilsCls.sumArray(k)+2*I.length)*(L+N)+4*U+2*$+j*I.length,P=(R+2)*(L+N)+2*q+$):(E=110+j,M=E*I.length,P=(R+2)*(L+N)+2*q,P+=20),Object.keys(i.chainsMapping).length>0&&(M*=3),t?(i.scatterplotWidth=2*P,H=i.scatterplotWidth,D=n.scatterplotid):(i.linegraphWidth=2*P,H=i.linegraphWidth,D=n.linegraphid),s=0==I.length?"No interactions found for each structure"+I+' . There are three sections: "Interactions", "Common interactions", and "Different interactions". Each section has '+I.length+" graphs.";let B,z=0;T=0,B=this.drawGraphPerType(T,p,t,l,o,a,d,z,E,j,k,L,N,U),z=B.heightFinal,s+=B.html,Object.keys(i.chainsMapping).length>0&&(T=1,B=this.drawGraphPerType(T,p,t,h,m,u,d,z,E,j,k,L,N,U),z=B.heightFinal,s+=B.html,T=2,B=this.drawGraphPerType(T,p,t,f,b,C,d,z,E,j,k,L,N,U),z=B.heightFinal,s+=B.html),s+=" "}else if(t){let e,t,l,c,h=p[0],m=o.length,u=a.length,g=1,f=3*g,b=7*g,C=30;t=(m+2)*(f+b)+2*10+C,e=(u+2)*(f+b)+2*10+C,i.scatterplotWidth=2*e,c=i.scatterplotWidth,l=n.scatterplotid,s=r.length>0?"":"No interactions found for these two sets",s+=this.drawScatterplot_base(o,a,r,d,0),i.lineGraphStr+=i.getGraphCls.updateGraphJson(h,1,o,a,r),s+=" "}else{let e=p[0],t=o.length,l=a.length,c=1,h=3*c,m=7*c,u=110,g=10,f=t>l?t*(h+m)+2*g:l*(h+m)+2*g;i.linegraphWidth=2*f,s=r.length>0?"":"No interactions found for these two sets",s+=this.drawLineGraph_base(o,a,r,d,0),i.lineGraphStr+=i.getGraphCls.updateGraphJson(e,1,o,a,r),s+=" "}return i.lineGraphStr+="}\n",i.scatterplotStr=i.lineGraphStr,t?$("#"+i.pre+"scatterplotDiv").html(s):$("#"+i.pre+"linegraphDiv").html(s),s}drawGraphPerType(e,t,s,i,n,l,r,o,a,d,c,h,p,m){let u=this.icn3d;u.icn3dui;let g,f,b="",C=2==t.length&&"2"==t[1].replace(t[0],"");0==e?(g="Interactions in ",f=""):1==e?(g="Common interactions in ",f="_common"):2==e&&(g="Different interactions in ",f="_diff");for(let y=0,v=t.length;y0&&(u.lineGraphStr+=", \n"):u.lineGraphStr+=", \n",u.lineGraphStr+=u.getGraphCls.updateGraphJson(t[y],y+f,i[y],n[y],l[y])}return{heightFinal:o,html:b}}getIdArrayFromNode(e){let t=this.icn3d.icn3dui,s=[];s.push(""),s.push("");let i=e.r.substr(4);return s=s.concat(t.utilsCls.getIdArray(i)),s}drawLineGraph_base(e,t,s,i,n,l,r){let o,a,d=this.icn3d,c=d.icn3dui,h="",p=e.length,m=t.length;p>m?(o=10,a=10*Math.abs(p-m)*.5+10):(a=10,o=10*Math.abs(p-m)*.5+10),l&&(h+=""+l+" ");let u=30+n,g=80+n,f="",b={},C={};for(let t=0;t";let u=1==t.n?"Interaction":t.n+" interactions";t.n>1&&(h+=""+u+" of residue "+n.id+" with residue "+l.id+" "),h+=""+r+" ");let g=n+u-(50+(3+m)),f=40+(3+m),b="",C={},y={};for(let t=0;t";let i=1==e.n?"Interaction":e.n+" interactions";e.n>1&&(h+=""+i+" of residue "+t.id+" with residue "+s.id+" "),h+=l?" "}return h}copyStylesInline(e,t){this.icn3d.icn3dui;let s=["svg","g"];for(let i=0;ir[d])&&(r[d]=e,i.domainid2refpdbname[d]=c,o[d]=a[0].segs,i.domainid2ig2kabat[d]=a[0].ig2kabat,i.domainid2ig2imgt[d]=a[0].ig2imgt)}else console.log("domainid: "+d),(!r.hasOwnProperty(d)||a[0].score>r[d])&&(r[d]=a[0].score,i.domainid2refpdbname[d]=c,o[d]=a[0].segs,i.domainid2ig2kabat[d]=a[0].ig2kabat,i.domainid2ig2imgt[d]=a[0].ig2imgt)}if(s){n.bNode||console.log("Start round 2 alignment with the reference culsters "+JSON.stringify(i.domainid2refpdbname));let e=[],t=[],s=n.htmlCls.baseUrl+"tmalign/tmalign.cgi";for(let l in i.domainid2refpdbname){let r=[],o=i.domainid2refpdbname[l],a=l.substr(0,l.indexOf("-"));if(i.refpdbHash.hasOwnProperty(a)&&(o=a,n.bNode||console.log("Adjusted refpdbname for domainid "+l+": "+o)),!i.refpdbHash[o])continue;for(let e=0,t=i.refpdbHash[o].length;e0){if(i.bShowRefnum=!0,i.hAtomsRefnum={},i.bAnnoShown)for(let e in i.protein_chainid){let t=i.protein_chainid[e];i.showSeqCls.showSeq(e,t,"protein")}else await i.showAnnoCls.showAnnotations();i.annotationCls.setAnnoViewAndDisplay("detailed view")}else alert("No Ig reference numbers are assigned based on the reference structures in iCn3D...")}getLabelFromRefnum(e,t,s){this.icn3d.icn3dui;let i=parseInt(e);if(!(i<900))return i>=900&&i<1e3?" "+e:i>=1e3&&i<1100?"A-"+e:i>=1100&&i<1200?"A"+e:i>=1200&&i<1300?"A'"+e:i>=1300&&i<2e3?t&&"A"==t.substr(0,1)?t+e:"A"+e:i>=2e3&&i<3e3?"B"+e:i>=3e3&&i<4e3?"C"+e:i>=4e3&&i<5e3?"C'"+e:i>=5e3&&i<6e3?"C''"+e:i>=6e3&&i<7e3?"D"+e:i>=7e3&&i<8e3?"E"+e:i>=8e3&&i<9e3?"F"+e:i>=9e3&&i<9300||i>=9300?"G"+e:void 0}async parseCustomRefFile(e){let t=this.icn3d;t.icn3dui,t.bShowCustomRefnum=!0;let s=e.split("\n");t.resid2refnum||(t.resid2refnum={}),t.refnum2residArray||(t.refnum2residArray={}),t.chainsMapping||(t.chainsMapping={});let i=[];for(let e=0,t=s.length;e",C=e.id;return c.resid2refnum[p]&&(C+="=>"+c.resid2refnum[p]),b+=""+C+" ",o?(b+=""+g+" "):(b+=""+g+" "),b+="",b}getNodeTopBottom(e,t,s,i,n){let l=this.icn3d.icn3dui,r=this,o=[],a=[],d={};for(let s in e){let e=t[s];if(e){if(1==i||2==i){if(e=l.hashUtilsCls.cloneHash(e),1==i){let t=n[s]?n[s]:"-";e.id+="=>"+t}else{let t=n[s]?n[s]:"--";e.id+="==>"+t}d[e.id]=e}"a"==e.s?o.push(e):"b"==e.s?a.push(e):"ab"==e.s&&(o.push(e),a.push(e))}}return o.sort((function(e,t){return r.compNode(e,t)})),a.sort((function(e,t){return r.compNode(e,t,s)})),{nodeArray1:o,nodeArray2:a,name2node:d}}updateGraphJson(e,t,s,i,n){let l=this.icn3d.icn3dui,r="";return r+='"structure'+t+'": {"id": "'+e+'", "nodes1":[',r+=l.utilsCls.getJSONFromArray(s),r+='], \n"nodes2":[',r+=l.utilsCls.getJSONFromArray(i),r+='], \n"links":[',r+=l.utilsCls.getJSONFromArray(n),r+="]}",r}updateGraphColor(){let e=this.icn3d,t=e.icn3dui;if(void 0!==e.graphStr){let s=JSON.parse(e.graphStr),i={};for(let t in e.residues){let s=e.firstAtomObjCls.getFirstAtomObj(e.residues[t]);i[t]=s.color.getHexString().toUpperCase()}let n={};for(let e=0,l=s.nodes.length;e0&&c==e.chain&&(n.resid2ncbi[e.resi]==n.resid2ncbi[p]+1||n.resid2ncbi[e.resi]==n.resid2ncbi[p])&&(o.push('{"source": "'+h+'", "target": "'+u+'", "v": '+d+', "c": "'+f+'"}'),e.ssbegin&&(d=l.htmlCls.ssValue),e.ssend&&(d=l.htmlCls.coilValue)),c=e.chain,h=u,p=e.resi,++a}}return{node:r,link:o}}getHbondLinksForSet(e,t){let s=this.icn3d,i=s.icn3dui,n={},l=parseFloat($("#"+s.pre+"hbondthreshold").val()),r=e,o=r;if(Object.keys(o).length>0&&Object.keys(r).length>0){let e=!1;s.hBondCls.calculateChemicalHbonds(i.hashUtilsCls.hash2Atoms(o,s.atoms),i.hashUtilsCls.hash2Atoms(r,s.atoms),parseFloat(l),e,"graph",!0),n=i.hashUtilsCls.cloneHash(s.resid2Residhash)}return this.getGraphLinks(n,n,i.htmlCls.hbondInsideColor,t,i.htmlCls.hbondInsideValue)}getIonicLinksForSet(e,t){let s=this.icn3d,i=s.icn3dui,n={},l=parseFloat($("#"+s.pre+"saltbridgethreshold").val()),r=e,o=r;if(Object.keys(o).length>0&&Object.keys(r).length>0){let e=!1;s.saltbridgeCls.calculateIonicInteractions(i.hashUtilsCls.hash2Atoms(o,s.atoms),i.hashUtilsCls.hash2Atoms(r,s.atoms),parseFloat(l),e,"graph",!0),n=i.hashUtilsCls.cloneHash(s.resid2Residhash)}return this.getGraphLinks(n,n,i.htmlCls.ionicInsideColor,t,i.htmlCls.ionicInsideValue)}getHalogenPiLinksForSet(e,t){let s,i=this.icn3d,n=i.icn3dui,l={},r=e,o=r,a="";return s=parseFloat($("#"+i.pre+"halogenthreshold").val()),Object.keys(o).length>0&&Object.keys(r).length>0&&(i.piHalogenCls.calculateHalogenPiInteractions(n.hashUtilsCls.hash2Atoms(r,i.atoms),n.hashUtilsCls.hash2Atoms(o,i.atoms),parseFloat(s),"graph","halogen",!0),l=n.hashUtilsCls.cloneHash(i.resid2Residhash)),a+=this.getGraphLinks(l,l,n.htmlCls.halogenInsideColor,t,n.htmlCls.halogenInsideValue),s=parseFloat($("#"+i.pre+"picationthreshold").val()),Object.keys(o).length>0&&Object.keys(r).length>0&&(i.piHalogenCls.calculateHalogenPiInteractions(n.hashUtilsCls.hash2Atoms(r,i.atoms),n.hashUtilsCls.hash2Atoms(o,i.atoms),parseFloat(s),"graph","pi-cation",!0),l=n.hashUtilsCls.cloneHash(i.resid2Residhash)),a+=this.getGraphLinks(l,l,n.htmlCls.picationInsideColor,t,n.htmlCls.picationInsideValue),s=parseFloat($("#"+i.pre+"pistackingthreshold").val()),Object.keys(o).length>0&&Object.keys(r).length>0&&(i.piHalogenCls.calculateHalogenPiInteractions(n.hashUtilsCls.hash2Atoms(r,i.atoms),n.hashUtilsCls.hash2Atoms(o,i.atoms),parseFloat(s),"graph","pi-stacking",!0),l=n.hashUtilsCls.cloneHash(i.resid2Residhash)),a+=this.getGraphLinks(l,l,n.htmlCls.pistackingInsideColor,t,n.htmlCls.pistackingInsideValue),a}getContactLinksForSet(e,t,s){let i=this.icn3d;i.icn3dui;let n=[],l="",r="",o={};for(let t in e){let e=i.atoms[t];e.ss==l&&e.chain==r||(Object.keys(o).length>0&&n.push(o),o={}),o[e.serial]=1,l=e.ss,r=e.chain}Object.keys(o).length>0&&n.push(o);let a=n.length,d="";for(let e=0;ed?s?-1:1:ah?1:c0&&Object.keys(a).length>0)){let t,s=c.hBondCls.calculateChemicalHbonds(h.hashUtilsCls.hash2Atoms(d,c.atoms),h.hashUtilsCls.hash2Atoms(a,c.atoms),parseFloat(e),n);n?(c.resid2ResidhashSaltbridge=h.hashUtilsCls.cloneHash(c.resid2Residhash),t="all atoms that have salt bridges with the selected atoms"):(c.resid2ResidhashHbond=h.hashUtilsCls.cloneHash(c.resid2Residhash),t="all atoms that are hydrogen-bonded with the selected atoms");let i={};for(let e in s){i[c.atoms[e].structure+"_"+c.atoms[e].chain+"_"+c.atoms[e].resi]=1}c.hAtoms={};for(let e in i)for(let t in c.residues[e])c.hAtoms[t]=1,c.atoms[t].style2="stick";let l=r+"_auto";c.selectionCls.addCustomSelection(Object.keys(i),l,t,o,!0),c.selectionCls.saveSelectionIfSelected(),c.drawCls.draw()}}showHydrogens(){let e=this.icn3d;if(void 0!==e.icn3dui.cfg.cid)for(let t in e.hAtoms){let s=e.atoms[t];if("H"!==s.elem.substr(0,1)){e.atoms[s.serial].bonds=e.atoms[s.serial].bonds2.concat(),e.atoms[s.serial].bondOrder=e.atoms[s.serial].bondOrder2.concat();for(let t=0,i=e.atoms[s.serial].bonds.length;t0){let i=e.atoms[t].bonds[0];e.atoms[i].bonds.push(s.serial),e.atoms[i].bondOrder&&e.atoms[i].bondOrder.push(1)}e.dAtoms[t]=1}}e.bShowHighlight=!1}hideHydrogens(){let e=this.icn3d;e.icn3dui;for(let t in e.hAtoms){let s=e.atoms[t];if("H"===s.elem.substr(0,1)){if(e.atoms[s.serial].bonds.length>0){let t=e.atoms[s.serial].bonds[0],i=e.atoms[t].bonds?e.atoms[t].bonds.indexOf(s.serial):-1;-1!==i&&(e.atoms[t].bonds.splice(i,1),e.atoms[t].bondOrder&&e.atoms[t].bondOrder.splice(i,1))}delete e.dAtoms[s.serial],delete e.hAtoms[s.serial]}}}hideExtraBonds(){let e=this.icn3d;e.icn3dui;for(let t in e.atoms)e.atoms[t].style2="nothing";for(let t in e.sidec)e.hAtoms.hasOwnProperty(t)&&(e.atoms[t].style2=e.opts.sidec);for(let t in e.water)e.hAtoms.hasOwnProperty(t)&&(e.atoms[t].style=e.opts.water)}hideHbondsContacts(){let e=this.icn3d,t=e.icn3dui,s="set hbonds off";t.htmlCls.clickMenuCls.setLogCmd(s,!0),e.hBondCls.hideHbonds(),s="set salt bridge off",t.htmlCls.clickMenuCls.setLogCmd(s,!0),e.saltbridgeCls.hideSaltbridge(),s="set contact off",t.htmlCls.clickMenuCls.setLogCmd(s,!0),e.contactCls.hideContact(),s="set halogen pi off",t.htmlCls.clickMenuCls.setLogCmd(s,!0),e.piHalogenCls.hideHalogenPi(),this.hideExtraBonds()}showIonicInteractions(e,t,s,i,n,l){let r,o,a,d,c=this.icn3d,h=c.icn3dui;if(!i&&(r="saltbridge",o="salt bridge "+e+" | sets "+t+" "+s+" | "+i,c.opts.saltbridge="yes",a=c.definedSetsCls.getAtomsFromNameArray(t),d=c.definedSetsCls.getAtomsFromNameArray(s),c.firstAtomObjCls.getFirstAtomObj(a),Object.keys(d).length>0&&Object.keys(a).length>0)){let t,s=c.saltbridgeCls.calculateIonicInteractions(h.hashUtilsCls.hash2Atoms(d,c.atoms),h.hashUtilsCls.hash2Atoms(a,c.atoms),parseFloat(e),n);c.resid2ResidhashSaltbridge=h.hashUtilsCls.cloneHash(c.resid2Residhash),t="all atoms that have ionic interactions with the selected atoms";let i={};for(let e in s){i[c.atoms[e].structure+"_"+c.atoms[e].chain+"_"+c.atoms[e].resi]=1}c.hAtoms={};for(let e in i)for(let t in c.residues[e])c.hAtoms[t]=1,c.atoms[t].style2="stick",c.ions.hasOwnProperty(t)&&(c.atoms[t].style2="sphere");let l="saltbridge_auto";c.selectionCls.addCustomSelection(Object.keys(i),l,t,o,!0),c.selectionCls.saveSelectionIfSelected(),c.drawCls.draw()}}showHalogenPi(e,t,s,i,n,l){let r=this.icn3d,o=r.icn3dui;if(i)return;let a,d,c=l+" "+e+" | sets "+t+" "+s+" | "+i;if(r.opts[l]="yes",a=r.definedSetsCls.getAtomsFromNameArray(t),d=r.definedSetsCls.getAtomsFromNameArray(s),r.firstAtomObjCls.getFirstAtomObj(a),Object.keys(d).length>0&&Object.keys(a).length>0){let t,s=r.piHalogenCls.calculateHalogenPiInteractions(o.hashUtilsCls.hash2Atoms(a,r.atoms),o.hashUtilsCls.hash2Atoms(d,r.atoms),parseFloat(e),n,l);"halogen"==l?(r.resid2ResidhashHalogen=o.hashUtilsCls.cloneHash(r.resid2Residhash),t="all atoms that have halogen bonds with the selected atoms"):"pi-cation"==l?(r.resid2ResidhashPication=o.hashUtilsCls.cloneHash(r.resid2Residhash),t="all atoms that have pi-cation interactions with the selected atoms"):"pi-stacking"==l&&(r.resid2ResidhashPistacking=o.hashUtilsCls.cloneHash(r.resid2Residhash),t="all atoms that have pi-stacking with the selected atoms");let i={};for(let e in s){i[r.atoms[e].structure+"_"+r.atoms[e].chain+"_"+r.atoms[e].resi]=1}r.hAtoms={};for(let e in i)for(let t in r.residues[e])r.hAtoms[t]=1,r.atoms[t].style2="stick",r.ions.hasOwnProperty(t)&&(r.atoms[t].style2="sphere");let h=l+"_auto";r.selectionCls.addCustomSelection(Object.keys(i),h,t,c,!0),r.selectionCls.saveSelectionIfSelected(),r.drawCls.draw()}}showClbonds(){let e=this.icn3d,t=e.icn3dui;e.opts.clbonds="yes";let s=e.applyClbondsCls.applyClbondsOptions();for(let i in s)e.hAtoms=t.hashUtilsCls.unionHash(e.hAtoms,e.residues[i]);if(Object.keys(s).length>0){let t="clbonds",i="all atoms that have cross-linkages";e.selectionCls.addCustomSelection(Object.keys(s),t,i,"cross linkage",!0),e.selectionCls.saveSelectionIfSelected(),e.drawCls.draw()}}showSsbonds(){let e=this.icn3d,t=e.icn3dui;e.opts.ssbonds="yes";let s={},i=Object.keys(e.structures);for(let n=0,l=i.length;n0){let t="ssbonds",i="all atoms that have disulfide bonds";e.selectionCls.addCustomSelection(Object.keys(s),t,i,"disulfide bonds",!0),e.selectionCls.saveSelectionIfSelected(),e.drawCls.draw()}}pickCustomSphere(e,t,s,i,n,l){let r=this.icn3d,o=r.icn3dui;if(i)return;let a,d,c="select zone cutoff "+e+" | sets "+t+" "+s+" | "+i;n&&(c="interactions "+e+" | sets "+t+" "+s+" | "+i,r.opts.contact="yes"),a=r.definedSetsCls.getAtomsFromNameArray(t),d=r.definedSetsCls.getAtomsFromNameArray(s);let h,p,m=this.pickCustomSphere_base(e,a,d,i,n,l,c,!0),u=Object.keys(m.residues);r.hAtoms={};for(let e=0,t=u.length;e1?"structure":v>1?"chain":"residue";let w=[];if(n&&w.push("hbonds"),l&&w.push("salt bridge"),r&&w.push("interactions"),o&&w.push("halogen"),a&&w.push("pi-cation"),d&&w.push("pi-stacking"),s||(p.resids2inter={},p.resids2interAll={}),l){let n=parseFloat($("#"+p.pre+"saltbridgethreshold").val());n&&!isNaN(n)||(n=p.tsIonic),s||(p.hAtoms=m.hashUtilsCls.cloneHash(f),p.showInterCls.showIonicInteractions(n,e,t,s,!0,i)),g=m.hashUtilsCls.unionHash(g,p.hAtoms)}if(n){let n=parseFloat($("#"+p.pre+"hbondthreshold").val());n&&!isNaN(n)||(n=p.tsHbond),s||(p.hAtoms=m.hashUtilsCls.cloneHash(f),p.showInterCls.showHbonds(n,e,t,s,void 0,i)),g=m.hashUtilsCls.unionHash(g,p.hAtoms)}let S,A,x,k,O="";if(n&&(O+=this.exportHbondPairs(i,u)),l&&(O+=this.exportSaltbridgePairs(i,u)),o){let n=parseFloat($("#"+p.pre+"halogenthreshold").val());n&&!isNaN(n)||(n=p.tsHalogen),s||(p.hAtoms=m.hashUtilsCls.cloneHash(f),p.showInterCls.showHalogenPi(n,e,t,s,i,"halogen")),g=m.hashUtilsCls.unionHash(g,p.hAtoms),O+=this.exportHalogenPiPairs(i,u,"halogen")}if(a){let n=parseFloat($("#"+p.pre+"picationthreshold").val());n&&!isNaN(n)||(n=p.tsPication),s||(p.hAtoms=m.hashUtilsCls.cloneHash(f),p.showInterCls.showHalogenPi(n,e,t,s,i,"pi-cation")),g=m.hashUtilsCls.unionHash(g,p.hAtoms),O+=this.exportHalogenPiPairs(i,u,"pi-cation")}if(d){let n=parseFloat($("#"+p.pre+"pistackingthreshold").val());n&&!isNaN(n)||(n=p.tsPistacking),s||(p.hAtoms=m.hashUtilsCls.cloneHash(f),p.showInterCls.showHalogenPi(n,e,t,s,i,"pi-stacking")),g=m.hashUtilsCls.unionHash(g,p.hAtoms),O+=this.exportHalogenPiPairs(i,u,"pi-stacking")}if(r){let n=b?c:parseFloat($("#"+p.pre+"contactthreshold").val());if(n&&!isNaN(n)||(n=p.tsContact),1!=e.length||1!=t.length||e[0]!=t[0])s||(p.hAtoms=m.hashUtilsCls.cloneHash(f),p.showInterCls.pickCustomSphere(n,e,t,s,!0,i)),g=m.hashUtilsCls.unionHash(g,p.hAtoms),O+=this.exportSpherePairs(!0,i,u);else{if(!s){let l={},o={};if(b){let e=!0,t=p.showInterCls.pickCustomSphere_base(n,C,y,s,!0,void 0,void 0,!0,e);l=m.hashUtilsCls.unionHash(l,t.residues);for(let e in t.resid2Residhash)o[e]=m.hashUtilsCls.unionHash(o[e],t.resid2Residhash[e])}else{let r=[],a="",d="",c={};for(let e in C){let t=p.atoms[e];t.ss==a&&t.chain==d||(Object.keys(c).length>0&&r.push(c),c={}),c[t.serial]=1,a=t.ss,d=t.chain}Object.keys(c).length>0&&r.push(c);let h=r.length;A="interactions "+n+" | sets "+e+" "+t+" | true",p.opts.contact="yes";for(let e=0;eHighlight in 3D Highlight in 3D The interfaces are: Highlight in 3D Highlight in 3D
',T+='Note : Each checkbox below selects the corresponding residue. You can click "Save Selection" in the "Select" menu to save the selection and click on "Highlight" button to clear the checkboxes.
Interactions Sorted on '+e+' : Show Count Only Show Details
';let t=this.getAllInteractionTable(i);T+=t.html,h=t.bondCnt,$("#"+p.pre+"dl_interactionsorted_html").html(T),m.htmlCls.dialogCls.openDlg("dl_interactionsorted","Show sorted interactions")}else if("view"==i)$("#"+p.pre+"dl_allinteraction_html").html(T),m.htmlCls.dialogCls.openDlg("dl_allinteraction","Show interactions");else if("linegraph"==i){m.htmlCls.dialogCls.openDlg("dl_linegraph","Show interactions between two lines of residue nodes"),p.graphStr=p.getGraphCls.getGraphData(C,y,e,t,T,u),p.bLinegraph=!0;let s=p.lineGraphCls.drawLineGraph(p.graphStr);$("#"+p.pre+"linegraphDiv").html(s)}else if("scatterplot"==i){m.htmlCls.dialogCls.openDlg("dl_scatterplot","Show interactions as scatterplot"),p.graphStr=p.getGraphCls.getGraphData(C,y,e,t,T,u),p.bScatterplot=!0;let s=p.lineGraphCls.drawLineGraph(p.graphStr,!0);$("#"+p.pre+"scatterplotDiv").html(s)}else if(b){m.htmlCls.dialogCls.openDlg("dl_contactmap","Show contact map");let s=!0,i=p.getGraphCls.getGraphData(C,y,e,t,T,u,s);p.bContactMap=!0;let n=p.contactMapCls.drawContactMap(i);$("#"+p.pre+"contactmapDiv").html(n)}else if("graph"==i){if(p.graphStr=p.getGraphCls.getGraphData(C,y,e,t,T,u),p.bGraph=!0,Object.keys(y).length+Object.keys(C).length>Object.keys(p.dAtoms).length&&(p.graphStr=p.selectionCls.getGraphDataForDisplayed()),void 0===p.bD3){let e="https://www.ncbi.nlm.nih.gov/Structure/icn3d/script/d3v4-force-all.min.js";await m.getAjaxPromise(e,"script"),p.bD3=!0}$("#"+m.svgid).empty(),m.htmlCls.dialogCls.openDlg("dl_graph","Force-directed graph"),p.drawGraphCls.drawGraph(p.graphStr,p.pre+"dl_graph")}return{interactionTypes:w.toString(),bondCnt:h}}clearInteractions(){let e=this.icn3d;e.icn3dui,e.lines.hbond=[],e.hbondpnts=[],e.lines.saltbridge=[],e.saltbridgepnts=[],e.lines.contact=[],e.contactpnts=[],e.lines.halogen=[],e.lines["pi-cation"]=[],e.lines["pi-stacking"]=[],e.halogenpnts=[],e.picationpnts=[],e.pistackingpnts=[]}resetInteractionPairs(){let e=this.icn3d;e.icn3dui,e.bHbondCalc=!1,e.showInterCls.hideHbondsContacts(),e.hlUpdateCls.clearHighlight(),e.resids2inter={},e.resids2interAll={}}async retrieveInteractionData(){let e=this.icn3d,t=e.icn3dui;if(!e.b2DShown)if(void 0!==t.cfg.align){let s=Object.keys(e.structures);if(2==t.cfg.atype){let t=!0;await e.alignParserCls.downloadAlignment(s[0]+","+s[1],t)}await e.ParserUtilsCls.set2DDiagramsForAlign(s[0].toUpperCase(),s[1].toUpperCase())}else void 0!==t.cfg.chainalign?(Object.keys(e.structures),await e.ParserUtilsCls.set2DDiagramsForChainalign(e.chainidArray)):e.ParserUtilsCls.download2Ddgm(e.inputid.toUpperCase())}getAllInteractionTable(e){let t=this.icn3d,s=t.icn3dui,i=[],n=Object.keys(t.resids2inter);("save1"==e||"save2"==e)&&n.sort((function(t,i){return s.utilsCls.compResid(t,i,e)}));let l,r,o="",a="",d="",c="",h="",p="",m="",u="",g="",f=0,b=0,C=0,y=0,v=0,_=0,w="";for(let s=0,S=n.length;s0&&l!=a&&(i.push({res1:a,res2:w,cntHbond:f,cntIonic:b,cntContact:C,cntHalegen:y,cntPication:v,cntPistacking:_}),o+=this.getInteractionPerResidue(d,c,h,p,m,u,g,f,b,C,y,v,_),c="",h="",p="",m="",u="",g="",f=0,b=0,C=0,y=0,v=0,_=0,w=""),x=t.resids2inter[S].hbond,k=this.getInteractionPairDetails(x,e,"hbond"),c+=k.html,f+=k.cnt,k.cnt>0&&(w+=r+":hbond_"+k.cnt+" "),x=t.resids2inter[S].ionic,k=this.getInteractionPairDetails(x,e,"ionic"),h+=k.html,b+=k.cnt,k.cnt>0&&(w+=r+":ionic_"+k.cnt+" "),x=t.resids2inter[S].contact,k=this.getContactPairDetails(x,e,"contact"),p+=k.html,C+=k.cnt,k.cnt>0&&(w+=r+":contact_"+k.cnt+" "),x=t.resids2inter[S].halogen,k=this.getInteractionPairDetails(x,e,"halogen"),m+=k.html,y+=k.cnt,k.cnt>0&&(w+=r+":halogen_"+k.cnt+" "),x=t.resids2inter[S]["pi-cation"],k=this.getInteractionPairDetails(x,e,"pi-cation"),u+=k.html,v+=k.cnt,k.cnt>0&&(w+=r+":pi-cation_"+k.cnt+" "),x=t.resids2inter[S]["pi-stacking"],k=this.getInteractionPairDetails(x,e,"pi-stacking"),g+=k.html,_+=k.cnt,k.cnt>0&&(w+=r+":pi-stacking_"+k.cnt+" "),a=l,d=O}i.push({res1:a,res2:w,cntHbond:f,cntIonic:b,cntContact:C,cntHalegen:y,cntPication:v,cntPistacking:_}),o+=this.getInteractionPerResidue(d,c,h,p,m,u,g,f,b,C,y,v,_);let S="";if(n.length>0){S+='',S+="Residue # Hydrogen # Salt Bridge # Contact ",S+="# Halogen # π-Cation # π-Stacking ",S+="Hydrogen Bond (backbone atoms: @CA, @N, @C, @O) Salt Bridge/Ionic Interaction Contact ",S+="Halogen Bond π-Cation π-Stacking ";let e='Atom1 Atom2 Distance(Å) Highlight in 3D
Atom1 Atom2 # Contacts Min Distance(Å) C-alpha Distance(Å) Highlight in 3D
",S+=" ",S+=o,S+="
'+e[3]+e[2]+" "+o+" "+a+" "+d+" "+c+" "+h+" "+p+" ";let u=[t,s,i,n,l,r];for(let e in u){m+=' ';if(void 0!==e)for(let a in e){let d=a.split(","),c="save1"==t?d[0]:d[1],h="save1"==t?d[1]:d[0],p=i.getGraphCls.convertLabel2Resid(c),m=i.firstAtomObjCls.getFirstAtomObj(i.residues[p]),u=m.color?m.color.getHexString():"",g=i.getGraphCls.convertLabel2Resid(h),f=i.firstAtomObjCls.getFirstAtomObj(i.residues[g]),b=f.color?f.color.getHexString():"",C=Math.sqrt(e[a]).toFixed(1);n+=''+C+" ",n+='Highlight ';if(void 0!==e)for(let o in e){let a=o.split(","),d="save1"==t?a[0]:a[1],c="save1"==t?a[1]:a[0],h=s.getGraphCls.convertLabel2Resid(d),p=s.firstAtomObjCls.getFirstAtomObj(s.residues[h]),m=p.color?p.color.getHexString():"",u=s.getGraphCls.convertLabel2Resid(c),g=s.firstAtomObjCls.getFirstAtomObj(s.residues[u]),f=g.color?g.color.getHexString():"",b=e[o].split("_"),C=b[0],y=b[1],v=b[2],_=b[3],w=b[4];i+=''+w+' '+C+' '+y+" ",i+='Highlight Interacting residues :
Base Chain: Residues Interacting Chain "+t+": ",s+=e.resid2specCls.residueids2spec(e.chainname2residues[t][i]),s+=" "+n+"
"+n[e]+" Cys "+n[e+1]+" Cys ",++i}}let n=''+i+" disulfide pairs :
Residue ID 1 Residue ID 2
"+r+" "+t.resn+" "+o+" "+n.resn+" ",++i}n[r+"_"+o]=1,n[o+"_"+r]=1}}let l=''+i+" cross-linkage pairs :
Residue ID 1 Residue ID 2
';for(let t in s.resid2ResidhashHbond){let i=s.getGraphCls.convertLabel2Resid(t),a=s.firstAtomObjCls.getFirstAtomObj(s.residues[i]),d=a.color?a.color.getHexString():"";for(let i in s.resid2ResidhashHbond[t]){let a=s.getGraphCls.convertLabel2Resid(i),c=s.firstAtomObjCls.getFirstAtomObj(s.residues[a]),h=c.color?c.color.getHexString():"",p=Math.sqrt(s.resid2ResidhashHbond[t][i]).toFixed(1);n+=''+p+" ","view"==e&&(n+='Highlight '+l+" hydrogen bond pairs (backbone atoms: @CA, @N, @C, @O):
Atom 1 Atom 2 Distance(Å) ","view"==e&&(a+='Highlight in 3D '),a+="
';for(let t in s.resid2ResidhashSaltbridge){let i=s.getGraphCls.convertLabel2Resid(t),a=s.firstAtomObjCls.getFirstAtomObj(s.residues[i]),d=a.color?a.color.getHexString():"";for(let i in s.resid2ResidhashSaltbridge[t]){let a=s.getGraphCls.convertLabel2Resid(i),c=s.firstAtomObjCls.getFirstAtomObj(s.residues[a]),h=c.color?c.color.getHexString():"",p=Math.sqrt(s.resid2ResidhashSaltbridge[t][i]).toFixed(1);n+=''+p+" ","view"==e&&(n+='Highlight '+l+" salt bridge/ionic interaction pairs :
Atom 1 Atom 2 Distance(Å) ","view"==e&&(a+='Highlight in 3D '),a+="
';"halogen"==s?(l=i.resid2ResidhashHalogen,r=n.htmlCls.halogenColor,o=n.htmlCls.halogenValue):"pi-cation"==s?(l=i.resid2ResidhashPication,r=n.htmlCls.picationColor,o=n.htmlCls.picationValue):"pi-stacking"==s&&(l=i.resid2ResidhashPistacking,r=n.htmlCls.pistackingColor,o=n.htmlCls.pistackingValue);for(let t in l){let n=i.getGraphCls.convertLabel2Resid(t),r=i.firstAtomObjCls.getFirstAtomObj(i.residues[n]),o=r.color?r.color.getHexString():"";for(let n in l[t]){let r=i.getGraphCls.convertLabel2Resid(n),p=i.firstAtomObjCls.getFirstAtomObj(i.residues[r]),m=p.color?p.color.getHexString():"",u=Math.sqrt(l[t][n]).toFixed(1);a+=''+u+" ","view"==e&&(a+='Highlight '+d+" "+s+" pairs :
Atom 1 Atom 2 Distance(Å) ","view"==e&&(p+='Highlight in 3D '),p+="
';for(let s in o){let n=i.getGraphCls.convertLabel2Resid(s),c=i.firstAtomObjCls.getFirstAtomObj(i.residues[n]),h=c.color?c.color.getHexString():"";for(let n in o[s]){let p=i.getGraphCls.convertLabel2Resid(n),m=i.firstAtomObjCls.getFirstAtomObj(i.residues[p]),u=m.color?m.color.getHexString():"",g=o[s][n].split("_"),f=g[0],b=g[1];c=g[2],m=g[3];let C=g[4];e?(l+=''+C+' '+f+' '+b+" ","view"==t&&(l+='Highlight "+s+" "+n+' '+C+' '+f+' '+b+" '+r+" residue pairs in "+(e?"the contacts":"sphere")+" :
Residue 1 Residue 2 Num Contacts Min Distance(Å) C-alpha Distance(Å) ',"view"==t&&(c+='Highlight in 3D '),c+="Residue 1 Residue 2 Num Contacts Min Distance(Å) C-alpha Distance(Å)
0?n.structures[0]:n.defaultPdbId;p=10*(a.length+2)+20+30,h=10*(d.length+2)+20+30,t?(n.alignerrormapWidth=2*h,u=n.alignerrormapWidth,m=l.alignerrormapid):(n.contactmapWidth=2*h,u=n.contactmapWidth,m=l.contactmapid),i=o.length>0?"":"No interactions found for these two sets";if(t){n.hex2id={};let e=29/s;n.hex2skip={};let t=1e3;for(let s=0;se&&(n.hex2skip[d]=c)}}if(i+=n.lineGraphCls.drawScatterplot_base(a,d,o,c,0,!0,void 0,void 0,t),g+=n.getGraphCls.updateGraphJson(f,1,a,d,o),i+=" ",g+="}\n",t){n.alignerrormapStr=g,$("#"+n.pre+"alignerrormapDiv").html(i);let e=$("#"+l.alignerrormapid+"_scale").val();$("#"+l.alignerrormapid).attr("width",(n.alignerrormapWidth*parseFloat(e)).toString()+"px")}else n.contactmapStr=g,$("#"+n.pre+"contactmapDiv").html(i);return i}}class Bt{constructor(e){this.icn3d=e}async downloadAlignment(e,t){let s=this.icn3d,i=s.icn3dui,n=this;s.opts.proteins="c alpha trace";let l=e.split(","),r="ids="+e,o=i.htmlCls.baseUrl+"vastplus/vastplus.cgi?v=3&cmd=c&b=1&s=1&w3d&"+r;void 0!==i.cfg.inpara&&(o+=i.cfg.inpara),s.pdbid_chain2title={},void 0===s.chainids2resids&&(s.chainids2resids={});let a={},d="These two MMDB IDs "+l+' do not have 3D alignment data in the VAST+ database. You can try the VAST alignment by visiting the VAST+ page https://www.ncbi.nlm.nih.gov/Structure/vastplus/vastplus.cgi?uid=[PDB ID] (e.g., uid=1KQ2), and clicking "Original VAST"',c=await i.getAjaxPromise(o,"jsonp",!0,d);if(a=c.seqalign,void 0===a)return alert(d),!1;s.pdbid_molid2chain={},s.chainsColor={};for(let e=0,t=2;e5){let t=!1,s=!0;d=await r.pdbParserCls.loadPdbData(e,n,!1,t,"target",h,s)}else{let t=!0;d=await r.mmdbParserCls.parseMmdbData(e,"target",i[0],0,h,t)}for(let e=0,s=t.length;e5){let s=!0,i=!0;c=await r.pdbParserCls.loadPdbData(t[e],l,!1,s,"query",h,i)}else{let s=!0;c=await r.mmdbParserCls.parseMmdbData(t[e],"query",i[e+1],e,h,s)}d=o.hashUtilsCls.unionHash(d,c)}if(o.cfg.resnum)await r.realignParserCls.realignChainOnSeqAlign(s,i);else if(o.cfg.resdef)await r.realignParserCls.realignChainOnSeqAlign(s,i,void 0,!0);else{await r.pdbParserCls.applyCommandDssp(!0);for(let e in r.pdbChainIndexHash){let t=r.pdbChainIndexHash[e].split("_");l=t[0],t[1],n=t[2],t[3],a.transformStructure(l,e-1,"query")}let e=[],t=[],c=[],h=o.htmlCls.baseUrl+"vastdyn/vastdyn.cgi",p=o.htmlCls.baseUrl+"tmalign/tmalign.cgi";for(let s in r.afChainIndexHash){let i=r.afChainIndexHash[s].split("_");l=i[0];let a=i[1];n=i[2];let d,m=i[3];if("tmalign"!=o.cfg.aligntool){let e={domains1:r.domain3dCls.getDomainJsonForAlign(r.chains[l+"_"+a]),domains2:r.domain3dCls.getDomainJsonForAlign(r.chains[n+"_"+m])};d=o.getAjaxPostPromise(h,e)}else{let e={pdb_query:r.saveFileCls.getAtomPDB(r.chains[l+"_"+a]),pdb_target:r.saveFileCls.getAtomPDB(r.chains[n+"_"+m])};d=o.getAjaxPostPromise(p,e)}e.push(d),t.push(s-1),c.push(l)}let m=Promise.allSettled(e),u=await m;await a.downloadChainalignmentPart2b(s,i,d,u,t,n,c)}}async downloadChainalignmentPart2b(e,t,s,i,n,l,r){let o=this.icn3d,a=o.icn3dui;for(let e=0,t=i.length;ec&&(c=l[t[0]],a=t[0]),l[t[1]]>c&&(c=l[t[1]],a=t[1])}let h={},p={},m={},u={};for(let e in r){let t,s,i=e.split("_"),n=r[e].split(","),l=n[2];a==i[0]?(t=i[0],s=i[1]):a==i[1]?(t=i[1],s=i[0]):(t=i[0],s=i[1]),m[t]=1,m.hasOwnProperty(s)||(m[s]=1,u[e]=r[e],d="target",this.transformStructure(t,l,d),d="query",this.transformStructure(s,l,d),h[n[0]]=1,h[n[1]]=1)}for(let e in u)if(void 0!==i.q_rotation){let t=u[e].split(","),s=[t[1],t[0],t[2]],l=i.setSeqAlignCls.setSeqAlignChain(void 0,void 0,s);p=n.hashUtilsCls.unionHash(p,l);let r=!1,o=n.htmlCls.alignSeqCls.getAlignSequencesAnnotations(Object.keys(i.alnChains),void 0,void 0,!1,void 0,r),a=$("#"+i.pre+"dl_sequence2").html();$("#"+i.pre+"dl_sequence2").html(a+o.sequencesHtml),$("#"+i.pre+"dl_sequence2").width(n.htmlCls.RESIDUE_WIDTH*o.maxSeqCnt+200)}i.dAtoms=n.hashUtilsCls.cloneHash(p),i.hAtoms=n.hashUtilsCls.cloneHash(p);let g="protein_aligned";i.selectionCls.saveSelection(g,g),i.opts.color="identity",i.setColorCls.setColorByOptions(i.opts,i.hAtoms),n.htmlCls.dialogCls.openDlg("dl_alignment","Select residues in aligned sequences"),i.drawCls.draw(),i.transformCls.zoominSelection(),i.hlUpdateCls.updateHlAll()}transformStructure(e,t,s,i){let n=this.icn3d,l=n.icn3dui,r=n.structures[e];for(let e=0,o=r.length;e2){let e=i.firstAtomObjCls.getResiduesFromAtoms(s),t="protein_aligned",n="protein aligned",l="select "+i.resid2specCls.residueids2spec(Object.keys(e));i.selectionCls.addCustomSelection(Object.keys(e),t,n,l,!0)}i.hlUpdateCls.updateHlAll(),n.htmlCls.dialogCls.openDlg("dl_alignment","Select residues in aligned sequences"),void 0!==n.cfg.rotate&&i.resizeCanvasCls.rotStruc(n.cfg.rotate,!0),i.html2ddgm="",n.cfg.show2d&&i.bFullUi&&(n.htmlCls.dialogCls.openDlg("dl_2ddgm","Interactions"),i.bFullUi&&(i.bChainAlign?await i.ParserUtilsCls.set2DDiagramsForChainalign(t):i.ParserUtilsCls.download2Ddgm(i.inputid.toUpperCase())))}addPostfixForChainids(e){this.icn3d.icn3dui;let t={};for(let s=0,i=e.length;s5?(d="https://alphafold.ebi.ac.uk/files/AF-"+i.mmdbid_t+"-F1-model_"+i.AFUniprotVersion+".pdb",a=n.getAjaxPromise(d,"text")):(d=n.htmlCls.baseUrl+"mmdb/mmdb_strview.cgi?v=2&program=icn3d&b=1&s=1&ft=1&bu="+n.cfg.bu+"&uid="+i.mmdbid_t,void 0!==n.cfg.inpara&&(d+=n.cfg.inpara),a=n.getAjaxPromise(d,"jsonp")),c.push(a),i.ParserUtilsCls.setYourNote(e.toUpperCase()+" in iCn3D"),i.pdbid_chain2title={},void 0===i.chainids2resids&&(i.chainids2resids={}),i.afChainIndexHash={},i.pdbChainIndexHash={};for(let e=1,t=l.length;e5?(t="https://alphafold.ebi.ac.uk/files/AF-"+i.mmdbid_q+"-F1-model_"+i.AFUniprotVersion+".pdb",s=n.getAjaxPromise(t,"text")):(t=n.htmlCls.baseUrl+"mmdb/mmdb_strview.cgi?v=2&program=icn3d&b=1&s=1&ft=1&bu="+n.cfg.bu+"&uid="+i.mmdbid_q,void 0!==n.cfg.inpara&&(t+=n.cfg.inpara),s=n.getAjaxPromise(t,"jsonp")),c.push(s)}for(let e=1,t=l.length;e0?r[e]+","+r[0]:void 0;if("tmalign"!=n.cfg.aligntool&&4==i.mmdbid_t.length&&4==i.mmdbid_q.length){let o;o=r.length>0?n.htmlCls.baseUrl+"vastdyn/vastdyn.cgi?domainpairs="+l:n.htmlCls.baseUrl+"vastdyn/vastdyn.cgi?chainpairs="+t;let a=n.getAjaxPromise(o,"jsonp");c.push(a),i.pdbChainIndexHash[e]=s+"_"+i.chain_q+"_"+i.mmdbid_t+"_"+i.chain_t}else i.afChainIndexHash[e]=i.mmdbid_q+"_"+i.chain_q+"_"+i.mmdbid_t+"_"+i.chain_t}}let h=Promise.allSettled(c),p=await h;await this.parseChainAlignData(p,l,i.mmdbid_t,i.chain_t)}async parseChainAlignData(e,t,s,i){let n=this.icn3d,l=n.icn3dui,r=e[0].value,o="HEADER "+s+"\n";isNaN(s)&&s.length>5&&(r=o+r),n.t_trans_add=[],n.q_trans_sub=[],"tmalign"==l.cfg.aligntool&&(n.q_trans_add=[]),n.q_rotation=[],n.qt_start_end=[],n.mmdbidArray=[],n.mmdbidArray.push(s);let a=[];for(let s=1,i=t.length;s5&&(i=o+i),void 0===i||-1!==JSON.stringify(i).indexOf("Oops there was a problem"))return void alert("The coordinate data can NOT be retrieved for the structure "+r+"...");n.mmdbidArray.push(r),a.push(i)}let d=0;for(let r=1,o=t.length;r";"tmalign"==o.cfg.aligntool&&(n+="TM-score : "+e[0].score.toPrecision(4)+"5)t="https://alphafold.ebi.ac.uk/files/AF-"+l+"-F1-model_"+i.AFUniprotVersion+".pdb",s=n.getAjaxPromise(t,"text");else{let e=l;5==l.length&&(e=l.substr(0,4)),t=n.htmlCls.baseUrl+"mmdb/mmdb_strview.cgi?v=2&program=icn3d&b=1&s=1&ft=1&bu="+n.cfg.bu+"&uid="+e,void 0!==n.cfg.inpara&&(t+=n.cfg.inpara),s=n.getAjaxPromise(t,"jsonp")}o.push(s)}i.ParserUtilsCls.setYourNote(i.structArray+" in iCn3D"),i.ParserUtilsCls.showLoading();let a=Promise.allSettled(o),d=await a;await this.parseMMdbAfData(d,r,t,s),void 0===s&&i.ParserUtilsCls.hideLoading()}async parseMMdbAfData(e,t,s,i){let n=this.icn3d,l=n.icn3dui,r=[];for(let s=0,i=t.length;s5&&(i=n+i),void 0===i||-1!==JSON.stringify(i).indexOf("Oops there was a problem"))return void alert("The coordinate data can NOT be retrieved for the structure "+t[s]+"...");r.push(i)}let o={},a={},d=!1;n.opts.color=n.structArray.length>1?"structure":t[0].length>5?"confidence":"chain";for(let e=0,i=t.length;e5){let s=!1;a=await n.pdbParserCls.loadPdbData(r[e],t[e],!1,c,i,d,s)}else{let s=!0,l=t[e];a=await n.mmdbParserCls.parseMmdbData(r[e],i,void 0,void 0,d,s,l)}o=l.hashUtilsCls.unionHash(o,a)}if(n.structArray.length>1&&(n.opts.color="structure"),n.setColorCls.setColorByOptions(n.opts,n.atoms),await n.ParserUtilsCls.renderStructure(),void 0!==l.cfg.rotate&&n.resizeCanvasCls.rotStruc(l.cfg.rotate,!0),s&&l.cfg.matchedchains){let e=!0,t=!0;await n.realignParserCls.realignChainOnSeqAlign(void 0,n.chainidArray,e,t),$("#"+n.pre+"dl_annotations").html(""),n.bAnnoShown=!1,$("#"+l.pre+"dl_selectannotations").hasClass("ui-dialog-content")&&$("#"+n.pre+"dl_selectannotations").dialog("isOpen")&&$("#"+n.pre+"dl_selectannotations").dialog("close")}else if(void 0!==i){let e=Object.keys(n.structures);await n.vastplusCls.vastplusAlign(e,i)}}}class Gt{constructor(e){this.icn3d=e}async dsn6Parser(e,t,s){this.icn3d.icn3dui;let i="https://edmaps.rcsb.org/maps/"+e.toLowerCase()+"_"+t+".dsn6";await this.dsn6ParserBase(i,t,s)}async dsn6ParserBase(e,t,s){let i=this.icn3d,n=i.icn3dui,l=this;if("2fofc"==t&&i.bAjax2fofc)i.mapData.sigma2=s,i.setOptionCls.setOption("map",t);else if("fofc"==t&&i.bAjaxfofc)i.mapData.sigma=s,i.setOptionCls.setOption("map",t);else{let r=await n.getXMLHttpRqstPromise(e,"GET","arraybuffer","rcsbEdmaps");l.loadDsn6Data(r,t,s),"2fofc"==t?i.bAjax2fofc=!0:"fofc"==t&&(i.bAjaxfofc=!0),i.setOptionCls.setOption("map",t)}}loadDsn6Data(e,t,s){let i=this.icn3d;i.icn3dui;let n,l,r={},o=e.buffer&&e.buffer instanceof ArrayBuffer?e.buffer:e,a=new Int16Array(o),d=new Uint8Array(o),c=String.fromCharCode.apply(null,d.subarray(0,512));if(0==c.indexOf(":-)"))r.xStart=parseInt(c.substr(10,5)),r.yStart=parseInt(c.substr(15,5)),r.zStart=parseInt(c.substr(20,5)),r.xExtent=parseInt(c.substr(32,5)),r.yExtent=parseInt(c.substr(38,5)),r.zExtent=parseInt(c.substr(42,5)),r.xRate=parseInt(c.substr(52,5)),r.yRate=parseInt(c.substr(58,5)),r.zRate=parseInt(c.substr(62,5)),r.xlen=1*parseFloat(c.substr(73,10)),r.ylen=1*parseFloat(c.substr(83,10)),r.zlen=1*parseFloat(c.substr(93,10)),r.alpha=parseFloat(c.substr(103,10)),r.beta=parseFloat(c.substr(113,10)),r.gamma=parseFloat(c.substr(123,10)),n=parseFloat(c.substr(138,12))/100,l=parseInt(c.substr(155,8)),r.sigma=100*parseFloat(c.substr(170,12));else{if(100!==a[18])for(let e=0,t=a.length;e>8&255}r.zStart=a[2],r.xStart=a[0],r.yStart=a[1],r.xExtent=a[3],r.yExtent=a[4],r.zExtent=a[5],r.xRate=a[6],r.yRate=a[7],r.zRate=a[8];let e=1/a[17],t=1*e;r.xlen=a[9]*t,r.ylen=a[10]*t,r.zlen=a[11]*t,r.alpha=a[12]*e,r.beta=a[13]*e,r.gamma=a[14]*e,n=a[15]/a[18],l=a[16]}let h=new Float32Array(r.xExtent*r.yExtent*r.zExtent),p=512,m=Math.ceil(r.xExtent/8),u=Math.ceil(r.yExtent/8),g=Math.ceil(r.zExtent/8);for(let e=0;es.maxatomcnt&&(s.bAssembly=!0)}if("mmtfid"===t&&void 0!==o.missingseq){let t=0,n="";for(let l=0,r=o.missingseq.length;lt)&&(s.chainMissingResidueArray[c].push(h),t=d,n=a)}s.loadPDBCls.adjustSeq(s.chainMissingResidueArray)}}async loadMmcifData(e,t){let s=this.icn3d;if(s.icn3dui,t||(t=e.mmcif),t||(t=s.defaultPdbId),void 0===e.atoms)return!1;s.init(),void 0!==e.emd&&(s.emd=e.emd),void 0!==e.organism&&(s.organism=e.organism),void 0!==s.emd?($("#"+s.pre+"mapWrapper1").hide(),$("#"+s.pre+"mapWrapper2").hide(),$("#"+s.pre+"mapWrapper3").hide()):($("#"+s.pre+"emmapWrapper1").hide(),$("#"+s.pre+"emmapWrapper2").hide(),$("#"+s.pre+"emmapWrapper3").hide()),await s.opmParserCls.loadOpmData(e,t,void 0,"mmcif")}}class Wt{constructor(e){this.icn3d=e}async downloadMmdb(e,t){let s,i=this.icn3d,n=i.icn3dui;try{if(s=await this.loadMmdbPrms(e,t),!s||s.error)return void this.getNoData(e,t)}catch(s){return void this.getNoData(e,t)}if(0!=Object.keys(s.atoms).length)if(n.utilsCls.isCalphaPhosOnly(s.atoms)||s.atomCount<=i.maxatomcnt)await this.parseMmdbData(s);else{let s;try{s=await this.loadMmdbPrms(e,t,!0)}catch(s){return void this.getNoData(e,t)}await this.parseMmdbData(s)}else{let e=s.pdbId;await i.mmtfParserCls.downloadMmtf(e)}}async downloadGi(e){let t=this.icn3d;t.icn3dui,t.bCid=void 0;await this.downloadMmdb(e,!0)}async downloadBlast_rep_id(e){let t=this.icn3d,s=t.icn3dui,i=e.split(",");s.cfg.query_id=i[0],s.cfg.blast_rep_id=i[1];let n=s.cfg.blast_rep_id.split("_")[0];4==n.length?await this.downloadMmdb(n):(t.blastAcxn=s.cfg.blast_rep_id.split(".")[0],await this.downloadRefseq(t.blastAcxn,!0))}async downloadRefseq(e,t){let s=this.icn3d,i=s.icn3dui,n=i.htmlCls.baseUrl+"vastdyn/vastdyn.cgi?refseq2uniprot="+e;i.cfg.refseqid=e;let l=await i.getAjaxPromise(n,"jsonp",!1,"The protein accession "+e+" can not be mapped to AlphaFold UniProt ID...");if(!l||!l.uniprot)return void alert("The accession "+e+" can not be mapped to AlphaFold UniProt ID. It will be treated as a UniProt ID instead.");i.cfg.afid=l.uniprot,s.uniprot2acc||(s.uniprot2acc={}),s.uniprot2acc[l.uniprot]=e,t&&(i.cfg.blast_rep_id=i.cfg.afid+"_A");await s.pdbParserCls.downloadPdb(i.cfg.afid,!0)}async downloadProteinname(e){let t=this.icn3d,s=t.icn3dui;s.icn3d.bCid=void 0;let i=s.htmlCls.baseUrl+"vastdyn/vastdyn.cgi?protein2acc="+e,n=(await s.getAjaxPromise(i,"jsonp")).acc;if(0==n.length)return void(s.bNode||alert("The protein/gene name "+e+" can not be mapped to RefSeq proteins..."));let l=[];for(let e=0,t=n.length;e=20231001||!i.cfg.date&&parseInt(i.utilsCls.getDateDigitStr())>=20231001)&&(h=h.replace(/_/g,"")),void 0===d[h]?d[h]=1:++d[h];let p=n+"_"+(1===d[h]?h:h+d[h].toString());r[e]=c,o[p]=e,a[e]=p,s.chainsColor[p]=void 0===t||i.cfg.mmdbafid?i.parasCls.thr(c):i.parasCls.thr(i.htmlCls.GREY8);let m=void 0===l[e].geneId?"":l[e].geneId,u=void 0===l[e].geneSymbol?"":l[e].geneSymbol,g=void 0===l[e].geneDesc?"":l[e].geneDesc;s.chainsGene[p]={geneId:m,geneSymbol:u,geneDesc:g}}s.molid2chain=a,$("#"+s.pre+"accordion5").show()}loadMmdbPrms(e,t,s){let i,n=this.icn3d,l=n.icn3dui;return i=t?l.htmlCls.baseUrl+"mmdb/mmdb_strview.cgi?v=2&program=icn3d&b=1&s=1&ft=1&bu="+l.cfg.bu+"&simple=1&gi="+e:l.htmlCls.baseUrl+"mmdb/mmdb_strview.cgi?v=2&program=icn3d&b=1&s=1&ft=1&bu="+l.cfg.bu+"&simple=1&uid="+e,void 0!==l.cfg.blast_rep_id&&(i+="&bu=0"),void 0!==l.cfg.inpara&&(i+=l.cfg.inpara),s&&(i+="&complexity=2"),void 0===n.chainids2resids&&(n.chainids2resids={}),l.getAjaxPromise(i,"jsonp",!0)}}class Yt{constructor(e){this.icn3d=e}async downloadMmtf(e){let t=this.icn3d,s=t.icn3dui;t.ParserUtilsCls.setYourNote(e.toUpperCase()+"(MMTF) in iCn3D");let i=await s.getMmtfReducedPromise(e);if(10*i.numAtoms>t.maxatomcnt){let s=!1;if(0==Object.keys(i).length)return void alert("This PDB structure is not found at RCSB...");await t.opmParserCls.loadOpmData(i,e,s,"mmtf")}else{let i=await s.getMmtfPromise(e),n=!0;if(0==Object.keys(i).length)return void alert("This PDB structure is not found at RCSB...");await t.opmParserCls.loadOpmData(i,e,n,"mmtf")}}async parseMmtfData(e,t,s){let i=this.icn3d,n=i.icn3dui;e.numAtoms,i.init();let l=new THREE.Vector3(9999,9999,9999),r=new THREE.Vector3(-9999,-9999,-9999),o=new THREE.Vector3,a=e.structureId;if(i.molTitle=e.title,void 0!==e.bioAssemblyList&&void 0!==e.bioAssemblyList[0]&&e.bioAssemblyList[0].transformList.length>1){i.biomtMatrices=[];for(let t=0,s=e.bioAssemblyList[0].transformList.length;t1&&($("#"+i.pre+"assemblyWrapper").show(),i.asuCnt=i.biomtMatrices.length);let d,c,h,p,m,u,g,f,b,C,y,v,_,w,S,A,x,k,O,R={},I=[],T="coil",E="",P=0,M=0,D={onModel:function(e){d=0===e.modelIndex?a:a+(e.modelIndex+1).toString()},onChain:function(e){c=e.chainName;let t=d+"_"+c;void 0===i.structures[d]&&(i.structures[d]=[]),i.structures[d].push(t)},onGroup:function(e){h=e.groupName,p=e.groupId;let t=d+"_"+c+"_"+p;m=0===e.secStruct||2===e.secStruct||4===e.secStruct?"helix":3===e.secStruct?"sheet":-1===e.secStruct?"other":"coil";let s=!1;if(c!==E){if(x=void 0,O=void 0,"coil"!==m&&"other"!==m?(u=!0,g=!1):(u=!1,g=!1),"coil"!==T&&"other"!==T){let e=d+"_"+E+"_"+P.toString();for(let t in i.residues[e])i.atoms[t].ssbegin=!1,i.atoms[t].ssend=!0}}else x=A,O=k,m!==T?"coil"===T||"other"===T?(u=!0,g=!1):"coil"===m||"other"===m?(s=!0,u=!1,g=!1):("sheet"===T&&"helix"===m||"helix"===T&&"sheet"===m)&&(s=!0,u=!0,g=!1):(u=!1,g=!1);if(s&&!isNaN(p)){let e=d+"_"+c+"_"+(p-1).toString();for(let t in i.residues[e])i.atoms[t].ssbegin=!1,i.atoms[t].ssend=!0}T=m,E=c,P=p,f=!1,b=!1,C=!1,"non-polymer"===e.chemCompType.toLowerCase()||"other"===e.chemCompType.toLowerCase()||-1!==e.chemCompType.toLowerCase().indexOf("saccharide")?f=!0:-1!==e.chemCompType.toLowerCase().indexOf("peptide")?b=!0:-1!==e.chemCompType.toLowerCase().indexOf("dna")||-1!==e.chemCompType.toLowerCase().indexOf("rna")?C=!0:b=!0;let l=d+"_"+c,r={};r.resi=p,r.name=n.utilsCls.residueName2Abbr(h),i.residueId2Name[t]=r.name,r.resi%10==0&&r.resi.toString();let o="-";"helix"===m?o="H":"sheet"===m?o="E":"coil"===m?o="c":"other"===m&&(o="o"),void 0===i.chainsSeq[l]&&(i.chainsSeq[l]=[]),i.bFullUi&&i.chainsSeq[l].push(r),i.secondaries[t]=o},onAtom:function(e){if(y=e.element,v=e.atomName,_=new THREE.Vector3(e.xCoord,e.yCoord,e.zCoord),w=e.bFactor,S=e.altLoc,"\0"===e.altLoc&&(S=""),""===S||"A"===S){++M,"SG"===v&&I.push(M),R[e.atomIndex]=M;let t={het:f,serial:M,name:v,alt:S,resn:h,structure:d,chain:c,resi:p,coord:_,b:w,elem:y,bonds:[],bondOrder:[],ss:m,ssbegin:u,ssend:g};if(t.het||"C"!==t.name||(A=M),t.het||"O"!==t.name||(k=M),!t.het&&"N"===t.name&&void 0!==x&&void 0!==O){let e=i.atoms[x].coord.distanceTo(i.atoms[O].coord),s=t.coord.x+(i.atoms[x].coord.x-i.atoms[O].coord.x)/e,n=t.coord.y+(i.atoms[x].coord.y-i.atoms[O].coord.y)/e,l=t.coord.z+(i.atoms[x].coord.z-i.atoms[O].coord.z)/e;t.hcoord=new THREE.Vector3(s,n,l)}i.atoms[M]=t,l.min(_),r.max(_),o.add(_);let a=d+"_"+c,T=a+"_"+p;void 0===i.chains[a]&&(i.chains[a]={}),i.chains[a][M]=1,void 0===i.residues[T]&&(i.residues[T]={}),i.residues[T][M]=1,b?(i.proteins[M]=1,"CA"===v&&(i.calphas[M]=1),"N"!==v&&"H"!==v&&"CA"!==v&&"HA"!==v&&"C"!==v&&"O"!==v&&(i.sidec[M]=1)):C?(i.nucleotides[M]=1,(!s||"O3'"!=v&&"O3*"!=v)&&(s||"P"!=v)||(i.nucleotidesO3[M]=1),-1===n.parasCls.nuclMainArray.indexOf(v)&&(i.ntbase[M]=1)):y.toLowerCase()===h.toLowerCase()?i.ions[M]=1:"HOH"===h||"WAT"===h||"SQL"===h||"H2O"===h||"W"===h||"DOD"===h||"D3O"===h?i.water[M]=1:i.chemicals[M]=1,i.dAtoms[M]=1,i.hAtoms[M]=1}},onBond:function(e){let t=R[e.atomIndex1],s=R[e.atomIndex2];if(R.hasOwnProperty(e.atomIndex1)&&R.hasOwnProperty(e.atomIndex2)&&(i.atoms[t].bonds.push(s),i.atoms[s].bonds.push(t),f)){let n=e.bondOrder;i.atoms[t].bondOrder.push(n),i.atoms[s].bondOrder.push(n),2===n?(i.doublebonds[t+"_"+s]=1,i.doublebonds[s+"_"+t]=1):3===n&&(i.triplebonds[t+"_"+s]=1,i.triplebonds[s+"_"+t]=1)}}};MMTF.traverse(e,D),i.loadPDBCls.setResidMapping();for(let e=0,t=I.length;ei.maxatomcnt||void 0!==i.biomtMatrices&&i.biomtMatrices.length*i.cnt>10*i.maxatomcnt)&&(i.opts.proteins="c alpha trace",i.opts.nucleotides="o3 trace"),i.pmin=l,i.pmax=r,i.center=i.ParserUtilsCls.getGeoCenter(i.pmin,i.pmax),i.maxD=i.ParserUtilsCls.getStructureSize(i.atoms,i.pmin,i.pmax,i.center),i.maxD<5&&(i.maxD=5),i.oriMaxD=i.maxD,i.oriCenter=i.center.clone(),i.ParserUtilsCls.transformToOpmOri(t),void 0===n.cfg.align&&1==Object.keys(i.structures).length&&$("#"+i.pre+"alternateWrapper").hide(),i.setStyleCls.setAtomStyleByOptions(i.opts),i.setColorCls.setColorByOptions(i.opts,i.atoms),await i.ParserUtilsCls.renderStructure(),i.saveFileCls.showTitle(),void 0!==n.cfg.rotate&&i.resizeCanvasCls.rotStruc(n.cfg.rotate,!0)}}class Xt{constructor(e){this.icn3d=e}async loadMol2Data(e){let t=this.icn3d,s=t.icn3dui,i=this.loadMol2AtomData(e);void 0===s.cfg.align&&1==Object.keys(t.structures).length&&$("#"+t.pre+"alternateWrapper").hide(),i?(t.setStyleCls.setAtomStyleByOptions(t.opts),t.setColorCls.setColorByOptions(t.opts,t.atoms),await t.ParserUtilsCls.renderStructure(),void 0!==s.cfg.rotate&&t.resizeCanvasCls.rotStruc(s.cfg.rotate,!0)):alert("The Mol2 file has the wrong format...")}loadMol2AtomData(e){let t=this.icn3d;t.icn3dui;let s=e.split(/\r?\n|\r/);if(s.length<4)return!1;t.init();let i,n,l="LIG",r={},o="1_A",a=0,d=0,c=1,h=!1,p=!1,m={},u={};for(let e=0,o=s.length;eMOLECULE"==o){t.molTitle=s[e+1].trim();let l=s[e+2].trim().replace(/\s+/g," ").split(" ");i=l[0],n=l[1],e+=4}else"@ATOM"==o?(c=1,h=!0,++e):"@BOND"==o?(p=!0,h=!1,++e):"@SUBSTRUCTURE"==o&&(p=!1,++e);if(o=s[e].trim(),""!==o&&"#"!==o.substr(0,1)){if(h&&a1&&($("#"+l.pre+"assemblyWrapper").show(),l.asuCnt=l.biomtMatrices.length),l.setStyleCls.setAtomStyleByOptions(l.opts),l.setColorCls.setColorByOptions(l.opts,l.atoms),await l.ParserUtilsCls.renderStructure(),void 0!==r.cfg.rotate&&l.resizeCanvasCls.rotStruc(r.cfg.rotate,!0)}else"pdb"===i?await l.pdbParserCls.loadPdbData(e,t):"align"===i&&(l.bOpm?await l.alignParserCls.downloadAlignmentPart2(t):void 0!==n?await this.loadOpmData(e,n,s,i):await l.alignParserCls.downloadAlignmentPart2(t))}}class Jt{constructor(e){this.icn3d=e}async downloadPdb(e,t){let s,i=this.icn3d,n=i.icn3dui;t?(s="https://alphafold.ebi.ac.uk/files/AF-"+e+"-F1-model_"+i.AFUniprotVersion+".pdb",n.cfg.refseqid?i.ParserUtilsCls.setYourNote(n.cfg.refseqid.toUpperCase()+"(NCBI Protein Acc.) in iCn3D"):n.cfg.protein?i.ParserUtilsCls.setYourNote(n.cfg.protein+"(NCBI Protein/Gene) in iCn3D"):i.ParserUtilsCls.setYourNote(e.toUpperCase()+"(AlphaFold) in iCn3D")):(s="https://files.rcsb.org/view/"+e+".pdb",e=e.toUpperCase(),i.ParserUtilsCls.setYourNote(e+"(PDB) in iCn3D"));let l=await n.getAjaxPromise(s,"text",!0,"The ID "+e+" can not be found in the server "+s+"...");if(t){l="HEADER "+e+"\n"+l,await i.opmParserCls.parseAtomData(l,e,void 0,"pdb",void 0)}else await i.opmParserCls.loadOpmData(l,e,void 0,"pdb")}async downloadUrl(e,t,s){let i=this.icn3d,n=i.icn3dui,l=e.lastIndexOf("/");if(-1!=l){let t=e.lastIndexOf(".");i.filename=e.substr(l+1,t-l-1)}else{let t=e.lastIndexOf(".");i.filename=e.substr(0,t)}let r=await n.getAjaxPromise(e,"text",!0);if(i.InputfileData=i.InputfileData?i.InputfileData+"\nENDMDL\n"+r:r,i.InputfileType=t,"pdb"===t)await this.loadPdbData(r);else if("mmcif"===t){let e=n.htmlCls.baseUrl+"mmcifparser/mmcifparser.cgi",t={mmciffile:r},s=await n.getAjaxPostPromise(e,t,!0);await i.mmcifParserCls.loadMmcifData(s,void 0)}else if("mol2"===t)await i.mol2ParserCls.loadMol2Data(r);else if("sdf"===t)await i.sdfParserCls.loadSdfData(r);else if("xyz"===t)await i.xyzParserCls.loadXyzData(r);else if("mmcif"===t)await i.mmcifParserCls.loadMmcifData(r);else if("icn3dpng"===t)await n.htmlCls.setHtmlCls.loadPng(r,s);else if("pae"===t){n.htmlCls.dialogCls.openDlg("dl_alignerrormap","Show Predicted Aligned Error (PAE) map");let e=!0;i.contactMapCls.processAfErrorMap(JSON.parse(r),e)}}async loadPdbData(e,t,s,i,n,l,r,o){let a=this.icn3d,d=a.icn3dui;if(!i&&(void 0===n||"target"===n)){let e=!!a.bCommandLoad;a.bStatefile||a.init(e)}let c=a.loadPDBCls.loadPDB(e,t,s,void 0,void 0,i,n,o);void 0===d.cfg.opmid&&a.ParserUtilsCls.transformToOpmOri(t),void 0!==a.biomtMatrices&&a.biomtMatrices.length>1&&(d.bNode||$("#"+a.pre+"assemblyWrapper").show(),a.asuCnt=a.biomtMatrices.length),d.bNode||(void 0!==a.emd?($("#"+a.pre+"mapWrapper1").hide(),$("#"+a.pre+"mapWrapper2").hide(),$("#"+a.pre+"mapWrapper3").hide()):($("#"+a.pre+"emmapWrapper1").hide(),$("#"+a.pre+"emmapWrapper2").hide(),$("#"+a.pre+"emmapWrapper3").hide()));let h=!1;return a.bSecondaryStructure&&1==Object.keys(a.structures).length?h=!1:d.cfg.mmtfid||d.cfg.pdbid||d.cfg.opmid||d.cfg.mmdbid||d.cfg.gi||d.cfg.uniprotid||d.cfg.blast_rep_id||d.cfg.cid||d.cfg.mmcifid||d.cfg.align||d.cfg.chainalign||(h=!0),(!a.bSecondaryStructure||h)&&Object.keys(a.proteins).length>0&&!r?await this.applyCommandDssp(i):(await this.loadPdbDataRender(i),d.bNode||await a.ParserUtilsCls.checkMemProteinAndRotate()),c}async applyCommandDssp(e){let t=this.icn3d,s=t.icn3dui,i=s.utilsCls.isCalphaPhosOnly(s.hashUtilsCls.hash2Atoms(t.proteins,t.atoms));await t.dsspCls.applyDssp(i,e)}async loadPdbDataRender(e){let t=this.icn3d,s=t.icn3dui;void 0===s.cfg.align&&1==Object.keys(t.structures).length&&$("#"+t.pre+"alternateWrapper").hide(),(s.cfg.afid&&!t.bAfMem||t.bEsmfold)&&(t.opts.color="confidence"),t.setStyleCls.setAtomStyleByOptions(t.opts),t.setColorCls.setColorByOptions(t.opts,t.hAtoms),await t.ParserUtilsCls.renderStructure(),t.saveFileCls.showTitle(),void 0!==s.cfg.rotate&&t.resizeCanvasCls.rotStruc(s.cfg.rotate,!0),e&&!s.bNode&&t.definedSetsCls.setModeAndDisplay("all")}}class Qt{constructor(e){this.icn3d=e}async downloadCid(e){let t=this.icn3d,s=t.icn3dui;t.ParserUtilsCls.setYourNote("PubChem CID "+e+" in iCn3D"),t.bCid=!0;let i="https://pubchem.ncbi.nlm.nih.gov/rest/pug/compound/cid/"+t.inputid+"/cids/JSONP?cids_type=parent",n="https://pubchem.ncbi.nlm.nih.gov/rest/pug/compound/cid/"+(await s.getAjaxPromise(i,"jsonp",!0,"Can not retrieve the parant CID...")).IdentifierList.CID[0]+"/record/SDF/?record_type=3d&response_type=display",l=await s.getAjaxPromise(n,"text",!0,"This CID may not have 3D structure..."),r=this.loadSdfAtomData(l,e);void 0===s.cfg.align&&1==Object.keys(t.structures).length&&$("#"+t.pre+"alternateWrapper").hide(),r?(t.setStyleCls.setAtomStyleByOptions(t.opts),t.setColorCls.setColorByOptions(t.opts,t.atoms),await t.ParserUtilsCls.renderStructure(),void 0!==s.cfg.rotate&&t.resizeCanvasCls.rotStruc(s.cfg.rotate,!0)):alert("The SDF of CID "+e+" has the wrong format...")}async loadSdfData(e){let t=this.icn3d,s=t.icn3dui,i=this.loadSdfAtomData(e);void 0===s.cfg.align&&1==Object.keys(t.structures).length&&$("#"+t.pre+"alternateWrapper").hide(),i?(t.setStyleCls.setAtomStyleByOptions(t.opts),t.setColorCls.setColorByOptions(t.opts,t.atoms),await t.ParserUtilsCls.renderStructure(),void 0!==s.cfg.rotate&&t.resizeCanvasCls.rotStruc(s.cfg.rotate,!0)):alert("The SDF file has the wrong format...")}loadSdfAtomData(e,t){let s=this.icn3d;s.icn3dui;let i=e.split(/\r?\n|\r/);if(i.length<4)return!1;s.init();let n=t||1,l="LIG",r=n,o=n+"_A",a=o+"_1",d=parseInt(i[3].substr(0,3));if(isNaN(d)||d<=0)return!1;let c=parseInt(i[3].substr(3,3)),h=4;if(i.lengthr||(Math.abs(t.coord.y-i.coord.y)>r||Math.abs(t.coord.z-i.coord.z)>r||l.utilsCls.hasCovalentBond(t,i)&&(n.atoms[o[e]].bonds.push(o[s]),n.atoms[o[s]].bonds.push(o[e])))}}}loadXyzAtomData(e){let t=this.icn3d;t.icn3dui;let s=e.split(/\r?\n|\r/);if(s.length<3)return!1;t.init();let i,n,l,r={},o=0,a=1;t.molTitle="";for(let e=0,d=s.length;e1&&(t.molTitle+="; "),t.molTitle+=s[e+1].trim(),e+=2),d=s[e].trim(),""===d)continue;let c=d.replace(/,/," ").replace(/\s+/g," ").split(" "),h=c[0],p=parseFloat(c[1]),m=parseFloat(c[2]),u=parseFloat(c[3]),g={het:!0,serial:a,name:h,resn:"LIG",structure:l,chain:"A",resi:1,coord:new THREE.Vector3(p,m,u),b:0,elem:h,bonds:[],ss:"coil",ssbegin:!1,ssend:!1,bondOrder:[]};t.atoms[a]=g,r[a]=1,++a}return this.setXyzAtomSeq(r,o,i,n),t.ParserUtilsCls.setMaxD(),t.saveFileCls.showTitle(),!0}}class es{constructor(e){this.icn3d=e}realign(){let e=this.icn3d,t=e.icn3dui;e.selectionCls.saveSelectionPrep();let s="alseq_"+Object.keys(e.defNames2Atoms).length;e.selectionCls.saveSelection(s,s),t.htmlCls.clickMenuCls.setLogCmd("realign",!0);let i={},n={};e.realignResid={};let l="";for(let s in e.hAtoms){let r=e.atoms[s],o=r.structure+"_"+r.chain;if(e.proteins.hasOwnProperty(s)&&"CA"==r.name||e.nucleotides.hasOwnProperty(s)&&("O3'"==r.name||"O3*"==r.name)){if(r.structure+"_"+r.resi==l)continue;i.hasOwnProperty(r.structure)||(i[r.structure]=[]),i[r.structure].push(r.coord.clone()),e.realignResid.hasOwnProperty(o)||(e.realignResid[o]=[]),e.realignResid[o].push({resid:o+"_"+r.resi,resn:t.utilsCls.residueName2Abbr(r.resn.substr(0,3)).substr(0,1)}),n[r.structure]=r.structure+"_"+r.chain,l=r.structure+"_"+r.resi}}let r=Object.keys(i),o=r[0],a=[];e.qt_start_end=[],a.push(n[o]);for(let t=1,s=r.length;t5){let e=r.cfg.chainalign.split(",");e.length>0&&(l.hAtoms=l.definedSetsCls.getAtomsFromNameArray(e)),r.cfg.aligntool="tmalign",await l.realignParserCls.realignOnStructAlign()}else l.hAtoms=l.chainalignParserCls.setMsa(e),l.transformCls.zoominSelection(),await l.chainalignParserCls.downloadChainalignmentPart3(void 0,e,l.hAtoms)}async parseChainRealignData(e,t,s,i,n,l,r){let o=this.icn3d,a=o.icn3dui,d=s[0].substr(0,s[0].indexOf("_"));r||(d=d.toUpperCase());let c={};o.realignResid={},o.opts.color="grey",o.setColorCls.setColorByOptions(o.opts,o.dAtoms),o.qt_start_end=[];for(let t=0,h=e.length;t=6&&C.length>=6&&!a.cfg.command&&o.bRender&&alert("These sequences can not be aligned to each other")):o.bRender&&alert("Please do not align residues in the same structure")}if(r){o.hAtoms=o.chainalignParserCls.setMsa(s);let e="protein_aligned";if(o.selectionCls.saveSelection(e,e),o.bAfMem?(o.selectionCls.selectAll_base(),o.opts.chemicals="stick",o.opts.color="confidence",o.setColorCls.setColorByOptions(o.opts,o.atoms)):(o.transformCls.zoominSelection(),o.dAtoms=a.hashUtilsCls.cloneHash(o.hAtoms),o.opts.color="identity",o.setColorCls.setColorByOptions(o.opts,o.hAtoms)),o.drawCls.draw(),o.hlUpdateCls.updateHlAll(),o.bAfMem){let e=new THREE.Vector3(1,0,0),t=-.5*Math.PI;o.transformCls.setRotation(e,t)}}else o.hAtoms=o.chainalignParserCls.setMsa(s),o.transformCls.zoominSelection(),await o.chainalignParserCls.downloadChainalignmentPart3(t,s,o.hAtoms)}async realignOnSeqAlign(e){let t=this.icn3d;t.icn3dui;let s=t.firstAtomObjCls.getChainsFromAtoms(t.hAtoms),i=Object.keys(s),n=[],l="";for(let e=0,t=i.length;ei){n[e][o]=a;break}}}let l=[],r=[],o=s.htmlCls.baseUrl+"vastdyn/vastdyn.cgi",a=s.htmlCls.baseUrl+"tmalign/tmalign.cgi",d=Object.keys(n);e&&(d=d.reverse());for(let e=0,i=d.length;ei){n[r]=o;break}}let l=[],r=[],o=[],a=s.htmlCls.baseUrl+"vastdyn/vastdyn.cgi",d=s.htmlCls.baseUrl+"tmalign/tmalign.cgi",c=e[0],h=c.substr(0,c.indexOf("_")),p=t.domain3dCls.getDomainJsonForAlign(n[c]);for(let i=1,m=e.length;if&&(f=s)}}}return{data:n,min:g,max:f}}(e.getCategory("_volume_data_3d").getColumn("values"),o,n.sampleCount,l);return{name:n.name,spacegroup:function(e,t,s){let i=Math.PI/180*s[0],n=Math.PI/180*s[1],l=Math.PI/180*s[2],r=t[0],o=t[1],a=t[2],d=Math.cos(n),c=(Math.cos(i)-Math.cos(n)*Math.cos(l))/Math.sin(l),h=Math.sqrt(1-d*d-c*c);return{number:e,size:t,angles:s,basis:{x:[r,0,0],y:[Math.cos(l)*o,Math.sin(l)*o,0],z:[d*a,c*a,h*a]}}}(n.spacegroupNumber,n.cellSize,n.cellAngles),box:{origin:r(n.origin),dimensions:r(n.dimensions),sampleCount:o},data:a.data,valuesInfo:{min:a.min,max:a.max,mean:n.mean,sigma:n.sigma}}}BinaryParse(e){this.icn3d.icn3dui;let t=new Uint8Array(e),s=this.MessagePackParse({buffer:t,offset:0,dataView:new DataView(t.buffer)}),i=function(){function e(e){this.additionalData={},this.header=e.header,this.categoryList=e.categories.map((function(e){return new n(e)})),this.categoryMap=new Map;for(let e=0,t=this.categoryList;e=0;s--)t=c(t,e.encoding[s]);return t}function p(e){if(!e.data.data)return _UndefinedColumn;let t,s=h(e.data);return e.mask&&(t=h(e.mask)),s.buffer&&s.byteLength&&s.BYTES_PER_ELEMENT?t?new f(s,t):new g(s):t?new C(s,t):new b(s)}function m(e,t,s){let i=0,n=1;for(45===e.charCodeAt(t)&&(n=-1,t++);t9||s<0)return n*i|0;i=10*i+s|0}return n*i}function u(e,t,s){let i=1,n=0,l=0,r=1;for(45===e.charCodeAt(t)&&(i=-1,++t);t=0&&o<10)){if(-2===o){for(++t;t=0&&o<10))return 53===o||21===o?parseScientific(i*(n+l/r),e,t+1,s):i*(n+l/r);l=10*l+o,r*=10,++t}return i*(n+l/r)}if(53===o||21===o)return parseScientific(i*n,e,t+1,s);break}n=10*n+o,++t}return i*n}let g=function(){function e(e){this.data=e,this.isDefined=!0}return e.prototype.getString=function(e){return""+this.data[e]},e.prototype.getInteger=function(e){return 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i(e)}))}return e.prototype.toJSON=function(){return this.dataBlocks.map((function(e){return e.toJSON()}))},e}();return new y(s)}MessagePackParse(e){this.icn3d.icn3dui;let t=this;function s(e,s){let i={};for(let n=0;n0&&(i[i.length]=l.slice(0,a).join(""));return i.join("")}(e.buffer,e.offset,t);return e.offset+=t,s}let r=function(){let e=[];for(let t=0;t<1024;t++)e[t]=String.fromCharCode(t);return e}();let o,a,d=e.buffer[e.offset];if(0==(128&d))return e.offset++,d;if(128==(240&d))return a=15&d,e.offset++,s(e,a);if(144==(240&d))return a=15&d,e.offset++,n(e,a);if(160==(224&d))return a=31&d,e.offset++,l(e,a);if(224==(224&d))return o=e.dataView.getInt8(e.offset),e.offset++,o;switch(d){case 192:return e.offset++,null;case 194:return e.offset++,!1;case 195:return e.offset++,!0;case 196:return a=e.dataView.getUint8(e.offset+1),e.offset+=2,i(e,a);case 197:return a=e.dataView.getUint16(e.offset+1),e.offset+=3,i(e,a);case 198:return a=e.dataView.getUint32(e.offset+1),e.offset+=5,i(e,a);case 202:return o=e.dataView.getFloat32(e.offset+1),e.offset+=5,o;case 203:return o=e.dataView.getFloat64(e.offset+1),e.offset+=9,o;case 204:return o=e.buffer[e.offset+1],e.offset+=2,o;case 205:return o=e.dataView.getUint16(e.offset+1),e.offset+=3,o;case 206:return o=e.dataView.getUint32(e.offset+1),e.offset+=5,o;case 208:return o=e.dataView.getInt8(e.offset+1),e.offset+=2,o;case 209:return o=e.dataView.getInt16(e.offset+1),e.offset+=3,o;case 210:return o=e.dataView.getInt32(e.offset+1),e.offset+=5,o;case 217:return a=e.dataView.getUint8(e.offset+1),e.offset+=2,l(e,a);case 218:return a=e.dataView.getUint16(e.offset+1),e.offset+=3,l(e,a);case 219:return a=e.dataView.getUint32(e.offset+1),e.offset+=5,l(e,a);case 220:return a=e.dataView.getUint16(e.offset+1),e.offset+=3,n(e,a);case 221:return a=e.dataView.getUint32(e.offset+1),e.offset+=5,n(e,a);case 222:return a=e.dataView.getUint16(e.offset+1),e.offset+=3,s(e,a);case 223:return a=e.dataView.getUint32(e.offset+1),e.offset+=5,s(e,a)}}}class ss{constructor(e){this.icn3d=e}alignCoords(e,t,s,i,n,l,r,o){let a,d=this.icn3d,c=d.icn3dui,h=e.length=4&&(d.bAfMem?d.rmsd_suprTmp=c.rmsdSuprCls.getRmsdSuprCls(t,e,h):d.rmsd_suprTmp=c.rmsdSuprCls.getRmsdSuprCls(e,t,h),void 0!==d.rmsd_suprTmp.rot)){let e=d.rmsd_suprTmp.rot;null===e[0]&&alert("Please select more residues in each structure...");let t=d.rmsd_suprTmp.trans1,i=d.rmsd_suprTmp.trans2;if(a=d.rmsd_suprTmp.rmsd,a){c.htmlCls.clickMenuCls.setLogCmd("realignment RMSD: "+a.toPrecision(4),!1);let e="Realignment RMSD : "+a.toPrecision(4)+" Å"+s.diagram2dCls.set2DdgmNote(!0),$("#"+s.pre+"dl_2ddgm_html").html(s.html2ddgm),s.b2DShown=!0}async set2DDiagramsForChainalign(e){let t=this.icn3d.icn3dui,s=this;t.htmlCls.dialogCls.openDlg("dl_2ddgm","Interactions");let i=[];for(let s=0,n=e.length;s"+s.diagram2dCls.set2DdgmNote(!0),s.b2DShown=!0,$("#"+s.pre+"dl_2ddgm_html").html(s.html2ddgm),i.cfg.show2d&&i.htmlCls.dialogCls.openDlg("dl_2ddgm","Interactions")}download2Ddgm(e,t){this.set2DDiagrams(e)}set2DDiagrams(e){let t=this.icn3d;t.icn3dui.htmlCls.dialogCls.openDlg("dl_2ddgm","Interactions"),void 0!==t.b2DShown&&t.b2DShown||(t.html2ddgm="",t.diagram2dCls.draw2Ddgm(t.interactionData,e),t.html2ddgm+="=4)if(i.rmsd_supr=n.rmsdSuprCls.getRmsdSuprCls(o,a,d),void 0!==i.rmsd_supr.rot&&i.rmsd_supr.rmsd<.1){let s=i.rmsd_supr.rot,l=i.rmsd_supr.trans1,r=i.rmsd_supr.trans2,o=i.rmsd_supr.rmsd;n.htmlCls.clickMenuCls.setLogCmd("RMSD of alignment to OPM: "+o.toPrecision(4),!1);let a=0;for(let e in i.atoms){let t=i.atoms[e];t.coord=i.surfaceCls.transformMemPro(t.coord,s,l,r);let n=t.coord.x*t.coord.x+t.coord.y*t.coord.y;Math.abs(t.coord.z)<=25&&n>a&&(a=n)}i.center=t.center,i.oriCenter=i.center.clone(),this.addMemAtoms(i.halfBilayerSize,e,Math.sqrt(a)),i.bStopRotate=!0,i.bOpm=!0,$("#"+i.pre+"togglememli").show(),$("#"+i.pre+"adjustmemli").show(),$("#"+i.pre+"selectplaneli").show()}else i.bOpm=!1;else i.bOpm=!1}}addOneDumAtom(e,t,s,i,n,l){let r=this.icn3d,o=r.icn3dui,a={het:!0,serial:++l,name:t,alt:void 0,resn:"DUM",structure:e,chain:"MEM",resi:1,coord:new THREE.Vector3(s,i,n),b:void 0,elem:t,bonds:[],ss:"",ssbegin:!1,ssend:!1,color:o.parasCls.atomColors[t]};return r.atoms[l]=a,r.chains[e+"_MEM"][l]=1,r.residues[e+"_MEM_1"][l]=1,r.chemicals[l]=1,r.dAtoms[l]=1,r.hAtoms[l]=1,l}addMemAtoms(e,t,s){let i=this.icn3d;if(i.icn3dui,!t)return;t=t?t.toUpperCase():i.defaultPdbId,i.structures[t].push(t+"_MEM"),i.chains[t+"_MEM"]={},i.residues[t+"_MEM_1"]={},i.chainsSeq[t+"_MEM"]=[{name:"DUM",resi:1}];let n=Object.keys(i.atoms).length;for(let e=0;e<1e3;++e)if(!i.atoms.hasOwnProperty(n+e)){n=n+e-1;break}for(let i=0;i<81;++i)for(let l=0;l<81;++l){let r=2*i-80,o=2*l-80;if(Math.sqrt(r*r+o*o)=2?$("#"+e.pre+"mn2_alternateWrap").show():$("#"+e.pre+"mn2_alternateWrap").hide(),setTimeout((async function(){if(e.bInitial){if(void 0!==t.cfg.align||void 0!==t.cfg.chainalign){let s=e.pre+"selection";if($("#"+s).show(),$("#"+s+"_expand").hide(),$("#"+s+"_shrink").show(),void 0!==t.cfg.align&&2!=t.cfg.atype){let s=!1,i=t.htmlCls.alignSeqCls.getAlignSequencesAnnotations(Object.keys(e.alnChains),void 0,void 0,s);$("#"+e.pre+"dl_sequence2").html(i.sequencesHtml),$("#"+e.pre+"dl_sequence2").width(t.htmlCls.RESIDUE_WIDTH*i.maxSeqCnt+200)}}if(t.cfg.showanno){let s="view annotations";t.htmlCls.clickMenuCls.setLogCmd(s,!0),await e.showAnnoCls.showAnnotations()}(t.cfg.closepopup||t.cfg.imageonly)&&e.resizeCanvasCls.closeDialogs()}else e.hlUpdateCls.updateHlAll();$("#"+e.pre+"atomsCustom").length>0&&$("#"+e.pre+"atomsCustom")[0].blur(),e.bInitial=!1,t.cfg.imageonly&&e.saveFileCls.saveFile(void 0,"png",void 0,!0)}),0)}processCommand(){let e=this.icn3d,t=e.icn3dui;if(1==Object.keys(e.structures).length){let s=Object.keys(e.structures)[0];t.cfg.command=t.cfg.command.replace(new RegExp("!","g"),s+"_")}}getMassCenter(e,t){return this.icn3d.icn3dui,e.multiplyScalar(1/t)}getGeoCenter(e,t){return this.icn3d.icn3dui,e.clone().add(t).multiplyScalar(.5)}getStructureSize(e,t,s,i){let n=this.icn3d;n.icn3dui;let l=0;for(let r in e){let e=n.atoms[r].coord;if(Math.round(t.x)==Math.round(e.x)||Math.round(t.y)==Math.round(e.y)||Math.round(t.z)==Math.round(e.z)||Math.round(s.x)==Math.round(e.x)||Math.round(s.y)==Math.round(e.y)||Math.round(s.z)==Math.round(e.z)){let t=2*e.distanceTo(i);t>l&&(l=t)}}return l}async checkMemProteinAndRotate(){let e=this.icn3d,t=e.icn3dui;if(!e.bCheckMemProtein){e.bCheckMemProtein=!0;let s=t.cfg.afid?t.cfg.afid:t.cfg.mmdbafid;if(await e.ParserUtilsCls.checkMemProtein(s),t.cfg.url&&-1!=t.cfg.url.indexOf("membranome")){let t=new THREE.Vector3(1,0,0),s=-.5*Math.PI;e.transformCls.setRotation(t,s)}}}async checkMemProtein(e){let t=this.icn3d,s=t.icn3dui;try{let i=s.htmlCls.baseUrl+"vastdyn/vastdyn.cgi?afid2mem="+e,n=await s.getAjaxPromise(i,"jsonp");if(n&&n.pdbid){let e='This is a single-spanning (bitopic) transmembrane protein according to the Membranome database. Do you want to align the protein with the model from Membranome? If you click "OK", you can press the letter "a" to alternate the structures.';if("off"==s.cfg.afmem);else if("on"==s.cfg.afmem||confirm(e))try{let e="https://storage.googleapis.com/membranome-assets/pdb_files/proteins/"+n.pdbid+".pdb",i=await s.getAjaxPromise(e,"text");t.bAfMem=!0,s.bNode||$("#"+s.pre+"togglememli").show();let l=n.pdbid.substr(0,n.pdbid.indexOf("_")),r=!0,o=!0;await t.pdbParserCls.loadPdbData(i,l,r,o),o&&(t.bSetChainsAdvancedMenu&&t.definedSetsCls.showSets(),t.bAnnoShown&&await t.showAnnoCls.showAnnotations());let a=n.segment.replace(/ /gi,"").split("(")[0];t.afmem_start_end=a.split("-"),t.hAtoms={},t.dAtoms={};for(let e in t.atoms)t.atoms[e].structure!=l&&(t.hAtoms[e]=1),t.dAtoms[e]=1;for(let e=parseInt(t.afmem_start_end[0]);e<=parseInt(t.afmem_start_end[1]);++e)t.hAtoms=s.hashUtilsCls.unionHash(t.hAtoms,t.residues[l+"_A_"+e]);await t.realignParserCls.realignOnSeqAlign(l)}catch(e){return void console.log("Error in retrieving matched PDB from Membranome...")}}}catch(e){return void console.log("Error in finding matched PDB in Membranome...")}}getResi(e,t){let s=this.icn3d;s.icn3dui;let i=s.ncbi2resid[e+"_"+(t+1).toString()];return i?i.substr(i.lastIndexOf("_")+1):""}getResiNCBI(e,t){let s=this.icn3d;s.icn3dui;let i=s.resid2ncbi[e+"_"+t];return i?parseInt(i.substr(i.lastIndexOf("_")+1)):0}}class is{constructor(e){this.icn3d=e}loadAtomDataIn(e,t,s,i,n,l,r,o,a){let d=this.icn3d,c=d.icn3dui;d.pmin=new THREE.Vector3(9999,9999,9999),d.pmax=new THREE.Vector3(-9999,-9999,-9999),d.psum=new THREE.Vector3;let h=e.atoms,p=d.atoms?Object.keys(d.atoms).length:0,m={},u={};d.pmid=e.pubmedId,void 0===d.chainid2title&&(d.chainid2title={}),void 0===d.chainid2sid&&(d.chainid2sid={});let g={},f={};if("align"===s){d.pmid="",d.molTitle="",c.cfg.inpara&&-1!==c.cfg.inpara.indexOf("atype=1")?d.molTitle="Invariant Core Structure Alignment (VAST) of ":c.cfg.inpara&&-1!==c.cfg.inpara.indexOf("atype=2")?d.molTitle="Structure Alignment (TM-align) of ":d.molTitle="Structure Alignment (VAST) of ";let t=!1;for(let s=0,i=e.alignedStructures[0].length;s'+i.pdbId.toUpperCase()+"",void 0!==i.descr&&(d.pmid+=i.descr.pubmedid),0===s&&(d.molTitle+=" and ",void 0!==i.descr&&(d.pmid+="_")),t=!0}d.molTitle+=" from VAST+",t||(d.molTitle="")}else if(void 0!==e.descr&&(d.molTitle+=e.descr.name),"mmdbid"===s){let s=isNaN(t)?t:e.pdbId,i={};void 0===d.alignmolid2color&&(d.alignmolid2color=[]);let n=1;for(let t in e.moleculeInfor){if(0===Object.keys(e.moleculeInfor[t]).length)continue;let l=e.moleculeInfor[t].chain.trim();(parseInt(c.cfg.date)>=20231001||!c.cfg.date&&parseInt(c.utilsCls.getDateDigitStr())>=20231001)&&(l=l.replace(/_/g,""));let r=s+"_"+l;i.hasOwnProperty(l)?(++i[l],r+=i[l]):i[l]=1,void 0!==d.mmdbid_q&&(d.mmdbid_q,d.mmdbid_t);let o=e.moleculeInfor[t].kind,a=e.moleculeInfor[t].color,h=e.moleculeInfor[t].sid;if(g[r]=o,f[r]=a,"protein"==o&&(d.organism=e.moleculeInfor[t].taxonomyName.toLowerCase()),void 0!==h&&(d.chainid2sid[r]=h),void 0===d.pdbid_chain2title&&(d.pdbid_chain2title={}),d.pdbid_chain2title[r]=e.moleculeInfor[t].name,l==r.substr(r.lastIndexOf("_"))){let e={};e[t]=n.toString(),d.alignmolid2color.push(e)}++n}}"mmdbid"===s&&(d.molTitleHash||(d.molTitleHash={}),d.molTitleHash[t]=d.molTitle);let b,C,y,v,_,w={},S="",A="",x="",k="",O="",R="",I=0,T=0,E="",P=!0,M=!1,D="",H=c.utilsCls.isCalphaPhosOnly(h),F=0,L={};for(let e in h){++p,w[e]=p;let i,n=h[e];n.serial=p,"mmdbid"===s||"mmcifid"===s?i=t:"align"===s&&(i=m[p]);let l=!1;if(void 0!==n.chain||"mmdbid"!==s&&"align"!==s)n.chain=""===n.chain?"Misc":n.chain;else if("mmdbid"===s)if(b=n.ids.m,void 0!==d.molid2chain[b]){let e=d.molid2chain[b].indexOf("_");n.chain=d.molid2chain[b].substr(e+1)}else{let e="Misc";("protein"===g[O]&&"nucleotide"===g[O]&&n.resi!=T||"protein"!==g[O]&&"nucleotide"!==g[O]&&(n.resn.substr(0,3)!=E.substr(0,3)||n.resi!=T||"solvent"===g[O]||"HOH"===n.resn))&&++F,n.resi_ori=n.resi,n.resi=F,l=!0,n.chain=e}else if("align"===s)if(b=n.ids.m,void 0!==d.pdbid_molid2chain[i+"_"+b])n.chain=d.pdbid_molid2chain[i+"_"+b];else{let e="Misc";("protein"===g[O]&&"nucleotide"===g[O]&&n.resi!=T||"protein"!==g[O]&&"nucleotide"!==g[O]&&(n.resn.substr(0,3)!=E.substr(0,3)||n.resi!=T||"solvent"===g[O]||"HOH"===n.resn))&&(++F,n.resi_ori=n.resi,n.resi=F,l=!0),n.chain=e}if(n.chain=n.chain.trim(),(parseInt(c.cfg.date)>=20231001||!c.cfg.date&&parseInt(c.utilsCls.getDateDigitStr())>=20231001)&&(n.chain=n.chain.replace(/_/g,"")),"mmdbid"!==s&&"align"!==s||(n.structure=i,"mmdbid"===s&&void 0!==d.mmdbid_q&&(d.mmdbid_q,d.mmdbid_t)),k=n.structure,O=k+"_"+n.chain,"mmdbid"===s||"align"===s){l||(n.resi_ori=n.resi,d.bUsePdbNum?n.resi=n.resi_ori:n.resi=n.ids.r);let e=n.resn.indexOf(" ");-1!==e&&0!=e&&(n.resn=n.resn.substr(0,e))}O!==A&&(I=0),n.resi!==I&&(O!==A?(y=void 0,_=void 0):(y=C,_=v)),n.coord="mmdbid"===s?new THREE.Vector3(n.coord[0],n.coord[1],n.coord[2]):new THREE.Vector3(n.coord.x,n.coord.y,n.coord.z);let r=c.utilsCls.residueName2Abbr(n.resn.substr(0,3));"mmdbid"!==s&&"align"!==s||!d.bFullUi||(void 0===d.mmdbMolidResid2mmdbChainResi&&(d.mmdbMolidResid2mmdbChainResi={}),d.mmdbMolidResid2mmdbChainResi[i+"_"+n.ids.m+"_"+n.ids.r]=i+"_"+n.chain+"_"+n.resi),d.pmin.min(n.coord),d.pmax.max(n.coord),d.psum.add(n.coord);let o=void 0===c.cfg.mmcifid&&"mmcif"!=d.InputfileType?"protein"===g[O]:"p"===n.mt,a=void 0===c.cfg.mmcifid&&"mmcif"!=d.InputfileType?"nucleotide"===g[O]:"n"===n.mt,u=void 0===c.cfg.mmcifid&&"mmcif"!=d.InputfileType?"solvent"===g[O]:"s"===n.mt,N=void 0===c.cfg.mmcifid&&"mmcif"!=d.InputfileType?"ligand"===g[O]||void 0!==g[O]&&-1!==g[O].indexOf("other")||void 0===g[O]:"l"===n.mt;if("Misc"!==n.chain&&"other"!==g[O]||"protein"===L[O]||"nucleotide"===L[O]||("CA"===n.name&&"C"===n.elem?L[O]="protein":"P"===n.name&&"P"===n.elem?L[O]="nucleotide":L[O]="chemical"),o||a?(o?(d.proteins[p]=1,"CA"===n.name&&(d.calphas[p]=1),"N"!==n.name&&"H"!==n.name&&"CA"!==n.name&&"HA"!==n.name&&"C"!==n.name&&"O"!==n.name&&(d.sidec[p]=1)):a&&(d.nucleotides[p]=1,("O3'"==n.name||"O3*"==n.name||H&&"P"==n.name)&&(d.nucleotidesO3[p]=1),-1===c.parasCls.nuclMainArray.indexOf(n.name)&&(d.ntbase[p]=1)),n.het=!1):u?(d.water[p]=1,n.het=!0):N&&("HOH"===n.resn||"O"===n.resn?d.water[p]=1:n.elem===n.resn?d.ions[p]=1:d.chemicals[p]=1,n.het=!0),"mmdbid"===s?n.het?n.color=c.parasCls.atomColors[n.elem]||c.parasCls.defaultAtomColor:n.color=void 0!==f[O]?c.parasCls.thr(f[O]):c.parasCls.chargeColors[n.resn]:void 0!==n.color&&(n.color=c.parasCls.thr(n.color))," "!==n.resn.charAt(0)&&" "===n.resn.charAt(1)&&(n.resn=n.resn.charAt(0)),n.het||"C"!==n.name||(C=p),n.het||"O"!==n.name||(v=p),!n.het&&"N"===n.name&&void 0!==y&&void 0!==_){let e=d.atoms[y].coord.distanceTo(d.atoms[_].coord),t=n.coord.x+(d.atoms[y].coord.x-d.atoms[_].coord.x)/e,s=n.coord.y+(d.atoms[y].coord.y-d.atoms[_].coord.y)/e,i=n.coord.z+(d.atoms[y].coord.z-d.atoms[_].coord.z)/e;n.hcoord=new THREE.Vector3(t,s,i)}"HOH"==n.resn&&(d.water[p]=1),d.atoms[p]=n,d.dAtoms[p]=1,d.hAtoms[p]=1;let q=n.structure+"_"+n.chain;void 0===d.chains[q]&&(d.chains[q]={}),d.chains[q][p]=1;let U=q+"_"+n.resi;void 0===d.residues[U]&&(d.residues[U]={}),d.residues[U][p]=1,R=O+"_"+n.resi,R!==x&&O!==A&&(P=!0,""!==S&&(void 0===d.structures[S]&&(d.structures[S]=[]),d.structures[S].push(A))),d.residueId2Name[U]=r;let $="-";if("helix"===n.ss?$="H":"sheet"===n.ss?$="E":n.het||a?$="o":(!n.het&&c.parasCls.residueColors.hasOwnProperty(n.resn.toUpperCase())||"coil"===n.ss)&&($="c"),d.secondaries[n.structure+"_"+n.chain+"_"+n.resi]=$,(n.resi!=I||b!=D)&&d.bFullUi&&(void 0===d.chainsSeq[q]&&(d.chainsSeq[q]=[],P=!1),!isNaN(n.resi)))if(P&&!M&&void 0!==d.chainsSeq[q][n.resi-1])d.chainsSeq[q][n.resi-1].name=r;else if(!P||!d.chainsSeq[q].hasOwnProperty(n.resi-1)){let e={};e.resi=n.resi,e.name=r,n.resi%10==0&&n.resi.toString(),d.chainsSeq[q].push(e),M=!0}I=n.resi,T=n.resi_ori,E=n.resn,S=k,A=O,x=R,D=b}for(let e in d.chemicals){let t=d.atoms[e];if("P"==t.elem&&t.bonds.length>=4)for(let e=t.bonds.length-1;e>=0;--e){"P"==d.atoms[t.bonds[e]].elem&&t.bonds.splice(e,1)}}for(let e in L)if(!(Object.keys(d.chains[e]).length<10)&&"chemical"!==L[e])for(let t in d.chains[e]){let s=d.atoms[t];delete d.chemicals[t],s.het=!1,"protein"===L[e]?(d.proteins[t]=1,"CA"===s.name&&(d.calphas[t]=1),"N"!==s.name&&"H"!==s.name&&"CA"!==s.name&&"HA"!==s.name&&"C"!==s.name&&"O"!==s.name&&(d.sidec[t]=1)):"nucleotide"===L[e]&&(d.nucleotides[t]=1,("O3'"==s.name||"O3*"==s.name||H&&"P"==s.name)&&(d.nucleotidesO3[t]=1),-1===c.parasCls.nuclMainArray.indexOf(s.name)&&(d.ntbase[t]=1))}if(void 0===d.structures[k]&&(d.structures[k]=[]),d.structures[k].push(O),d.bFullUi)if("mmdbid"===s||"mmcifid"===s)for(let i in e.sequences){let n=e.sequences[i],l=t+"_"+i;void 0!==d.mmdbid_q&&(d.mmdbid_q,d.mmdbid_t),d.ParserUtilsCls.getMissingResidues(n,s,l)}else if("align"===s)for(let e in d.chainid2seq){let t=d.chainid2seq[e];d.ParserUtilsCls.getMissingResidues(t,s,e)}if(d.loadPDBCls.setResidMapping(),"mmcifid"!==s)for(let e in h){let t=w[e],s=void 0===d.atoms[t].bonds?0:d.atoms[t].bonds.length;for(let e=0;ed.maxatomcnt||void 0!==d.biomtMatrices&&d.biomtMatrices.length*d.cnt>10*d.maxatomcnt)&&(d.opts.proteins="c alpha trace",d.opts.nucleotides="o3 trace"),d.center=d.ParserUtilsCls.getGeoCenter(d.pmin,d.pmax),d.maxD=d.ParserUtilsCls.getStructureSize(d.atoms,d.pmin,d.pmax,d.center),d.maxD<5&&(d.maxD=5),d.oriMaxD=d.maxD,("align"===s||o)&&(d.ssbondpnts={},d.loadPDBCls.setSsbond()),"mmdbid"===s&&1==Object.keys(d.structures).length){let t=e.disulfides;if(void 0!==t)for(let e=0,s=t.length;ep&&(p=e)),c[e]={resi:t,resn:i,aligned:n}}r=e[t][1];let u=r.moleculeId,g=s.pdbid_molid2chain[l+"_"+u],f=l+"_"+g;void 0===s.alnChainsAnTtl[d]&&(s.alnChainsAnTtl[d]=[]),void 0===s.alnChainsAnTtl[d][0]&&(s.alnChainsAnTtl[d][0]=[]),void 0===s.alnChainsAnTtl[d][1]&&(s.alnChainsAnTtl[d][1]=[]),void 0===s.alnChainsAnTtl[d][2]&&(s.alnChainsAnTtl[d][2]=[]),void 0===s.alnChainsAnTtl[d][3]&&(s.alnChainsAnTtl[d][3]=[]),void 0===s.alnChainsAnTtl[d][4]&&(s.alnChainsAnTtl[d][4]=[]),void 0===s.alnChainsAnTtl[d][5]&&(s.alnChainsAnTtl[d][5]=[]),void 0===s.alnChainsAnTtl[d][6]&&(s.alnChainsAnTtl[d][6]=[]),s.alnChainsAnTtl[d][0].push(f),s.alnChainsAnTtl[d][1].push(d),s.alnChainsAnTtl[d][2].push(""),s.alnChainsAnTtl[d][3].push(""),s.alnChainsAnTtl[d][4].push(f),s.alnChainsAnTtl[d][5].push(d),s.alnChainsAnTtl[d][6].push("");let b=1;s.chainsMapping[d]||(s.chainsMapping[d]={}),s.chainsMapping[f]||(s.chainsMapping[f]={});for(let e=h;e<=p;++e){let t,o,p,m=s.bUsePdbNum?s.ParserUtilsCls.getResi(f,r.sequence[e][0]-1):r.sequence[e][0],u="~"===r.sequence[e][2]?"-":r.sequence[e][2],C=r.sequence[e][3]?1:0,y=c[e].aligned+C;2===y?(c[e].resn===u?(t="#FF0000",p="icn3d-cons",s.consHash1[d+"_"+c[e].resi]=1,s.consHash2[f+"_"+m]=1):(t="#0000FF",p="icn3d-ncons",s.nconsHash1[d+"_"+c[e].resi]=1,s.nconsHash2[f+"_"+m]=1),s.chainsMapping[d][d+"_"+c[e].resi]=c[e].resn+c[e].resi,s.chainsMapping[f][f+"_"+m]=c[e].resn+c[e].resi,o="#"+s.showAnnoCls.getColorhexFromBlosum62(c[e].resn,u)):(t=i.htmlCls.GREY8,p="icn3d-nalign",s.nalignHash1[d+"_"+c[e].resi]=1,s.nalignHash2[f+"_"+m]=1),void 0===s.alnChainsSeq[d]&&(s.alnChainsSeq[d]=[]);let v={};v.mmdbid=n,v.chain=a,v.resi=c[e].resi,v.resn=""===v.resi||"icn3d-nalign"===p?c[e].resn.toLowerCase():c[e].resn,v.aligned=y,v.color=""===v.resi?i.htmlCls.GREYC:t,v.color2=""===v.resi?i.htmlCls.GREYC:o,v.class=p,s.alnChainsSeq[d].push(v),""!==c[e].resi&&(void 0===s.alnChains[d]&&(s.alnChains[d]={}),$.extend(s.alnChains[d],s.residues[d+"_"+c[e].resi])),void 0===s.alnChainsSeq[f]&&(s.alnChainsSeq[f]=[]),v={},v.mmdbid=l,v.chain=g,v.resi=m,v.resn=""===v.resi||"icn3d-nalign"===p?u.toLowerCase():u,v.aligned=y,v.color=""===v.resi?i.htmlCls.GREYC:t,v.color2=""===v.resi?i.htmlCls.GREYC:o,v.class=p,s.alnChainsSeq[f].push(v),""!==v.resi&&(void 0===s.alnChains[f]&&(s.alnChains[f]={}),$.extend(s.alnChains[f],s.residues[f+"_"+m])),void 0===s.alnChainsAnno[d]&&(s.alnChainsAnno[d]=[]),void 0===s.alnChainsAnno[d][0]&&(s.alnChainsAnno[d][0]=[]),void 0===s.alnChainsAnno[d][1]&&(s.alnChainsAnno[d][1]=[]),void 0===s.alnChainsAnno[d][2]&&(s.alnChainsAnno[d][2]=[]),void 0===s.alnChainsAnno[d][3]&&(s.alnChainsAnno[d][3]=[]),e===h&&(void 0===s.alnChainsAnno[d][4]&&(s.alnChainsAnno[d][4]=[]),void 0===s.alnChainsAnno[d][5]&&(s.alnChainsAnno[d][5]=[]),void 0===s.alnChainsAnno[d][6]&&(s.alnChainsAnno[d][6]=[]),s.alnChainsAnno[d][4].push(s.pdbid_chain2title[f]),s.alnChainsAnno[d][5].push(s.pdbid_chain2title[d]),s.alnChainsAnno[d][6].push(""));let _=d+"_"+c[e].resi,w=f+"_"+m,S=s.secondaries[_],A=s.secondaries[w];A?s.alnChainsAnno[d][0].push(A):s.alnChainsAnno[d][0].push("-"),S?s.alnChainsAnno[d][1].push(S):s.alnChainsAnno[d][1].push("-");let x=".";b%5==0&&(x="*"),b%10==0&&(x="|"),s.alnChainsAnno[d][2].push(x);let k="";b%10==0&&(k=b.toString()),s.alnChainsAnno[d][3].push(k),++b}}e={}}getPosFromResi(e,t){let s=this.icn3d;s.icn3dui;let i,n=s.resid2ncbi[e+"_"+t];if(n){i=n.substr(n.lastIndexOf("_")+1)-1}return i}getResnFromResi(e,t){let s=this.icn3d;s.icn3dui;let i=e+"_"+t,n=s.residueId2Name[i];return n||(n="?"),n}getResiAferAlign(e,t,s){let i,n=this.icn3d,l=n.icn3dui;if(t&&"tmalign"==l.cfg.aligntool)i=s;else if(n.posid2resid){let t=n.posid2resid[e+"_"+s];i=t.substr(t.lastIndexOf("_")+1)}else i=n.chainsSeq[e][s].resi;return i}setSeqAlignChain(e,t,s){let i,n,l,r,o,a,d,c,h,p,m,u=this.icn3d,g=u.icn3dui,f={},b=!!s;if(b){if(o=s[1],a=s[0],t=s[2],d=o.indexOf("_"),c=a.indexOf("_"),i=o.substr(0,d).toUpperCase(),n=a.substr(0,c).toUpperCase(),l=o.substr(d+1),r=a.substr(d+1),i==n&&l==r){let e=u.chainsSeq[n+"_"+r].length;u.qt_start_end[t]={q_start:1,q_end:e,t_start:1,t_end:e}}}else{let d=s[0].indexOf("_"),c=e.indexOf("_");if(i=u.mmdbid_t,n=e.substr(0,c).toUpperCase(),l=s[0].substr(d+1),r=e.substr(c+1),i==n&&l==r){let e=u.chainsSeq[u.mmdbid_q+"_"+u.chain_q].length;u.qt_start_end[t]={q_start:1,q_end:e,t_start:1,t_end:e}}o=i+"_"+l,a=n+"_"+r,void 0!==n&&u.mmdbid_t}u.conservedName1=o+"_cons",u.nonConservedName1=o+"_ncons",u.notAlignedName1=o+"_nalign",u.conservedName2=a+"_cons",u.nonConservedName2=a+"_ncons",u.notAlignedName2=a+"_nalign",u.consHash1={},u.nconsHash1={},u.nalignHash1={},u.consHash2={},u.nconsHash2={},u.nalignHash2={},u.alnChains={},u.alnChainsSeq[o]=[],u.alnChains[o]={},u.alnChainsSeq[a]=[],u.alnChains[a]={},u.alnChainsAnno[o]=[],u.alnChainsAnTtl[o]=[],void 0===u.alnChainsAnTtl[o]&&(u.alnChainsAnTtl[o]=[]);for(let e=0;e<7;++e)void 0===u.alnChainsAnTtl[o][e]&&(u.alnChainsAnTtl[o][e]=[]);u.alnChainsAnTtl[o][0].push(a),u.alnChainsAnTtl[o][1].push(o),u.alnChainsAnTtl[o][2].push(""),u.alnChainsAnTtl[o][3].push(""),u.alnChainsAnTtl[o][4].push(a),u.alnChainsAnTtl[o][5].push(o),u.alnChainsAnTtl[o][6].push("");let C=0,y=0;if(void 0===u.qt_start_end[t])return;let v=1;u.chainsMapping[o]||(u.chainsMapping[o]={}),u.chainsMapping[a]||(u.chainsMapping[a]={});let _={},w={};for(let e=0,s=u.qt_start_end[t].length;e0){let e=v;for(let t=C+1,i=s;tc&&(c=t)}}}"tmalign"==n.cfg.aligntool&&(s=!0);let p=Object.keys(a);p.sort((function(e,t){return parseInt(e)-parseInt(t)}));let m=-999,u=0,g=0,f=[],b=0;for(let e=0,t=p.length;e0&&i.resid2ncbi[t]!=i.resid2ncbi[m]+1&&i.resid2ncbi[t]!=i.resid2ncbi[m]){g=m;for(let e=0,t=f.length;ec)continue;let o={},p=r.indexOf("_");o.mmdbid=r.substr(0,p),o.chain=r.substr(p+1),o.resi=t,o.resn=a[t]?i.chainsSeq[r][e].name.toUpperCase():i.chainsSeq[r][e].name.toLowerCase(),o.aligned=!!a[t],o.color=a[t]?"#FF0000":n.htmlCls.GREYC,o.color2=a[t]?"#FF0000":n.htmlCls.GREYC,o.class=a[t]?"icn3d-align":"icn3d-nalign",i.alnChainsSeq[r].push(o),a[t]&&($.extend(i.alnChains[r],i.residues[r+"_"+o.resi]),l=n.hashUtilsCls.unionHash(l,i.residues[r+"_"+o.resi]))}let C=[0];for(let i=0,r=t.length;in)for(let e=0,t=u-m;e=n)for(let e=0,s=t-n;en)for(let e=0,t=d-a;e=n)for(let t=0,s=e-n;t0?void 0!==n?p.alnChainsAnno[t][0].push(n):p.alnChainsAnno[t][0].push("-"):console.log("Error: ic.alnChainsAnno[chainid1] is undefined")}}}class ls{constructor(e){this.icn3d=e}getStructureId(e,t,s){let i=this.icn3d;i.icn3dui;let n=e;return(e==i.defaultPdbId||s||i.structures.hasOwnProperty(e))&&(n=1===t?e:e+t.toString()),n}loadPDB(e,t,s,i,n,l,r,o){let a,d,c=this.icn3d,h=c.icn3dui,p={},m=!1,u=e.split("\n"),g={},f={};c.atoms||(l=!1),n||l?(c.oriNStru=c.structures?Object.keys(c.structures).length:0,d=c.oriNStru+1,a=c.atoms?Object.keys(c.atoms).length:0):(c.init(),d=1,a=0);let b,C,y,v,_,w,S,A=[],x=[],k=[],O=[],R=[],I=[],T="",E="",P="",M={},D=t||c.defaultPdbId,H=D,F="",L=!1,N=!0;for(let e in u){let r=u[e],q=r.substr(0,6);if("HEADER"!==q||L||t)if("TITLE "===q){let e=r.substr(10).replace(/ALPHAFOLD MONOMER V2.0 PREDICTION FOR /gi,"");c.molTitle+=e.trim()+" ",o&&c.esmTitle&&(c.molTitle=c.esmTitle),c.molTitleHash||(c.molTitleHash={}),c.molTitleHash[H]=c.molTitle}else if("HELIX "===q){c.bSecondaryStructure=!0;let e=""==r.substr(18,2).trim()?"A":r.substr(18,2).trim(),t=parseInt(r.substr(21,4)),s=parseInt(r.substr(33,4));for(let i=t;i<=s;++i){let n=H+"_"+e+"_"+i;O.push(n),i===t&&R.push(n),i===s&&I.push(n)}}else if("SHEET "===q){void 0!==s&&s||(c.bSecondaryStructure=!0);let e=""==r.substr(20,2).trim()?"A":r.substr(20,2).trim(),t=parseInt(r.substr(22,4)),i=parseInt(r.substr(33,4));for(let s=t;s<=i;++s){let n=H+"_"+e+"_"+s;A.push(n),s===t&&x.push(n),s===i&&k.push(n)}}else if("HBOND "===q)void 0!==s&&s||(c.bSecondaryStructure=!0);else if("SSBOND"===q){c.bSsbondProvided=!0;let e=D+"_"+(" "==r.substr(15,1)?"A":r.substr(15,1))+"_"+r.substr(17,4).trim(),t=D+"_"+(" "==r.substr(29,1)?"A":r.substr(29,1))+"_"+r.substr(31,4).trim();void 0===c.ssbondpnts[D]&&(c.ssbondpnts[D]=[]),c.ssbondpnts[D].push(e),c.ssbondpnts[D].push(t)}else if("REMARK"===q){let e=parseInt(r.substr(7,3));if(-1!==r.indexOf("1/2 of bilayer thickness:"))c.halfBilayerSize=parseFloat(r.substr(r.indexOf(":")+1).trim());else if(210==e)"EXPERIMENT TYPE"==r.substr(11,32).trim()&&"NMR"==r.substr(45).trim()&&(m=!0);else if(350==e&&"BIOMT"==r.substr(13,5)){let e=parseInt(r[18])-1,t=parseInt(r.substr(21,2))-1;null==c.biomtMatrices[t]&&(c.biomtMatrices[t]=(new THREE.Matrix4).identity()),c.biomtMatrices[t].elements[e]=parseFloat(r.substr(24,9)),c.biomtMatrices[t].elements[e+4]=parseFloat(r.substr(34,9)),c.biomtMatrices[t].elements[e+8]=parseFloat(r.substr(44,9)),c.biomtMatrices[t].elements[e+12]=parseFloat(r.substr(54,14))}else if(465==e&&" "==r.substr(18,1)&&" "==r.substr(20,1)&&"S"!=r.substr(21,1)){let e=r.substr(15,3),t=r.substr(18,2).trim(),s=r.substr(21,5).trim(),i=D+"_"+t;void 0===c.chainMissingResidueArray[i]&&(c.chainMissingResidueArray[i]=[]);let n={};n.resi=s,n.name=h.utilsCls.residueName2Abbr(e).toLowerCase(),""!=F&&t==F&&t!=F||(c.chainMissingResidueArray[i].push(n),F=t)}else 900==e&&void 0===c.emd&&"RELATED DB: EMDB"==r.substr(34).trim()&&(c.emd=r.substr(23,11).trim())}else if("SOURCE"===q&&void 0===c.organism&&"ORGANISM_COMMON"==r.substr(11,15).trim())c.organism=r.substr(28).toLowerCase().trim(),c.organism=c.organism.substr(0,c.organism.length-1);else if("ENDMDL"===q)++d,D=c.defaultPdbId,H=this.getStructureId(D,d,n),m||(A=[],x=[],k=[],O=[],R=[],I=[]),L=!1;else if("JRNL "===q)"PMID"===r.substr(12,4)&&(c.pmid=r.substr(19).trim());else if("ATOM "===q||"HETATM"===q){N&&(H=this.getStructureId(D,d,n),N=!1);let e=r.substr(16,1);++a,M[parseInt(r.substr(6,5))]=a;let t=r.substr(76,2).trim();""===t&&(t=r.substr(12,2).trim());let l=r.substr(12,4).trim(),u=r.substr(17,3),F=r.substr(20,2).trim();""===F&&(F="A");let L=r.substr(22,5).trim(),U=L;if(s&&"DUM"===u&&(t=l,F="MEM",U=1,L=1),i&&"DUM"===u)break;b=H+"_"+F,y=b+"_"+L,C=b+"_"+U;let $=parseFloat(r.substr(30,8)),j=parseFloat(r.substr(38,8)),B=parseFloat(r.substr(46,8)),z=new THREE.Vector3($,j,B),G=parseFloat(r.substr(60,8));o&&(G*=100);let V={het:"H"===q[0],serial:a,name:l,alt:e,resn:u,structure:H,chain:F,resi:U,coord:z,b:G,elem:t,bonds:[],ss:"coil",ssbegin:!1,ssend:!1};if(V.het||"C"!==V.name||(v=a),V.het||"O"!==V.name||(w=a),!V.het&&"N"===V.name&&void 0!==_&&void 0!==S){let e=c.atoms[_].coord.distanceTo(c.atoms[S].coord),t=V.coord.x+(c.atoms[_].coord.x-c.atoms[S].coord.x)/e,s=V.coord.y+(c.atoms[_].coord.y-c.atoms[S].coord.y)/e,i=V.coord.z+(c.atoms[_].coord.z-c.atoms[S].coord.z)/e;V.hcoord=new THREE.Vector3(t,s,i)}c.atoms[a]=V,c.dAtoms[a]=1,c.hAtoms[a]=1,p[a]=1,this.isSecondary(C,A,m)?(c.atoms[a].ss="sheet",this.isSecondary(C,x,m)&&(c.atoms[a].ssbegin=!0),this.isSecondary(C,k,m)&&(c.atoms[a].ssend=!0)):this.isSecondary(C,O,m)&&(c.atoms[a].ss="helix",this.isSecondary(C,R,m)&&(c.atoms[a].ssbegin=!0),this.isSecondary(C,I,m)&&(c.atoms[a].ssend=!0));let W="-";if(W="helix"===c.atoms[a].ss?"H":"sheet"===c.atoms[a].ss?"E":!c.atoms[a].het&&h.parasCls.residueColors.hasOwnProperty(c.atoms[a].resn.toUpperCase())?"c":"o",c.secondaries[C]=W,y!==P){let e=h.utilsCls.residueName2Abbr(u);if(c.residueId2Name[C]=e,1!==a&&""!==E&&(c.residues[E]=f),C!==E&&(f={}),b!==T){_=void 0,S=void 0,1!==a&&""!==T&&(void 0===c.chains[T]&&(c.chains[T]={}),c.chains[T]=h.hashUtilsCls.unionHash(c.chains[T],g)),g={},void 0===c.structures[H.toString()]&&(c.structures[H.toString()]=[]),c.structures[H.toString()].includes(b)||c.structures[H.toString()].push(b),void 0===c.chainsSeq[b]&&(c.chainsSeq[b]=[]);let t={};t.resi=U,t.name=e,c.chainsSeq[b].push(t)}else{_=v,S=w;let t={};t.resi=U,t.name=e,c.chainsSeq[b].push(t)}}g[a]=1,f[a]=1,T=b,E=C,P=y}else if("CONECT"===q){let e=parseInt(r.substr(6,5));for(let t=0;t<4;++t){let s=parseInt(r.substr([11,16,21,26][t],5));isNaN(s)||void 0!==c.atoms[M[e]]&&c.atoms[M[e]].bonds.push(M[s])}}else q.substr(0,3);else D=r.substr(62).trim(),""==D&&(D=l?c.defaultPdbId:c.inputid&&-1==c.inputid.indexOf("/")?c.inputid.substr(0,10):c.defaultPdbId),H=this.getStructureId(D,d,n),c.molTitle="",c.molTitleHash={},L=!0}c.residues[C]=f,void 0===c.chains[b]&&(c.chains[b]={}),c.chains[b]=h.hashUtilsCls.unionHash2Atoms(c.chains[b],g,c.atoms),this.adjustSeq(c.chainMissingResidueArray);let q=Object.keys(c.structures);for(let e=0,t=q.length;e=l?n:l,o=new Array(s+i),a=0,d=0,c=0,h=!1;for(;ar&&i>r&&(h=!0),s<=r&&i>r?s>i||h?(o[c]=t[d],d++):(o[c]=e[a],a++):s>r&&i<=r?s<=i||h?(o[c]=e[a],a++):(o[c]=t[d],d++):s<=i?(o[c]=e[a],a++):(o[c]=t[d],d++),c++}if(a4||Math.abs(l.y-r.y)>4||Math.abs(l.z-r.z)>4||(l.x-r.x)*(l.x-r.x)+(l.y-r.y)*(l.y-r.y)+(l.z-r.z)*(l.z-r.z)<16&&(void 0===t.ssbondpnts[e]&&(t.ssbondpnts[e]=[]),t.ssbondpnts[e].push(o),t.ssbondpnts[e].push(a)))}}}getChainCalpha(e,t,s,i){let n=this.icn3d,l=n.icn3dui,r={};for(let o in e){if(void 0!==i){if(o.split("_")[0]!==i)continue}let a=Object.keys(e[o]),d=[],c=0,h=0;for(let e=0,i=a.length;e3?i.resn.trim().substr(0,3):i.resn.trim();if(!l.parasCls.chargeColors.hasOwnProperty(e))continue;s?i.resi_ori:i.resi,d.push(i.coord.clone()),++c,h=i.resi}}if(c>0){r[t[a[0]].chain]=d}}return{chainresiCalphaHash:r,center:n.center.clone()}}isSecondary(e,t,s){if(this.icn3d.icn3dui,s){let s=e.substr(e.indexOf("_")+1),i=!1;for(let e=0,n=t.length;e0&&(d=!0);for(let n=0,l=t.length;na&&(a=l),s.push(l)}o.push(s)}if(!d)return void(n.bRender&&alert("These structures can not be aligned..."));a<1e-6&&(a=1);for(let e=0,s=t.length;ep[e]=4&&(n.rmsd_suprTmp=l.rmsdSuprCls.getRmsdSuprCls(c,a,p),void 0!==n.rmsd_suprTmp.rot))){let e=n.rmsd_suprTmp.rot;if(null===e[0])continue;let i=n.rmsd_suprTmp.trans1,r=n.rmsd_suprTmp.trans2,a=n.rmsd_suprTmp.rmsd;if(aRealignment RMSD : "+a.toPrecision(4)+" Å8)return s;let g=[];g[0]=n[0]*r[0]+n[1]*r[1]+n[2]*r[2],g[1]=n[3]*r[0]+n[4]*r[1]+n[5]*r[2],g[2]=n[6]*r[0]+n[7]*r[1]+n[8]*r[2],g[0]-=n[0]*a[0]+n[1]*a[1]+n[2]*a[2],g[1]-=n[3]*a[0]+n[4]*a[1]+n[5]*a[2],g[2]-=n[6]*a[0]+n[7]*a[1]+n[8]*a[2];let f=0;return f=c[0]*g[0],f+=c[1]*g[1],f+=c[2]*g[2],f/=p*m,f<.866?s:(g[0]=l[0]*r[0]+l[1]*r[1]+l[2]*r[2],g[1]=l[3]*r[0]+l[4]*r[1]+l[5]*r[2],g[2]=l[6]*r[0]+l[7]*r[1]+l[8]*r[2],g[0]-=l[0]*a[0]+l[1]*a[1]+l[2]*a[2],g[1]-=l[3]*a[0]+l[4]*a[1]+l[5]*a[2],g[2]-=l[6]*a[0]+l[7]*a[1]+l[8]*a[2],f=c[0]*g[0],f+=c[1]*g[1],f+=c[2]*g[2],f/=p*m,f<.866?s:(u=0,u+=Math.pow(e.q_rotation.x1-t.q_rotation.x1,2),u+=Math.pow(e.q_rotation.y1-t.q_rotation.y1,2),u+=Math.pow(e.q_rotation.z1-t.q_rotation.z1,2),u+=Math.pow(e.q_rotation.x2-t.q_rotation.x2,2),u+=Math.pow(e.q_rotation.y2-t.q_rotation.y2,2),u+=Math.pow(e.q_rotation.z2-t.q_rotation.z2,2),u+=Math.pow(e.q_rotation.x3-t.q_rotation.x3,2),u+=Math.pow(e.q_rotation.y3-t.q_rotation.y3,2),u+=Math.pow(e.q_rotation.z3-t.q_rotation.z3,2),Math.sqrt(u)))}GetRotMatrix(e,t,s){this.icn3d.icn3dui;let i=[];return i&&(i[0]=e.q_rotation.x1/t,i[1]=e.q_rotation.y1/t,i[2]=e.q_rotation.z1/t,i[3]=e.q_rotation.x2/t,i[4]=e.q_rotation.y2/t,i[5]=e.q_rotation.z2/t,i[6]=e.q_rotation.x3/t,i[7]=e.q_rotation.y3/t,i[8]=e.q_rotation.z3/t,2!=s?(i[9]=e.t_trans_add.x/t,i[10]=e.t_trans_add.y/t,i[11]=e.t_trans_add.z/t,i[12]=-e.q_trans_sub.x/t,i[13]=-e.q_trans_sub.y/t,i[14]=-e.q_trans_sub.z/t):(i[9]=-e.q_trans_add.x/t,i[10]=-e.q_trans_add.y/t,i[11]=-e.q_trans_add.z/t,i[12]=0,i[13]=0,i[14]=0)),i}cbu_dist(e,t,s){return er&&(s.push(e[n].leaves),i.push(e[n].dist));return{clusters:s,scores:i}}}class os{constructor(e){this.icn3d=e}async applyCommand(e){let t=this.icn3d,s=t.icn3dui;t.bAddCommands=!1;let i=e.split("|||")[0].split("%7C%7C%7C")[0].replace(/\s+/g," ").trim(),n=i.toLowerCase();if("share link"==n)await t.shareLinkCls.shareLink();else if("export state file"==n);else if(0==n.indexOf("export canvas"))setTimeout((async function(){let e=n.substr(13).trim();t.scaleFactor=""===e?1:parseInt(e);let s=""!==e;await t.shareLinkCls.shareLink(!0,s)}),500);else if("export interactions"==n)t.viewInterPairsCls.exportInteractions();else if("export stl file"==n)setTimeout((function(){t.export3DCls.exportStlFile("")}),500);else if("export vrml file"==n)setTimeout((function(){t.export3DCls.exportVrmlFile("")}),500);else if("export stl stabilizer file"==n)setTimeout((function(){t.threeDPrintCls.hideStabilizer(),t.threeDPrintCls.resetAfter3Dprint(),t.threeDPrintCls.addStabilizer(),t.export3DCls.exportStlFile("_stab")}),500);else if("export vrml stabilizer file"==n)setTimeout((function(){t.threeDPrintCls.hideStabilizer(),t.threeDPrintCls.resetAfter3Dprint(),t.threeDPrintCls.addStabilizer(),t.export3DCls.exportVrmlFile("_stab")}),500);else if("export pdb"==n)s.htmlCls.setHtmlCls.exportPdb();else if("export pdb missing atoms"==n)await t.scapCls.exportPdbProfix(!1);else if("export pdb hydrogen"==n)await t.scapCls.exportPdbProfix(!0);else if(-1!=n.indexOf("export refnum ")){let e=n.substr(14);t.refnumCls.exportRefnum(e)}else if("export secondary structure"==n)s.htmlCls.setHtmlCls.exportSecondary();else if("select all"==n)t.selectionCls.selectAll();else if("show all"==n)t.selectionCls.showAll();else if("select complement"==n)t.resid2specCls.selectComplement();else if("set pk atom"==n)t.pk=1,t.opts.pk="atom";else if("set pk off"==n)t.pk=0,t.opts.pk="no",t.drawCls.draw(),t.hlObjectsCls.removeHlObjects();else if("set pk residue"==n)t.pk=2,t.opts.pk="residue";else if("set pk strand"==n)t.pk=3,t.opts.pk="strand";else if("set pk domain"==n)t.pk=4,t.opts.pk="domain";else if("set pk chain"==n)t.pk=5,t.opts.pk="chain";else if("set surface wireframe on"==n)t.opts.wireframe="yes",t.applyMapCls.applySurfaceOptions();else if("set surface wireframe off"==n)t.opts.wireframe="no",t.applyMapCls.applySurfaceOptions();else if("set map wireframe on"==n)t.opts.mapwireframe="yes",t.applyMapCls.applyMapOptions();else if("set map wireframe off"==n)t.opts.mapwireframe="no",t.applyMapCls.applyMapOptions();else if("set emmap wireframe on"==n)t.opts.emmapwireframe="yes",t.applyMapCls.applyEmmapOptions();else if("set emmap wireframe off"==n)t.opts.emmapwireframe="no",t.applyMapCls.applyEmmapOptions();else if("set surface neighbors on"==n)t.bConsiderNeighbors=!0,t.applyMapCls.applySurfaceOptions();else if("set surface neighbors off"==n)t.bConsiderNeighbors=!1,t.applyMapCls.applySurfaceOptions();else if("set axis on"==n)t.opts.axis="yes";else if("set pc1 axis"==n)t.pc1=!0,t.axesCls.setPc1Axes();else if("set axis off"==n)t.opts.axis="no",t.pc1=!1;else if("set fog on"==n)t.opts.fog="yes",t.fogCls.setFog(!0);else if("set fog off"==n)t.opts.fog="no",t.fogCls.setFog(!0);else if("set slab on"==n)t.opts.slab="yes";else if("set slab off"==n)t.opts.slab="no";else if("set assembly on"==n)t.bAssembly=!0;else if("set assembly off"==n)t.bAssembly=!1;else if("set chemicalbinding show"==n)t.setOptionCls.setOption("chemicalbinding","show");else if("set chemicalbinding hide"==n)t.setOptionCls.setOption("chemicalbinding","hide");else if("set hbonds off"==n)t.hBondCls.hideHbonds(),t.showInterCls.hideExtraBonds(),t.drawCls.draw();else if("set salt bridge off"==n)t.saltbridgeCls.hideSaltbridge(),t.showInterCls.hideExtraBonds(),t.drawCls.draw();else if("set contact off"==n)t.contactCls.hideContact(),t.showInterCls.hideExtraBonds(),t.drawCls.draw();else if("set halogen pi off"==n)t.piHalogenCls.hideHalogenPi(),t.showInterCls.hideExtraBonds(),t.drawCls.draw();else if("hydrogens"==n)t.showInterCls.showHydrogens(),t.drawCls.draw();else if("set hydrogens off"==n)t.showInterCls.hideHydrogens(),t.drawCls.draw();else if("close popup"==n)t.resizeCanvasCls.closeDialogs();else if("set stabilizer off"==n)t.threeDPrintCls.hideStabilizer(),t.drawCls.draw();else if("set disulfide bonds off"==n)t.opts.ssbonds="no",t.drawCls.draw();else if("set cross linkage off"==n)t.opts.clbonds="no",t.drawCls.draw();else if("set lines off"==n)t.labels.distance=[],t.lines.distance=[],t.drawCls.draw();else if("set labels off"==n){for(let e in t.labels)t.labels[e]=[];t.drawCls.draw()}else if("set mode all"==n)t.definedSetsCls.setModeAndDisplay("all");else if("set mode selection"==n)t.definedSetsCls.setModeAndDisplay("selection");else if("set view detailed view"==n)t.annotationCls.setAnnoViewAndDisplay("detailed view");else if("set view overview"==n)t.annotationCls.setAnnoViewAndDisplay("overview");else if("set annotation custom"==n)t.annotationCls.setAnnoTabCustom();else if("set annotation interaction"==n)t.annotationCls.setAnnoTabInteraction();else if("set annotation ptm"==n)await t.annotationCls.setAnnoTabPTM();else if("set annotation cdd"==n)t.annotationCls.setAnnoTabCdd();else if("set annotation site"==n)t.annotationCls.setAnnoTabSite();else if("set annotation ssbond"==n)t.annotationCls.setAnnoTabSsbond();else if("set annotation crosslink"==n)t.annotationCls.setAnnoTabCrosslink();else if("set annotation transmembrane"==n)await t.annotationCls.setAnnoTabTransmem();else if("highlight level up"==n)t.resid2specCls.switchHighlightLevelUp();else if("highlight level down"==n)t.resid2specCls.switchHighlightLevelDown();else if(0==n.indexOf("hide annotation")){let e=n.lastIndexOf(" "),s=n.substr(e+1);"all"==s?t.annotationCls.hideAnnoTabAll():"custom"==s?t.annotationCls.hideAnnoTabCustom():"clinvar"==s?t.annotationCls.hideAnnoTabClinvar():"snp"==s?t.annotationCls.hideAnnoTabSnp():"cdd"==s?t.annotationCls.hideAnnoTabCdd():"3ddomain"==s?t.annotationCls.hideAnnoTab3ddomain():"site"==s?t.annotationCls.hideAnnoTabSite():"ptm"==s?t.annotationCls.hideAnnoTabPTM():"interaction"==s?t.annotationCls.hideAnnoTabInteraction():"ssbond"==s?t.annotationCls.hideAnnoTabSsbond():"crosslink"==s?t.annotationCls.hideAnnoTabCrosslink():"transmembrane"==s&&t.annotationCls.hideAnnoTabTransmem()}else if("add residue labels"==n)t.residueLabelsCls.addResidueLabels(t.hAtoms),t.drawCls.draw();else if("add residue number labels"==n)t.residueLabelsCls.addResidueLabels(t.hAtoms,void 0,void 0,!0),t.drawCls.draw();else if("add reference number labels"==n)t.residueLabelsCls.addResidueLabels(t.hAtoms,void 0,void 0,void 0,!0),t.drawCls.draw();else if("add atom labels"==n)t.residueLabelsCls.addAtomLabels(t.hAtoms),t.drawCls.draw();else if("add element labels"==n)t.residueLabelsCls.addAtomLabels(t.hAtoms,!0),t.drawCls.draw();else if("add chain labels"==n)t.analysisCls.addChainLabels(t.hAtoms),t.drawCls.draw();else if("add terminal labels"==n)t.analysisCls.addTerminiLabels(t.hAtoms),t.drawCls.draw();else if("rotate left"==n)t.bStopRotate=!1,t.ROT_DIR="left",t.transformCls.rotateCountMax=6e3,t.resizeCanvasCls.rotStruc("left");else if("rotate right"==n)t.bStopRotate=!1,t.ROT_DIR="right",t.transformCls.rotateCountMax=6e3,t.resizeCanvasCls.rotStruc("right");else if("rotate up"==n)t.bStopRotate=!1,t.ROT_DIR="up",t.transformCls.rotateCountMax=6e3,t.resizeCanvasCls.rotStruc("up");else if("rotate down"==n)t.bStopRotate=!1,t.ROT_DIR="down",t.transformCls.rotateCountMax=6e3,t.resizeCanvasCls.rotStruc("down");else if("rotate x"==n){let e=new THREE.Vector3(1,0,0),s=.5*Math.PI;t.transformCls.setRotation(e,s)}else if("rotate y"==n){let e=new THREE.Vector3(0,1,0),s=.5*Math.PI;t.transformCls.setRotation(e,s)}else if("rotate z"==n){let e=new THREE.Vector3(0,0,1),s=.5*Math.PI;t.transformCls.setRotation(e,s)}else if("reset"===n)t.selectionCls.resetAll();else if("reset orientation"===n)t.transformCls.resetOrientation(),t.drawCls.draw();else if("reset thickness"==n)t.threeDPrintCls.resetAfter3Dprint(),t.drawCls.draw();else if("clear selection"==n)t.hlObjectsCls.removeHlObjects(),t.hlUpdateCls.removeHl2D(),t.bShowHighlight=!1,t.bSelectResidue=!1;else if("zoom selection"==n)t.transformCls.zoominSelection(),t.drawCls.draw();else if("center selection"==n)t.applyCenterCls.centerSelection(),t.drawCls.draw();else if("show selection"==n)t.selectionCls.showSelection();else if("hide selection"==n)t.selectionCls.hideSelection();else if("output selection"==n)t.threeDPrintCls.outputSelection();else if("toggle selection"==n)t.selectionCls.toggleSelection();else if("toggle highlight"==n)t.hlUpdateCls.toggleHighlight();else if("stabilizer"==n)t.threeDPrintCls.addStabilizer(),t.threeDPrintCls.prepareFor3Dprint();else if("disulfide bonds"==n)t.showInterCls.showSsbonds();else if("cross linkage"==n)t.showInterCls.showClbonds();else if("back"==n)await t.resizeCanvasCls.back();else if("forward"==n)await t.resizeCanvasCls.forward();else if("clear all"==n)t.selectionCls.selectAll();else if("defined sets"==n)t.definedSetsCls.showSets();else if("delete selected sets"==n)t.definedSetsCls.deleteSelectedSets();else if("view interactions"==n)void 0===s.cfg.mmdbid&&void 0===s.cfg.gi||t.ParserUtilsCls.set2DDiagrams(t.inputid);else if("show annotations all chains"==n)t.annotationCls.showAnnoAllChains();else if("save color"==n)t.setOptionCls.saveColor();else if("apply saved color"==n)t.setOptionCls.applySavedColor();else if("save style"==n)t.setOptionCls.saveStyle();else if("apply saved style"==n)t.setOptionCls.applySavedStyle();else if("select main chains"==n)t.selectionCls.selectMainChains();else if("select side chains"==n)t.selectionCls.selectSideChains();else if("select main side chains"==n)t.selectionCls.selectMainSideChains();else if("realign"==n)t.realignParserCls.realign();else if(-1!=n.indexOf("realign predefined ")){let e="realign predefined ",n=i.substr(e.length),l=n.indexOf(" "),r=n.substr(0,l).split(",");s.cfg.resdef=n.substr(l+1).replace(/:/gi,";"),await t.realignParserCls.realignChainOnSeqAlign(void 0,r,!0,!0)}else if("area"==n)t.analysisCls.calculateArea();else if("table inter count only"==n)$(".icn3d-border").hide();else if("table inter details"==n)$(".icn3d-border").show();else if("setoption map nothing"==n)t.setOptionCls.setOption("map","nothing");else if("setoption emmap nothing"==n)t.setOptionCls.setOption("emmap","nothing");else if("setoption phimap nothing"==n)t.setOptionCls.setOption("phimap","nothing");else if("setoption phisurface nothing"==n)t.setOptionCls.setOption("phisurface","nothing");else if("clear symd symmetry"==n)t.symdArray=[];else if("show axis"==n)t.bAxisOnly=!0;else if(0==i.indexOf("define helix sets")){let e=i.split(" | ")[1].split(" ")[1];t.addTrackCls.defineSecondary(e,"helix")}else if(0==i.indexOf("define sheet sets")){let e=i.split(" | ")[1].split(" ")[1];t.addTrackCls.defineSecondary(e,"sheet")}else if(0==i.indexOf("define coil sets")){let e=i.split(" | ")[1].split(" ")[1];t.addTrackCls.defineSecondary(e,"coil")}else if(0==i.indexOf("define igstrand sets")){let e=i.split(" | ")[1].split(" ")[1];t.addTrackCls.defineIgstrand(e,"igstrand")}else if(0==i.indexOf("define igloop sets")){let e=i.split(" | ")[1].split(" ")[1];t.addTrackCls.defineIgstrand(e,"igloop")}else if(0==i.indexOf("select interaction")){let e=i.substr(i.lastIndexOf(" ")+1).split(",");if(null!==e){let s=e[0].split("_")[0];t.b2DShown||t.ParserUtilsCls.download2Ddgm(s.toUpperCase()),t.diagram2dCls.selectInteraction(e[0],e[1])}}else if(0==i.indexOf("select saved atoms")||0==i.indexOf("select sets")){i=i.replace(/aligned_protein/g,"protein_aligned");let e=i.split(" | "),s=e[0].replace(/,/g," or "),n=19;0==i.indexOf("select sets")&&(n=12);let l=s.substr(n),r=l;2==e.length&&(r=e[1].substr(5)),t.definedSetsCls.selectCombinedSets(l,r)}else if(-1!==i.indexOf("select chain")){let e=i.substr(i.lastIndexOf(" ")+1).split(",");for(let s=0,i=e.length;s6?e[6].substr(e[6].lastIndexOf(" ")+1):0,d=e.length>7?e[7].substr(e[7].lastIndexOf(" ")+1):1;t.analysisCls.addLine(parseFloat(s[1]),parseFloat(s[3]),parseFloat(s[5]),parseFloat(i[1]),parseFloat(i[3]),parseFloat(i[5]),l,r,o,parseFloat(a),parseFloat(d)),t.drawCls.draw()}else if(0==n.indexOf("add sphere"))this.addShape(n,"sphere");else if(0==n.indexOf("add cube"))this.addShape(n,"cube");else if(0==n.indexOf("clear shape"))t.shapeCmdHash={};else if(0==n.indexOf("clear line between sets"))t.lines.cylinder=[];else if(0==i.indexOf("add label")){let e,n,l,r,o,a,d,c=i.split(" | "),h=c[0].substr("add label".length+1),p=!1;for(let t=1,s=c.length;t=5&&(e=l[4].substr(5)),l.length>=6&&(s=l[5].substr(6)),l.length>=7&&(n=l[6].substr(4)),$("#"+t.pre+"anno_custom")[0]&&($("#"+t.pre+"anno_custom")[0].checked=!0),$("[id^="+t.pre+"custom]").show(),"0"==s&&(s=void 0),t.addTrackCls.checkGiSeq(r,o,a,e,s,n,0)}else if(0==n.indexOf("remove one stabilizer")){let e=n.split(" | ")[1].split(" "),s=[];s.push(parseInt(e[0])),s.push(parseInt(e[1])),t.threeDPrintCls.removeOneStabilizer(s),t.drawCls.draw()}else if(0==n.indexOf("add one stabilizer")){let e=n.split(" | ")[1].split(" ");void 0===t.pairArray&&(t.pairArray=[]),t.pairArray.push(parseInt(e[0])),t.pairArray.push(parseInt(e[1])),t.drawCls.draw()}else if(0==n.indexOf("select planes z-axis")){let e=n.split(" ");if(5==e.length){let s=parseFloat(e[3]),i=parseFloat(e[4]);t.selectionCls.selectBtwPlanes(s,i)}}else if(0==n.indexOf("adjust membrane z-axis")){let e=n.split(" ");if(5==e.length){let s=parseFloat(e[3]),i=parseFloat(e[4]);t.selectionCls.adjustMembrane(s,i)}}else if(0==n.indexOf("toggle membrane"))t.selectionCls.toggleMembrane();else if(0==i.indexOf("calc buried surface")){let e=i.split(" | ");if(2==e.length){let s=e[1].split(" ");if(2==s.length){let e=s[0].split(","),i=s[1].split(",");t.analysisCls.calcBuriedSurface(e,i)}}}else if(0==i.indexOf("dist ")){let e=i.split(" | ");if(2==e.length){let s=e[1].split(" ");if(2==s.length){let e=s[0].split(","),i=s[1].split(",");t.analysisCls.measureDistTwoSets(e,i)}}}else if(0==i.indexOf("disttable")){let e=i.split(" | ");if(2==e.length){let i=e[1].split(" ");if(2==i.length){let e=i[0].split(","),n=i[1].split(",");t.analysisCls.measureDistManySets(e,n),s.htmlCls.dialogCls.openDlg("dl_disttable","Distance among the sets")}}}else if(0==i.indexOf("display interaction 3d")||0==i.indexOf("view interaction pairs")||0==i.indexOf("save1 interaction pairs")||0==i.indexOf("save2 interaction pairs")||0==i.indexOf("line graph interaction pairs")||0==i.indexOf("scatterplot interaction pairs")){let e=i.split(" | ");if(e.length>=3){let s=e[1].split(" ");if(2==s.length){let n,l,r=s[0].split(","),o=s[1].split(","),a=-1!==e[2].indexOf("hbonds"),d=-1!==e[2].indexOf("salt bridge"),c=-1!==e[2].indexOf("interactions"),h=-1!==e[2].indexOf("halogen"),p=-1!==e[2].indexOf("pi-cation"),m=-1!==e[2].indexOf("pi-stacking");if(e.length>=4&&(n="true"==e[3]),e.length>=5){let s=e[4].split(" ");s.length>=4&&($("#"+t.pre+"hbondthreshold").val(s[1]),$("#"+t.pre+"saltbridgethreshold").val(s[2]),$("#"+t.pre+"contactthreshold").val(s[3]),7==s.length&&($("#"+t.pre+"halogenthreshold").val(s[4]),$("#"+t.pre+"picationthreshold").val(s[5]),$("#"+t.pre+"pistackingthreshold").val(s[6])))}0==i.indexOf("display interaction 3d")?l="3d":0==i.indexOf("view interaction pairs")?l="view":0==i.indexOf("save1 interaction pairs")?l="save1":0==i.indexOf("save2 interaction pairs")?l="save2":0==i.indexOf("line graph interaction pairs")?l="linegraph":0==i.indexOf("scatterplot interaction pairs")&&(l="scatterplot"),await t.viewInterPairsCls.viewInteractionPairs(r,o,n,l,a,d,c,h,p,m)}}}else if(0==i.indexOf("export pairs")){let e=i.split(" | ");if(3==e.length){let i=e[1].split(" ");if(2==i.length){let n=i[0].split(","),l=i[1].split(","),r=e[2].split(" ")[1];t.showInterCls.pickCustomSphere(r,n,l,t.bSphereCalc),t.bSphereCalc=!0;let o=t.viewInterPairsCls.exportSpherePairs(),a=Object.keys(s.utilsCls.getHlStructures()).join(",");t.saveFileCls.saveFile(a+"_sphere_pairs.html","html",o)}}}else if(0==n.indexOf("graph label")){let e=n.lastIndexOf(" "),t=n.substr(e+1);$("#"+s.svgid+"_label").val(t),$("#"+s.svgid+" text").removeClass(),$("#"+s.svgid+" text").addClass(t)}else if(0==n.indexOf("cartoon label")){let e=n.lastIndexOf(" "),t=n.substr(e+1);$("#"+s.svgid_ct+"_label").val(t),$("#"+s.svgid_ct+" text").removeClass(),$("#"+s.svgid_ct+" text").addClass(t)}else if(0==n.indexOf("line graph scale")){let e=n.lastIndexOf(" "),i=n.substr(e+1);$("#"+s.linegraphid+"_scale").val(i),$("#"+s.linegraphid).attr("width",(t.linegraphWidth*parseFloat(i)).toString()+"px")}else if(0==n.indexOf("scatterplot scale")){let e=n.lastIndexOf(" "),i=n.substr(e+1);$("#"+s.scatterplotid+"_scale").val(i),$("#"+s.scatterplotid).attr("width",(t.scatterplotWidth*parseFloat(i)).toString()+"px")}else if(0==n.indexOf("contactmap scale")){let e=n.lastIndexOf(" "),i=n.substr(e+1);$("#"+s.contactmapid+"_scale").val(i),$("#"+s.contactmapid).attr("width",(t.contactmapWidth*parseFloat(i)).toString()+"px")}else if(0==n.indexOf("alignerrormap scale")){let e=n.lastIndexOf(" "),i=n.substr(e+1);$("#"+s.alignerrormapid+"_scale").val(i),$("#"+s.alignerrormapid).attr("width",(t.alignerrormapWidth*parseFloat(i)).toString()+"px")}else if(0==n.indexOf("graph force")){let e=n.lastIndexOf(" ");s.htmlCls.force=parseInt(n.substr(e+1)),$("#"+s.svgid+"_force").val(s.htmlCls.force),t.getGraphCls.handleForce()}else if(0==n.indexOf("hide edges")){let e=n.lastIndexOf(" ");s.htmlCls.hideedges=parseInt(n.substr(e+1)),$("#"+s.svgid+"_hideedges").val(s.htmlCls.hideedges),s.htmlCls.hideedges?(s.htmlCls.contactInsideColor="FFF",s.htmlCls.hbondInsideColor="FFF",s.htmlCls.ionicInsideColor="FFF"):(s.htmlCls.contactInsideColor="DDD",s.htmlCls.hbondInsideColor="AFA",s.htmlCls.ionicInsideColor="8FF"),void 0!==t.graphStr&&t.bRender&&s.htmlCls.force&&t.drawGraphCls.drawGraph(t.graphStr,t.pre+"dl_graph")}else if(0==n.indexOf("reset interaction pairs"))t.viewInterPairsCls.resetInteractionPairs();else if(0==n.indexOf("side by side")){let e=n.split(" | ")[1],t="_blank";window.open(e,t)}else if(0==i.indexOf("your note")){let e=i.split(" | ");t.yournote=e[1],$("#"+t.pre+"yournote").val(t.yournote),s.cfg.shownote&&(document.title=t.yournote)}else if(0==n.indexOf("cross structure interaction"))t.crossstrucinter=parseInt(n.substr(n.lastIndexOf(" ")+1)),$("#"+t.pre+"crossstrucinter").val(t.crossstrucinter);else if("replay on"==n)await t.resizeCanvasCls.replayon();else if("replay off"==n)await t.resizeCanvasCls.replayoff();else if(0==n.indexOf("contact map")){let e=n.split(" | ");if(3===e.length){let s=parseFloat(e[1].split(" ")[1]),i=e[2].split(" ")[1];await t.contactMapCls.contactMap(s,i)}}else if(0==n.indexOf("pickatom")){let e=parseInt(n.substr(n.lastIndexOf(" ")+1));t.pAtom=t.atoms[e],t.pickingCls.showPicking(t.pAtom)}else if(0==i.indexOf("set color spectrum")){let e=i.split(" | ");if(2==e.length){let s=e[1].split(","),i=!0;t.setColorCls.setColorAcrossSets(s,i)}}else if(0==i.indexOf("set residues color spectrum")){let e=i.split(" | ");if(2==e.length){let s=e[1].split(","),i=!0;t.setColorCls.setColorBySets(s,i)}}else if(0==i.indexOf("set color rainbow")){let e=i.split(" | ");if(2==e.length){let s=e[1].split(","),i=!1;t.setColorCls.setColorAcrossSets(s,i)}}else if(0==i.indexOf("set residues color rainbow")){let e=i.split(" | ");if(2==e.length){let s=e[1].split(","),i=!1;t.setColorCls.setColorBySets(s,i)}}else if(0==i.indexOf("color")){let e=i.split(" | "),n=e[0].substr(e[0].indexOf(" ")+1);if(t.opts.color=n,"residue custom"==n&&2==e.length){t.customResidueColors=JSON.parse(e[1]);for(let e in t.customResidueColors)t.customResidueColors[e.toUpperCase()]=s.parasCls.thr("#"+t.customResidueColors[e])}else if("align custom"==n&&3==e.length){let s=e[1],i=e[2].split(", ");t.queryresi2score={},t.queryresi2score[s]={};for(let e=0,n=i.length;e=4?this.setQueryresi2score(e):"area"==n&&2==e.length&&(t.midpercent=e[1],$("#"+t.pre+"midpercent").val(t.midpercent));t.setColorCls.setColorByOptions(t.opts,t.hAtoms),t.hlUpdateCls.updateHlAll(),t.getGraphCls.updateGraphColor()}else if(0==i.indexOf("remove legend"))$("#"+s.pre+"legend").hide();else if(0==i.indexOf("custom tube")){let e=i.split(" | ");this.setQueryresi2score(e),t.setOptionCls.setStyle("proteins","custom tube")}else if(0==n.indexOf("style")){let e=n.substr(n.indexOf(" ")+1),s=e.substr(0,e.indexOf(" ")),i=e.substr(e.indexOf(" ")+1);t.setOptionCls.setStyle(s,i)}else if(0==n.indexOf("window")){let e=n.substr(n.indexOf(" ")+1);setTimeout((function(){"aligned sequences"==e?s.htmlCls.dialogCls.openDlg("dl_alignment","Select residues in aligned sequences"):"interaction table"==e?s.htmlCls.dialogCls.openDlg("dl_allinteraction","Show interactions"):"interaction graph"==e?s.htmlCls.dialogCls.openDlg("dl_linegraph","Show interactions between two lines of residue nodes"):"interaction scatterplot"==e?s.htmlCls.dialogCls.openDlg("dl_scatterplot","Show interactions as scatterplot"):"force-directed graph"==e&&s.htmlCls.dialogCls.openDlg("dl_graph","Force-directed graph")}),1e3)}else if(0==n.indexOf("set theme")){let e=n.substr(n.lastIndexOf(" ")+1);s.htmlCls.setMenuCls.setTheme(e)}else if(0==n.indexOf("set double color")){let e=n.substr(n.lastIndexOf(" ")+1);"on"==e?(t.bDoublecolor=!0,t.setOptionCls.setStyle("proteins","ribbon")):"off"==e&&(t.bDoublecolor=!1)}else if(0==n.indexOf("adjust dialog")){let e=n.substr(n.lastIndexOf(" ")+1);t.scapCls.adjust2DWidth(e)}else if(0==n.indexOf("glycans cartoon")){let e=n.substr(n.lastIndexOf(" ")+1);t.bGlycansCartoon="yes"==e}else if(0==n.indexOf("save html")){let e=n.substr(n.lastIndexOf(" ")+1);s.htmlCls.eventsCls.saveHtml(e)}else if(0==n.indexOf("resdef"))s.cfg.resdef=n.substr(n.indexOf(" ")+1);else if(0==n.indexOf("vast_search_chainid")){t.chainidArray=i.substr(i.indexOf(" ")+1).split(",");let e=!0,s=!0;await t.realignParserCls.realignChainOnSeqAlign(void 0,t.chainidArray,e,s)}else if(0==n.indexOf("ig refnum off"))await t.refnumCls.hideIgRefNum();else if(0==n.indexOf("custom refnum")){let e=i.split(" | ")[1].replace(/\\n/g,"\n");await t.refnumCls.parseCustomRefFile(e)}else if(0==n.indexOf("show ref number"))t.bShownRefnum=!0;else if(0==n.indexOf("hide ref number"))t.bShownRefnum=!1;else if(-1!==n.indexOf("select displayed set"))t.hAtoms=s.hashUtilsCls.cloneHash(t.viewSelectionAtoms),t.hlUpdateCls.updateHlAll();else if(-1!==n.indexOf("select prop")){let e,s,n=i.split(" | "),l=n[0].substr("select prop".length+1);if(2==n.length){let t=n[1].split("_");e=t[0],s=t[1]}t.resid2specCls.selectProperty(l,e,s)}else if(-1!==n.indexOf("select each residue"))t.selectionCls.saveEachResiInSel();else if(0==n.indexOf("select")&&-1!==n.indexOf("name")){let e=i.split(" | "),s="",n="",l="";for(let t=0,i=e.length;t1&&(n=e[1].substr(e[1].indexOf(" ")+1)),e.length>2&&(l=e[2].substr(e[2].indexOf(" ")+1)),-1!==s.indexOf(" or ")?await t.selByCommCls.selectByCommand(s,n,l):await t.selByCommCls.selectBySpec(s,n,l)}s.htmlCls.clickMenuCls.setLogCmd(i,!1),t.bAddCommands=!0}setStrengthPara(e){let t=this.icn3d;if(t.icn3dui,e.length>=5){let s=e[4].split(" ");s.length>=4&&($("#"+t.pre+"hbondthreshold").val(s[1]),$("#"+t.pre+"saltbridgethreshold").val(s[2]),$("#"+t.pre+"contactthreshold").val(s[3]),s.length>=7&&($("#"+t.pre+"halogenthreshold").val(s[4]),$("#"+t.pre+"picationthreshold").val(s[5]),$("#"+t.pre+"pistackingthreshold").val(s[6])))}if(6==e.length){let s=e[5].split(" 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e=parseInt(n[0]),s=0;e<=parseInt(n[1]);++e,++s)"_"!=l[s]&&(t.queryresi2score[i][e]=11.11111111111111*parseInt(l[s]));if(e.length>4){let i=e[4].split(" ");t.startColor=i[1],t.midColor=i[2],t.endColor=i[3];let n=s.htmlCls.clickMenuCls.setLegendHtml();$("#"+s.pre+"dl_legend_html").html(n),s.htmlCls.dialogCls.openDlg("dl_legend","Color Range")}}addShape(e,t){let s=this.icn3d,i=s.icn3dui;s.shapeCmdHash[e]=1;let n=e.split(" | "),l=n[1].split(" "),r=n[2].substr(n[2].lastIndexOf(" ")+1),o=n[3].substr(n[3].lastIndexOf(" ")+1),a=n[4].substr(n[4].lastIndexOf(" ")+1);r="#"+r.replace(/\#/g,"");let d=i.parasCls.thr(r),c=new THREE.Vector3(parseFloat(l[1]),parseFloat(l[3]),parseFloat(l[5]));"sphere"==t?s.sphereCls.createSphereBase(c,d,parseFloat(a),void 0,void 0,void 0,parseFloat(o)):s.boxCls.createBox_base(c,parseFloat(a),d,void 0,void 0,void 0,parseFloat(o))}getMenuFromCmd(e){this.icn3d.icn3dui;let t="Windows > View Sequences & Annotations",s="Analysis > Interactions",i=s+" > 2D Graph(Force-Directed)",n="View > Rotate > Auto Rotation > Rotate ",l="View > Rotate > Rotate 90 deg > ",r="Select > Select on 3D > ",o="Analysis > Label > ",a="File > 3D Printing > ";return 0==(e=e.trim()).indexOf("load")?"File > Retrieve by ID, Align":0==e.indexOf("set map")&&-1==e.indexOf("set map wireframe")?"Style > Electron Density":0==e.indexOf("set emmap")&&-1==e.indexOf("set emmap wireframe")?"Style > EM Density Map":0==e.indexOf("set phi")?"Analysis > Load Potential > URL(CORS) Phi/Cube":0==e.indexOf("set delphi")?"Analysis > DelPhi Potential":0==e.indexOf("setoption map")?"Style > Remove Map":0==e.indexOf("setoption emmap")?"Style > Remove EM Map":0==e.indexOf("view annotations")?t:0==e.indexOf("set annotation all")?t+': "All" checkbox':0==e.indexOf("set annotation clinvar")?t+': "ClinVar" checkbox':0==e.indexOf("set annotation snp")?t+': "SNP" checkbox':0==e.indexOf("set annotation 3ddomain")?t+': "3D Domains" checkbox':0==e.indexOf("view interactions")?"Windows > View 2D Diagram":0==e.indexOf("symmetry")?"Analysis > Symmetry":0==e.indexOf("realign on seq align")?"File > Realign Selection > on Sequence Alignment":0==e.indexOf("realign")?"File > Realign Selection > Residue by Residue":0==e.indexOf("graph interaction pairs")?s+" > 2D Graph(Force-Directed)":0==e.indexOf("export canvas")?"File > Save File > iCn3D PNG Image":"export stl file"==e?a+"STL":"export vrml file"==e?a+"VRML(Color)":"export stl stabilizer file"==e?a+"STL W/ Stabilizers":"export vrml stabilizer file"==e?a+"VRML(Color, W/ Stabilizers)":"select all"==e?'Select > All; or Toggle to "All"(next to "Help")':"show all"==e?"View > View Full Structure":"select complement"==e?"Select > Inverse":"set pk atom"==e?r+"Atom":"set pk residue"==e?r+"Residue":"set pk strand"==e?r+"Strand/Helix":"set pk domain"==e?r+"3D Domain":"set pk chain"==e?r+"Chain":"set surface wireframe on"==e?"Style > Surface Wireframe > Yes":"set surface wireframe off"==e?"Style > Surface Wireframe > No":"set map wireframe on"==e?"Style > Map Wireframe > Yes":"set map wireframe off"==e?"Style > Map Wireframe > No":"set emmap wireframe on"==e?"Style > EM Map Wireframe > Yes":"set emmap wireframe off"==e?"Style > EM Map Wireframe > No":"set surface neighbors on"==e?"Style > Surface Type > ... with Context":"set axis on"==e?"View > XYZ-axes > Show":"set axis off"==e?"View > XYZ-axes > Hide":"set fog on"==e?"View > Fog for Selection > On":"set fog off"==e?"View > Fog for Selection > Off":"set slab on"==e?"View > Slab for Selection > On":"set slab off"==e?"View > Slab for Selection > Off":"set assembly on"==e?"Analysis > Assembly > Biological Assembly":"set assembly off"==e?"Analysis > Assembly > Asymmetric Unit":"set chemicalbinding show"==e?"Analysis > Chem. Binding > Show":"set chemicalbinding hide"==e?"Analysis > Chem. Binding > Hide":"set hbonds off"==e||"set salt bridge off"==e||"set contact off"==e||"set halogen pi off"==e?s+" > Reset":"hydrogens"==e?"Style > Hydrogens > Show":"set hydrogens off"==e?"Style > Hydrogens > Hide":"set stabilizer off"==e?"File > 3D Printing > Remove All Stabilizers":"set disulfide bonds off"==e?"Analysis > Disulfide Bonds > Hide":"set cross linkage off"==e?"Analysis > Cross-Linkages > Hide":"set lines off"==e?"Analysis > Distance > Hide":"set labels off"==e?"Analysis > Label > Remove":"set mode all"==e?'Toggle to "All"(next to "Help")':"set mode selection"==e?'Toggle to "Selection"(next to "Help")':"set view detailed view"==e?t+': "Details" tab':"set view overview"==e?t+': "Summary" tab':"set annotation custom"==e?t+': "Custom" checkbox':"set annotation interaction"==e?t+': "Interactions" checkbox':"set annotation ptm"==e?t+': "PTM" checkbox':"set annotation cdd"==e?t+': "Conserved Domains" checkbox':"set annotation site"==e?t+': "Functional Sites" checkbox':"set annotation ssbond"==e?t+': "Disulfide Bonds" checkbox':"set annotation crosslink"==e?t+': "Cross-Linkages" checkbox':"set annotation transmembrane"==e?t+': "Transmembrane" checkbox':"highlight level up"==e?"Keyboard Arrow Up":"highlight level down"==e?"Keyboard Arrow Down":0==e.indexOf("hide annotation")?t+": checkboxes off":"add residue labels"==e?o+"per Residue":"add residue number labels"==e?o+"per Residue & Number":"add atom labels"==e?o+"per Atom":"add chain labels"==e?o+"per Chain":"add terminal labels"==e?o+"N- & C- Termini":"rotate left"==e?n+"Left; or Key l":"rotate right"==e?n+"Right; or Key j":"rotate up"==e?n+"Up; or Key i":"rotate down"==e?n+"Down; or Key m":"rotate x"==e?l+"X-axis":"rotate y"==e?l+"Y-axis":"rotate z"==e?l+"Z-axis":"reset"==e?"View > Reset > All":"reset orientation"==e?"View > Reset > Orientation":"clear selection"==e?"Select > Clear Selection":"zoom selection"==e?"Select > Zoom in Selection":"center selection"==e?"Select > Center Selection":"show selection"==e?"Select > View Only Selection":"hide selection"==e?"Select > Hide Selection":"output selection"==e?"Select > Clear Selection":"toggle highlight"==e?"Select > Toggle Highlight":"stabilizer"==e?"File > 3D Printing > Add all Stabilizers":"disulfide bonds"==e?"Analysis > Disulfide Bonds > Show":"cross linkage"==e?"Analysis > Cross-Linkages > Show":"back"==e?"View > Undo":"forward"==e?"View > Redo":"clear all"==e?"Select > Clear Selection":"defined sets"==e?"Windows > Defined Sets":"delete selected sets"==e?'Windows > Defined Sets: "Delete Selected Sets" button':"view interactions"==e?"Windows > View Interactions":"show annotations all chains"==e?t+': "Show All Chains" button':"save color"==e?"Color > Save Color":"apply saved color"==e?"Color > Apply Saved Color":"save style"==e?"Style > Save Style":"apply saved style"==e?"Style > Apply Saved Style":"select main chains"==e?"Select > Main Chains":"select side chains"==e?"Select > Side Chains":"select main side chains"==e?"Select > Main & Side Chains":"area"==e?"View > Surface Area":"table inter count only"==e?s+': "Set 1" button: "Show Count Only" button':"table inter details"==e?s+': "Set 1" button: "Show Details" button':0==e.indexOf("define helix sets")?t+': "Helix Sets" button':0==e.indexOf("define sheet sets")?t+': "Sheet Sets" button':0==e.indexOf("define coil sets")?t+': "Coil Sets" button':0==e.indexOf("select interaction")?"Windows > View 2D Diagram: click on edges":0==e.indexOf("select saved atoms")||0==e.indexOf("select sets")?"Windows > Defined Sets: select in menu":-1!==e.indexOf("select chain")?t+": click on chain names":-1!==e.indexOf("select alignChain")?"Windows > View Aligned Sequences: click on chain names":0==e.indexOf("select zone cutoff")?"Select > by Distance":0==e.indexOf("set surface opacity")?"Style > Surface Opacity":0==e.indexOf("set label scale")?"View > Label Scale":0==e.indexOf("set surface")?"Style > Surface Type":0==e.indexOf("set camera")?"View > Camera":0==e.indexOf("set background")?"Style > Background":0==e.indexOf("set thickness")?"File > 3D Printing > Set Thickness":0==e.indexOf("set highlight color")?"Select > Highlight Color":0==e.indexOf("set highlight style")?"Select > Highlight Style":0==e.indexOf("add line")||0==e.indexOf("add label")?"Analysis > Distance > between Two Atoms":0==e.indexOf("dist")?"Analysis > Distance > between Two Sets":0==e.indexOf("msa")?t+': "Add Track" button: "FASTA Alignment" button':0==e.indexOf("add track")?t+': "Add Track" button':0==e.indexOf("remove one stabilizer")?"File > 3D Printing > Remove One Stablizer":0==e.indexOf("add one stabilizer")?"File > 3D Printing > Add One Stablizer":0==e.indexOf("select planes z-axis")?"View > Select between Two X-Y Planes":0==e.indexOf("adjust membrane z-axis")?"View > Adjust Membrane":0==e.indexOf("toggle membrane")?"View > Toggle Membrane":0==e.indexOf("calc buried surface")?s+': "Buried Surface Area" button':0==e.indexOf("display interaction 3d")?s+': "3D Display Interactions" button':0==e.indexOf("view interaction pairs")?s+': "Highlight Interactions in Table" button':0==e.indexOf("save1 interaction pairs")?s+': "Set 1" button':0==e.indexOf("save2 interaction pairs")?s+': "Set 2" button':0==e.indexOf("line graph interaction pairs")?s+': "2D Interaction Network" button':0==e.indexOf("scatterplot interaction pairs")?s+': "2D Interaction Map" button':0==e.indexOf("graph label")?i+': "Label Size" menu':0==e.indexOf("graph force")?i+': "Force on Nodes" menu':0==e.indexOf("hide edges")?i+': "Internal Edges" menu':0==e.indexOf("reset interaction pairs")?s+" > Reset":0==e.indexOf("side by side")?"View > Side by Side":0==e.indexOf("your note")?"Windows > Your Notes / Window Title":0==e.indexOf("pickatom")?"Hold Alt key and click on 3D structure":0==e.indexOf("color")?"Color menu":0==e.indexOf("custom tube")?t+': "Custom Color/Tube" button: "Custom Tube" button':0==e.indexOf("style")?"Style menu":-1!==e.indexOf("select displayed set")?"Select > Displayed Set":-1!==e.indexOf("select prop")?"Select > by Property":0==e.indexOf("select")&&-1!==e.indexOf("name")?t+": drag on residues to select":-1!==e.indexOf("select $")||-1!==e.indexOf("select .")||-1!==e.indexOf("select :")||-1!==e.indexOf("select @")?"Select > Advanced; or other selection":-1!==e.indexOf("replay on")?"File > Replay Each Step > On":-1!==e.indexOf("replay off")?"File > Replay Each Step > Off":-1!==e.indexOf("set theme")?"Style > Theme Color":-1!==e.indexOf("set double color")?"Style > Two-color Helix":""}}class as{constructor(e){this.icn3d=e}setProtNuclLigInMenu(){let e=this.icn3d;if(e.icn3dui,Object.keys(e.proteins).length>0&&(e.defNames2Residues.proteins=Object.keys(e.firstAtomObjCls.getResiduesFromAtoms(e.proteins)),e.defNames2Descr.proteins="proteins",e.defNames2Command.proteins="select :proteins"),Object.keys(e.nucleotides).length>0&&(e.defNames2Residues.nucleotides=Object.keys(e.firstAtomObjCls.getResiduesFromAtoms(e.nucleotides)),e.defNames2Descr.nucleotides="nucleotides",e.defNames2Command.nucleotides="select :nucleotides"),Object.keys(e.chemicals).length>0)if(e.bOpm){let t={},s={};for(let i in e.chemicals){let n=e.atoms[i],l=n.structure+"_"+n.chain+"_"+n.resi;"DUM"===n.resn?s[l]=1:t[l]=1}Object.keys(t).length>0&&(e.defNames2Residues.chemicals=Object.keys(t),e.defNames2Descr.chemicals="chemicals",e.defNames2Command.chemicals="select :chemicals"),Object.keys(s).length>0&&(e.defNames2Residues.membrane=Object.keys(s),e.defNames2Descr.membrane="membrane",e.defNames2Command.membrane="select :membrane")}else e.defNames2Residues.chemicals=Object.keys(e.firstAtomObjCls.getResiduesFromAtoms(e.chemicals)),e.defNames2Descr.chemicals="chemicals",e.defNames2Command.chemicals="select :chemicals";Object.keys(e.ions).length>0&&(e.defNames2Residues.ions=Object.keys(e.firstAtomObjCls.getResiduesFromAtoms(e.ions)),e.defNames2Descr.ions="ions",e.defNames2Command.ions="select :ions"),Object.keys(e.water).length>0&&(e.defNames2Residues.water=Object.keys(e.firstAtomObjCls.getResiduesFromAtoms(e.water)),e.defNames2Descr.water="water",e.defNames2Command.water="select :water"),this.setTransmemInMenu(e.halfBilayerSize,-e.halfBilayerSize)}setPredefinedInMenu(){let e=this.icn3d,t=e.icn3dui;if(this.setChainsInMenu(),this.setProtNuclLigInMenu(),void 0!==t.cfg.mmdbid||void 0!==t.cfg.gi||void 0!==t.cfg.chainalign||void 0!==t.cfg.mmdbafid)for(let t in e.tddomains)e.selectionCls.selectResidueList(e.tddomains[t],t,t,!1,!1);if((void 0!==t.cfg.align||void 0!==t.cfg.chainalign&&2==e.chainidArray.length)&&e.bFullUi){e.selectionCls.selectResidueList(e.consHash1,e.conservedName1,e.conservedName1,!1,!1),e.selectionCls.selectResidueList(e.consHash2,e.conservedName2,e.conservedName2,!1,!1),e.selectionCls.selectResidueList(e.nconsHash1,e.nonConservedName1,e.nonConservedName1,!1,!1),e.selectionCls.selectResidueList(e.nconsHash2,e.nonConservedName2,e.nonConservedName2,!1,!1),e.selectionCls.selectResidueList(e.nalignHash1,e.notAlignedName1,e.notAlignedName1,!1,!1),e.selectionCls.selectResidueList(e.nalignHash2,e.notAlignedName2,e.notAlignedName2,!1,!1);let s={};for(let i in e.alnChains)s=t.hashUtilsCls.unionHash(s,e.alnChains[i]);let i=e.firstAtomObjCls.getResiduesFromAtoms(s),n="protein_aligned",l="aligned protein and nucleotides",r="select "+e.resid2specCls.residueids2spec(Object.keys(i));e.selectionCls.addCustomSelection(Object.keys(i),n,l,r,!0)}}setAtomMenu(e){let t=this.icn3d;t.icn3dui;let s="",i=void 0!==t.defNames2Residues?Object.keys(t.defNames2Residues):[],n=void 0!==t.defNames2Atoms?Object.keys(t.defNames2Atoms):[],l=i.concat(n).sort(),r=[];l.forEach((e=>{-1===$.inArray(e,r)&&r.push(e)}));for(let i=0,n=r.length;i0&&(n=t.atoms[e[0]])}else if(void 0!==t.defNames2Residues&&t.defNames2Residues.hasOwnProperty(o)){let e=t.defNames2Residues[o];e.length>0&&(l=t.residues[e[0]],l&&(n=t.atoms[Object.keys(l)[0]]))}let a=void 0===n||void 0===n.color||"FFFFFF"===n.color.getHexString().toUpperCase()?"DDDDDD":n.color.getHexString(),d=void 0!==n&&void 0!==n.color?a:"000000";-1!=e.indexOf(o)?s+=""+o+" ":s+=""+o+" "}return s}setChainsInMenu(){let e=this.icn3d;e.icn3dui;for(let t in e.chains)if(e.chainsSeq[t]&&e.chainsSeq[t].length>1){e.defNames2Residues[t]=Object.keys(e.firstAtomObjCls.getResiduesFromAtoms(e.chains[t])),e.defNames2Descr[t]=t;let s=t.indexOf("_"),i=t.substr(0,s),n=t.substr(s+1);e.defNames2Command[t]="select $"+i+"."+n}if(1==Object.keys(e.structures)){let t=Object.keys(e.structures)[0];e.defNames2Residues[t]=Object.keys(e.residues),e.defNames2Descr[t]=t,e.defNames2Command[t]="select $"+t}else{let t=Object.keys(e.residues),s={};for(let e=0,i=t.length;ee?l[a]=1:o.coord.z0&&(i.defNames2Residues["transmembrane"+o]=Object.keys(n),i.defNames2Descr["transmembrane"+o]="transmembrane"+o,i.defNames2Command["transmembrane"+o]="select :transmembrane"+o),Object.keys(l).length>0&&(i.defNames2Residues["extracellular"+o]=Object.keys(l),i.defNames2Descr["extracellular"+o]="extracellular"+o,i.defNames2Command["extracellular"+o]="select :extracellular"+o),Object.keys(r).length>0&&(i.defNames2Residues["intracellular"+o]=Object.keys(r),i.defNames2Descr["intracellular"+o]="intracellular"+o,i.defNames2Command["intracellular"+o]="select :intracellular"+o)}}showSets(){let e=this.icn3d,t=e.icn3dui;t.bNode||(t.htmlCls.dialogCls.openDlg("dl_definedsets","Select sets"),$("#"+e.pre+"dl_setsmenu").show(),$("#"+e.pre+"dl_setoperations").show(),$("#"+e.pre+"dl_command").hide(),$("#"+e.pre+"atomsCustom").resizable());let s=t.hashUtilsCls.cloneHash(e.hAtoms),i=t.hashUtilsCls.cloneHash(e.dAtoms);void 0!==e.bSetChainsAdvancedMenu&&e.bSetChainsAdvancedMenu&&!e.bResetSets||(this.setPredefinedInMenu(),e.bSetChainsAdvancedMenu=!0),e.hAtoms=t.hashUtilsCls.cloneHash(s),e.dAtoms=t.hashUtilsCls.cloneHash(i),e.hlUpdateCls.updateHlMenus()}clickCustomAtoms(){let e=this.icn3d,t=e.icn3dui,s=this;$("#"+e.pre+"atomsCustom").change((function(e){let i=s.icn3d,n=$(this).val();if(i.nameArray=n,null!==n){let e=!1;s.changeCustomAtoms(n,e),t.htmlCls.clickMenuCls.setLogCmd("select sets "+n.join(" "+i.setOperation+" "),!0),i.bSelectResidue=!1}})),t.myEventCls.onIds("#"+e.pre+"atomsCustom","focus",(function(e){let i=s.icn3d;t.utilsCls.isMobile()&&$("#"+i.pre+"atomsCustom").val("")}))}deleteSelectedSets(){let e=this.icn3d;e.icn3dui;let t=$("#"+e.pre+"atomsCustom").val();for(let s=0;s0)for(let n=0,l=t.defNames2Residues[e].length;n0)for(let s=0,n=t.defNames2Atoms[e].length;s0&&(n[0]=i.commands[0]);let l=e.trim().split("\n");i.commands=l;let r=l[0].indexOf("command=");if(t&&-1!=r){let e=l[0].substr(0,r-1);i.commands.splice(0,1,e)}i.STATENUMBER=i.commands.length,i.commands=n.concat(i.commands),i.STATENUMBER=i.commands.length,i.CURRENTNUMBER=0,i.bReplay?await this.replayFirstStep(i.CURRENTNUMBER):await this.execCommands(i.CURRENTNUMBER,i.STATENUMBER-1,i.STATENUMBER,s)}async execCommands(e,t,s,i){let n=this.icn3d;n.icn3dui,n.bRender=!1,i||n.reinitAfterLoad(),await this.execCommandsBase(e,t,s)}getNameArray(e){let t=this.icn3d;t.icn3dui;let s=e.split(" | "),i=[];return 2==s.length&&(i=s[1].split(","),t.hAtoms=t.definedSetsCls.getAtomsFromNameArray(i)),i}async execCommandsBase(e,t,s,i){let n,l=this.icn3d,r=l.icn3dui,o=this;for(n=e;n<=t;++n){let i=n===s-1;if(!l.commands[n].trim())continue;if(0==Object.keys(l.atoms).length&&-1==l.commands[n].indexOf("load"))continue;let a=l.commands[n].split("|||"),d=a[0].trim();if(l.inputid&&(l.bNotLoadStructure=!0),-1!==d.indexOf("load")){if(0===t&&e===t)return void(l.bNotLoadStructure?(l.hAtoms=r.hashUtilsCls.cloneHash(l.atoms),1===l.commands.length&&(l.bAddCommands=!0),i&&this.renderFinalStep(s)):(await o.applyCommandLoad(l.commands[n]),1===l.commands.length&&(l.bAddCommands=!0),i&&o.renderFinalStep(s)));l.bNotLoadStructure?(l.hAtoms=r.hashUtilsCls.cloneHash(l.atoms),l.backForward&&this.renderFinalStep(1)):(await o.applyCommandLoad(l.commands[n]),l.backForward&&o.renderFinalStep(1))}else if(0==d.indexOf("set map")&&-1==d.indexOf("set map wireframe")){let e=a[0].trim().split(" | ")[0].substr(8).split(" ");3==e.length&&"sigma"==e[1]&&(e[2],e[0],await o.applyCommandMap(a[0].trim()))}else if(0==d.indexOf("set emmap")&&-1==d.indexOf("set emmap wireframe")){let e=a[0].trim().substr(10).split(" ");2==e.length&&"percentage"==e[0]&&(e[1],await o.applyCommandEmmap(a[0].trim()))}else if(0==d.indexOf("set phi"))await l.delphiCls.applyCommandPhi(a[0].trim());else if(0==d.indexOf("set delphi"))await l.delphiCls.applyCommandDelphi(a[0].trim());else if(0==d.indexOf("view annotations"))Object.keys(l.proteins).length>0&&await o.applyCommandAnnotationsAndCddSite(a[0].trim());else if(0==d.indexOf("set annotation clinvar"))Object.keys(l.proteins).length>0&&await o.applyCommandClinvar(a[0].trim());else if(0==d.indexOf("set annotation snp"))Object.keys(l.proteins).length>0&&await o.applyCommandSnp(a[0].trim());else if(0==d.indexOf("set annotation ptm"))Object.keys(l.proteins).length>0&&await o.applyCommandPTM(a[0].trim());else if(0==d.indexOf("ig refnum on"))await l.refnumCls.showIgRefNum();else if(0==d.indexOf("ig template")){let e=d.substr(d.lastIndexOf(" ")+1);await l.refnumCls.showIgRefNum(e)}else if(0==d.indexOf("set annotation 3ddomain"))Object.keys(l.proteins).length>0&&o.applyCommand3ddomain(a[0].trim());else if(0==d.indexOf("set annotation all"))Object.keys(l.proteins).length>0&&(await o.applyCommandClinvar(a[0].trim()),await o.applyCommandSnp(a[0].trim()),o.applyCommand3ddomain(a[0].trim())),await l.annotationCls.setAnnoTabAll();else if(0==d.indexOf("view interactions")&&void 0!==r.cfg.align)await o.applyCommandViewinteraction(a[0].trim());else if(0==d.indexOf("symmetry")){l.bAxisOnly=!1;let e=d.substr(d.indexOf(" ")+1);l.symmetrytitle="none"===e?void 0:e,"none"!==e&&await l.symdCls.retrieveSymmetry(Object.keys(l.structures)[0]),l.drawCls.draw()}else if(0==d.indexOf("symd symmetry"))l.bAxisOnly=!1,await l.symdCls.applyCommandSymd(d),l.drawCls.draw();else if(0==d.indexOf("scap"))await l.scapCls.applyCommandScap(d);else if(0==d.indexOf("realign on seq align"))this.getNameArray(d),await o.applyCommandRealign(d);else if(0==d.indexOf("realign on structure align msa")){let e=this.getNameArray(d);r.cfg.aligntool="vast",await l.realignParserCls.realignOnStructAlignMsa(e)}else if(0==d.indexOf("realign on structure align"))this.getNameArray(d),r.cfg.aligntool="vast",await l.realignParserCls.realignOnStructAlign();else if(0==d.indexOf("realign on tmalign msa")){let e=this.getNameArray(d);r.cfg.aligntool="tmalign",await l.realignParserCls.realignOnStructAlignMsa(e)}else if(0==d.indexOf("realign on tmalign"))this.getNameArray(d),r.cfg.aligntool="tmalign",await l.realignParserCls.realignOnStructAlign();else if(0==d.indexOf("realign on vastplus"))o.getHAtoms(l.commands[n]),await l.vastplusCls.realignOnVastplus();else if(0==d.indexOf("graph interaction pairs"))await o.applyCommandGraphinteraction(d);else if(0==d.indexOf("cartoon 2d domain"))await o.applyCommandCartoon2d(d);else if(0==d.indexOf("set half pae map"))await o.applyCommandAfmap(d);else if(0==d.indexOf("set full pae map"))await o.applyCommandAfmap(d,!0);else if(0==d.indexOf("export pqr"))await r.htmlCls.setHtmlCls.exportPqr();else if(0==d.indexOf("cartoon 2d chain")||0==d.indexOf("cartoon 2d secondary")){let e=d.lastIndexOf(" "),t=d.substr(e+1);await l.cartoon2dCls.draw2Dcartoon(t)}else if(0==d.indexOf("add msa track")){let e=d.split(" | "),t=e[1].substr(8),s=e[2].substr(9),i=e[3].substr(5),n=e[4].substr(10);$("#"+l.pre+"anno_custom")[0]&&($("#"+l.pre+"anno_custom")[0].checked=!0),$("[id^="+l.pre+"custom]").show(),await l.addTrackCls.addMsaTracks(t,s,i,n)}else if(0==d.indexOf("add exon track")){let e=d.split(" | "),t=e[1].substr(8),s=e[2].substr(7),i=e[3].substr(9),n=e[4].substr(5);$("#"+l.pre+"anno_custom")[0]&&($("#"+l.pre+"anno_custom")[0].checked=!0),$("[id^="+l.pre+"custom]").show(),await l.addTrackCls.addExonTracks(t,s,i,n)}else await l.applyCommandCls.applyCommand(l.commands[n])}(n===s||i)&&this.renderFinalStep(n)}pressCommandtext(){let e=this.icn3d,t=e.icn3dui,s=this;$("#"+e.pre+"logtext").keypress((async function(e){let i=s.icn3d;if(i.bAddLogs=!1,13==(e.keyCode?e.keyCode:e.which)){e.preventDefault();let n=$(this).val();i.bRender=!0;let l=n.split("\n"),r=i.logs.length;for(let e=r,n=l.length;e "+i.logs.join("\n> ")+"\n> ").scrollTop($("#"+i.pre+"logtext")[0].scrollHeight)}i.bAddLogs=!0}))}async applyCommandLoad(e){let t=this.icn3d,s=t.icn3dui;t.bAddCommands=!1;let i=e.split("|||")[0].replace(/\s\s/g," ").trim();if(-1!==i.indexOf("load")){let e=i.split(" | "),n=e[0];if(e.length>1){let t=e[e.length-1].indexOf(" ");s.cfg.inpara=e[e.length-1].substr(t+1),"undefined"===s.cfg.inpara&&(s.cfg.inpara="")}let l=n.substr(n.lastIndexOf(" ")+1);if(4==l.length&&(l=l.toUpperCase()),t.bInputPNGWithData||t.structures&&t.structures.hasOwnProperty(l))return;if(t.inputid=l,-1!==i.indexOf("load mmtf"))s.cfg.mmtfid=l,await t.mmtfParserCls.downloadMmtf(l);else if(-1!==i.indexOf("load pdb"))s.cfg.pdbid=l,await t.pdbParserCls.downloadPdb(l);else if(-1!==i.indexOf("load af"))s.cfg.afid=l,await t.pdbParserCls.downloadPdb(l,!0);else if(-1!==i.indexOf("load opm"))s.cfg.opmid=l,await t.opmParserCls.downloadOpm(l);else if(-1!==i.indexOf("load mmcif"))s.cfg.mmcifid=l,await t.mmcifParserCls.downloadMmcif(l);else if(-1!==i.indexOf("load mmdb ")||-1!==i.indexOf("load mmdb1 "))s.cfg.mmdbid=l,s.cfg.bu=1,await t.mmdbParserCls.downloadMmdb(l);else if(-1!==i.indexOf("load mmdb0"))s.cfg.mmdbid=l,s.cfg.bu=0,await t.mmdbParserCls.downloadMmdb(l);else if(-1!==i.indexOf("load mmdbaf1"))s.cfg.mmdbafid=l,s.cfg.bu=1,await t.chainalignParserCls.downloadMmdbAf(l);else if(-1!==i.indexOf("load mmdbaf0"))s.cfg.mmdbafid=l,s.cfg.bu=0,await t.chainalignParserCls.downloadMmdbAf(l);else if(-1!==i.indexOf("load gi"))s.cfg.gi=l,await t.mmdbParserCls.downloadGi(l);else if(-1!==i.indexOf("load refseq"))s.cfg.refseqid=l,await t.mmdbParserCls.downloadRefseq(l);else if(-1!==i.indexOf("load protein"))s.cfg.protein=l,await t.mmdbParserCls.downloadProteinname(l);else if(-1!==i.indexOf("load seq_struct_ids "))t.bSmithwm=!1,t.bLocalSmithwm=!1,await t.mmdbParserCls.downloadBlast_rep_id(l);else if(-1!==i.indexOf("load seq_struct_ids_smithwm "))t.bSmithwm=!0,await t.mmdbParserCls.downloadBlast_rep_id(l);else if(-1!==i.indexOf("load seq_struct_ids_local_smithwm "))t.bLocalSmithwm=!0,await t.mmdbParserCls.downloadBlast_rep_id(l);else if(-1!==i.indexOf("load cid"))s.cfg.cid=l,await t.sdfParserCls.downloadCid(l);else if(-1!==i.indexOf("load alignment"))if(s.cfg.align=l,s.cfg.inpara||-1==s.cfg.inpara.indexOf("atype=2"))await t.alignParserCls.downloadAlignment(s.cfg.align);else{let e=2;await t.chainalignParserCls.downloadMmdbAf(s.cfg.align,void 0,e)}else if(-1!==i.indexOf("load chainalignment")){let e=i.split(" | ");e.length>1&&-1!=e[1].indexOf("resnum")&&(s.cfg.resnum=e[1].substr(e[1].indexOf("resnum")+7)),e.length>2&&-1!=e[2].indexOf("resdef")&&(s.cfg.resdef=e[2].substr(e[1].indexOf("resdef")+7)),e.length>3&&-1!=e[3].indexOf("aligntool")&&(s.cfg.aligntool=e[3].substr(e[1].indexOf("aligntool")+10)),s.cfg.chainalign=l,await t.chainalignParserCls.downloadChainalignment(l,s.cfg.resnum,s.cfg.resdef)}else if(-1!==i.indexOf("load url")){let i=e[1],n=void 0!==i?i.indexOf("type "):-1,r="pdb";-1!==n&&(r=i.substr(n+5)),s.cfg.url=l,await t.pdbParserCls.downloadUrl(l,r)}}t.bAddCommands=!0}async applyCommandMap(e){let t=this.icn3d;t.icn3dui;let s=e.split(" | "),i=s[0].substr(8).split(" ");if(3==i.length&&"sigma"==i[1]){let e=i[2],n=i[0];2==s.length?await t.dsn6ParserCls.dsn6ParserBase(s[1],n,e):await t.dsn6ParserCls.dsn6Parser(t.inputid,n,e)}}async applyCommandEmmap(e){let t=this.icn3d;t.icn3dui;let s=e.substr(10).split(" ");if(2==s.length&&"percentage"==s[0]){let e=s[1],i="em";await t.densityCifParserCls.densityCifParser(t.inputid,i,e,t.emd)}}async applyCommandRealign(e){let t=this.icn3d;t.icn3dui,await t.realignParserCls.realignOnSeqAlign()}async applyCommandRealignByStruct(e){let t=this.icn3d;t.icn3dui,t.drawCls.draw(),await t.realignParserCls.realignOnStructAlign()}async applyCommandAfmap(e,t){let s=this.icn3d;s.icn3dui;let i=e.substr(e.lastIndexOf(" ")+1);await s.contactMapCls.afErrorMap(i,t)}async applyCommandGraphinteraction(e){let t=this.icn3d;t.icn3dui;let s=e.split(" | ");if(s.length>=3){let e,i=s[1].split(" "),n=i[0].split(","),l=i[1].split(","),r=-1!==s[2].indexOf("hbonds"),o=-1!==s[2].indexOf("salt bridge"),a=-1!==s[2].indexOf("interactions"),d=-1!==s[2].indexOf("halogen"),c=-1!==s[2].indexOf("pi-cation"),h=-1!==s[2].indexOf("pi-stacking");s.length>=4&&(e="true"==s[3]),t.applyCommandCls.setStrengthPara(s),await t.viewInterPairsCls.viewInteractionPairs(n,l,e,"graph",r,o,a,d,c,h)}}async applyCommandCartoon2d(e){let t=this.icn3d;t.icn3dui;let s=e.substr(e.lastIndexOf(" ")+1);await t.cartoon2dCls.draw2Dcartoon(s)}async applyCommandAnnotationsAndCddSite(e){let t=this.icn3d;t.icn3dui,"view annotations"==e&&await t.showAnnoCls.showAnnotations()}async applyCommandClinvar(e){let t=this.icn3d;t.icn3dui;let s=e.lastIndexOf(" ");e.substr(s+1),await t.annotationCls.setAnnoTabClinvar()}async applyCommandSnp(e){let t=this.icn3d;t.icn3dui;let s=e.lastIndexOf(" ");e.substr(s+1),await t.annotationCls.setAnnoTabSnp()}async applyCommandPTM(e){let t=this.icn3d;t.icn3dui;let s=e.lastIndexOf(" ");e.substr(s+1),await t.annotationCls.setAnnoTabPTM()}applyCommand3ddomain(e){let t=this.icn3d;t.icn3dui;let s=e.lastIndexOf(" "),i=e.substr(s+1);"3ddomain"!=i&&"all"!=i||t.annotationCls.setAnnoTab3ddomain()}async applyCommandViewinteraction(e){let t=this.icn3d,s=t.icn3dui;if(void 0!==s.cfg.align||void 0!==s.cfg.chainalign){let e=Object.keys(t.structures);await t.ParserUtilsCls.set2DDiagramsForAlign(e[0].toUpperCase(),e[1].toUpperCase())}}async renderFinalStep(e){let t=this.icn3d,s=t.icn3dui;t.bCommandLoad=!1,t.ParserUtilsCls.hideLoading(),e+1===t.commands.length&&(t.bAddCommands=!0),t.bRender=!0;let i=t.commands[e-1]?t.commands[e-1].split("|||"):[];if(2==i.length){let e=JSON.parse(i[1]);t._zoomFactor=e.factor,t.mouseChange.x=e.mouseChange.x,t.mouseChange.y=e.mouseChange.y,t.quaternion._x=e.quaternion._x,t.quaternion._y=e.quaternion._y,t.quaternion._z=e.quaternion._z,t.quaternion._w=e.quaternion._w}if(t.selectionCls.oneStructurePerWindow(),1===e||t.hAtoms&&t.atoms&&Object.keys(t.hAtoms).length===Object.keys(t.atoms).length||void 0!==t.optsHistory[e-1]&&t.optsHistory[e-1].hasOwnProperty("hlatomcount")&&t.optsHistory[e-1].hlatomcount===Object.keys(t.atoms).length)if(t.optsHistory.length>=e){let s=t.optsHistory[e-1].pk;"no"===s?t.pk=0:"atom"===s?t.pk=1:"residue"===s?t.pk=2:"strand"===s&&(t.pk=3),t.hlUpdateCls.updateHlAll(),t.drawCls.draw()}else t.hlUpdateCls.updateHlAll(),t.drawCls.draw();else t.hlUpdateCls.updateHlAll(),t.drawCls.draw();(s.cfg.closepopup||s.cfg.imageonly)&&(setTimeout((function(){t.resizeCanvasCls.closeDialogs()}),100),t.resizeCanvasCls.resizeCanvas(s.htmlCls.WIDTH,s.htmlCls.HEIGHT,!0)),t.bTransparentSurface&&t.bRender&&t.drawCls.render(),s.cfg.imageonly&&t.saveFileCls.saveFile(void 0,"png",void 0,!0)}async replayFirstStep(e){let t=this.icn3d,s=t.icn3dui;t.reinitAfterLoad(),await this.execCommandsBase(e,e,t.STATENUMBER);let i=t.commands[e],n=t.commands[e].indexOf("|");-1!=n&&(i=t.commands[e].substr(0,n));let l=i.length>20?i.substr(0,20)+"...":i,r=t.applyCommandCls.getMenuFromCmd(i);$("#"+t.pre+"replay_cmd").html("Cmd: "+l),$("#"+t.pre+"replay_menu").html("Menu: "+r),s.htmlCls.clickMenuCls.setLogCmd(i,!0),t.bCommandLoad=!1,t.ParserUtilsCls.hideLoading(),t.bRender=!0,t.drawCls.draw()}getHAtoms(e){let t=this.icn3d;t.icn3dui;let s=e.split("|||")[0].trim().split(" | ");if(2==s.length){let e=s[1].split(",");t.hAtoms=t.definedSetsCls.getAtomsFromNameArray(e)}}}class cs{constructor(e){this.icn3d=e}async selectByCommand(e,t,s){let i=this.icn3d,n=i.icn3dui;if(0===e.indexOf("saved atoms")){let s=12,n=e.substr(s);i.definedSetsCls.selectCombinedSets(n,t)}else{let l=e.replace(/ AND /g," and ").replace(/ OR /g," or ").replace(/ or and /g," and ").replace(/ and /g," or and ").replace(/ or not /g," not ").replace(/ not /g," or not "),r=("select"===l.trim().substr(0,6)?l.trim().substr(7):l.trim()).split(" or "),o={};for(let e=0,t=r.length;e1||1==o.length&&"*"!==o[0])&&(h=!1);let C,y,v,_,w=[],S=[];if(w="*"===t?Object.keys(l.structures):t.split(","),"*"===s){let e=Object.keys(l.chains);for(let t=0,s=e.length;t1&&"3"===x[t][0]&&isNaN(x[t][1])&&"-"!==x[t][0]){i=x[t].toUpperCase().substr(1),m=!0}else if(""===x[t]||isNaN(parseInt(x[t]))){if("*"===x[t])h=!0;else if("proteins"!==x[t]&&"nucleotides"!==x[t]&&"chemicals"!==x[t]&&"ions"!==x[t]&&"water"!==x[t]&&"anchors"!==x[t]&&"strands"!==x[t]&&"loops"!==x[t]){s=x[t].toUpperCase(),p=!0}}else v=x[t],_=v,n=!0;for(let a=0,u=S.length;a1?e.substr(0,l-1)===n.atoms[i].name.substr(0,l-1)&&(0===s?t[i]=1:t.hasOwnProperty(i)||delete t[i]):"*"!==e&&e!==n.atoms[i].name||(0===s?t[i]=1:t.hasOwnProperty(i)||delete t[i]),t}}class hs{constructor(e){this.icn3d=e}selectAll(){let e=this.icn3d;e.icn3dui,this.selectAll_base(),e.hlObjectsCls.removeHlObjects(),e.hlUpdateCls.removeHl2D(),e.hlUpdateCls.removeHlMenus(),e.bSelectResidue=!1,e.bSelectAlignResidue=!1,e.hlUpdateCls.removeSeqResidueBkgd(),e.hlUpdateCls.update2DdgmContent(),$("#"+e.pre+"dl_annotations > .icn3d-annotation").show(),e.definedSetsCls.setMode("all"),e.saveFileCls.showTitle()}selectAll_base(){let e=this.icn3d,t=e.icn3dui;e.hAtoms={},e.dAtoms={};for(let s in e.chains)e.hAtoms=t.hashUtilsCls.unionHash(e.hAtoms,e.chains[s]);e.dAtoms=t.hashUtilsCls.cloneHash(e.hAtoms),e.viewSelectionAtoms=t.hashUtilsCls.cloneHash(e.hAtoms),e.ALTERNATE_STRUCTURE=-1}selectAChain(e,t,s,i){let n=this.icn3d,l=n.icn3dui;t=t.replace(/\s/g,"");let r=void 0!==s||s?"select alignChain "+e:"select chain "+e;void 0!==i&&i?(n.hAtoms=l.hashUtilsCls.unionHash(n.hAtoms,n.chains[e]),void 0===n.nameArray&&(n.nameArray=[])):(n.hAtoms={},n.nameArray=[]),n.nameArray.push(e);let o,a=s?n.alnChainsSeq[e]:n.chainsSeq[e];o=void 0===a?0:a.length;let d={};for(let t=0,s=o;t0){if(void 0!==i&&i?void 0===r.nameArray&&(r.nameArray=[]):(r.hAtoms={},r.nameArray=[]),l)for(let t in e)r.hAtoms[t]=1;else for(let t in e)for(let e in r.residues[t])r.hAtoms[e]=1;let o,a;t=t.replace(/\s/g,""),r.nameArray.push(t),l?(o="select "+r.resid2specCls.atoms2spec(r.hAtoms),a=!1):(o="select "+r.resid2specCls.residueids2spec(Object.keys(e)),a=!0);let d=Object.keys(e);this.addCustomSelection(d,t,s,o,a),(void 0===n||n)&&r.hlUpdateCls.updateHlAll(r.nameArray,void 0,i)}}selectMainChains(){let e=this.icn3d,t=e.icn3dui.hashUtilsCls.cloneHash(e.hAtoms);e.hAtoms=e.applyDisplayCls.selectMainChainSubset(t),e.hlUpdateCls.showHighlight()}selectSideChains(){let e=this.icn3d,t=e.icn3dui,s=t.hashUtilsCls.cloneHash(e.hAtoms);e.hAtoms={};for(let i in s)(e.proteins.hasOwnProperty(i)&&"N"!==e.atoms[i].name&&"H"!==e.atoms[i].name&&"C"!==e.atoms[i].name&&"O"!==e.atoms[i].name&&("CA"!==e.atoms[i].name||"C"!==e.atoms[i].elem)&&"HA"!==e.atoms[i].name||e.nucleotides.hasOwnProperty(i)&&-1===t.parasCls.nuclMainArray.indexOf(e.atoms[i].name))&&(e.hAtoms[i]=1);e.hlUpdateCls.showHighlight()}selectMainSideChains(){let e=this.icn3d,t=e.icn3dui,s=e.firstAtomObjCls.getResiduesFromAtoms(e.hAtoms);e.hAtoms={};for(let i in s)e.hAtoms=t.hashUtilsCls.unionHash(e.hAtoms,e.residues[i]),e.dAtoms=t.hashUtilsCls.unionHash(e.dAtoms,e.residues[i]);e.drawCls.draw(),e.hlUpdateCls.showHighlight()}clickShow_selected(){let e=this.icn3d,t=e.icn3dui,s=this;t.myEventCls.onIds(["#"+e.pre+"show_selected","#"+e.pre+"mn2_show_selected"],"click",(function(e){s.icn3d,s.showSelection(),t.htmlCls.clickMenuCls.setLogCmd("show selection",!0)}))}clickHide_selected(){let e=this.icn3d,t=e.icn3dui,s=this;t.myEventCls.onIds("#"+e.pre+"mn2_hide_selected","click",(function(e){s.icn3d,s.hideSelection(),t.htmlCls.clickMenuCls.setLogCmd("hide selection",!0)}))}getGraphDataForDisplayed(){let e=this.icn3d;e.icn3dui;let t=JSON.parse(e.graphStr),s=e.firstAtomObjCls.getResiduesFromAtoms(e.dAtoms),i=[],n=[],l={};for(let e=0,n=t.nodes.length;e0)if(1==s.pk){let n=!0;this.selectResidueList(s.hAtoms,e,t,void 0,void 0,n),this.updateSelectionNameDesc(),i.htmlCls.clickMenuCls.setLogCmd("select "+s.resid2specCls.atoms2spec(s.hAtoms)+" | name "+e,!0)}else this.selectResidueList(s.selectedResidues,e,t),this.updateSelectionNameDesc(),i.htmlCls.clickMenuCls.setLogCmd("select "+s.resid2specCls.residueids2spec(Object.keys(s.selectedResidues))+" | name "+e,!0)}saveSelInCommand(){let e=this.icn3d,t=e.icn3dui;e.selectedResidues=e.firstAtomObjCls.getResiduesFromCalphaAtoms(e.hAtoms),t.htmlCls.clickMenuCls.setLogCmd("select "+e.resid2specCls.residueids2spec(Object.keys(e.selectedResidues)),!0)}saveEachResiInSel(){let e=this.icn3d;e.icn3dui,e.selectionCls.saveSelectionPrep(),e.selectedResidues={},e.selectedResidues=e.firstAtomObjCls.getResiduesFromCalphaAtoms(e.hAtoms);for(let t in e.selectedResidues){let s={};s[t]=1;let i=t+"_"+e.selectedResidues[t];this.selectResidueList(s,i,i)}}removeSelection(){let e=this.icn3d;e.icn3dui,e.bAnnotations||e.hlUpdateCls.removeSeqChainBkgd(),e.bCtrl||e.bShift||(e.hlUpdateCls.removeSeqResidueBkgd(),e.hlUpdateCls.removeSeqChainBkgd()),e.selectedResidues={},e.bSelectResidue=!1,e.hAtoms={},e.hlObjectsCls.removeHlObjects(),e.hlUpdateCls.removeHl2D()}resetAll(){let e=this.icn3d,t=e.icn3dui;e.maxD=e.oriMaxD,e.center=e.oriCenter.clone(),e.opts=t.hashUtilsCls.cloneHash(e.optsOri),e.setOptionCls.setStyle("sidec","nothing"),e.reinitAfterLoad(),e.definedSetsCls.setMode("all"),e.selectionCls.selectAll(),t.htmlCls.clickMenuCls.setLogCmd("reset",!0),e.hlUpdateCls.removeSeqChainBkgd(),e.hlUpdateCls.removeSeqResidueBkgd(),e.hlUpdateCls.removeHl2D(),e.hlUpdateCls.removeHlMenus(),e.loadScriptCls.renderFinalStep(1)}async loadSelection(e){let t=this.icn3d,s=t.icn3dui,i=e.trim().split("\n");for(let e=0,n=i.length;e=t&&l.coord.z<=e)){i[l.structure+"_"+l.chain+"_"+l.resi]=1}}let n="z_planes_"+e+"_"+t,l=n;this.selectResidueList(i,n,l,!1)}}class ps{constructor(e){this.icn3d=e}residueids2spec(e){var t=this.icn3d;t.icn3dui;let s="";if(void 0!==e){let i,n,l,r,o,a,d,c=e.sort((function(e,t){if(""!==e&&!isNaN(e))return parseInt(e)-parseInt(t);{let s=e.lastIndexOf("_"),i=t.lastIndexOf("_");if(e.substr(0,s)t.substr(0,i))return 1;if(e.substr(0,s)==t.substr(0,i)){if(parseInt(e.substr(s+1))parseInt(t.substr(i+1)))return 1;if(parseInt(e.substr(s+1))==parseInt(t.substr(i+1)))return 0}}})),h="",p=0,m=1!=Object.keys(t.structures).length;for(let e=0,u=c.length;e0&&(s+=p===d?m?"$"+o+"."+a+":"+d+" or ":"."+a+":"+d+" or ":m?"$"+o+"."+a+":"+d+"-"+p+" or ":"."+a+":"+d+"-"+p+" or "),d=n;else if(h===i){let e=t.ParserUtilsCls.getResiNCBI(h,p);t.ParserUtilsCls.getResiNCBI(i,n)!=e+1&&(s+=p===d?m?"$"+o+"."+a+":"+d+" or ":"."+a+":"+d+" or ":m?"$"+o+"."+a+":"+d+"-"+p+" or ":"."+a+":"+d+"-"+p+" or ",d=n)}h=i,p=n}}r=h.indexOf("_"),o=h.substr(0,r),a=h.substr(r+1),s+=p===d?m?"$"+o+"."+a+":"+d:"."+a+":"+d:m?"$"+o+"."+a+":"+d+"-"+p:"."+a+":"+d+"-"+p}return s}atoms2spec(e){var t=this.icn3d;t.icn3dui;let s,i="",n=0,l={},r={},o={};for(let a in e)s=t.atoms[a],n>0&&(i+=" or "),i+="$"+s.structure+"."+s.chain+":"+s.resi+"@"+s.name,l[s.structure]=1,r[s.structure+"_"+s.chain]=1,o[s.structure+"_"+s.chain+"_"+s.resi]=1,++n;if(1==Object.keys(o).length){let e="\\$"+s.structure+"\\."+s.chain+":"+s.resi;i=i.replace(new RegExp(e,"g"),"")}else if(1==Object.keys(r).length){let e="\\$"+s.structure+"\\."+s.chain;i=i.replace(new RegExp(e,"g"),"")}else if(1==Object.keys(l).length){let e="\\$"+s.structure;i=i.replace(new RegExp(e,"g"),"")}return i}atoms2residues(e){var t=this.icn3d;t.icn3dui;let s={};for(let t=0,i=e.length;t=parseInt(t)&&e.b<=parseInt(s)&&(i.hAtoms=n.hashUtilsCls.unionHash(i.hAtoms,i.residues[e.structure+"_"+e.chain+"_"+e.resi]))}}else if("percent out"==e){i.bCalcArea=!0,i.opts.surface="solvent accessible surface",i.applyMapCls.applySurfaceOptions(),i.bCalcArea=!1,i.hAtoms={};for(let e in i.resid2area){let l=e.lastIndexOf("_"),r=e.substr(l+1);if(n.parasCls.residueArea.hasOwnProperty(r)){let o=parseInt(i.resid2area[e]/n.parasCls.residueArea[r]*100);if(o>=t&&o<=s){let t=e.substr(0,l);i.hAtoms=n.hashUtilsCls.unionHash(i.hAtoms,i.residues[t])}}}}i.hAtoms=n.hashUtilsCls.intHash(i.hAtoms,l),i.drawCls.draw(),i.hlUpdateCls.updateHlAll()}selectComplement(){let e=this.icn3d,t=e.icn3dui,s={};for(let t in e.atoms)e.hAtoms.hasOwnProperty(t)||(s[t]=1);e.hAtoms=t.hashUtilsCls.cloneHash(s),e.hlUpdateCls.updateHlAll()}switchHighlightLevel(){var e=this.icn3d.icn3dui;if(e.bNode)return;let t=this;document.addEventListener("keydown",(function(s){let i=t.icn3d;38===s.keyCode?(s.preventDefault(),0!=Object.keys(i.pickedAtomList).length&&i.hAtoms.hasOwnProperty(i.firstAtomObjCls.getFirstAtomObj(i.pickedAtomList).serial)||(i.pickedAtomList=e.hashUtilsCls.cloneHash(i.hAtoms)),t.switchHighlightLevelUp(),e.htmlCls.clickMenuCls.setLogCmd("highlight level up",!0)):40===s.keyCode&&(s.preventDefault(),0!=Object.keys(i.pickedAtomList).length&&i.hAtoms.hasOwnProperty(i.firstAtomObjCls.getFirstAtomObj(i.pickedAtomList).serial)||(i.pickedAtomList=e.hashUtilsCls.cloneHash(i.hAtoms)),t.switchHighlightLevelDown(),e.htmlCls.clickMenuCls.setLogCmd("highlight level down",!0))}))}switchHighlightLevelUp(){var e=this.icn3d,t=e.icn3dui;if(!t.bNode){if(e.bShift||e.bCtrl||e.hlObjectsCls.removeHlObjects(),void 0!==e.pickedAtomList&&0!==Object.keys(e.pickedAtomList).length||(e.pickedAtomList=t.hashUtilsCls.cloneHash(e.hAtoms)),0===Object.keys(e.pickedAtomList).length&&(e.pickedAtomList=e.dAtoms),1===e.highlightlevel){e.highlightlevel=2;let s=e.firstAtomObjCls.getFirstAtomObj(e.pickedAtomList);e.bShift||e.bCtrl?e.hAtoms=t.hashUtilsCls.unionHash(e.hAtoms,e.residues[s.structure+"_"+s.chain+"_"+s.resi]):e.hAtoms=t.hashUtilsCls.cloneHash(e.residues[s.structure+"_"+s.chain+"_"+s.resi])}else if(2===e.highlightlevel){e.highlightlevel=3;let s=e.firstAtomObjCls.getFirstAtomObj(e.pickedAtomList);e.bShift||e.bCtrl?e.hAtoms=t.hashUtilsCls.unionHash(e.hAtoms,e.pickingCls.selectStrandHelixFromAtom(s)):e.hAtoms=t.hashUtilsCls.cloneHash(e.pickingCls.selectStrandHelixFromAtom(s))}else if(3===e.highlightlevel){let s;if(void 0!==t.cfg.mmdbid||void 0!==t.cfg.gi){e.highlightlevel=4;let i=e.firstAtomObjCls.getFirstAtomObj(e.pickedAtomList);s=e.pickingCls.select3ddomainFromAtom(i),e.bShift||e.bCtrl?e.hAtoms=t.hashUtilsCls.unionHash(e.hAtoms,s):e.hAtoms=t.hashUtilsCls.cloneHash(s)}if(void 0===t.cfg.mmdbid&&void 0===t.cfg.gi||0==Object.keys(s).length){e.highlightlevel=5;let s=e.firstAtomObjCls.getFirstAtomObj(e.pickedAtomList);e.bShift||e.bCtrl?e.hAtoms=t.hashUtilsCls.unionHash(e.hAtoms,e.chains[s.structure+"_"+s.chain]):e.hAtoms=t.hashUtilsCls.cloneHash(e.chains[s.structure+"_"+s.chain])}}else if(4===e.highlightlevel){e.highlightlevel=5;let s=e.firstAtomObjCls.getFirstAtomObj(e.pickedAtomList);e.bShift||e.bCtrl?e.hAtoms=t.hashUtilsCls.unionHash(e.hAtoms,e.chains[s.structure+"_"+s.chain]):e.hAtoms=t.hashUtilsCls.cloneHash(e.chains[s.structure+"_"+s.chain])}else if(5===e.highlightlevel||6===e.highlightlevel){e.highlightlevel=6;let s=e.firstAtomObjCls.getFirstAtomObj(e.pickedAtomList);e.bShift||e.bCtrl||(e.hAtoms={});let i=e.structures[s.structure];for(let s=0,n=i.length;s3e4)return void(e?console.log("The maximum number of allowed atoms is 30,000. Please try it again with selected chains..."):alert("The maximum number of allowed atoms is 30,000. Please try it again with selected chains..."));let o="";return o+=s.cfg.cid?t.saveFileCls.getAtomPDB(n,!0,void 0,void 0,void 0,void 0,true):t.saveFileCls.getAtomPDB(n,void 0,void 0,void 0,void 0,void 0,true),o+=t.saveFileCls.getAtomPDB(i,!0,void 0,!0),o}async CalcPhi(e,t,s,i,n){let l=this.icn3d;l.icn3dui;let r=await this.CalcPhiPrms(e,t,s,i,n);this.loadPhiData(r,s,i),l.bAjaxPhi=!0,i?l.setOptionCls.setOption("phisurface","phi"):l.setOptionCls.setOption("phimap","phi")}CalcPhiPrms(e,t,s,i,n){let l=this.icn3d,r=l.icn3dui;l.loadPhiFrom="delphi";let o=r.htmlCls.baseUrl+"delphi/delphi.cgi",a=r.cfg.cid?r.cfg.cid:Object.keys(l.structures).toString(),d={};if(n)d={pqr2phi:n,gsize:e,salt:t,pdbid:a};else{let s=this.getPdbStr();d={pdb2phi:s,gsize:e,salt:t,pdbid:a}}return new Promise((function(e,t){$.ajax({url:o,type:"POST",data:d,dataType:"binary",responseType:"arraybuffer",cache:!0,beforeSend:function(){l.ParserUtilsCls.showLoading()},complete:function(){l.ParserUtilsCls.hideLoading()},success:function(t){e(t)},error:function(e,t,s){}})}))}async PhiParser(e,t,s,i){let n,l=this.icn3d,r=l.icn3dui,o=this;n="phiurl"==t||"phiurl2"==t?"arraybuffer":"text";let a=await r.getXMLHttpRqstPromise(e,"GET",n,"potential");"phiurl"==t||"phiurl2"==t?o.loadPhiData(a,s,i):o.loadCubeData(a,s,i),l.bAjaxPhi=!0,i?l.setOptionCls.setOption("phisurface","phi"):l.setOptionCls.setOption("phimap","phi")}loadPhiData(e,t,s){let i=this.icn3d;i.icn3dui;let n={filetype:"phi"},l=e.buffer&&e.buffer instanceof ArrayBuffer?e.buffer:e,r=new Float32Array(l.slice(l.byteLength-24,l.byteLength-8));n.scale=r[0];let o=r[1],a=r[2],d=r[3];n.n=new Int32Array(l.slice(l.byteLength-8,l.byteLength-4)),n.xExtent=n.yExtent=n.zExtent=n.n;let c=1/n.scale*((n.n-1)/2);n.ori=new THREE.Vector3(o-c,a-c,d-c);let h=new Float32Array(l.slice(110,l.byteLength-56));n.bSurface=s,i.mapData.headerPhi=n,i.mapData.dataPhi=h,i.mapData.contourPhi=t;let p=new THREE.Matrix4;p.identity(),p.multiply((new THREE.Matrix4).makeTranslation(n.ori.x,n.ori.y,n.ori.z)),i.mapData.matrixPhi=p}loadCubeData(e,t,s){let i=this.icn3d;i.icn3dui;let n={filetype:"cube"},l=e.split("\n"),r=[];r.push(parseFloat(l[0].substr(0,10))),r.push(parseFloat(l[0].substr(10,6))),r.push(parseFloat(l[0].substr(16,10))),r.push(parseFloat(l[0].substr(26,10))),r.push(parseFloat(l[0].substr(36,10))),n.scale=r[0];let o=r[2],a=r[3],d=r[4];n.n=r[1],n.xExtent=n.yExtent=n.zExtent=n.n;let c=1/n.scale*((n.n-1)/2);n.ori=new THREE.Vector3(o-c,a-c,d-c);let h=[];for(let e=7,t=l.length;e1e4)return void alert("The maximum number of allowed atoms is 10,000. Please try it again with smaller sets...");let o="";o+=e.saveFileCls.getAtomPDB(n);let a,d={pdb:o,pdbid:Object.keys(e.structures).toString()};try{a=await t.getAjaxPostPromise(i,d,!0);let n,l,o,c=a.rcsb_struct_symmetry,h="none";if(void 0!==c){let i;void 0!==e.rmsd_supr&&void 0!==e.rmsd_supr.rot&&(n=e.rmsd_supr.rot,l=e.rmsd_supr.trans1,o=e.rmsd_supr.trans2),void 0===e.symdArray&&(e.symdArray=[]);for(let t=0,n=c.length;tThe selected residues have no detected symmetry with a Z score of "+a.zscore+" from the program SymD ."),t.htmlCls.dialogCls.openDlg("dl_symd","Dynamically Calculated Symmetry Using SymD");else{let n=a.seqalign.replace(/ /g,"").split(","),l=a.nres,o=a.shift,d=a.rmsd,h=Object.keys(r),p={},m={},u=[],g=[],f=0,b=0,C={};for(let e=0,s=n[0].length;et&&(t=C[s].length,e=s);let s=Object.keys(p),i=Object.keys(m);for(let t=0,n=C[e].length;tSymD. The Z score "+a.zscore+" is greater than the threshold Z score 8. The RMSD is "+d+' angstrom. SymD ."),t.htmlCls.dialogCls.openDlg("dl_symd","Dynamically Calculated Symmetry Using SymD");e.symdtitle="none"===h?void 0:h,e.drawCls.draw()}catch(s){return $("#"+e.pre+"dl_symd").html("This structure has no symmetry."),void i.htmlCls.dialogCls.openDlg("dl_symmetry","Symmetry")}let r,o,a,d=t.rcsb_struct_symmetry;if(void 0!==d){void 0!==s.rmsd_supr&&void 0!==s.rmsd_supr.rot&&(r=s.rmsd_supr.rot,o=s.rmsd_supr.trans1,a=s.rmsd_supr.trans2),s.symmetryHash={};for(let e=0,t=d.length;eThis structure has no symmetry.");else{let e="None ",t=0;for(let i in s.symmetryHash){e+=""+i+" ",++t}$("#"+s.pre+"selectSymmetry").html(e)}}else $("#"+s.pre+"dl_symmetry").html("0&&(s=-s),i=0;i=2&&"number"==typeof t[0]&&"number"==typeof t[1]){if(null==s)return null;let e="number"==typeof s?s:s[s.length-1]+1;i=this.bsa_gen_score_matrix(e,t[0],t[1])}else i=t;for(let e=0;eo.length?d:o.length;l=null==l||l<0?c:l;let h,p,m=o.target>d?o.target-d:d-o.target;l=l>m?l:m,"number"==typeof n?(h=0,p=n>0?n:-n):(h=n[0]>0?n[0]:-n[0],p=n[1]>0?n[1]:-n[1]);let u,g=h+p,f=-1073741824,b=[],C=[],y=[],v=0,_=-1,w=-1;if(e)for(let e=0;e<=d;++e)b[e]=C[e]=0;else{b[0]=0,C[0]=-g-g;for(let e=1;e<=d;++e)e>=l?b[e]=C[e]=f:(b[e]=-(g+p*(e-1)),C[e]=-(g+g+p*e))}for(let t=0;tl?t-l:0,u=t+l+10?f:-(g+p*t),n=m>0?f:-(g+g+p*t));for(let t=m;t=o?0:1,a=a>=o?a:o,l=a>=n?l:2,a=a>=n?a:n,l=!e||a>0?l:64,i=a,c=r>a?c:t,r=r>a?r:a,a-=g,a=!e||a>0?a:0,o-=p,l|=o>a?4:0,o=o>a?o:a,C[t]=o,n-=p,l|=n>a?32:0,n=n>a?n:a,s[t]=l}b[u]=i,C[u]=e?0:f,r>v&&(v=r,_=t,w=c)}if(e&&0==v)return null;u=e?v:b[d];let S,A,x,k=[],O=0,R=0;for(e?(A=_,x=w,w!=d-1&&this.push_cigar(k,4,d-1-w)):(A=o.length-1,x=(A+l+1=0&&x>=0&&(S=y[A][x-(A>l?A-l:0)],O=S>>(O<<1)&3,!(0==O&&S>>6));)0==O&&(O=3&S),0==O?(this.push_cigar(k,0,1),--A,--x):1==O?(this.push_cigar(k,2,1),--A):(this.push_cigar(k,1,1),--x);e?(x>=0&&this.push_cigar(k,4,x+1),R=A+1):(A>=0&&this.push_cigar(k,2,A+1),x>=0&&this.push_cigar(k,1,x+1));for(let e=0;e>1;++e)S=k[e],k[e]=k[k.length-1-e],k[k.length-1-e]=S;return[u,R,k]}push_cigar(e,t,s){this.icn3d.icn3dui,0==e.length||t!=(15&e[e.length-1])?e.push(s<<4|t):e[e.length-1]+=s<<4}bsa_cigar2gaps(e,t,s,i){this.icn3d.icn3dui;let n="",l="",r="",o=0,a=s;for(let s=0;s>4;0==r?(n+=t.substr(o,d),l+=e.substr(a,d),o+=d,a+=d):1==r?(n+=t.substr(o,d),l+=Array(d+1).join("-"),o+=d):2==r?(n+=Array(d+1).join("-"),l+=e.substr(a,d),a+=d):4==r&&(o+=d)}let d=l.toUpperCase(),c=n.toUpperCase();for(let e=0;e>4).toString()+"MIDNSHP=XB".charAt(15&e[s]));return t.join("")}}class ys{constructor(e){this.icn3d=e}calculateArea(){var e=this.icn3d,t=e.icn3dui;e.bCalcArea=!0,e.opts.surface="solvent accessible surface",e.applyMapCls.applySurfaceOptions(),$("#"+e.pre+"areavalue").val(e.areavalue),$("#"+e.pre+"areatable").html(e.areahtml),t.htmlCls.dialogCls.openDlg("dl_area","Surface area calculation"),e.bCalcArea=!1}calcBuriedSurface(e,t){var s=this.icn3d,i=s.icn3dui;if(0==e.length)alert("Please select the first set");else{let n=i.hashUtilsCls.cloneHash(s.hAtoms),l=s.definedSetsCls.getAtomsFromNameArray(e),r=s.definedSetsCls.getAtomsFromNameArray(t);s.bCalcArea=!0,s.opts.surface="solvent accessible surface",s.hAtoms=i.hashUtilsCls.cloneHash(l),s.applyMapCls.applySurfaceOptions();let o=s.areavalue,a=i.hashUtilsCls.cloneHash(s.resid2area);s.hAtoms=i.hashUtilsCls.cloneHash(r),s.applyMapCls.applySurfaceOptions();let d=s.areavalue,c=i.hashUtilsCls.cloneHash(s.resid2area);s.hAtoms=i.hashUtilsCls.unionHash(s.hAtoms,l),s.applyMapCls.applySurfaceOptions();let h=s.areavalue,p=i.hashUtilsCls.cloneHash(s.resid2area),m=0,u=0,g=0,f=0;for(let e in a)p.hasOwnProperty(e)&&(f+=parseFloat(p[e]));u=(o-f).toFixed(2);for(let e in c)p.hasOwnProperty(e)&&(g+=parseFloat(p[e]));m=(d-g).toFixed(2),s.bCalcArea=!1,s.hAtoms=i.hashUtilsCls.cloneHash(n);let b=(parseFloat(d)+parseFloat(o)-parseFloat(h)).toFixed(2),C="2 2 2 Buried Surface for Set 1 : "+u+" Å2 Buried Surface for Set 2 : "+m+" Å2 "+t[e]+" (Å)"}r+="";for(let s=0,i=e.length;s"+i+" (Å)'+l[i][s]+" ":r+="0 "}r+=""}r+="
";p+=""+t.toUpperCase()+" ";let m={},u=[],g="",f="",b={};if(i)for(let e in n.dAtoms){let t=n.atoms[e];b[c[t.structure+"_"+t.chain]]=1}let C=Object.keys(e.moleculeInfor),y=Object.keys(e.intrac),v=[];for(let e=0,t=C.length;e0)for(let t in e.intrac){let s=e.intrac[t];for(let e=0,i=s.intrac.length;e0&&(y="#"+n.atoms[e[0]].color.getHexString().toUpperCase())}let S="";n.bInitial&&void 0!==s&&(void 0!==n.alignmolid2color&&n.alignmolid2color[s].hasOwnProperty(l)?(S=n.alignmolid2color[s][l],y="#FF0000"):y="#FFFFFF");let A=d[l],x=" ",k=" ";if(void 0!==c){let e=c.indexOf("_");k=c.substr(e+1),x=k.length>1?k.substr(0,1)+"..":k}else c="Misc";void 0===y&&(y="#FFFFFF");let O=1;if(n.bInitial&&void 0!==n.alnChains[c]){let e=0;for(let t in n.alnChains[c]){let s=n.atoms[t].color.getHexString().toUpperCase();"FF0000"!==s&&"00FF00"!==s||++e}O=1*e/Object.keys(n.chains[c]).length}if(O<.2&&(O=.2),-1===v.indexOf(l)){for(let e=0,t=h.intrac.length;e1){let s=0,i=0;for(let e=0,t=_[l].length;e",p+="Interaction of chain "+c+" with chain "+h+" ",p+="",p+="Interaction of chain "+h+" with chain "+c+" ",p+=" "}return p+=f+g,p+=" ",p+="",n.html2ddgm+=p,$("#"+n.pre+"dl_2ddgm_html").html(n.html2ddgm),p}set2DdgmNote(e){let t="Nodes :◯ Protein▢ Nucleotide♢ Chemical▢ BiopolymerO Protein▢ Nucleotide◇ Chemical▢ BiopolymerLines :Numbers in red :
1)s="inter_"+e+"_"+t;else{let i=e.indexOf("_"),n=t.indexOf("_");s="inter_"+e.substr(i+1)+"_"+t.substr(n+1)}i="select the atoms in chain "+e+" interacting with chain "+t+" in a distance of 4 angstrom";let o="select interaction "+e+","+t;n.selectionCls.addCustomSelection(r,s,i,o,!0)}draw2DProtein(e,t,s,i,n,l,r,o,a,d,c){this.icn3d.icn3dui;let h=20*d,p="";return p+="Chain "+i+": "+l+" ",p+=""+n+" ",""!==r&&(p+=""+r+" "),p+=" ",p}draw2DNucleotide(e,t,s,i,n,l,r,o,a,d,c){this.icn3d.icn3dui;let h=30*d,p=30*d,m="";return m+="Chain "+i+": "+l+" ",m+=""+n+" ",""!==r&&(m+=""+r+" "),m+=" ",m}draw2DChemical(e,t,s,i,n,l,r,o,a,d,c,h){this.icn3d.icn3dui;let p,m,u,g,f,b,C,y,v=30*d;if(h){let s=.5*v/Math.sqrt(3),i=.5*v;p=e-s,m=t-i,u=e+3*s,g=t-i,f=e+s,b=t+i,C=e-3*s,y=t+i}else{let s=.5*v,i=.5*v;p=e-s,m=t,u=e,g=t+i,f=e+s,b=t,C=e,y=t-i}let _=p-e,w=m-t,S=u-e,A=g-t,x=f-e,k=b-t,O=C-e,R=y-t,I="";return I+="Chain "+i+": "+l+" ",I+=""+n+" ",""!==r&&(I+=""+r+" "),I+=" ",I}}class _s{constructor(e){this.icn3d=e}async draw2Dcartoon(e,t){let s=this.icn3d,i=s.icn3dui,n=this;if(i.htmlCls.clickMenuCls.setLogCmd("cartoon 2d "+e,!0),s.cartoon2dType=e,t){let t=n.getCartoonSvg(e,s.graphStr);$("#"+i.svgid_ct).html(t)}else{await this.getNodesLinksForSetCartoon(e),s.graphStr=n.getCartoonData(e,s.node_link);let t=n.getCartoonSvg(e,s.graphStr);$("#"+i.svgid_ct).html(t),n.setEventsForCartoon2d(),i.htmlCls.dialogCls.openDlg("dl_2dctn","2D Cartoon")}}getCartoonSvg(e,t){let s=this.icn3d,i=s.icn3dui,n="",l="",r=JSON.parse(t);s.ctnNodeHash={};for(let t=0,i=r.nodes.length;t":"domain"==e?n+="":"secondary"==e&&(a=s.ctnNodeHash[l].x2,d=i.htmlCls.width2d-s.ctnNodeHash[l].y2,c=s.ctnNodeHash[o].x1,h=i.htmlCls.width2d-s.ctnNodeHash[o].y1,n+="");let p=l+"--"+o;n+="Interaction of "+e+" "+this.getLabelFromId(l,e)+" with "+e+" "+this.getLabelFromId(o,e)+" ",n+=" ",s.nodeid2lineid.hasOwnProperty(l)||(s.nodeid2lineid[l]=[]),s.nodeid2lineid.hasOwnProperty(o)||(s.nodeid2lineid[o]=[]),s.nodeid2lineid[l].push(p),s.nodeid2lineid[o].push(p)}return n+=l,n}setEventsForCartoon2d(){let e=this.icn3d,t=e.icn3dui;$("#"+t.svgid_ct+" .icn3d-ctnode").draggable({start:function(e,t){let s=parseFloat(e.target.getAttribute("cx")),i=parseFloat(e.target.getAttribute("cy"));e.target.setAttribute("cx",s),e.target.setAttribute("cy",i);let n=e.target.getAttribute("ang");if(n)e.target.setAttribute("transform","rotate("+n+","+s+","+i+")");else{let t=parseFloat(e.target.getAttribute("x1")),s=parseFloat(e.target.getAttribute("y1")),i=parseFloat(e.target.getAttribute("x2")),n=parseFloat(e.target.getAttribute("y2"));e.target.setAttribute("x1",t),e.target.setAttribute("y1",s),e.target.setAttribute("x2",i),e.target.setAttribute("y2",n)}},drag:function(s,i){let n=$("#"+t.svgid_ct).offset().left,l=$("#"+t.svgid_ct).offset().top,r=s.target.getAttribute("id"),o=s.target.getAttribute("ang"),a=s.clientX-n,d=s.clientY-l,c=parseFloat(s.target.getAttribute("cx")),h=parseFloat(s.target.getAttribute("cy")),p=(a-c)/e.resizeRatioX,m=(d-h)/e.resizeRatioY,u=parseFloat($("#"+r+"_text").attr("x")),g=parseFloat($("#"+r+"_text").attr("y"));if($("#"+r+"_text").attr("x",u+p),$("#"+r+"_text").attr("y",g+m),s.target.setAttribute("cx",a),s.target.setAttribute("cy",d),o)s.target.setAttribute("transform","rotate("+o+","+a+","+d+")");else{let e=parseFloat(s.target.getAttribute("x1")),t=parseFloat(s.target.getAttribute("y1")),i=parseFloat(s.target.getAttribute("x2")),n=parseFloat(s.target.getAttribute("y2"));if(s.target.setAttribute("x1",e+p),s.target.setAttribute("y1",t+m),s.target.setAttribute("x2",i+p),s.target.setAttribute("y2",n+m),"S"==r.substr(0,1)){let e=parseFloat($("#"+r+"_box").attr("x1")),t=parseFloat($("#"+r+"_box").attr("y1")),s=parseFloat($("#"+r+"_box").attr("x2")),i=parseFloat($("#"+r+"_box").attr("y2"));$("#"+r+"_box").attr("x1",e+p),$("#"+r+"_box").attr("y1",t+m),$("#"+r+"_box").attr("x2",s+p),$("#"+r+"_box").attr("y2",i+m)}}if(e.nodeid2lineid[r])for(let t=0,s=e.nodeid2lineid[r].length;t";return u+=""+e+" "+m+" ","H"==t.substr(0,1)?u+=""+m+" ",u+=" ",u}drawOval(e,t,s,i,n,l,r,o,a,d){let c=this.icn3d.icn3dui,h=this.getLabelFromId(t,e);i=c.htmlCls.width2d-i,r=180-r;let p="chain"==e?"":"";return p+=""+e+" "+h+" ",p+="",p+="",p+=" ",p+=" ",p+=""+h+" ",p+=" ",p}getCartoonData(e,t){let s=this.icn3d;s.icn3dui;let i,n,l=[],r=[];l=t.node;let o=[],a={},d=0;for(let e=0,t=l.length;e0?n.y=s.htmlCls.width2d-n.y:n.y=-n.y,n}async getNodesLinksForSetCartoon(e){let t,s,i,n,l,r=this.icn3d,o=r.icn3dui,a=this,d=[],c=[],h=0,p=o.htmlCls.defaultValue,m="",u="",g="",f=!1,b=!0;if("chain"==e){let e={};for(let t in r.hAtoms){let s=r.atoms[t];if("DUM"==s.chain)continue;let i=s.structure+"_"+s.chain;(r.proteins.hasOwnProperty(t)||r.nucleotides.hasOwnProperty(t))&&(e.hasOwnProperty(i)||(e[i]={}),e[i][s.serial]=s)}let t=r.contactCls.getExtent(r.atoms),s=9999,i=9999,n=-9999,a=-9999,h=-9999,p=[];for(let d in e){r.hAtom={},r.hAtoms=o.hashUtilsCls.cloneHash(r.chains[d]);let e=r.axesCls.setPc1Axes(),c=e[0],m=e[1].distanceTo(e[0]),u=e[2].distanceTo(e[0]),g=180*new THREE.Vector2(e[1].x-e[0].x,e[1].y-e[0].y).angle()/Math.PI;g>180&&(g-=180);let f=Object.keys(r.hAtoms)[0],b=r.atoms[f];l=d,c=this.projectTo2d(c);let C=c.x,y=c.y;Cn&&(n=C),ya&&(a=y);let v=.5;m=v*o.htmlCls.width2d*m/(t[1][0]-t[0][0]),u=v*o.htmlCls.width2d*u/(t[1][1]-t[0][1]),m>h&&(h=m),u>h&&(h=u),p.push({id:d,r:l,x:C,y:y,rx:m,ry:u,ang:g,c:b.color.getHexString()})}let m=h+2,u=n-s,g=a-i;for(let e=0,t=p.length;e1&&(e+="__"+S.structure),a.push(e)),g==S.chain&&f&&S.ssend){let o=this.projectTo2d(t.coord.clone()),d=o.x,g=o.y,x=this.projectTo2d(S.coord.clone()),k=x.x,O=x.y;s=.5*(d+k),i=.5*(g+O),d=.5*(s+d),g=.5*(i+g),k=.5*(s+k),O=.5*(i+O),d_&&(_=d),gw&&(w=g),k_&&(_=k),Ow&&(w=O),f=!1,b=!0,n+="-"+S.resi,l+="-"+S.resi,n+="__"+S.chain,Object.keys(r.structures).length>1&&(n+="__"+S.structure);for(let t=0,s=a.length;t0&&m==S.chain&&c.push('{"source": "'+u+'", "target": "'+n+'", "v": '+p+', "c": "'+t.color.getHexString().toUpperCase()+'"}'),A.push({id:n,r:l,ss:C,x:s,y:i,x1:d,y1:g,x2:k,y2:O,c:S.color.getHexString()}),m=S.chain,u=n,++h}}}let x=S+2,k=_-y,O=w-v;for(let e=0,t=A.length;e1&&(v+="__"+i.substr(0,i.indexOf("_")));let _=g[b],w=f[b];t.hAtoms={};for(let e=0,n=_.length;e180&&(O-=180);let R=Object.keys(t.hAtoms)[0],I=t.atoms[R];A=this.projectTo2d(A);let T=A.x,E=A.y;Tc&&(c=T),Eh&&(h=E);let P=.5;x=P*s.htmlCls.width2d*x/(o[1][0]-o[0][0]),k=P*s.htmlCls.width2d*k/(o[1][1]-o[0][1]),x>p&&(p=x),k>p&&(p=k),void 0!==C&&n.push('{"source": "'+C+'", "target": "'+v+'", "v": '+l+', "c": "'+y.color.getHexString().toUpperCase()+'"}'),m.push({id:v,from:_+"",to:w+"",x:T,y:E,rx:x,ry:k,ang:O,c:I.color.getHexString()}),C=v,y=I}}let g=p+2,f=c-a,b=h-d;for(let e=0,t=m.length;e=2?d+"_"+e[1]:Object.keys(i.chains)[0];for(let e=0,t=o.length;e0&&(void 0===i||i)&&n.drawCls.draw()}}windowResize(){let e=this.icn3d.icn3dui,t=this;e.cfg.resize&&!e.utilsCls.isMobile()&&$(window).resize((function(){let s=t.icn3d;e.utilsCls.setViewerWidthHeight(s.icn3dui);let i=e.htmlCls.WIDTH,n=e.htmlCls.HEIGHT;void 0===s||s.bFullscreen||t.resizeCanvas(i,n)}))}openFullscreen(e){this.icn3d.icn3dui.bNode||document.fullscreenElement||document.mozFullScreenElement||document.webkitFullscreenElement||document.msFullscreenElement||(e.requestFullscreen?e.requestFullscreen():e.mozRequestFullScreen?e.mozRequestFullScreen():e.webkitRequestFullscreen?e.webkitRequestFullscreen():e.msRequestFullscreen&&e.msRequestFullscreen())}rotStruc(e,t){var s=this.icn3d;s.icn3dui;let i=this;if(s.bStopRotate)return!1;if(s.transformCls.rotateCount>s.transformCls.rotateCountMax)return s.transformCls.resetOrientation(),!1;if(++s.transformCls.rotateCount,t)if("left"===e)s.ROT_DIR="left";else if("right"===e)s.ROT_DIR="right";else if("up"===e)s.ROT_DIR="up";else{if("down"!==e)return!1;s.ROT_DIR="down"}if("left"===e&&"left"===s.ROT_DIR)s.transformCls.rotateLeft(1);else if("right"===e&&"right"===s.ROT_DIR)s.transformCls.rotateRight(1);else if("up"===e&&"up"===s.ROT_DIR)s.transformCls.rotateUp(1);else{if("down"!==e||"down"!==s.ROT_DIR)return!1;s.transformCls.rotateDown(1)}setTimeout((function(){i.rotStruc(e)}),100)}async back(){var e=this.icn3d;e.icn3dui,e.backForward=!0,e.STATENUMBER--,e.bAddCommands=!1,e.bAddLogs=!1,e.bNotLoadStructure=!0,e.STATENUMBER<1?e.STATENUMBER=1:await e.loadScriptCls.execCommands(0,e.STATENUMBER-1,e.STATENUMBER,!0),e.setStyleCls.adjustIcon(),e.bAddCommands=!0,e.bAddLogs=!0}async forward(){var e=this.icn3d;e.icn3dui,e.backForward=!0,e.STATENUMBER++,e.bAddCommands=!1,e.bAddLogs=!1,e.bNotLoadStructure=!0,e.STATENUMBER>e.commands.length?e.STATENUMBER=e.commands.length:await e.loadScriptCls.execCommands(0,e.STATENUMBER-1,e.STATENUMBER,!0),e.setStyleCls.adjustIcon(),e.bAddCommands=!0,e.bAddLogs=!0}async replayon(){var e=this.icn3d;e.icn3dui,e.CURRENTNUMBER=0,e.bReplay=1,$("#"+e.pre+"replay").show(),e.commands.length>0&&await e.loadScriptCls.replayFirstStep(e.CURRENTNUMBER)}async replayoff(){var e=this.icn3d;e.icn3dui,e.bReplay=0,$("#"+e.pre+"replay").hide(),++e.CURRENTNUMBER,await e.loadScriptCls.execCommands(e.CURRENTNUMBER,e.STATENUMBER-1,e.STATENUMBER)}closeDialogs(){var e=this.icn3d,t=e.icn3dui;let s=["dl_2ddgm","dl_2dctn","dl_alignment","dl_sequence2","dl_definedsets","dl_setsmenu","dl_command","dl_setoperations","dl_vast","dl_foldseek","dl_mmtfid","dl_pdbid","dl_afid","dl_opmid","dl_pdbfile","dl_pdbfile_app","dl_rescolorfile","dl_customcolor","dl_align","dl_alignaf","dl_chainalign","dl_chainalign2","dl_chainalign3","dl_mutation","dl_mol2file","dl_sdffile","dl_xyzfile","dl_afmapfile","dl_urlfile","dl_mmciffile","dl_mmcifid","dl_mmdbid","dl_mmdbafid","dl_blast_rep_id","dl_yournote","dl_proteinname","dl_refseqid","dl_cid","dl_pngimage","dl_state","dl_fixedversion","dl_selection","dl_dsn6","dl_dsn6url","dl_clr","dl_symmetry","dl_symd","dl_contact","dl_hbonds","dl_realign","dl_realignbystruct","dl_allinteracton","dl_interactionsorted","dl_linegraph","dl_linegraphcolor","dl_scatterplot","dl_scatterploitcolor","dl_contactmap","dl_alignerrormap","dl_elecmap2fofc","dl_elecmapfofc","dl_emmap","dl_aroundsphere","dl_adjustmem","dl_selectplane","dl_addlabel","dl_addlabelselection","dl_labelColor","dl_distance","dl_stabilizer","dl_disttwosets","dl_distmanysets","dl_stabilizer_rm","dl_thickness","dl_thickness2","dl_addtrack","dl_addtrack_tabs","dl_saveselection","dl_copyurl","dl_selectannotations","dl_annotations_tabs","dl_anno_view_tabs","dl_annotations","dl_graph","dl_svgcolor","dl_area","dl_colorbyarea","dl_rmsd","dl_buriedarea","dl_propbypercentout","dl_propbybfactor","dl_legend","dl_disttable"];for(let i in s){let n=s[i];t.cfg.notebook?$("#"+e.pre+n).hide():$("#"+e.pre+n).hasClass("ui-dialog-content")&&$("#"+e.pre+n).dialog("isOpen")&&$("#"+e.pre+n).dialog("close").remove()}t.cfg.notebook||this.resizeCanvas(t.htmlCls.WIDTH,t.htmlCls.HEIGHT,!0)}}class Ss{constructor(e){this.icn3d=e}resetOrientation(){let e=this.icn3d;e.icn3dui;let t=!1;if(e.commands.length>0){let s=e.commands[0].split("|||");if(2==s.length){let i=JSON.parse(s[1]);e._zoomFactor=i.factor,e.mouseChange.x=i.mouseChange.x,e.mouseChange.y=i.mouseChange.y,e.quaternion._x=i.quaternion._x,e.quaternion._y=i.quaternion._y,e.quaternion._z=i.quaternion._z,e.quaternion._w=i.quaternion._w,t=!0}}t||(e._zoomFactor=1,e.mouseChange=new THREE.Vector2(0,0),e.quaternion=new THREE.Quaternion(0,0,0,1)),e.maxD=e.oriMaxD,e.center=e.oriCenter.clone(),"show"==e.ori_chemicalbinding?e.bSkipChemicalbinding=!1:"hide"==e.ori_chemicalbinding&&(e.bSkipChemicalbinding=!0)}rotateLeft(e){let t=this.icn3d,s=t.icn3dui,i=new THREE.Vector3(0,1,0),n=-e/180*Math.PI;t.bControlGl&&!s.bNode?i.applyQuaternion(window.cam.quaternion).normalize():i.applyQuaternion(t.cam.quaternion).normalize();let l=new THREE.Quaternion;l.setFromAxisAngle(i,-n);let r={};r.quaternion=l,r.update=!0,t.bControlGl&&!s.bNode?window.controls.update(r):t.controls.update(r),t.bRender&&t.drawCls.render()}rotateRight(e){let t=this.icn3d,s=t.icn3dui,i=new THREE.Vector3(0,1,0),n=e/180*Math.PI;t.bControlGl&&!s.bNode?i.applyQuaternion(window.cam.quaternion).normalize():i.applyQuaternion(t.cam.quaternion).normalize();let l=new THREE.Quaternion;l.setFromAxisAngle(i,-n);let r={};r.quaternion=l,r.update=!0,t.bControlGl&&!s.bNode?window.controls.update(r):t.controls.update(r),t.bRender&&t.drawCls.render()}rotateUp(e){this.icn3d.icn3dui,this.rotate_base(-e)}rotateDown(e){this.icn3d.icn3dui,this.rotate_base(e)}rotate_base(e){let t=this.icn3d,s=t.icn3dui,i=new THREE.Vector3(1,0,0),n=e/180*Math.PI;t.bControlGl&&!s.bNode?i.applyQuaternion(window.cam.quaternion).normalize():i.applyQuaternion(t.cam.quaternion).normalize();let l=new THREE.Quaternion;l.setFromAxisAngle(i,-n);let r={};r.quaternion=l,r.update=!0,t.bControlGl&&!s.bNode?window.controls.update(r):t.controls.update(r),t.bRender&&t.drawCls.render()}setRotation(e,t){let s=this.icn3d,i=s.icn3dui;s.bControlGl&&!i.bNode&&window.cam?e.applyQuaternion(window.cam.quaternion).normalize():s.cam&&e.applyQuaternion(s.cam.quaternion).normalize();let n=new THREE.Quaternion;n.setFromAxisAngle(e,-t);let l={};l.quaternion=n,l.update=!0,s.bControlGl&&!i.bNode&&window.controls?window.controls.update(l):s.controls&&s.controls.update(l),s.bRender&&s.drawCls.render()}translateLeft(e){this.icn3d.icn3dui,this.translate_base(-e,0)}translateRight(e){this.icn3d.icn3dui,this.translate_base(e,0)}translateUp(e){this.icn3d.icn3dui,this.translate_base(0,-e)}translateDown(e){this.icn3d.icn3dui,this.translate_base(0,e)}translate_base(e,t){let s=this.icn3d,i=s.icn3dui,n=new THREE.Vector2(0,0);n.x+=e/100,n.y+=t/100;let l={};l.mouseChange=n,l.update=!0,s.bControlGl&&!i.bNode?window.controls.update(l):s.controls.update(l),s.bRender&&s.drawCls.render()}zoominSelection(e){let t=this.icn3d,s=t.icn3dui,i={};if(i._zoomFactor=1/t._zoomFactor,i.update=!0,t.bControlGl&&!s.bNode?window.controls&&window.controls.update(i):t.controls&&t.controls.update(i),void 0===e&&(e=s.hashUtilsCls.hash2Atoms(t.hAtoms,t.atoms)),Object.keys(e).length>1){let s=t.applyCenterCls.centerAtoms(e);t.maxD=s.maxD,t.maxD<5&&(t.maxD=5),t.center=s.center,t.applyCenterCls.setCenter(t.center),t.cameraCls.setCamera()}}getTransformationStr(e){this.icn3d.icn3dui;let t={factor:1,mouseChange:{x:0,y:0},quaternion:{_x:0,_y:0,_z:0,_w:1}};return t.factor=parseFloat(e.factor).toPrecision(4),t.mouseChange.x=parseFloat(e.mouseChange.x).toPrecision(4),t.mouseChange.y=parseFloat(e.mouseChange.y).toPrecision(4),t.quaternion._x=parseFloat(e.quaternion._x).toPrecision(4),t.quaternion._y=parseFloat(e.quaternion._y).toPrecision(4),t.quaternion._z=parseFloat(e.quaternion._z).toPrecision(4),t.quaternion._w=parseFloat(e.quaternion._w).toPrecision(4),"1.0000"==t.factor&&(t.factor=1),"0.0000"==t.mouseChange.x&&(t.mouseChange.x=0),"0.0000"==t.mouseChange.y&&(t.mouseChange.y=0),"0.0000"==t.quaternion._x&&(t.quaternion._x=0),"0.0000"==t.quaternion._y&&(t.quaternion._y=0),"0.0000"==t.quaternion._z&&(t.quaternion._z=0),"1.0000"==t.quaternion._w&&(t.quaternion._w=1),JSON.stringify(t)}}class As{constructor(e){this.icn3d=e}saveFile(e,t,s,i){let n,l=this.icn3d,r=l.icn3dui,o=this;if("command"===t){let e=l.loadCmd?l.loadCmd+"\n":"";for(let t=0,s=l.commands.length;t4e3||0!==s.indexOf("http")||l.bInputfile&&!l.bInputUrlfile?$("#"+l.pre+"viewer").html("'+""+document.getElementById(e).innerHTML+" "}savePng(e,t,s){let i=this.icn3d,n=i.icn3dui;if(n.bNode)return"";let l=$("#"+e).width(),r=$("#"+e).height();s&&(r=l);let o=document.getElementById(e),a=o.getBBox(),d=o.cloneNode(!0);i.lineGraphCls.copyStylesInline(d,o);let c=document.createElement("CANVAS");c.width=l,c.height=r;let h=c.getContext("2d");h.clearRect(0,0,a.width,a.height);let p=this.getSvgXml(e,l,r,s),m=window.URL||window.webkitURL||window,u=new Blob([p],{type:"image/svg+xml;charset=utf-8"}),g=new Image;g.src=m.createObjectURL(u),g.onload=function(){if(h.drawImage(g,0,0),m.revokeObjectURL(this.src),n.utilsCls.isIE()){let e=c.msToBlob();e&&(saveAs(e,t),c.remove())}else c.toBlob((function(e){e&&(saveAs(e,t),c.remove())}))}}exportCustomAtoms(e){var t=this.icn3d;t.icn3dui;let s="",i=void 0!==t.defNames2Residues?Object.keys(t.defNames2Residues).sort():[];for(let n=0,l=i.length;n0)if(s){let s={};for(let e=0,l=t.length;eparseInt(p)+1&&(s.ss=" ",f.push(s)),"helix"==t.ss?(s.ss="H",f.push(s)):"sheet"==t.ss&&(s.ss="S",f.push(s)),t.ssend){let e=a.hashUtilsCls.cloneHash(s);e.ss=" ",f.push(e)}p=t.resi}let b,C,y=0,v=!1,_=!1;for(let e=0,t=f.length;e1,A=1,x="",k="",O=0,R="",I={};for(let l in e){let e=o.atoms[l];if(s&&e.het)continue;if(e.structure!=x){r&&S||(d+=w,w="",A>1&&(d+="\nENDMDL\n"),S&&(d+="MODEL "+A+"\n"));let t=n?"Mutated chain_residue "+Object.keys(n)+"; ":"";i||r&&S||(d+=this.getPDBHeader(A-1,g,t,e.structure)),++A}e.chain!=k&&e.structure==x&&k&&(d+="TER\n");let p=e.chain+"_"+e.resi;if(n&&n.hasOwnProperty(p)){I.hasOwnProperty(p)||(d+=n[p],I[p]=1);continue}let m="";m+=e.het?"HETATM":"ATOM ",m+=l.toString().padStart(5," "),m+=" ";let u=e.name.trim();isNaN(u.substr(0,1))||(u=u.substr(1)+u.substr(0,1)),4==u.length?m+=u:(m+=" ",u=u.replace(/\*/g,"'"),"O1P"==u?u="OP1":"O2P"==u?u="OP2":"C5M"==u&&(u="C7 "),m+=u.padEnd(3," ")),m+=" ";let f=e.resn;if(m+=f.length<=3?f.padStart(3," "):f.substr(0,3),r&&A>2&&(o.proteins.hasOwnProperty(e.serial)||o.nucleotides.hasOwnProperty(e.serial)))e.structure==x&&e.chain==k||(R=O<36?"abcdefghijklmnopqrstuvwxyz0123456789"[O]:"?",++O),m+=" "+R;else if(e.chain.length>=2){m+=e.chain.replace(/_/gi,"").substr(0,2)}else 1==e.chain.length?m+=" "+e.chain.substr(0,1):0==e.chain.length&&(m+=" A");let b=e.resi;!isNaN(b)&&e.chain.length>3&&!isNaN(e.chain.substr(3))&&(b=b-1+parseInt(e.chain.substr(3)));let C=parseInt(b);m+=C.toString().length<=4?C.toString().padStart(4," "):C.toString().substr(0,4);let y=e.resi.toString().substr(e.resi.toString().length-1,1);if(isNaN(y)?m+=y:m+=" ",m+=" ".padStart(3," "),m+=e.coord.x.toFixed(3).toString().padStart(8," "),m+=e.coord.y.toFixed(3).toString().padStart(8," "),m+=e.coord.z.toFixed(3).toString().padStart(8," "),t&&e.het){let t=1.5,s=0;"C"==e.elem?t=1.908:"N"==e.elem?t=1.824:"O"==e.elem?t=1.6612:"H"==e.elem?t=1.25:"S"==e.elem?t=2:"P"==e.elem?t=2.1:a.parasCls.vdwRadii.hasOwnProperty(e.elem)&&(t=a.parasCls.vdwRadii[e.elem]),void 0!==a.cfg.cid&&void 0!==e.crg?s=e.crg:c.hasOwnProperty(l)?s=1.38:h.hasOwnProperty(l)?s=-.595:a.parasCls.ionCharges.hasOwnProperty(e.elem)&&(s=a.parasCls.ionCharges[e.elem]),m+=s.toFixed(4).toString().padStart(8," "),m+=t.toFixed(4).toString().padStart(7," ")}else m+="1.00".padStart(6," "),m+=e.b?parseFloat(e.b).toFixed(2).toString().padStart(6," "):" ".padStart(6," "),m+=" ".padStart(10," "),m+=e.elem.padStart(2," "),m+=" ".padStart(2," ");if(e.het&&e.bonds.length>0){w+="CONECT"+l.toString().padStart(5," ");let t={};for(let s=0,i=e.bonds.length;s50?n.molTitle.substr(0,47)+"...":n.molTitle;-1!=e.indexOf('"')&&(e=""),s&&(e=s+e),l+="TITLE "+e+"\n"}return t&&t[r]&&(l+=t[r]),l}showTitle(){var e=this.icn3d,t=e.icn3dui;let s=e.molTitle?e.molTitle:"",i="black"==e.opts.background?t.htmlCls.GREYD:"black";if(void 0===e.inputid)s.length>40&&(s=s.substr(0,40)+"..."),$("#"+e.pre+"title").html(s);else if(void 0!==t.cfg.cid){let t=this.getLinkToStructureSummary();$("#"+e.pre+"title").html("PubChem CID "+e.inputid.toUpperCase()+" : "+s)}else if(void 0!==t.cfg.align)s="VAST+ alignment of "+Object.keys(e.structures),$("#"+e.pre+"title").html(s);else if(void 0!==t.cfg.chainalign){s="Dynamic Structure Alignment of Chains: "+t.cfg.chainalign.split(","),$("#"+e.pre+"title").html(s)}else{let n=Object.keys(t.utilsCls.getStructures(e.dAtoms));if(n.length>1){s="Multiple structures: ";for(let e=0,t=n.length;e'+n[e]+"",e5?"https://alphafold.ebi.ac.uk/entry/"+n[0]:"https://www.ncbi.nlm.nih.gov/structure/?term="+n[0];this.setStructureTitle(e,s,i)}}}setStructureTitle(e,t,s){var i=this.icn3d,n=i.icn3dui;t.length>40&&(t=t.substr(0,40)+"...");let l,r,o=i.inputid;if(-1!=o.indexOf("http"))r="Data from",e=o,l=o;else{let e=n.utilsCls.getHlStructures(),s=!1,a=!1;for(let t in e)t.length>5?a=!0:s=!0;let d=Object.keys(e);if(o=d.join(","),l=n.cfg.refseqid||n.cfg.protein?i.inputid:o.toUpperCase(),s&&a?r="AlphaFold/PDB ID":s?r="PDB ID":a&&(r="AlphaFold ID"),d.length>1&&(r+="s"),i.molTitleHash){t="";for(let e=0,s=d.length;e20&&(e=e.substr(0,17)+"..."),l="Query: "+e+"; target: "+s,$("#"+i.pre+"title").html(l+", "+t)}else $("#"+i.pre+"title").html(r+" "+l+" : "+t);else $("#"+i.pre+"title").html(t)}getLinkToStructureSummary(e){var t=this.icn3d,s=t.icn3dui;let i="https://www.ncbi.nlm.nih.gov/structure/?term=";if(i=void 0!==s.cfg.cid?"https://www.ncbi.nlm.nih.gov/pccompound/?term=":void 0!==s.cfg.refseqid?"https://www.ncbi.nlm.nih.gov/protein/":void 0!==s.cfg.afid?"https://alphafold.ebi.ac.uk/search/text/":Object.keys(t.structures).length>1?"https://www.ncbi.nlm.nih.gov/structure/?term=":s.htmlCls.baseUrl+"pdb/",void 0===t.inputid)i="https://www.ncbi.nlm.nih.gov/pccompound/?term="+t.molTitle;else{let n=t.inputid.split("_");1===n.length?(i+=t.inputid,e&&s.htmlCls.clickMenuCls.setLogCmd("link to "+t.inputid+": "+i,!1)):2===n.length&&(s.cfg.afid?i+=n[0]+" "+n[1]:i+=n[0]+" OR "+n[1],e&&s.htmlCls.clickMenuCls.setLogCmd("link to structures "+n[0]+" and "+n[1]+": "+i,!1))}return i}setEntrezLinks(e){var t=this.icn3d,s=t.icn3dui;let i,n=Object.keys(t.structures);if(1===n.length){i="https://www.ncbi.nlm.nih.gov/"+e+"/?term="+n[0],s.htmlCls.clickMenuCls.setLogCmd("Entrez "+e+" about PDB "+n[0]+": "+i,!1);let l=t.structures&&Object.keys(t.structures).length>0?"_blank":"_self";window.open(i,l)}else if(2===n.length){i="https://www.ncbi.nlm.nih.gov/"+e+"/?term="+n[0]+" OR "+n[1],s.htmlCls.clickMenuCls.setLogCmd("Entrez "+e+" about PDB "+n[0]+" OR "+n[1]+": "+i,!1);let l=t.structures&&Object.keys(t.structures).length>0?"_blank":"_self";window.open(i,l)}}}class xs{constructor(e){this.icn3d=e}async shareLink(e,t){let s=this.icn3d,i=s.icn3dui,n=this.shareLinkUrl(),l=n.length>4e3||0!==n.indexOf("http"),r=Object.keys(s.structures).join("_");if(r==s.defaultPdbId&&(s.filename?r=s.filename:s.inputid&&(r=s.inputid)),e){if(t||s.bInputfile||l)return void s.saveFileCls.saveFile(r+"_icn3d_loadable.png","png")}else{if(s.bInputfile&&!s.bInputUrlfile)return void alert("Share Link does NOT work when the data are from custom files. Please save 'iCn3D PNG Image' in the File menu and open it in iCn3D.");if(l)return void alert("The url is more than 4000 characters and may not work. Please save 'iCn3D PNG Image' or 'State File' and open them in iCn3D.");i.htmlCls.clickMenuCls.setLogCmd("share link: "+n,!1)}let o="Problem in getting shortened URL";if(!i.cfg.notebook){let t=await this.getShareLinkPrms(n,e);if(void 0!==t.shortLink&&(o=t.shortLink,e)){let e=o.split("/"),t=e[e.length-1];s.saveFileCls.saveFile(r+"-"+t+".png","png");let i='\n\n",s.saveFileCls.saveFile(r+"-"+t+".html","html",i)}e&&void 0===t.shortLink&&s.saveFileCls.saveFile(r+"_icn3d_loadable.png","png");let i=o.split("page.link/");2==i.length&&(o="https://structure.ncbi.nlm.nih.gov/icn3d/share.html?"+i[1]),$("#"+s.pre+"short_url").val(o),$("#"+s.pre+"short_url_title").val(o+"&t="+s.yournote)}let a=this.shareLinkUrl(void 0,!0),d="view = icn3dpy.view(q='"+(i.cfg.url?"url="+i.cfg.url:i.cfg.idname+"="+i.cfg.idvalue)+"',command='"+a+"')\nview";(i.cfg.url||i.cfg.idname)&&$("#"+s.pre+"jn_commands").val(d),$("#"+s.pre+"ori_url").val(n),e||i.htmlCls.dialogCls.openDlg("dl_copyurl","Copy a Share Link URL or Jupyter Notebook Commands")}getShareLinkPrms(e,t){let s=this.icn3d,i=s.icn3dui;return new Promise((function(n,l){$.ajax({url:"https://firebasedynamiclinks.googleapis.com/v1/shortLinks?key=AIzaSyBxl9CgM0dY5lagHL4UOhEpLWE1fuwdnvc",type:"POST",data:{longDynamicLink:"https://icn3d.page.link/?link="+encodeURIComponent(e)},dataType:"json",success:function(e){n(e)},error:function(n,l,r){let o="Problem in getting shortened URL";$("#"+s.pre+"ori_url").val(e),$("#"+s.pre+"short_url").val(o),$("#"+s.pre+"short_url_title").val(o+"&t="+s.yournote),t||i.htmlCls.dialogCls.openDlg("dl_copyurl","Copy a Share Link URL")}})}))}shareLinkUrl(e,t){let s=this.icn3d,i=s.icn3dui,n=i.htmlCls.baseUrl+"icn3d/?",l="";if(i.cfg.bSidebyside&&(n=i.htmlCls.baseUrl+"icn3d/full2.html?"),s.bInputUrlfile){n=window.location.href.split("?")[0]+"?"+s.inputurl+"&"}let r,o={};for(let e in s.cfg){let t=s.cfg[e];"inpara"!==e&&"command"!==e&&"usepdbnum"!==e&&"date"!==e&&"v"!==e&&void 0!==t&&("width"===e&&"100%"===t||"height"===e&&"100%"===t||"resize"===e&&!0===t||"showmenu"===e&&!0===t||"showtitle"===e&&!0===t||"showcommand"===e&&!0===t||"mobilemenu"===e&&!1===t||"showanno"===e&&!1===t||"showseq"===e&&!1===t||"showalignseq"===e&&!1===t||"show2d"===e&&!1===t||"showsets"===e&&!1===t||"rotate"===e&&"right"===t||"command"!==e&&("options"===e?Object.keys(t).length>0&&(o[e]=JSON.stringify(t)):!0===t?o[e]=1:!1===t?o[e]=0:""!==t&&(o[e]=t)))}s.bAfMem?o.afmem="on":(i.cfg.afid||1==Object.keys(s.structures).length&&Object.keys(s.structures)[0].length>5)&&(o.afmem="off");let a=-1;void 0!==i.cfg.inpara&&(a=i.cfg.inpara.indexOf("&command=")),r=-1!==a?i.cfg.inpara.substr(0,a):i.cfg.inpara;let d=!1;if(!s.bInputUrlfile){let e=r&&r.substr(1)?r.substr(1).split("&"):[];for(let t=0,s=e.length;tc){u=s.commands[c].split("|||")[0].split("&command=")[0].trim(),-1!==u.indexOf(g)&&++f}let b,C=c+1,y="";for(let e=s.commands.length;C0&&f%2==0&&u!==g&&(y+=g+"; "),y+=u+"|||"+s.transformCls.getTransformationStr(p),m+=u+"|||"+s.transformCls.getTransformationStr(p)+"\n"),n+=y,l=y,m=m.replace(/!/g,Object.keys(s.structures)[0]+"_"),(s.bEsmfold||s.bInputfile&&!s.bInputUrlfile||s.bInputUrlfile&&s.bAppend||n.length>4e3)&&(n=m),void 0!==s.structures&&1==Object.keys(s.structures).length&&void 0!==s.inputid&&(b=Object.keys(s.structures)[0],n=n.replace(new RegExp(b+"_","g"),"!"),l=l.replace(new RegExp(b+"_","g"),"!")),void 0!==i.cfg.blast_rep_id&&(n=n.replace(new RegExp("blast_rep_id=!","g"),"blast_rep_id="+b+"_")),t?l:n}getPngText(){let e,t=this.icn3d;t.icn3dui;let s="";if(t.bInputfile)e=this.shareLinkUrl(true),"http"==e.substr(0,4)?s+="\nShare Link: "+e:(s+="\nStart of type file======\n",s+=t.InputfileType+"\n",s+="End of type file======\n",s+="Start of data file======\n",s+=t.saveFileCls.getAtomPDB(t.atoms),s+="End of data file======\n",s+="Start of state file======\n",s+=e+"\n",s+="End of state file======\n");else{e=this.shareLinkUrl(),e.length>4e3||0!==e.indexOf("http")?(e=this.shareLinkUrl(true),s+="\nStart of state file======\n",s+=e+"\n",s+="End of state file======\n"):s+="\nShare Link: "+e}return s=s.replace(/!/g,Object.keys(t.structures)[0]+"_"),s}}class ks{constructor(e){this.icn3d=e}setThichknessFor3Dprint(){let e=this.icn3d,t=e.icn3dui;e.lineRadius=1,e.coilWidth=1.2,e.cylinderRadius=.8,e.crosslinkRadius=.8,e.traceRadius=1,e.dotSphereScale=.6,e.sphereRadius=1.5,e.ribbonthickness=1,e.helixSheetWidth=2,e.nucleicAcidWidth=1.4,t.htmlCls.setHtmlCls.setCookieForThickness()}prepareFor3Dprint(){let e=this.icn3d,t=e.icn3dui;if(e.bShowHighlight=!1,e.hlObjectsCls.removeHlObjects(),e.bDashedLines=!1,e.bSetThickness||void 0!==t.cfg.cid||this.setThichknessFor3Dprint(),void 0!==e.lines.hbond)for(let t=0,s=e.lines.hbond.length;tt.substr(0,s))return 1;if(e.substr(0,s)==t.substr(0,s)){if(parseInt(e.substr(s+1))parseInt(t.substr(i+1)))return 1;if(parseInt(e.substr(s+1))==parseInt(t.substr(i+1)))return 0}}})),n="Structure Chain Residue Number "+i[e].substr(0,t)+" "+i[e].substr(t+1,s-t-1)+" "+i[e].substr(s+1)+" "}let l=Object.keys(t.utilsCls.getHlStructures()).join(",");e.saveFileCls.saveFile(l+"_residues.txt","html",n)}addStabilizer(){let e=this.icn3d,t=e.icn3dui,s=3.5;if(Object.keys(e.dAtoms).length>0){let i,n={},l=12.25,r=3.2*3.2;for(let t in e.dAtoms){let s=e.atoms[t];!e.nucleotides.hasOwnProperty(s.serial)||"N1"!==s.name&&"N2"!==s.name&&"N3"!==s.name&&"N4"!==s.name&&"N6"!==s.name&&"O2"!==s.name&&"O6"!==s.name||(i=s.structure+"_"+s.chain+"_"+s.resi+"_"+s.name,n[i]=s)}let o=Object.keys(n),a=o.length;void 0===e.pairArray&&(e.pairArray=[]);for(let t=0;ts)continue;let h=Math.abs(n[a].coord.y-n[d].coord.y);if(h>s)continue;let p=Math.abs(n[a].coord.z-n[d].coord.z);if(p>s)continue;let m=c*c+h*h+p*p;m>l||ms+1||rs+2||rs+4||r0&&o.length>0)if(a){let t=parseInt((r.length+.5)/2);e.pairArray.push(o[0]),e.pairArray.push(r[t])}else{let t=10,s=parseInt(r.length/(t+1));for(let i=0,n=o.length;i1&&t.bAssembly&&(t.threshbox=180/Math.pow(t.biomtMatrices.length,.33),t.applyMapCls.removeSurfaces(),t.applyMapCls.applySurfaceOptions(),t.applyMapCls.removeMaps(),t.applyMapCls.applyMapOptions(),t.applyMapCls.removeEmmaps(),t.applyMapCls.applyEmmapOptions());let i=this.saveStlFile(),n=Object.keys(s.utilsCls.getHlStructures()).join(",");if(t.saveFileCls.saveFile(n+e+".stl","binary",i),void 0!==t.biomtMatrices&&t.biomtMatrices.length>1&&t.bAssembly&&Object.keys(t.dAtoms).length*t.biomtMatrices.length>t.maxAtoms3DMultiFile){alert(t.biomtMatrices.length+" files will be generated for this assembly. Please merge these files using some software and 3D print the merged file.");let s=new THREE.Matrix4;s.identity();let l=1;for(let r=0;r1&&t.bAssembly&&(t.threshbox=180/Math.pow(t.biomtMatrices.length,.33),t.applyMapCls.removeSurfaces(),t.applyMapCls.applySurfaceOptions(),t.applyMapCls.removeMaps(),t.applyMapCls.applyMapOptions(),t.applyMapCls.removeEmmaps(),t.applyMapCls.applyEmmapOptions());let i=this.saveVrmlFile(),n=Object.keys(s.utilsCls.getHlStructures()).join(",");if(t.saveFileCls.saveFile(n+e+".wrl","text",i),void 0!==t.biomtMatrices&&t.biomtMatrices.length>1&&t.bAssembly&&Object.keys(t.dAtoms).length*t.biomtMatrices.length>t.maxAtoms3DMultiFile){alert(t.biomtMatrices.length+" files will be generated for this assembly. Please merge these files using some software and 3D print the merged file.");let s=new THREE.Matrix4;s.identity();let n=1;for(let l=0;l7e4)return alert("Please display a subset of the structure to export 3D files. Then merge the files for 3D printing..."),[""];t.threeDPrintCls.prepareFor3Dprint();let i=0;i+=this.getFaceCnt(t.mdl),i+=this.getFaceCnt(t.mdl_ghost);let n=[],l=new Uint8Array(84),r="STL file for the structure(s) ",o=Object.keys(t.structures);for(let e=0,t=o.length;e80&&(r=r.substr(0,80));for(let e=0;e<80;++e)e1&&t.bAssembly&&Object.keys(t.dAtoms).length*t.biomtMatrices.length<=t.maxAtoms3DMultiFile?this.updateArray(l,s.convertTypeCls.passInt32([i*t.biomtMatrices.length]),80):this.updateArray(l,s.convertTypeCls.passInt32([i]),80),n.push(new Blob([l],{type:"application/octet-stream"})),n=this.processStlMeshGroup(t.mdl,n,e),n=this.processStlMeshGroup(t.mdl_ghost,n,e),void 0!==t.biomtMatrices&&t.biomtMatrices.length>1&&t.bAssembly&&Object.keys(t.dAtoms).length*t.biomtMatrices.length<=t.maxAtoms3DMultiFile){let e=new THREE.Matrix4;e.identity();for(let s=0;s5e4)return alert("Please display a subset of the structure to export 3D files. Then merge the files for 3D printing..."),[""];t.threeDPrintCls.prepareFor3Dprint();let s=[];s.push("#VRML V2.0 utf8\n");let i=0,n=this.processVrmlMeshGroup(t.mdl,s,i,e);if(s=n.vrmlStrArray,i=n.vertexCnt,n=this.processVrmlMeshGroup(t.mdl_ghost,s,i,e),s=n.vrmlStrArray,i=n.vertexCnt,void 0!==t.biomtMatrices&&t.biomtMatrices.length>1&&t.bAssembly&&Object.keys(t.dAtoms).length*t.biomtMatrices.length<=t.maxAtoms3DMultiFile){let e=new THREE.Matrix4;e.identity();for(let l=0;l0?h.z=-1:h.z=1,s.cam===s.perspectiveCamera?(s.cam_z>0?h.z=-1:h.z=1,h.unproject(s.cam),s.raycaster.set(s.cam.position,h.sub(s.cam.position).normalize())):s.cam===s.orthographicCamera&&(s.cam_z>0?h.z=1:h.z=-1,h.unproject(s.cam),s.raycaster.set(h,new THREE.Vector3(0,0,-1).transformDirection(s.cam.matrixWorld)));let p=this.isIntersect(s.objects,s.mdl,t,d,c);p||(p=this.isIntersect(s.objects_ghost,s.mdl_ghost,t,d,c))}isIntersect(e,t,s,i,n){let l=this.icn3d;l.icn3dui;let r=l.raycaster.intersectObjects(e),o=!1,a=t.position;if(r.length>0){r[0].point.sub(a);let e=l.rayThreshold,t=this.getAtomsFromPosition(r[0].point,e);for(;!t&&e<10;)e+=.5,t=this.getAtomsFromPosition(r[0].point,e);t?(o=!0,l.pickpair?s&&(l.pAtomNum%2==0?l.pAtom=t:l.pAtom2=t,++l.pAtomNum):l.pAtom=t,s?l.pickingCls.showPicking(t):l.pickingCls.showPicking(t,i,n)):console.log("No atoms were found in 10 andstrom range")}return o}getAtomsFromPosition(e,t){let s,i=this.icn3d,n=i.icn3dui;for(s in null==t&&(t=1),i.dAtoms){let l=i.atoms[s];if(i.ions.hasOwnProperty(s)&&"sphere"===i.opts.ions){let s=n.parasCls.vdwRadii[l.elem.toUpperCase()];if(Math.abs(l.coord.x-e.x)-s>t)continue;if(Math.abs(l.coord.y-e.y)-s>t)continue;if(Math.abs(l.coord.z-e.z)-s>t)continue}else{if(l.coord.xe.x+t)continue;if(l.coord.ye.y+t)continue;if(l.coord.ze.z+t)continue}return l}return null}}class Is{constructor(e){this.icn3d=e}setControl(){let e=this.icn3d,t=e.icn3dui;if(t.bNode)return;let s=this;e.WIDTH=e.container.width(),e.HEIGHT=e.container.height(),e.applyCenterCls.setWidthHeight(e.WIDTH,e.HEIGHT),e._zoomFactor=1,e.mouseChange=new THREE.Vector2(0,0),e.quaternion=new THREE.Quaternion(0,0,0,1),e.container.bind("contextmenu",(function(e){e.preventDefault()})),e.typetext=!1,$(document).bind("keyup",(function(t){16===t.keyCode&&(e.bShift=!1),17!==t.keyCode&&224!==t.keyCode&&91!==t.keyCode||(e.bCtrl=!1)})),$("input[type=text], textarea").focus((function(){e.typetext=!0})),$("input[type=text], textarea").blur((function(){e.typetext=!1})),$(document).bind("keydown",(async function(s){if((s.shiftKey||16===s.keyCode)&&(e.bShift=!0),(s.ctrlKey||17===s.keyCode||224===s.keyCode||91===s.keyCode)&&(e.bCtrl=!0),!e.bControlGl&&!e.controls||e.bControlGl&&!window.controls)return;e.bStopRotate=!0;let i=e.bShift?90:5;if(!e.typetext)if(90===s.keyCode){let s={};e.bControlGl&&!t.bNode?window.cam===e.perspectiveCamera?s._zoomFactor=.9:window.cam===e.orthographicCamera&&(e._zoomFactor<.1?e._zoomFactor=.1:e._zoomFactor>1&&(e._zoomFactor=1),s._zoomFactor=.8*e._zoomFactor,s._zoomFactor<.1&&(s._zoomFactor=.1)):e.cam===e.perspectiveCamera?s._zoomFactor=.9:e.cam===e.orthographicCamera&&(e._zoomFactor<.1?e._zoomFactor=.1:e._zoomFactor>1&&(e._zoomFactor=1),s._zoomFactor=.8*e._zoomFactor,s._zoomFactor<.1&&(s._zoomFactor=.1)),s.update=!0,e.bControlGl&&!t.bNode?window.controls.update(s):e.controls.update(s),e.bRender&&e.drawCls.render()}else if(88===s.keyCode){let s={};e.bControlGl&&!t.bNode?window.cam===e.perspectiveCamera?s._zoomFactor=1.03:window.cam===e.orthographicCamera&&(e._zoomFactor>10?e._zoomFactor=10:e._zoomFactor<1&&(e._zoomFactor=1),s._zoomFactor=1.01*e._zoomFactor,s._zoomFactor>10&&(s._zoomFactor=10)):e.cam===e.perspectiveCamera?s._zoomFactor=1.03:e.cam===e.orthographicCamera&&(e._zoomFactor>10?e._zoomFactor=10:e._zoomFactor<1&&(e._zoomFactor=1),s._zoomFactor=1.01*e._zoomFactor,s._zoomFactor>10&&(s._zoomFactor=10)),s.update=!0,e.bControlGl&&!t.bNode?window.controls.update(s):e.controls.update(s),e.bRender&&e.drawCls.render()}else if(76===s.keyCode){let t=new THREE.Vector3(0,1,0),s=-i/180*Math.PI;e.transformCls.setRotation(t,s)}else if(74===s.keyCode){let t=new THREE.Vector3(0,1,0),s=i/180*Math.PI;e.transformCls.setRotation(t,s)}else if(73===s.keyCode){let t=new THREE.Vector3(1,0,0),s=-i/180*Math.PI;e.transformCls.setRotation(t,s)}else if(77===s.keyCode){let t=new THREE.Vector3(1,0,0),s=i/180*Math.PI;e.transformCls.setRotation(t,s)}else 65===s.keyCode&&Object.keys(e.structures).length>1&&await e.alternateCls.alternateWrapper()})),e.container.bind("mouseup",(function(t){e.isDragging=!1})),e.container.bind("touchend",(function(t){e.isDragging=!1})),e.container.bind("mousedown",(function(s){if(e.isDragging=!0,e.scene){if(e.bStopRotate=!0,e.pk&&(s.altKey||s.ctrlKey||s.shiftKey||18===s.keyCode||16===s.keyCode||17===s.keyCode||224===s.keyCode||91===s.keyCode)){e.highlightlevel=e.pk;let t=!0;e.rayCls.rayCaster(s,t)}e.bControlGl&&!t.bNode?(window.controls.handleResize(),window.controls.update()):(e.controls.handleResize(),e.controls.update()),e.bRender&&e.drawCls.render()}})),e.container.bind("touchstart",(function(s){if(s.preventDefault(),e.isDragging=!0,!e.scene)return;e.bStopRotate=!0,$("#"+e.pre+"popup").hide();e.rayCls.rayCaster(s,!0),e.bControlGl&&!t.bNode?(window.controls.handleResize(),window.controls.update()):(e.controls.handleResize(),e.controls.update()),e.bRender&&e.drawCls.render()})),e.container.bind("mousemove touchmove",(function(e){s.mouseMove(e)})),e.container.bind("mousewheel",(function(s){s.preventDefault(),e.scene&&(e.bStopRotate=!0,e.bControlGl&&!t.bNode?(window.controls.handleResize(),window.controls.update()):(e.controls.handleResize(),e.controls.update()),e.bRender&&e.drawCls.render())})),e.container.bind("DOMMouseScroll",(function(s){s.preventDefault(),e.scene&&(e.bStopRotate=!0,e.bControlGl&&!t.bNode?(window.controls.handleResize(),window.controls.update()):(e.controls.handleResize(),e.controls.update()),e.bRender&&e.drawCls.render())}))}mouseMove(e){let t=this.icn3d,s=t.icn3dui;if(s.bNode)return;if(e.preventDefault(),!t.scene)return;$("#"+t.pre+"popup").hide();if(t.rayCls.rayCaster(e,!1),t.bControlGl&&!s.bNode){window.controls.handleResize(),window.controls.update();for(let e in window.icn3duiHash){let t=window.icn3duiHash[e].icn3d;t.bRender&&t.drawCls.render()}}else t.controls.handleResize(),t.controls.update(),t.bRender&&t.drawCls.render()}}class Ts{constructor(e){this.icn3d=e}showPicking(e,t,s){let i=this.icn3d,n=i.icn3dui;if(void 0!==n.cfg.cid&&0!=i.pk&&(i.pk=1),i.highlightlevel=i.pk,this.showPickingBase(e,t,s),0!=i.pk)if(void 0!==t&&void 0!==s){null!=n.cfg.showmenu&&1==n.cfg.showmenu&&(s+=n.htmlCls.MENU_HEIGHT);let l=1==i.pk?e.resn+e.resi+"@"+e.name:e.resn+e.resi;void 0!==i.structures&&Object.keys(i.structures).length>1?(l=e.structure+"_"+e.chain+" "+l,$("#"+i.pre+"popup").css("width","160px")):$("#"+i.pre+"popup").css("width","80px"),$("#"+i.pre+"popup").html(l),$("#"+i.pre+"popup").css("top",s).css("left",t+20).show()}else{i.hlUpdateCls.updateHlAll();let t={};t.factor=i._zoomFactor,t.mouseChange=i.mouseChange,t.quaternion={},t.quaternion._x=parseFloat(i.quaternion._x).toPrecision(5),t.quaternion._y=parseFloat(i.quaternion._y).toPrecision(5),t.quaternion._z=parseFloat(i.quaternion._z).toPrecision(5),t.quaternion._w=parseFloat(i.quaternion._w).toPrecision(5),n.htmlCls.clickMenuCls.setLogCmd("pickatom "+e.serial,!0),i.selectionCls.saveSelInCommand(),i.bSphereCalc=!1,i.bHbondCalc=!1}}showPickingBase(e,t,s){this.icn3d.icn3dui,void 0===t&&void 0===s&&this.showPickingHilight(e)}getPickedAtomList(e,t){let s=this.icn3d;s.icn3dui;let i={};if(1===e)i[t.serial]=1;else if(2===e){let e=t.structure+"_"+t.chain+"_"+t.resi;i=s.residues[e]}else if(3===e)i=this.selectStrandHelixFromAtom(t);else if(4===e)i=this.select3ddomainFromAtom(t);else if(5===e){let e=t.structure+"_"+t.chain;i=s.chains[e]}return i}showPickingHilight(e){let t=this.icn3d,s=t.icn3dui;t.bShift||t.bCtrl||t.hlObjectsCls.removeHlObjects(),t.pickedAtomList=this.getPickedAtomList(t.pk,e),0===t.pk?t.bShowHighlight=!1:t.bShowHighlight=!0;let i=Object.keys(t.hAtoms).length==Object.keys(t.atoms).length?{}:s.hashUtilsCls.intHash(t.hAtoms,t.pickedAtomList),n=Object.keys(i).length;if(t.bShift||t.bCtrl)if(t.bShift){if(void 0===t.prevPickedAtomList)t.hAtoms=s.hashUtilsCls.unionHash(t.hAtoms,t.pickedAtomList);else{let e=t.firstAtomObjCls.getFirstAtomObj(t.prevPickedAtomList),i=t.firstAtomObjCls.getFirstAtomObj(t.pickedAtomList);if(e.structure+"_"+e.chain!=i.structure+"_"+i.chain)t.hAtoms=s.hashUtilsCls.unionHash(t.hAtoms,t.pickedAtomList);else{let e;e=s.hashUtilsCls.unionHash(e,t.prevPickedAtomList),e=s.hashUtilsCls.unionHash(e,t.pickedAtomList);let i=t.firstAtomObjCls.getFirstAtomObj(e),n=t.firstAtomObjCls.getLastAtomObj(e);for(let e=i.serial;e<=n.serial;++e)t.hAtoms[e]=1}}t.prevPickedAtomList=s.hashUtilsCls.cloneHash(t.pickedAtomList)}else t.bCtrl&&(t.hAtoms=n>0?s.hashUtilsCls.exclHash(t.hAtoms,t.pickedAtomList):s.hashUtilsCls.unionHash(t.hAtoms,t.pickedAtomList));else t.hAtoms=s.hashUtilsCls.cloneHash(t.pickedAtomList);t.hlObjectsCls.removeHlObjects(),t.hlObjectsCls.addHlObjects()}select3ddomainFromAtom(e){let t,s=this.icn3d,i=s.icn3dui,n=e.structure+"_"+e.chain,l=n+"_"+e.resi;for(let e in s.tddomains){let i=e.indexOf("_3d_domain");if(e.substr(0,i)==n&&-1!==Object.keys(s.tddomains[e]).indexOf(l)){t=e;break}}let r={};for(let e in s.tddomains[t])r=i.hashUtilsCls.unionHash(r,s.residues[e]);return r}selectStrandHelixFromAtom(e){let t=this.icn3d,s=t.icn3dui,i=e,n=e,l={},r=i.resi;if(!i.ssbegin&&!isNaN(i.resi)){for(let e=i.resi-1;e>0;--e){let s=i.structure+"_"+i.chain+"_"+e;if(!t.residues.hasOwnProperty(s))break;let n=t.firstAtomObjCls.getFirstCalphaAtomObj(t.residues[s]);if(r=n.resi,"coil"!==i.ss&&n.ss===i.ss&&n.ssbegin||"coil"===i.ss&&n.ss!==i.ss){"coil"===i.ss&&n.ss!==i.ss&&(r=parseInt(n.resi)+1);break}}for(let e=r;e<=i.resi;++e){let n=i.structure+"_"+i.chain+"_"+e;l=s.hashUtilsCls.unionHash(l,s.hashUtilsCls.hash2Atoms(t.residues[n],t.atoms))}}let o=n.resi,a=t.firstAtomObjCls.getLastAtomObj(t.chains[n.structure+"_"+n.chain]).resi;for(let e=parseInt(n.resi)+1;e<=parseInt(a);++e){let s=n.structure+"_"+n.chain+"_"+e;if(!t.residues.hasOwnProperty(s))break;let i=t.firstAtomObjCls.getFirstCalphaAtomObj(t.residues[s]);if(o=i.resi,"coil"!==n.ss&&i.ss===n.ss&&i.ssend||"coil"===n.ss&&i.ss!==n.ss){"coil"!==n.ss||i.ss===n.ss||isNaN(i.resi)||(o=i.resi-1);break}}for(let e=parseInt(n.resi)+1;e<=parseInt(o);++e){let i=n.structure+"_"+n.chain+"_"+e;l=s.hashUtilsCls.unionHash(l,s.hashUtilsCls.hash2Atoms(t.residues[i],t.atoms))}return l}}class Es{constructor(e){this.icn3d=e,this.xrSessionIsGranted=!1}createButton(e,t){let s=this.icn3d,i=s.icn3dui;t&&console.error('THREE.VRButton: The "options" parameter has been removed. Please set the reference space type via renderer.xr.setReferenceSpaceType() instead.');const n=document.createElement("button");function l(){n.style.display="",n.style.cursor="auto",n.style.left="calc(33% - 75px)",n.style.width="150px",n.onmouseenter=null,n.onmouseleave=null,n.onclick=null}let r=this;if("xr"in navigator)return n.id=i.pre+"VRButton",n.style.display="none",(o=n).style.position="absolute",o.style.bottom="20px",o.style.padding="12px 6px",o.style.border="1px solid #fff",o.style.borderRadius="4px",o.style.background="#000",o.style.color="#f8b84e",o.style.font="bold 13px sans-serif",o.style.textAlign="center",o.style.opacity="0.8",o.style.outline="none",o.style.zIndex="999",navigator.xr.isSessionSupported("immersive-vr").then((function(t){t?function(){let t=null;async function i(s){s.addEventListener("end",l),await e.xr.setSession(s),n.textContent="EXIT VR",t=s}function l(){s.transformCls.resetOrientation(),s.bVr=!1,s.drawCls.draw(),t.removeEventListener("end",l),n.textContent="ENTER VR",t=null}n.style.display="",n.style.cursor="pointer",n.style.left="calc(33% - 50px)",n.style.width="100px",n.textContent="ENTER VR",n.onmouseenter=function(){n.style.opacity="1.0"},n.onmouseleave=function(){n.style.opacity="0.8"},n.onclick=function(){if(s.bImpo=!1,s.bVr=!0,s.drawCls.draw(s.bVr),null===t){const e={optionalFeatures:["local-floor","bounded-floor","hand-tracking","layers"]};navigator.xr.requestSession("immersive-vr",e).then(i)}else t.end()}}():(l(),n.style.display="none"),t&&r.xrSessionIsGranted&&n.click()})).catch((function(e){l(),console.warn("Exception when trying to call xr.isSessionSupported",e),n.style.display="none"})),n;return document.createElement("span");var o}registerSessionGrantedListener(){"xr"in navigator&&navigator.xr.addEventListener("sessiongranted",(()=>{this.xrSessionIsGranted=!0}))}}class Ps{constructor(e){this.icn3d=e,this.xrSessionIsGranted=!1}createButton(e,t={}){let s=this.icn3d,i=s.icn3dui;const n=document.createElement("button");function l(){n.style.display="",n.style.cursor="auto",n.style.left="calc(66% - 50px)",n.style.width="150px",n.onmouseenter=null,n.onmouseleave=null,n.onclick=null}function r(e){e.style.position="absolute",e.style.bottom="20px",e.style.padding="12px 6px",e.style.border="1px solid #fff",e.style.borderRadius="4px",e.style.background="#000",e.style.color="#f8b84e",e.style.font="bold 13px sans-serif",e.style.textAlign="center",e.style.opacity="0.8",e.style.outline="none",e.style.zIndex="999"}if(i.utilsCls.isAndroid()&&i.utilsCls.isChrome()){if("xr"in navigator)return n.id=i.pre+"ARButton",n.style.display="none",r(n),navigator.xr.isSessionSupported("immersive-ar").then((function(i){i?function(){if(void 0===t.domOverlay){const e=document.createElement("div");e.style.display="none",document.body.appendChild(e);const s=document.createElementNS("http://www.w3.org/2000/svg","svg");s.setAttribute("width",38),s.setAttribute("height",38),s.style.position="absolute",s.style.right="20px",s.style.top="20px",s.addEventListener("click",(function(){i.end()})),e.appendChild(s);const n=document.createElementNS("http://www.w3.org/2000/svg","path");n.setAttribute("d","M 12,12 L 28,28 M 28,12 12,28"),n.setAttribute("stroke","#fff"),n.setAttribute("stroke-width",2),s.appendChild(n),void 0===t.optionalFeatures&&(t.optionalFeatures=[]),t.optionalFeatures.push("dom-overlay"),t.domOverlay={root:e}}let i=null;async function l(s){s.addEventListener("end",r),e.xr.setReferenceSpaceType("local"),await e.xr.setSession(s),n.textContent="STOP AR",t.domOverlay.root.style.display="",i=s}function r(){s.transformCls.resetOrientation(),s.bAr=!1,s.drawCls.draw(),i.removeEventListener("end",r),n.textContent="START AR",t.domOverlay.root.style.display="none",i=null}n.style.display="",n.style.cursor="pointer",n.style.left="calc(66% - 50px)",n.style.width="100px",n.textContent="START AR",n.onmouseenter=function(){n.style.opacity="1.0"},n.onmouseleave=function(){n.style.opacity="0.8"},n.onclick=function(){s.bImpo=!1,s.opts.background="transparent",s.bAr=!0,s.drawCls.draw(s.bAr),null===i?navigator.xr.requestSession("immersive-ar",t).then(l):i.end()}}():(l(),n.style.display="none")})).catch((function(e){l(),console.warn("Exception when trying to call xr.isSessionSupported",e),n.style.display="none"})),n;return document.createElement("span")}return n.id=i.pre+"ARButton",n.style.display="none",r(n),l(),n.style.display="none",n}}class Ms{constructor(e){let t,s,i,n=e;if(this.icn3dui=e,this.id=this.icn3dui.pre+"canvas",this.pre=this.icn3dui.pre,this.container=$("#"+this.id),this.oriContainer=$("#"+this.id),this.bControlGl=!1,this.maxatomcnt=1e5,this.overdraw=0,this.bDrawn=!1,this.bOpm=!1,this.crossstrucinter=0,this.bSecondaryStructure=!1,this.bHighlight=1,this.renderOrderPicking=-1,this.bInitial=!0,this.bDoublecolor=!1,this.originSize=1,this.ALTERNATE_STRUCTURE=-1,this.bUsePdbNum=!0,!this.icn3dui.bNode){let e=document.createElement("canvas");t=!(!window.WebGLRenderingContext||!e.getContext("webgl")&&!e.getContext("experimental-webgl")),e.remove(),e=document.createElement("canvas"),s=!(!window.WebGLRenderingContext||!e.getContext("webgl2")),e.remove(),i="xr"in navigator,t?(s&&i?(this.renderer=new THREE.WebGLRenderer({canvas:this.oriContainer.get(0),antialias:!0,preserveDrawingBuffer:!0,sortObjects:!1,alpha:!0}),this.renderer.xr.enabled=!0):this.renderer=new THREE.WebGL1Renderer({canvas:this.oriContainer.get(0),antialias:!0,preserveDrawingBuffer:!0,sortObjects:!1,alpha:!0}),this.overdraw=0):alert("Currently your web browser has a problem on WebGL. If you are using Chrome, open a new tab for the same URL and WebGL may work again.")}this.frac=new THREE.Color(.1,.1,.1),this.shininess=40,this.emissive=1118481,this.light1=.8,this.light2=.4,this.light3=.2,this.lineRadius=.1,this.coilWidth=.3,this.cylinderRadius=.4,this.crosslinkRadius=.4,this.traceRadius=.4,this.dotSphereScale=.3,this.sphereRadius=1.5,this.cylinderHelixRadius=1.6,this.ribbonthickness=.2,this.helixSheetWidth=1.3,this.nucleicAcidWidth=.8,this.scaleFactor=1,this.labelScale=1,this.resizeRatioX=1,this.resizeRatioY=1,this.bImpo=!0,this.bInstanced=!0,this.chainMissingResidueArray={},this._zoomFactor=1,this.transparentRenderOrder=!1,this.AFUniprotVersion="v4",this.defaultPdbId="stru",this.icn3dui.bNode||(s&&i?(this.bExtFragDepth=!0,this.bImpo=!0,this.bInstanced=!0):(this.bExtFragDepth=this.renderer.extensions.get("EXT_frag_depth"),this.bExtFragDepth?console.log("EXT_frag_depth is supported. All spheres and cylinders are drawn using shaders."):(this.bImpo=!1,console.log("EXT_frag_depth is NOT supported. All spheres and cylinders are drawn using geometry.")),this.bInstanced=this.renderer.extensions.get("ANGLE_instanced_arrays"),this.bInstanced?console.log("ANGLE_instanced_arrays is supported. Assembly is drawn with one copy of the asymmetric unit using hardware instancing."):console.log("ANGLE_instanced_arrays is NOT supported. Assembly is drawn by making copies of the asymmetric unit."))),this.posArray=new Array,this.colorArray=new Array,this.pos2Array=new Array,this.color2Array=new Array,this.radiusArray=new Array,this.posArraySphere=new Array,this.colorArraySphere=new Array,this.radiusArraySphere=new Array,this.axis=!1,this.pk=1,this.highlightlevel=1,this.pickpair=!1,this.pAtomNum=0,this.pAtom=void 0,this.pAtom2=void 0,this.bCtrl=!1,this.bShift=!1,this.bStopRotate=!1,this.bCalphaOnly=!1,this.bConsiderNeighbors=!1,this.bShowCrossResidueBond=!0,this.bExtrude=!0,this.effects={none:this.renderer},this.maxD=500,this.oriMaxD=this.maxD,this.cam_z=2*this.maxD,this.commands=[],this.optsHistory=[],this.logs=[],this.bRender=!0,this.hColor=new THREE.Color(16777011),this.sphereGeometry=new THREE.SphereGeometry(1,32,32),this.boxGeometry=new THREE.BoxGeometry(1,1,1),this.cylinderGeometry=new THREE.CylinderGeometry(1,1,1,32,1),this.cylinderGeometryOutline=new THREE.CylinderGeometry(1,1,1,32,1,!0),this.axisDIV=15,this.strandDIV=6,this.tubeDIV=8,this.nucleicAcidStrandDIV=6,this.linewidth=1,this.hlLineRadius=.1,this.threshbox=180,this.maxAtoms3DMultiFile=4e4,this.tsHbond=3.8,this.tsIonic=6,this.tsContact=4,this.tsHalogen=3.8,this.tsPication=6,this.tsPistacking=5.5,this.LABELSIZE=30,this.rayThreshold=.5,this.colorBlackbkgd="#ffff00",this.colorWhitebkgd="#000000",this.optsOri={},this.optsOri.camera="perspective",this.optsOri.background="black",this.optsOri.color="chain",this.optsOri.proteins="ribbon",this.optsOri.sidec="nothing",this.optsOri.nucleotides="nucleotide cartoon",this.optsOri.ntbase="nothing",this.optsOri.surface="nothing",this.optsOri.opacity="1.0",this.optsOri.wireframe="no",this.optsOri.map="nothing",this.optsOri.mapwireframe="yes",this.optsOri.emmap="nothing",this.optsOri.emmapwireframe="yes",this.optsOri.phimap="nothing",this.optsOri.phimapwireframe="yes",this.optsOri.phisurface="nothing",this.optsOri.phisurftype="nothing",this.optsOri.phisurfop="1.0",this.optsOri.phisurfwf="yes",this.optsOri.chemicals="stick",this.optsOri.water="nothing",this.optsOri.ions="sphere",this.optsOri.hbonds="no",this.optsOri.saltbridge="no",this.optsOri.contact="no",this.optsOri.halogen="no",this.optsOri["pi-cation"]="no",this.optsOri["pi-stacking"]="no",this.optsOri.ssbonds="yes",this.optsOri.clbonds="yes",this.optsOri.rotationcenter="molecule center",this.optsOri.axis="no",this.optsOri.fog="no",this.optsOri.slab="no",this.optsOri.pk="residue",this.optsOri.chemicalbinding="hide",this.opts=n.hashUtilsCls.cloneHash(this.optsOri),this.sheetcolor="green",this.bShowHighlight=!0,this.mapData={},this.bFullUi=!0,this.divid=this.icn3dui.cfg.divid,this.inputid="",this.setOperation="or",this.ROT_DIR="right",this.currSelectedSets=[],this.selectedResidues={},this.ncbi2resid={},this.resid2ncbi={},this.shapeCmdHash={},this.bHideSelection=!0,this.bSelectResidue=!1,this.bSelectAlignResidue=!1,this.bAnnoShown=!1,this.bSetChainsAdvancedMenu=!1,this.b2DShown=!1,this.bCrashed=!1,this.bAddCommands=!0,this.bAddLogs=!0,this.bNotLoadStructure=!1,this.InputfileData="",this.bVr=!1,this.bAr=!1,this.startColor="blue",this.midColor="white",this.endColor="red",this.startValue=0,this.midValue=50,this.endValue=100,this.crosslinkRadius=.4,this.sceneCls=new Ie(this),this.cameraCls=new Te(this),this.fogCls=new Ee(this),this.boxCls=new Pe(this),this.brickCls=new Me(this),this.curveStripArrowCls=new De(this),this.curveCls=new He(this),this.cylinderCls=new Fe(this),this.lineCls=new Le(this),this.reprSubCls=new Ne(this),this.sphereCls=new qe(this),this.stickCls=new Ue(this),this.strandCls=new $e(this),this.stripCls=new je(this),this.tubeCls=new Be(this),this.cartoonNuclCls=new ze(this),this.surfaceCls=new Qe(this),this.labelCls=new Ve(this),this.axesCls=new We(this),this.glycanCls=new Ye(this),this.applyCenterCls=new Ze(this),this.applyClbondsCls=new et(this),this.applyMissingResCls=new tt(this),this.applyDisplayCls=new st(this),this.applyMapCls=new rt(this),this.applyOtherCls=new it(this),this.applySsbondsCls=new nt(this),this.applySymdCls=new lt(this),this.hlObjectsCls=new Ht(this),this.residueLabelsCls=new ot(this),this.alternateCls=new ct(this),this.drawCls=new ht(this),this.firstAtomObjCls=new ms(this),this.impostorCls=new at(this),this.instancingCls=new dt(this),this.contactCls=new pt(this),this.hBondCls=new mt(this),this.piHalogenCls=new ut(this),this.saltbridgeCls=new gt(this),this.loadPDBCls=new ls(this),this.vastplusCls=new rs(this),this.transformCls=new Ss(this),this.setStyleCls=new ft(this),this.setColorCls=new bt(this),this.threeDPrintCls=new ks(this),this.export3DCls=new Os(this),this.annoCddSiteCls=new vt(this),this.annoContactCls=new _t(this),this.annoPTMCls=new wt(this),this.annoCrossLinkCls=new St(this),this.annoDomainCls=new At(this),this.annoSnpClinVarCls=new xt(this),this.annoSsbondCls=new kt(this),this.annoTransMemCls=new Ot(this),this.domain3dCls=new Rt(this),this.addTrackCls=new It(this),this.annotationCls=new Tt(this),this.showAnnoCls=new Et(this),this.showSeqCls=new Pt(this),this.hlSeqCls=new Mt(this),this.hlUpdateCls=new Dt(this),this.lineGraphCls=new Ft(this),this.getGraphCls=new Nt(this),this.showInterCls=new qt(this),this.viewInterPairsCls=new Ut(this),this.drawGraphCls=new $t(this),this.contactMapCls=new jt(this),this.alignParserCls=new Bt(this),this.chainalignParserCls=new zt(this),this.dsn6ParserCls=new Gt(this),this.mmcifParserCls=new Vt(this),this.mmdbParserCls=new Wt(this),this.mmtfParserCls=new Yt(this),this.mol2ParserCls=new Xt(this),this.opmParserCls=new Kt(this),this.pdbParserCls=new Jt(this),this.sdfParserCls=new Qt(this),this.xyzParserCls=new Zt(this),this.realignParserCls=new es(this),this.densityCifParserCls=new ts(this),this.ParserUtilsCls=new ss(this),this.loadAtomDataCls=new is(this),this.setSeqAlignCls=new ns(this),this.applyCommandCls=new os(this),this.definedSetsCls=new as(this),this.legendTableCls=new yt(this),this.loadScriptCls=new ds(this),this.selByCommCls=new cs(this),this.selectionCls=new hs(this),this.resid2specCls=new ps(this),this.delphiCls=new us(this),this.dsspCls=new gs(this),this.refnumCls=new Lt(this),this.scapCls=new fs(this),this.symdCls=new bs(this),this.alignSWCls=new Cs(this),this.analysisCls=new ys(this),this.resizeCanvasCls=new ws(this),this.saveFileCls=new As(this),this.setOptionCls=new Ct(this),this.shareLinkCls=new xs(this),this.diagram2dCls=new vs(this),this.cartoon2dCls=new _s(this),this.rayCls=new Rs(this),this.controlCls=new Is(this),this.pickingCls=new Ts(this),this.VRButtonCls=new Es(this),this.ARButtonCls=new Ps(this),this.matShader=this.setColorCls.setOutlineColor("yellow")}}Ms.prototype.init=function(e){this.init_base(),this.molTitle="",this.ssbondpnts={},this.clbondpnts={},this.biomtMatrices=[],this.bAssembly=!0,this.bDrawn=!1,this.bSecondaryStructure=!1,this.bHighlight=1,this.axes=[]},Ms.prototype.init_base=function(e){this.resetConfig(),this.structures={},this.chains={},this.tddomains={},this.residues={},this.secondaries={},this.alnChains={},this.chainsSeq={},this.chainsColor={},this.chainsGene={},this.chainsAn={},this.chainsAnTitle={},this.chainsMapping={},this.resid2refnum={},this.residIgLoop={},this.refnum2residArray={},this.bShowRefnum=!1,this.alnChainsSeq={},this.alnChainsAnno={},this.alnChainsAnTtl={},this.pickedAtomList={},this.prevHighlightObjects=[],this.prevHighlightObjects_ghost=[],this.prevSurfaces=[],this.prevMaps=[],this.prevEmmaps=[],this.prevPhimaps=[],this.prevOtherMesh=[],this.defNames2Residues={},this.defNames2Atoms={},this.defNames2Descr={},this.defNames2Command={},this.residueId2Name={},this.atoms={},this.dAtoms={},this.hAtoms={},this.proteins={},this.sidec={},this.ntbase={},this.nucleotides={},this.nucleotidesO3={},this.chemicals={},this.ions={},this.water={},this.calphas={},this.hbondpnts=[],this.saltbridgepnts=[],this.contactpnts=[],this.stabilizerpnts=[],this.halogenpnts=[],this.picationpnts=[],this.pistackingpnts=[],this.distPnts=[],this.doublebonds={},this.triplebonds={},this.aromaticbonds={},this.atomPrevColors={},this.style2atoms={},this.labels={},this.lines={},this.resids2inter={},this.resids2interAll={},this.transformCls.rotateCount=0,this.transformCls.rotateCountMax=20,e&&(this.commands=[]),this.axes=[],this.bGlycansCartoon=0,this.bMembrane=1,this.bCmdWindow=0,this.chainMissingResidueArray={},this.nTotalGap=0},Ms.prototype.reinitAfterLoad=function(){let e=this,t=e.icn3dui;e.resetConfig(),e.setStyleCls.setAtomStyleByOptions(),e.setColorCls.setColorByOptions(e.opts,e.atoms),e.dAtoms=t.hashUtilsCls.cloneHash(e.atoms),e.hAtoms=t.hashUtilsCls.cloneHash(e.atoms),e.prevHighlightObjects=[],e.prevHighlightObjects_ghost=[],e.prevSurfaces=[],e.prevMaps=[],e.prevEmmaps=[],e.prevPhimaps=[],e.prevOtherMesh=[],e.labels={},e.lines={},e.shapeCmdHash={},e.bAssembly=!0},Ms.prototype.resetConfig=function(){let e=this,t=e.icn3dui;if(this.opts=t.hashUtilsCls.cloneHash(this.optsOri),void 0===t.cfg.align&&void 0===t.cfg.chainalign||(this.opts.color="identity",this.opts.proteins="c alpha trace",this.opts.nucleotides="o3 trace"),void 0!==t.cfg.cid&&(this.opts.color="atom",this.opts.pk="atom",this.opts.chemicals="ball and stick"),(void 0!==t.cfg.afid||e.bEsmfold)&&(this.opts.color="confidence"),void 0!==t.cfg.blast_rep_id&&(this.opts.color="conservation"),void 0!==t.cfg.mmdbafid){let s=t.cfg.mmdbafid.split(",");if(s.length>1)e.opts.color="structure";else if(1==s.length){let t=s[0];isNaN(t)&&t.length>5?this.opts.color="confidence":e.opts.color="chain"}}void 0!==t.cfg.options&&$.extend(this.opts,t.cfg.options)};class Ds{constructor(e){this.cfg=e,this.pre=this.cfg.divid+"_",this.REVISION="3.28.4",this.bNode=Object.keys(window).length<2,void 0===this.cfg.command&&(this.cfg.command=""),void 0===this.cfg.width&&(this.cfg.width="100%"),void 0===this.cfg.height&&(this.cfg.height="100%"),void 0===this.cfg.resize&&(this.cfg.resize=!0),void 0===this.cfg.showmenu&&(this.cfg.showmenu=!0),void 0===this.cfg.showtitle&&(this.cfg.showtitle=!0),void 0===this.cfg.showcommand&&(this.cfg.showcommand=!0),void 0===this.cfg.mobilemenu&&(this.cfg.mobilemenu=!1),void 0===this.cfg.imageonly&&(this.cfg.imageonly=!1),void 0===this.cfg.closepopup&&(this.cfg.closepopup=!1),void 0===this.cfg.showanno&&(this.cfg.showanno=!1),void 0===this.cfg.showseq&&(this.cfg.showseq=!1),void 0===this.cfg.showalignseq&&(this.cfg.showalignseq=!1),void 0===this.cfg.show2d&&(this.cfg.show2d=!1),void 0===this.cfg.showsets&&(this.cfg.showsets=!1),void 0===this.cfg.rotate&&(this.cfg.rotate="right"),void 0===this.cfg.hidelicense&&(this.cfg.hidelicense=!1),this.hashUtilsCls=new t(this),this.utilsCls=new s(this),this.parasCls=new i(this),this.myEventCls=new n(this),this.rmsdSuprCls=new l(this),this.subdivideCls=new r(this),this.convertTypeCls=new o(this),this.htmlCls=new g(this)}allCustomEvents(){}}Ds.prototype.show3DStructure=async function(e){let t=this;t.cfg.menuicon?(t.htmlCls.wifiStr=' ',t.htmlCls.licenseStr=' '):(t.htmlCls.wifiStr="",t.htmlCls.licenseStr=""),t.setIcn3d();let s=t.icn3d;t.utilsCls.isSessionStorageSupported()&&s.setStyleCls.getCommandsBeforeCrash();let i=t.htmlCls.WIDTH,n=t.htmlCls.HEIGHT;t.oriWidth=i,t.oriHeight=n,t.htmlCls.eventsCls.allEventFunctions(),this.allCustomEvents();let l=0;if((null==t.cfg.showmenu||t.cfg.showmenu)&&(l+=t.htmlCls.MENU_HEIGHT),(null==t.cfg.showcommand||t.cfg.showcommand)&&(l+=t.htmlCls.CMD_HEIGHT),null!=t.cfg.showmenu&&0==t.cfg.showmenu?t.htmlCls.setMenuCls.hideMenu():t.htmlCls.setMenuCls.showMenu(),null!=t.cfg.showtitle&&0==t.cfg.showtitle?$("#"+s.pre+"title").hide():$("#"+s.pre+"title").show(),$("#"+s.pre+"viewer").width(i).height(parseInt(n)+l),$("#"+s.pre+"canvas").width(i).height(parseInt(n)),$("#"+s.pre+"canvas").resizable({resize:function(e,i){t.htmlCls.WIDTH=i.size.width,t.htmlCls.HEIGHT=i.size.height,void 0===s||t.icn3d.bFullscreen||s.resizeCanvasCls.resizeCanvas(t.htmlCls.WIDTH,t.htmlCls.HEIGHT,!0)}}),void 0!==t.cfg.usepdbnum?t.icn3d.bUsePdbNum=t.cfg.usepdbnum:void 0!==t.cfg.date?t.icn3d.bUsePdbNum=parseInt(t.cfg.date)>=20201222:"1tup"==t.cfg.mmdbid&&1==t.cfg.showanno&&1==t.cfg.show2d&&1==t.cfg.showsets||"118496"==t.cfg.mmdbid&&0==t.cfg.showanno&&-1!=t.cfg.inpara.indexOf("bu=1")||"163605,1,91105,1,1,1"==t.cfg.align&&-1!=t.cfg.inpara.indexOf("atype=1")?t.icn3d.bUsePdbNum=!1:t.icn3d.bUsePdbNum=!0,t.cfg.replay?(s.bReplay=1,$("#"+s.pre+"replay").show()):(s.bReplay=0,$("#"+s.pre+"replay").hide()),t.utilsCls.isMobile()&&(s.threshbox=60),t.cfg.controlGl&&(s.bControlGl=!0,s.container=s.bControlGl&&!t.bNode?$(document):$("#"+s.id)),s.setStyleCls.handleContextLost(),s.applyCenterCls.setWidthHeight(i,n),s.ori_chemicalbinding=s.opts.chemicalbinding,void 0!==t.cfg.bCalphaOnly&&(s.bCalphaOnly=t.cfg.bCalphaOnly),s.opts=t.hashUtilsCls.cloneHash(s.opts),s.STATENUMBER=s.commands.length,t.utilsCls.isSessionStorageSupported()&&s.bCrashed){s.bCrashed=!1;let e=s.commandsBeforeCrash.split("|||")[0],i=e.substr(e.lastIndexOf(" ")+1);if(i===t.cfg.mmtfid||i===t.cfg.pdbid||i===t.cfg.opmid||i===t.cfg.mmdbid||i===t.cfg.gi||i===t.cfg.blast_rep_id||i===t.cfg.cid||i===t.cfg.mmcifid||i===t.cfg.align||i===t.cfg.chainalign||i===t.cfg.mmdbafid)return void await s.loadScriptCls.loadScript(s.commandsBeforeCrash,!0)}if(s.molTitle="",s.loadCmd,t.htmlCls.clickMenuCls.getHiddenMenusFromCache(),t.htmlCls.clickMenuCls.applyShownMenus(),e){if(s.init(),s.bInputfile=!0,s.InputfileType="pdb",s.InputfileData=s.InputfileData?s.InputfileData+"\nENDMDL\n"+e:e,await s.pdbParserCls.loadPdbData(e),void 0!==t.cfg.resdef&&void 0!==t.cfg.chains){let e=Object.keys(s.structures),i=t.cfg.chains.split(" | "),n=[];if(e.length==i.length){for(let t=0,s=e.length;t0&&(l+=","),l+=n[e].substr(0,n[e].indexOf("_"));s.chainidArray=[e].concat(n),s.chainidArray=s.chainalignParserCls.addPostfixForChainids(s.chainidArray),t.htmlCls.clickMenuCls.setLogCmd("resdef "+t.cfg.resdef,!0),s.loadCmd="vast_search_chainid "+s.chainidArray,t.htmlCls.clickMenuCls.setLogCmd(s.loadCmd,!0),s.bMmdbafid=!0;let r=!0;await s.chainalignParserCls.downloadMmdbAf(l,r)}}else if(void 0!==t.cfg.url){s.bInputUrlfile=!0;let e=t.cfg.url.split("|"),i=e[0],n=e[1];s.molTitle="",s.inputid=n,s.inputurl="type="+i+"&url="+encodeURIComponent(n),s.loadCmd="load url "+n+" | type "+i,t.htmlCls.clickMenuCls.setLogCmd(s.loadCmd,!0),await s.pdbParserCls.downloadUrl(n,i,t.cfg.command)}else if(void 0!==t.cfg.mmtfid)s.inputid=t.cfg.mmtfid,s.loadCmd="load mmtf "+t.cfg.mmtfid,t.htmlCls.clickMenuCls.setLogCmd(s.loadCmd,!0),await s.mmtfParserCls.downloadMmtf(t.cfg.mmtfid);else if(void 0!==t.cfg.pdbid)s.inputid=t.cfg.pdbid,s.loadCmd="load pdb "+t.cfg.pdbid,t.htmlCls.clickMenuCls.setLogCmd(s.loadCmd,!0),await s.pdbParserCls.downloadPdb(t.cfg.pdbid);else if(void 0!==t.cfg.afid){s.inputid=t.cfg.afid,s.loadCmd="load af "+t.cfg.afid,t.htmlCls.clickMenuCls.setLogCmd(s.loadCmd,!0);let e=!0;await s.pdbParserCls.downloadPdb(t.cfg.afid,e)}else if(void 0!==t.cfg.opmid)s.inputid=t.cfg.opmid,s.loadCmd="load opm "+t.cfg.opmid,t.htmlCls.clickMenuCls.setLogCmd(s.loadCmd,!0),await s.opmParserCls.downloadOpm(t.cfg.opmid);else if(void 0!==t.cfg.mmdbid)s.inputid=t.cfg.mmdbid,s.loadCmd="load mmdb "+t.cfg.mmdbid+" | parameters "+t.cfg.inpara,t.htmlCls.clickMenuCls.setLogCmd(s.loadCmd,!0),await s.mmdbParserCls.downloadMmdb(t.cfg.mmdbid);else if(void 0!==t.cfg.gi)s.loadCmd="load gi "+t.cfg.gi,t.htmlCls.clickMenuCls.setLogCmd(s.loadCmd,!0),await s.mmdbParserCls.downloadGi(t.cfg.gi);else if(void 0!==t.cfg.refseqid)s.inputid=t.cfg.refseqid,s.loadCmd="load refseq "+t.cfg.refseqid,t.htmlCls.clickMenuCls.setLogCmd(s.loadCmd,!0),await s.mmdbParserCls.downloadRefseq(t.cfg.refseqid);else if(void 0!==t.cfg.protein)s.inputid=t.cfg.protein,s.loadCmd="load protein "+t.cfg.protein,t.htmlCls.clickMenuCls.setLogCmd(s.loadCmd,!0),await s.mmdbParserCls.downloadProteinname(t.cfg.protein);else if(void 0!==t.cfg.blast_rep_id)if(s.inputid=t.cfg.query_id+","+t.cfg.blast_rep_id,t.cfg.oriQuery_id=t.cfg.query_id,t.cfg.oriBlast_rep_id=t.cfg.blast_rep_id,"Query"!==t.cfg.query_id.substr(0,5)&&void 0===t.cfg.rid)"icn3d"==t.cfg.from&&"1TSR_A"==t.cfg.blast_rep_id&&"NP_001108451.1"==t.cfg.query_id&&(t.cfg.command="view annotations; set annotation cdd; set annotation site; set view detailed view; select chain 1TSR_A; show selection"),"smithwm"==t.cfg.alg?(s.loadCmd="load seq_struct_ids_smithwm "+t.cfg.query_id+","+t.cfg.blast_rep_id,s.bSmithwm=!0):"local_smithwm"==t.cfg.alg?(s.loadCmd="load seq_struct_ids_local_smithwm "+t.cfg.query_id+","+t.cfg.blast_rep_id,s.bLocalSmithwm=!0):(s.loadCmd="load seq_struct_ids "+t.cfg.query_id+","+t.cfg.blast_rep_id,s.bSmithwm=!1,s.bLocalSmithwm=!1),t.htmlCls.clickMenuCls.setLogCmd(s.loadCmd,!0),await s.mmdbParserCls.downloadBlast_rep_id(t.cfg.query_id+","+t.cfg.blast_rep_id);else if(void 0!==t.cfg.rid){let e="https://blast.ncbi.nlm.nih.gov/Blast.cgi?RESULTS_FILE=on&FORMAT_TYPE=JSON2_S&FORMAT_OBJECT=Alignment&CMD=Get&RID="+t.cfg.rid,i=await t.getAjaxPromise(e,"json",!1,"The RID "+t.cfg.rid+" may have expired...");for(let e=0,n=i.BlastOutput2.length;e
",s="All atoms Selection ";e.utilsCls.setViewerWidthHeight(e),e.utilsCls.isMobile()||e.cfg.mobilemenu?e.htmlCls.setMenuCls.setTopMenusHtmlMobile(e.cfg.divid,t,s):e.htmlCls.setMenuCls.setTopMenusHtml(e.cfg.divid,t,s),e.icn3d=new Ms(e),e.icn3d.controlCls.setControl(),e.setDialogAjax()},Ds.prototype.getMmtfPromise=function(e){return new Promise((function(t,s){MMTF.fetch(e,(async function(e){t(e)}),(function(e){s("error")}))}))},Ds.prototype.getMmtfReducedPromise=function(e){return new Promise((function(t,s){MMTF.fetchReduced(e,(async function(e){t(e)}),(function(e){s("error")}))}))},Ds.prototype.getXMLHttpRqstPromise=function(e,t,s,i){let n=this;return new Promise((function(l,r){let o=new XMLHttpRequest;o.open(t,e,!0),o.responseType=s,o.onreadystatechange=function(){if(4==this.readyState)if(200==this.status){let e=o.response;l(e)}else"2fofc"==i||"fofc"==i?alert("Density server at EBI has no corresponding electron density map for this structure."):"em"==i?alert("Density server at EBI has no corresponding EM density map for this structure."):"rcsbEdmaps"==i?alert("RCSB server has no corresponding eletron density map for this structure."):alert("The "+i+" file is unavailable..."),r("error");else n.icn3d.ParserUtilsCls.showLoading()},o.send()}))},Ds.prototype.getAjaxPromise=function(e,t,s,i,n,l,r){let o=this;return new Promise((function(r,a){$.ajax({url:e,dataType:t,cache:!0,beforeSend:function(){s&&o.icn3d.ParserUtilsCls.showLoading()},complete:function(){l&&o.icn3d.ParserUtilsCls.hideLoading()},success:function(e){r(e)},error:function(){i&&alert(i),n&&console.log(n),a("error")}})}))},Ds.prototype.getAjaxPostPromise=async function(e,t,s,i,n,l,r,o){let a=this;return r=r||"json",new Promise((function(o,d){$.ajax({url:e,type:"POST",data:t,dataType:r,cache:!0,beforeSend:function(){s&&a.icn3d.ParserUtilsCls.showLoading()},complete:function(){l&&a.icn3d.ParserUtilsCls.hideLoading()},success:function(e){o(e)},error:function(){i&&alert(i),n&&console.log(n),d("error")}})}))},Ds.prototype.setDialogAjax=function(){this.bNode||$.ui.dialog.prototype._makeDraggableBase||($.ui.dialog.prototype._makeDraggableBase=$.ui.dialog.prototype._makeDraggable,$.ui.dialog.prototype._makeDraggable=function(){this._makeDraggableBase(),this.uiDialog.draggable("option","containment",!1)}),$.ajaxTransport("+binary",(function(e,t,s){if(window.FormData&&(e.dataType&&"binary"==e.dataType||e.data&&(window.ArrayBuffer&&e.data instanceof ArrayBuffer||window.Blob&&e.data instanceof Blob)))return{send:function(t,s){let i=new XMLHttpRequest,n=e.url,l=e.type,r=e.async||!0,o=e.responseType||"blob",a=e.data||null;i.addEventListener("load",(function(){let t={};t[e.dataType]=i.response,s(i.status,i.statusText,t,i.getAllResponseHeaders())})),i.open(l,n,r);for(let e in t)i.setRequestHeader(e,t[e]);i.responseType=o,i.send(a)},abort:function(){s.abort()}}}))};return e.ARButton=Ps,e.AddTrack=It,e.AlignParser=Bt,e.AlignSW=Cs,e.AlignSeq=m,e.Alternate=ct,e.Analysis=ys,e.AnnoCddSite=vt,e.AnnoContact=_t,e.AnnoCrossLink=St,e.AnnoDomain=At,e.AnnoSnpClinVar=xt,e.AnnoSsbond=kt,e.AnnoTransMem=Ot,e.Annotation=Tt,e.ApplyCenter=Ze,e.ApplyClbonds=et,e.ApplyCommand=os,e.ApplyDisplay=st,e.ApplyMap=rt,e.ApplyOther=it,e.ApplySsbonds=nt,e.ApplySymd=lt,e.Axes=We,e.Box=Pe,e.Brick=Me,e.Camera=Te,e.CartoonNucl=ze,e.ChainalignParser=zt,e.ClickMenu=a,e.Contact=pt,e.Control=Is,e.ConvertTypeCls=o,e.Curve=He,e.CurveStripArrow=De,e.Cylinder=Fe,e.DefinedSets=as,e.Delphi=us,e.DensityCifParser=ts,e.Diagram2d=vs,e.Dialog=c,e.Domain3d=Rt,e.Draw=ht,e.DrawGraph=$t,e.Dsn6Parser=Gt,e.Dssp=gs,e.ElectronMap=Je,e.Events=p,e.Export3D=Os,e.FirstAtomObj=ms,e.Fog=Ee,e.GetGraph=Nt,e.Glycan=Ye,e.HBond=mt,e.HashUtilsCls=t,e.HlObjects=Ht,e.HlSeq=Mt,e.HlUpdate=Dt,e.Html=g,e.Impostor=at,e.Instancing=dt,e.Label=Ve,e.Line=Le,e.LineGraph=Ft,e.LoadAtomData=is,e.LoadPDB=ls,e.LoadScript=ds,e.MarchingCube=Xe,e.MmcifParser=Vt,e.MmdbParser=Wt,e.MmtfParser=Yt,e.Mol2Parser=Xt,e.MyEventCls=n,e.OpmParser=Kt,e.ParasCls=i,e.ParserUtils=ss,e.PdbParser=Jt,e.PiHalogen=ut,e.Picking=Ts,e.ProteinSurface=Ke,e.Ray=Rs,e.RealignParser=es,e.Refnum=Lt,e.ReprSub=Ne,e.Resid2spec=ps,e.ResidueLabels=ot,e.ResizeCanvas=ws,e.RmsdSuprCls=l,e.Saltbridge=gt,e.SaveFile=As,e.Scap=fs,e.Scene=Ie,e.SdfParser=Qt,e.SelectByCommand=cs,e.Selection=hs,e.SetColor=bt,e.SetDialog=h,e.SetHtml=u,e.SetMenu=d,e.SetOption=Ct,e.SetSeqAlign=ns,e.SetStyle=ft,e.ShareLink=xs,e.ShowAnno=Et,e.ShowInter=qt,e.ShowSeq=Pt,e.Sphere=qe,e.Stick=Ue,e.Strand=$e,e.Strip=je,e.SubdivideCls=r,e.Surface=Qe,e.Symd=bs,e.ThreeDPrint=ks,e.Transform=Ss,e.Tube=Be,e.UtilsCls=s,e.VRButton=Es,e.Vastplus=rs,e.ViewInterPairs=Ut,e.XyzParser=Zt,e.iCn3D=Ms,e.iCn3DUI=Ds,e.printMsg=class{constructor(){console.log("This is a message from the icn3d package")}},Object.defineProperty(e,"__esModule",{value:!0}),e}({});
+t+=this.getRadio("mn6_addlabel","mn6_addlabelRefnum","per Reference Number",void 0,1,2),t+=this.getRadio("mn6_addlabel","mn6_addlabelChains","per Chain",void 0,void 0,2),t+=this.getRadio("mn6_addlabel","mn6_addlabelTermini","N- & C-Termini",void 0,1,2)),t+=this.getMenuSep(),t+=this.getRadio("mn6_addlabel","mn6_labelColor","Change Label Color",void 0,1,2),t+=this.getRadio("mn6_addlabel","mn6_addlabelNo","Remove",!0,1,2),t+="",t+="",t+=this.getMenuText("labelscalewrap","Label Scale",void 0,1,1),t+="";for(let e=1;e<=4;++e){let s=2*e;t+=this.getRadio("mn6_labelscale","mn6_labelscale0"+s,"0."+s,void 0,1,2)}for(let e=1;e<=5;++e)t+=1==e?this.getRadio("mn6_labelscale","mn6_labelscale"+e+"0",e+".0",!0,1,2):this.getRadio("mn6_labelscale","mn6_labelscale"+e+"0",e+".0",void 0,1,2);if(t+=" ",t+="",t+=this.getMenuSep(),void 0===e.cfg.cid){t+=this.getMenuText("mn6_chemicalbindingwrap","Chem. Binding",void 0,void 0,1),t+="",t+=this.getRadio("mn6_chemicalbinding","mn6_chemicalbindingshow","Show",void 0,void 0,2),t+=this.getRadio("mn6_chemicalbinding","mn6_chemicalbindinghide","Hide",!0,void 0,2),t+=" ",t+="",t+=this.getMenuText("mn6_ssbondswrap","Disulfide Bonds",void 0,1,1),t+="",t+=this.getRadio("mn6_ssbonds","mn6_ssbondsYes","Show",!0,1,2),t+=this.getRadio("mn6_ssbonds","mn6_ssbondsExport","Export Pairs",void 0,void 0,2),t+=this.getRadio("mn6_ssbonds","mn6_ssbondsNo","Hide",void 0,1,2),t+=" ",t+="",t+=this.getMenuText("mn6_clbondswrap","Cross-Linkages",void 0,void 0,1),t+="",t+=this.getRadio("mn6_clbonds","mn6_clbondsYes","Show",!0,void 0,2),t+=this.getRadio("mn6_clbonds","mn6_clbondsExport","Export Pairs",void 0,void 0,2),t+=this.getRadio("mn6_clbonds","mn6_clbondsNo","Hide",void 0,void 0,2),t+=" ",t+="";let s=void 0!==e.cfg.mmtfid||void 0!==e.cfg.pdbid||void 0!==e.cfg.opmid||void 0!==e.cfg.mmcifid||void 0!==e.cfg.mmdbid||void 0!==e.cfg.mmdbafid||void 0!==e.cfg.gi||void 0!==e.cfg.blast_rep_id;s&&(t+=this.getMenuText("assemblyWrapper","Assembly",void 0,1,1),t+="",e.cfg.bu?(t+=this.getRadio("mn6_assembly","mn6_assemblyYes","Biological Assembly",!0,1,2),t+=this.getRadio("mn6_assembly","mn6_assemblyNo","Asymmetric Unit",void 0,1,2)):(t+=this.getRadio("mn6_assembly","mn6_assemblyYes","Biological Assembly",void 0,1,2),t+=this.getRadio("mn6_assembly","mn6_assemblyNo","Asymmetric Unit",!0,1,2)),t+=" ",t+=""),t+=this.getMenuText("mn6_symmetrywrap","Symmetry",void 0,void 0,1),t+="",s&&(t+=this.getLink("mn6_symmetry","from PDB(precalculated) "+e.htmlCls.wifiStr,void 0,2)),t+=this.getLink("mn6_symd","from SymD(Dynamic) "+e.htmlCls.wifiStr,void 0,2),t+=this.getLink("mn6_clear_sym","Clear SymD Symmetry",void 0,2),t+=this.getLink("mn6_axes_only","Show Axes Only",void 0,2),t+=" ",t+="",t+=this.getMenuText("mn6_igrefwrap","Ref. Number",void 0,void 0,1),t+="",
+//!!!
+t+=this.getLink("mn6_igrefYes","Show Ig Ref. Number",void 0,2),t+=this.getLink("mn6_igrefTpl","Ig w/ Specified Template",void 0,2),t+=this.getLink("mn6_igrefNo","Hide Ig Ref. Number",void 0,2),t+=this.getMenuSep(),t+=this.getLink("mn6_customref","Custom Ref. Number",void 0,2),t+=" ",t+="",t+=this.getMenuSep()}return t+=this.getLink("mn6_yournote","Window Title",void 0,1),void 0!==e.cfg.cid?(t+=this.getMenuText("mn1_linkwrap","Links",void 0,void 0,1),t+="",t+=this.getLink("mn1_link_structure","Compound Summary "+e.htmlCls.wifiStr,void 0,2),t+=this.getLink("mn1_link_vast","Similar Compounds "+e.htmlCls.wifiStr,void 0,2),t+=this.getLink("mn1_link_bind","Structures Bound "+e.htmlCls.wifiStr,void 0,2),t+=" ",t+=""):(t+=this.getMenuText("mn1_linkwrap","Links",void 0,void 0,1),t+="",t+=this.getLink("mn1_link_structure","Structure Summary "+e.htmlCls.wifiStr,void 0,2),t+=this.getLink("mn1_link_vast","Similar Structures "+e.htmlCls.wifiStr,void 0,2),t+=this.getLink("mn1_link_pubmed","Literature "+e.htmlCls.wifiStr,void 0,2),t+=this.getLink("mn1_link_protein","Protein "+e.htmlCls.wifiStr,void 0,2),t+=" ",t+=""),t+="",t+=this.getMenuUrl("abouticn3d",e.htmlCls.baseUrl+"icn3d/icn3d.html#about","About iCn3D "+e.REVISION+" ",1,1),t+=this.getMenuUrl("gallery",e.htmlCls.baseUrl+"icn3d/icn3d.html#gallery","Live Gallery "+e.htmlCls.wifiStr,1,1),t+=this.getMenuUrl("video",e.htmlCls.baseUrl+"icn3d/icn3d.html#videos","Videos & Tutorials",1,1),t+=this.getMenuText("mn6_faq","FAQ",void 0,1,1),t+="",t+=this.getMenuUrl("faq_viewstru",e.htmlCls.baseUrl+"icn3d/icn3d.html#viewstru","View structure",1,2),t+=this.getMenuUrl("faq_tfstru",e.htmlCls.baseUrl+"icn3d/icn3d.html#tfstru","Transform Structure",1,2),t+=this.getMenuUrl("faq_selsubset",e.htmlCls.baseUrl+"icn3d/icn3d.html#selsubset","Select Subsets",1,2),t+=this.getMenuUrl("faq_stylecolor",e.htmlCls.baseUrl+"icn3d/icn3d.html#changestylecolor","Change Style/Color",1,2),t+=this.getMenuUrl("faq_savework",e.htmlCls.baseUrl+"icn3d/icn3d.html#saveview","Save Work",1,2),t+=this.getMenuUrl("faq_showanno",e.htmlCls.baseUrl+"icn3d/icn3d.html#showanno","Show Annotations",1,2),t+=this.getMenuUrl("faq_exportanno",e.htmlCls.baseUrl+"icn3d/icn3d.html#exportanno","Export Annotations",1,2),t+=this.getMenuUrl("faq_interanal",e.htmlCls.baseUrl+"icn3d/icn3d.html#interanalysis","Interaction Analysis",1,2),t+=this.getMenuUrl("faq_mutanal",e.htmlCls.baseUrl+"icn3d/icn3d.html#mutationanalysis","Mutation Analysis",1,2),t+=this.getMenuUrl("faq_elecpot",e.htmlCls.baseUrl+"icn3d/icn3d.html#elecpot","Electrostatic Pot.",1,2),t+=this.getMenuUrl("faq_simipdb",e.htmlCls.baseUrl+"icn3d/icn3d.html#simivast","Similar PDB",1,2),t+=this.getMenuUrl("faq_simialphapdb",e.htmlCls.baseUrl+"icn3d/icn3d.html#simifoldseek","Similar AlphaFold/PDB",1,2),t+=this.getMenuUrl("faq_alnstru",e.htmlCls.baseUrl+"icn3d/icn3d.html#alignmul","Align Multiple Structures",1,2),t+=this.getMenuUrl("faq_batchanal",e.htmlCls.baseUrl+"icn3d/icn3d.html#batchanalysis","Batch Analysis",1,2),t+=this.getMenuUrl("faq_embedicn3d",e.htmlCls.baseUrl+"icn3d/icn3d.html#embedicn3d","Embed iCn3D",1,2),t+=" ",t+="",t+=this.getMenuUrl("citing",e.htmlCls.baseUrl+"icn3d/icn3d.html#citing","Citing iCn3D",void 0,1),t+=this.getMenuText("mn6_source","Source Code",void 0,1,1),t+="",t+=this.getMenuUrl("github","https://github.com/ncbi/icn3d","GitHub (browser) "+e.htmlCls.wifiStr,1,2),t+=this.getMenuUrl("npm","https://www.npmjs.com/package/icn3d","npm (Node.js) "+e.htmlCls.wifiStr,1,2),t+=this.getMenuUrl("notebook","https://pypi.org/project/icn3dpy","Jupyter Notebook "+e.htmlCls.wifiStr,1,2),t+=" ",t+="",t+=this.getMenuText("mn6_develop","Develop",void 0,void 0,1),t+="",t+=this.getMenuUrl("dev_embedicn3d2",e.htmlCls.baseUrl+"icn3d/icn3d.html#HowToUse","Embed iCn3D",void 0,2),t+=this.getMenuUrl("dev_urlpara",e.htmlCls.baseUrl+"icn3d/icn3d.html#parameters","URL Parameters",void 0,2),t+=this.getMenuUrl("dev_command",e.htmlCls.baseUrl+"icn3d/icn3d.html#commands","Commands",void 0,2),t+=this.getMenuUrl("dev_datastru",e.htmlCls.baseUrl+"icn3d/icn3d.html#datastructure","Data Structure",void 0,2),t+=this.getMenuUrl("dev_classstru",e.htmlCls.baseUrl+"icn3d/icn3d.html#classstructure","Class Structure",void 0,2),t+=this.getMenuUrl("dev_addclass",e.htmlCls.baseUrl+"icn3d/icn3d.html#addclass","Add New Classes",void 0,2),t+=this.getMenuUrl("dev_modfunc",e.htmlCls.baseUrl+"icn3d/icn3d.html#modifyfunction","Modify Functions",void 0,2),t+=this.getMenuUrl("dev_restful",e.htmlCls.baseUrl+"icn3d/icn3d.html#restfulapi","RESTful APIs",void 0,2),t+=this.getMenuUrl("dev_contributor",e.htmlCls.baseUrl+"icn3d/icn3d.html#contributors","iCn3D Contributors",void 0,2),t+=" ",t+="",t+=this.getMenuUrl("helpdoc",e.htmlCls.baseUrl+"icn3d/docs/icn3d_help.html","Help Doc "+e.htmlCls.wifiStr,1,1),t+=this.getMenuSep(),t+=this.getMenuText("mn6_tfhint","Transform Hints",void 0,1,1),t+="",t+=this.getMenuText("mn6_rotate","Rotate",void 0,1,2),t+="",t+="Left Mouse (Click & Drag) ",t+="Key l: Left ",t+="Key j: Right ",t+="Key i: Up ",t+="Key m: Down ",t+="Shift + Key l: Left 90° ",t+="Shift + Key j: Right 90° ",t+="Shift + Key i: Up 90° ",t+="Shift + Key m: Down 90° ",t+=" ",t+="",t+=this.getMenuText("mn6_zoom","Zoom",void 0,1,2),t+="",t+="Middle Mouse ",t+="Key z: Zoom in ",t+="Key x: Zoom out ",t+=" ",t+="",t+=this.getMenuText("mn6_translate","Translate",void 0,1,2),t+="",t+="Right Mouse ",t+=" ",t+="",t+=" ",t+="",t+=this.getMenuUrl("selhints",e.htmlCls.baseUrl+"icn3d/icn3d.html#selsubset","Selection Hints",void 0,1),t+=this.getMenuUrl("helpdesk","https://support.nlm.nih.gov/support/create-case/","Write to Help Desk",1,1),t+=" ",t}hideMenu(){let e=this.icn3dui;e.bNode||(void 0!==$("#"+e.pre+"mnlist")[0]&&($("#"+e.pre+"mnlist")[0].style.display="none"),void 0!==$("#"+e.pre+"mnLogSection")[0]&&($("#"+e.pre+"mnLogSection")[0].style.display="none"),void 0!==$("#"+e.pre+"cmdlog")[0]&&($("#"+e.pre+"cmdlog")[0].style.display="none"),$("#"+e.pre+"title")[0].style.margin="10px 0 0 10px")}showMenu(){let e=this.icn3dui;e.bNode||(void 0!==$("#"+e.pre+"mnlist")[0]&&($("#"+e.pre+"mnlist")[0].style.display="block"),void 0!==$("#"+e.pre+"mnLogSection")[0]&&($("#"+e.pre+"mnLogSection")[0].style.display="block"),void 0!==$("#"+e.pre+"cmdlog")[0]&&($("#"+e.pre+"cmdlog")[0].style.display="block"))}}class c{constructor(e){this.icn3dui=e}openDlg(e,t){let s=this.icn3dui;s.icn3d,s.bNode||(e=s.pre+e,s.cfg.notebook?this.openDlgNotebook(e,t):this.openDlgRegular(e,t),s.htmlCls.themecolor||(s.htmlCls.themecolor="blue"),s.htmlCls.setMenuCls.setTheme(s.htmlCls.themecolor))}addSaveButton(e){let t=this.icn3dui;t.icn3d,t.bNode||void 0!==this.dialogHashSave&&this.dialogHashSave.hasOwnProperty(e)||($("#"+e).parent().children(".ui-dialog-titlebar").append("
"),void 0===this.dialogHashSave&&(this.dialogHashSave={}),this.dialogHashSave[e]=1)}addHideButton(e){let t=this.icn3dui;t.icn3d,t.bNode||void 0!==this.dialogHashHide&&this.dialogHashHide.hasOwnProperty(e)||($("#"+e).parent().children(".ui-dialog-titlebar").append("
"),void 0===this.dialogHashHide&&(this.dialogHashHide={}),this.dialogHashHide[e]=1)}getDialogStatus(){let e=this.icn3dui;if(e.icn3d,e.bNode)return;let t={},s={},i=$("#"+e.pre+"dl_selectannotations").hasClass("ui-dialog-content"),n=$("#"+e.pre+"dl_graph").hasClass("ui-dialog-content"),l=$("#"+e.pre+"dl_linegraph").hasClass("ui-dialog-content"),r=$("#"+e.pre+"dl_scatterplot").hasClass("ui-dialog-content"),o=$("#"+e.pre+"dl_contactmap").hasClass("ui-dialog-content"),a=$("#"+e.pre+"dl_alignerrormap").hasClass("ui-dialog-content"),d=$("#"+e.pre+"dl_interactionsorted").hasClass("ui-dialog-content"),c=$("#"+e.pre+"dl_alignment").hasClass("ui-dialog-content"),h=$("#"+e.pre+"dl_2ddgm").hasClass("ui-dialog-content"),p=$("#"+e.pre+"dl_2dctn").hasClass("ui-dialog-content"),m=$("#"+e.pre+"dl_definedsets").hasClass("ui-dialog-content");return t.bSelectannotationsInit2=!1,t.bGraph2=!1,t.bLineGraph2=!1,t.bScatterplot2=!1,t.bTable2=!1,t.bAlignmentInit2=!1,t.bTwoddgmInit2=!1,t.bTwodctnInit2=!1,t.bSetsInit2=!1,s.dl_selectannotations="bSelectannotationsInit2",s.dl_graph="bGraph2",s.dl_linegraph="bLineGraph2",s.dl_scatterplot="bScatterplot2",s.dl_contactmap="bContactmap2",s.dl_alignerrormap="bAlignerrormap2",s.dl_interactionsorted="bTable2",s.dl_alignment="bAlignmentInit2",s.dl_2ddgm="bTwoddgmInit2",s.dl_2dctn="bTwodctnInit2",s.dl_definedsets="bSetsInit2",i&&(t.bSelectannotationsInit2=$("#"+e.pre+"dl_selectannotations").dialog("isOpen")),n&&(t.bGraph2=$("#"+e.pre+"dl_graph").dialog("isOpen")),l&&(t.bLineGraph2=$("#"+e.pre+"dl_linegraph").dialog("isOpen")),r&&(t.bScatterplot2=$("#"+e.pre+"dl_scatterplot").dialog("isOpen")),o&&(t.bContactmap2=$("#"+e.pre+"dl_contactmap").dialog("isOpen")),a&&(t.bAlignerror2=$("#"+e.pre+"dl_alignerrormap").dialog("isOpen")),d&&(t.bTable2=$("#"+e.pre+"dl_interactionsorted").dialog("isOpen")),c&&(t.bAlignmentInit2=$("#"+e.pre+"dl_alignment").dialog("isOpen")),h&&(t.bTwoddgmInit2=$("#"+e.pre+"dl_2ddgm").dialog("isOpen")),p&&(t.bTwodctnInit2=$("#"+e.pre+"dl_2dctn").dialog("isOpen")),m&&(t.bSetsInit2=$("#"+e.pre+"dl_definedsets").dialog("isOpen")),{status:t,id2flag:s}}openDlgHalfWindow(e,t,s,i){let n=this.icn3dui,l=n.icn3d;if(n.bNode)return;let r=this,o=n.htmlCls.width2d+20;l.resizeCanvasCls.resizeCanvas(n.htmlCls.WIDTH-s,n.htmlCls.HEIGHT,i);let a,d=n.htmlCls.HEIGHT,c=s;a=!n.cfg.showmenu||n.utilsCls.isMobile()||n.cfg.mobilemenu?{my:"left top",at:"right top",of:"#"+n.pre+"viewer",collision:"none"}:{my:"left top",at:"right top+40",of:"#"+n.pre+"viewer",collision:"none"},n.cfg.resize=!1,window.dialog=$("#"+e).dialog({autoOpen:!0,title:t,height:d,width:c,modal:!1,position:a,close:function(t){let s=r.getDialogStatus(),i=s.status,a=s.id2flag,d=!1;for(let t in a){let s=e===n.pre+t;for(let e in i)i.hasOwnProperty(e)||(s=s&&!i[e]);d=d||s}if(d)if(i.bTwoddgmInit2||i.bTwodctnInit2||i.bSetsInit2){let e=n.utilsCls.isMobile()?n.htmlCls.WIDTH:n.htmlCls.WIDTH-o;l.resizeCanvasCls.resizeCanvas(e,n.htmlCls.HEIGHT,!0),i.bTwoddgmInit2&&r.openDlg2Ddgm(n.pre+"dl_2ddgm",void 0,i.bSetsInit2),i.bTwodctnInit2&&r.openDlg2Ddgm(n.pre+"dl_2dctn",void 0,i.bSetsInit2),i.bSetsInit2&&r.openDlg2Ddgm(n.pre+"dl_definedsets")}else l.resizeCanvasCls.resizeCanvas(n.htmlCls.WIDTH,n.htmlCls.HEIGHT,!0)},resize:function(t){if(e==n.pre+"dl_selectannotations")l.annotationCls.hideFixedTitle();else if(e==n.pre+"dl_graph"){let t=$("#"+e).width(),s=$("#"+e).height();d3.select("#"+n.svgid).attr("width",t).attr("height",s)}else if(e==n.pre+"dl_linegraph"||e==n.pre+"dl_scatterplot"||e==n.pre+"dl_contactmap"||e==n.pre+"dl_alignerrormap"){let t=status.bTwoddgmInit2||status.bSetsInit2?(n.htmlCls.WIDTH-o)/2:n.htmlCls.WIDTH/2,s=$("#"+e).width()/t;if(e==n.pre+"dl_linegraph"){let e=l.linegraphWidth*s;$("#"+n.linegraphid).attr("width",e)}else if(e==n.pre+"dl_scatterplot"){let e=l.scatterplotWidth*s;$("#"+n.scatterplotid).attr("width",e)}else if(e==n.pre+"dl_contactmap"){let e=l.contactmapWidth*s;$("#"+n.contactmapid).attr("width",e)}else if(e==n.pre+"dl_alignerrormap"){let e=l.alignerrormapWidth*s;$("#"+n.alignerrormapid).attr("width",e)}}}}),this.addSaveButton(e),this.addHideButton(e)}openDlg2Ddgm(e,t,s){let i=this.icn3dui,n=i.icn3d;if(i.bNode)return;let l,r,o=this,a=i.htmlCls.width2d+20;e===i.pre+"dl_definedsets"?(l="right top",r="Select sets"):e!==i.pre+"dl_2ddgm"&&e!==i.pre+"dl_2dctn"||(l=s?"right top+240":"right top",r=e===i.pre+"dl_2ddgm"?"2D Diagram":"2D Cartoon");let d={my:"left top+"+i.htmlCls.MENU_HEIGHT,at:l,of:"#"+i.pre+"viewer",collision:"none"};window.dialog=$("#"+e).dialog({autoOpen:!0,title:r,height:"auto",width:a,modal:!1,position:d,close:function(e){let t=o.getDialogStatus().status;t.bSelectannotationsInit2||t.bGraph2||t.bLineGraph2||t.bScatterplot2||t.bTable2||t.bAlignmentInit2||n.resizeCanvasCls.resizeCanvas(i.htmlCls.WIDTH,i.htmlCls.HEIGHT,!0)},resize:function(t,s){e==i.pre+"dl_2dctn"&&(n.resizeRatioX=s.size.width/i.htmlCls.width2d,n.resizeRatioY=s.size.height/(i.htmlCls.width2d+70))},resizeStop:function(e,t){n.resizeRatioX=t.size.width/i.htmlCls.width2d,n.resizeRatioY=t.size.height/(i.htmlCls.width2d+70)}}),this.addSaveButton(e),this.addHideButton(e)}openDlgRegular(e,t){let s=this.icn3dui,i=s.icn3d;if(s.bNode)return;let n=400,l=150,r=s.htmlCls.width2d+20,o=this.getDialogStatus().status;if(e===s.pre+"dl_selectannotations"||e===s.pre+"dl_graph"||e===s.pre+"dl_linegraph"||e===s.pre+"dl_scatterplot"||e===s.pre+"dl_contactmap"||e===s.pre+"dl_alignerrormap"||e===s.pre+"dl_interactionsorted"||e===s.pre+"dl_alignment"){let a=.5*s.htmlCls.WIDTH-.5*r;if(s.htmlCls.WIDTH>=s.htmlCls.HEIGHT)this.openDlgHalfWindow(e,t,a,!0),(o.bTwoddgmInit2||o.bTwodctnInit2||o.bSetsInit2)&&(i.resizeCanvasCls.resizeCanvas(s.htmlCls.WIDTH-a-r,s.htmlCls.HEIGHT,!0),o.bTwoddgmInit2&&this.openDlg2Ddgm(s.pre+"dl_2ddgm",void 0,o.bSetsInit2),o.bTwodctnInit2&&this.openDlg2Ddgm(s.pre+"dl_2dctn",void 0,o.bSetsInit2),o.bSetsInit2&&this.openDlg2Ddgm(s.pre+"dl_definedsets"));else{i.resizeCanvasCls.resizeCanvas(s.htmlCls.WIDTH,.5*s.htmlCls.HEIGHT,!0),l=.5*s.htmlCls.HEIGHT,n=s.htmlCls.WIDTH;let a={my:"left top",at:"left bottom+32",of:"#"+s.pre+"canvas",collision:"none"};window.dialog=$("#"+e).dialog({autoOpen:!0,title:t,height:l,width:n,modal:!1,position:a,close:function(t){if(!((e!==s.pre+"dl_selectannotations"||o.bAlignmentInit2||o.bGraph2||o.bTable2||o.bLineGraph2||o.bScatterplot2||o.bContactmap2||o.bAlignerrormap2)&&(e!==s.pre+"dl_graph"||o.bSelectannotationsInit2||o.bAlignmentInit2||o.bTable2||o.bLineGraph2||o.bScatterplot2||o.bContactmap2||o.bAlignerrormap2)&&(e!==s.pre+"dl_alignment"||o.bSelectannotationsInit2||o.bGraph2||o.bTable2||o.bLineGraph2||o.bScatterplot2||o.bContactmap2||o.bAlignerrormap2)&&(e!==s.pre+"dl_interactionsorted"||o.bSelectannotationsInit2||o.bGraph2||o.bAlignmentInit2||o.bLineGraph2||o.bScatterplot2||o.bContactmap2||o.bAlignerrormap2)&&(e!==s.pre+"dl_linegraph"||o.bSelectannotationsInit2||o.bGraph2||o.bAlignmentInit2||o.bTable2||o.bScatterplot2||o.bContactmap2||o.bAlignerrormap2)&&(e!==s.pre+"dl_scatterplot"||o.bSelectannotationsInit2||o.bGraph2||o.bAlignmentInit2||o.bTable2||o.bLineGraph2||o.bContactmap2||o.bAlignerrormap2)&&(e!==s.pre+"dl_contactmap"||o.bSelectannotationsInit2||o.bGraph2||o.bAlignmentInit2||o.bTable2||o.bLineGraph2||o.bScatterplot2||o.bAlignerrormap2)&&(e!==s.pre+"dl_alignerrormap"||o.bSelectannotationsInit2||o.bGraph2||o.bAlignmentInit2||o.bTable2||o.bLineGraph2||o.bScatterplot2||o.bContactmap2)))if(o.bTwoddgmInit2||o.bTwodctnInit2||o.bSetsInit2){let e=s.utilsCls.isMobile()?s.htmlCls.WIDTH:s.htmlCls.WIDTH-r;i.resizeCanvasCls.resizeCanvas(e,s.htmlCls.HEIGHT,!0),o.bTwoddgmInit2&&thisClass.openDlg2Ddgm(s.pre+"dl_2ddgm",void 0,o.bSetsInit2),o.bTwodctnInit2&&thisClass.openDlg2Ddgm(s.pre+"dl_2dctn",void 0,o.bSetsInit2),o.bSetsInit2&&thisClass.openDlg2Ddgm(s.pre+"dl_definedsets")}else i.resizeCanvasCls.resizeCanvas(s.htmlCls.WIDTH,s.htmlCls.HEIGHT,!0)},resize:function(t){if(e==s.pre+"dl_selectannotations")i.annotationCls.hideFixedTitle();else if(e==s.pre+"dl_graph"){let t=$("#"+e).width(),i=$("#"+e).height();d3.select("#"+s.svgid).attr("width",t).attr("height",i)}else if(e==s.pre+"dl_linegraph"||e==s.pre+"dl_scatterplot"||e==s.pre+"dl_contactmap"||e==s.pre+"dl_alignerrormap"){let t=o.bTwoddgmInit2||o.bSetsInit2?(s.htmlCls.WIDTH-r)/2:s.htmlCls.WIDTH/2,n=$("#"+e).width()/t;if(e==s.pre+"dl_linegraph"){let e=i.linegraphWidth*n;$("#"+s.linegraphid).attr("width",e)}else if(e==s.pre+"dl_scatterplot"){let e=i.scatterplotWidth*n;$("#"+s.scatterplotid).attr("width",e)}else if(e==s.pre+"dl_contactmap"){let e=i.contactmapWidth*n;$("#"+s.contactmapid).attr("width",e)}else if(e==s.pre+"dl_alignerrormap"){let e=i.alignerrormapWidth*n;$("#"+s.alignerrormapid).attr("width",e)}}}}),this.addSaveButton(e),this.addHideButton(e)}}else if(e===s.pre+"dl_2ddgm"||e===s.pre+"dl_2dctn"){let t=0;if(s.htmlCls.WIDTH>=s.htmlCls.HEIGHT)(o.bSelectannotationsInit2||o.bGraph2||o.bLineGraph2||o.bScatterplot2||o.bTable2||o.bAlignmentInit2)&&(t=.5*s.htmlCls.WIDTH-.5*r),i.resizeCanvasCls.resizeCanvas(s.htmlCls.WIDTH-t-r,s.htmlCls.HEIGHT,!0),this.openDlg2Ddgm(e,void 0,o.bSetsInit2);else{let t=s.utilsCls.isMobile()?s.htmlCls.WIDTH:s.htmlCls.WIDTH-r;i.resizeCanvasCls.resizeCanvas(t,.5*s.htmlCls.HEIGHT,!0),this.openDlg2Ddgm(e,.5*s.htmlCls.HEIGHT),this.openDlg2Ddgm(e,.5*s.htmlCls.HEIGHT,o.bSetsInit2)}}else{let a;if(l="auto",n="auto",e===s.pre+"dl_addtrack"?n="50%":e===s.pre+"dl_menupref"&&(n=600,l=500),e===s.pre+"dl_definedsets"){let t=0;if(s.htmlCls.WIDTH>=s.htmlCls.HEIGHT)(o.bSelectannotationsInit2||o.bGraph2||o.bLineGraph2||o.bScatterplot2||o.bTable2||o.bAlignmentInit2)&&(t=.5*s.htmlCls.WIDTH-.5*r),i.resizeCanvasCls.resizeCanvas(s.htmlCls.WIDTH-t-r,s.htmlCls.HEIGHT,!0),this.openDlg2Ddgm(e),o.bTwoddgmInit2&&this.openDlg2Ddgm(s.pre+"dl_2ddgm",void 0,!0),o.bTwodctnInit2&&this.openDlg2Ddgm(s.pre+"dl_2dctn",void 0,!0);else{let t=s.utilsCls.isMobile()?s.htmlCls.WIDTH:s.htmlCls.WIDTH-r;i.resizeCanvasCls.resizeCanvas(t,.5*s.htmlCls.HEIGHT,!0),this.openDlg2Ddgm(e,.5*s.htmlCls.HEIGHT),o.bTwoddgmInit2&&this.openDlg2Ddgm(s.pre+"dl_2ddgm",.5*s.htmlCls.HEIGHT,!0),o.bTwodctnInit2&&this.openDlg2Ddgm(s.pre+"dl_2dctn",.5*s.htmlCls.HEIGHT,!0)}}else s.utilsCls.isMobile()?a={my:"left top",at:"left bottom-50",of:"#"+s.pre+"canvas",collision:"none"}:e===s.pre+"dl_allinteraction"||e===s.pre+"dl_buriedarea"?(a={my:"right top",at:"right top+50",of:"#"+i.divid,collision:"none"},n=700,l=500):a=e===s.pre+"dl_rmsd"||e===s.pre+"dl_legend"?{my:"left bottom",at:"left+20 bottom-20",of:"#"+s.pre+"canvas",collision:"none"}:e===s.pre+"dl_symd"?{my:"left top",at:"right-200 bottom-200",of:"#"+s.pre+"canvas",collision:"none"}:s.cfg.align?{my:"left top",at:"left top+90",of:"#"+s.pre+"canvas",collision:"none"}:e===s.pre+"dl_mmdbafid"?{my:"left top",at:"left top+130",of:"#"+s.pre+"canvas",collision:"none"}:{my:"left top",at:"left top+50",of:"#"+s.pre+"canvas",collision:"none"},window.dialog=$("#"+e).dialog({autoOpen:!0,title:t,height:l,width:n,modal:!1,position:a}),this.addSaveButton(e),this.addHideButton(e)}$(".ui-dialog .ui-button span").removeClass("ui-icon-closethick").addClass("ui-icon-close")}openDlgNotebook(e,t){let s=this.icn3dui,i=s.icn3d;if(s.bNode)return;let n=400,l=150,r=s.htmlCls.width2d+20;e===s.pre+"dl_selectannotations"||e===s.pre+"dl_graph"||e===s.pre+"dl_linegraph"||e===s.pre+"dl_scatterplot"||e===s.pre+"dl_contactmap"||e===s.pre+"dl_alignerrormap"||e===s.pre+"dl_interactionsorted"||e===s.pre+"dl_alignment"?($("#"+e).show(),$("#"+e+"_nb").show(),$("#"+e+"_title").html(t),l=.5*s.htmlCls.HEIGHT,n=s.htmlCls.WIDTH,$("#"+e).width(n),$("#"+e).height(l),$("#"+e).resize((function(t){let n=s.htmlCls.WIDTH/2,l=$("#"+e).width()/n;if(e==s.pre+"dl_selectannotations")i.annotationCls.hideFixedTitle();else if(e==s.pre+"dl_graph"){let t=$("#"+e).width(),i=$("#"+e).height();d3.select("#"+s.svgid).attr("width",t).attr("height",i)}else if(e==s.pre+"dl_linegraph"){let e=i.linegraphWidth*l;$("#"+s.linegraphid).attr("width",e)}else if(e==s.pre+"dl_scatterplot"){let e=i.scatterplotWidth*l;$("#"+s.scatterplotid).attr("width",e)}else if(e==s.pre+"dl_contactmap"){let e=i.contactmapWidth*l;$("#"+s.contactmapid).attr("width",e)}else if(e==s.pre+"dl_alignerrormap"){let e=i.alignerrormapWidth*l;$("#"+s.alignerrormapid).attr("width",e)}}))):(i.bRender&&($("#"+e).show(),$("#"+e+"_nb").show(),$("#"+e+"_title").html(t)),l="auto",n="auto",e===s.pre+"dl_addtrack"?n="50%":e===s.pre+"dl_2ddgm"||e===s.pre+"dl_2dctn"||e===s.pre+"dl_definedsets"?n=r:e!==s.pre+"dl_allinteraction"&&e!==s.pre+"dl_buriedarea"||(n=700,l=500),$("#"+e).width(n),$("#"+e).height(l))}}class h{constructor(e){this.icn3dui=e}setCustomDialogs(){let e=this.icn3dui;if(e.icn3d,e.bNode)return"";return""}getHtmlAlignResidueByResidue(e,t,s){let i=this.icn3dui;i.icn3d;let n="";return n+="All chains will be aligned to the first chain in the comma-separated chain IDs. Each chain ID has the form of PDBID_chain (e.g., 1HHO_A, case sensitive) or UniprotID (e.g., P69905 for AlphaFold structures).Chain IDs : "+i.htmlCls.inputTextStr+"id='"+i.pre+e+"' value='P69905,P01942,1HHO_A' size=50>Align Residue by Residue
'),n}setDialogs(){let e=this.icn3dui,t=e.icn3d;if(e.bNode)return"";let s="";e.htmlCls.optionStr="",s+=e.htmlCls.divStr+"dl_2ddgm' class='"+n+" icn3d-dl_2ddgm' style='background-color:white'>",s+=this.addNotebookTitle("dl_2ddgm","2D Diagram",!0),s+="",s+=e.htmlCls.divStr+"dl_2dctn' class='"+n+" icn3d-dl_2dctn' style='background-color:white'>",s+=this.addNotebookTitle("dl_2dctn","2D Cartoon"),e.svgid_ct=e.pre+"icn3d_cartoon";let l='Nodes can be dragged or clicked.",s+=e.htmlCls.divNowrapStr+l+e.svgid_ct+'_svg">SVG '+e.htmlCls.space2,s+=l+e.svgid_ct+'_png">PNG'+e.htmlCls.space2,s+=l+e.svgid_ct+'_json">JSONLabel : ",s+=e.htmlCls.optionStr+"'"+r+"0'>No ",s+=e.htmlCls.optionStr+"'"+r+"4'>4px",s+=e.htmlCls.optionStr+"'"+r+"8' selected>8px",s+=e.htmlCls.optionStr+"'"+r+"12'>12px",s+=e.htmlCls.optionStr+"'"+r+"16'>16px",s+=e.htmlCls.optionStr+"'"+r+"24'>24px",s+=e.htmlCls.optionStr+"'"+r+"32'>32px",s+="",s+="",s+="",s+=" ",s+="",s+=e.htmlCls.divStr+"dl_alignment' class='"+n+"' style='background-color:white;'>",s+=this.addNotebookTitle("dl_alignment","Dynamically Calculated Symmetry using SymD"),s+=e.htmlCls.divStr+"symd_info'>",s+=e.htmlCls.divStr+"alignseqguide_wrapper'>Defined Sets: ",s+=" ",s+=""+e.htmlCls.buttonStr+"deletesets'>Delete Selected Sets
",s+=' Set Operations :
"+e.htmlCls.inputRadioStr+"name='"+e.pre+"setOperation' id='"+e.pre+"setOr' checked> Union(or) "+e.htmlCls.inputRadioStr+"name='"+e.pre+"setOperation' id='"+e.pre+"setAnd'> Intersection(and) "+e.htmlCls.inputRadioStr+"name='"+e.pre+"setOperation' id='"+e.pre+"setNot'> Exclusion(not) ",s+="VAST+ finds other macromolecular structures that have a similar biological unit. To do this, VAST+ takes into consideration the complete set of 3D domains that VAST identified within a query structure, throughout all of its component protein molecules, and finds other macromolecular structures that have a similar set of proteins/3D domains.VAST identifies 3D domains (substructures) within each protein structure in the Molecular Modeling Database (MMDB), and then finds other protein structures that have one or more similar 3D domains, using purely geometric criteria. You have two ways to do a VAST search.Option 1 , search with your selection (all residues are selected by default) in the loaded structures:Option 2 , search with PDB ID and chain name:Option 3 , search with a PDB file:Foldseek web server.AlphaFold Uniprot ID: "+e.htmlCls.inputTextStr+"id='"+e.pre+"afid' value='"+o+"' size=10>Orientations of Proteins in Membranes(OPM) PDB ID: "+e.htmlCls.inputTextStr+"id='"+e.pre+"opmid' value='6JXR' size=8> ",s+=e.htmlCls.buttonStr+"reload_opm'>Load",s+="",s+=e.htmlCls.divStr+"dl_pdbfile' class='"+n+"'>",s+=this.addNotebookTitle("dl_pdbfile","Please input a PDB file"),s+='Note: Several PDB files could be concatenated into a single PDB file. Use the line "ENDMDL" to separate PDB files.The custom JSON file on residue colors has the following format for proteins("ALA" and "ARG") and nucleotides("G" and "A"):
The custom file for the structure has two columns separated by space or tab: ',s+='residue number, and score in the range of 0-100. If you click "Apply Custom Color" button, ',s+='the scores 0, 50 and 100 correspond to the three colors specified below. If you click "Apply Custom Tube", ',s+='the selected residues will be displayed in a style similar to "B-factor Tube".
Score to Color: 0: ",s+=e.htmlCls.optionStr+"'red'>Red",s+=e.htmlCls.optionStr+"'green'>Green",s+=e.htmlCls.optionStr+"'blue' selected>Blue",s+=" ",s+="50 : ",s+=e.htmlCls.optionStr+"'white' selected>White",s+=e.htmlCls.optionStr+"'black'>Black",s+=" ",s+="100 : ",s+=e.htmlCls.optionStr+"'red' selected>Red",s+=e.htmlCls.optionStr+"'green'>Green",s+=e.htmlCls.optionStr+"'blue'>Blue",s+=" You can define your own reference numbers in a custom file using Excel, and then export it as a CSV file. An example file is shown below with cells separated by commas.
',s+="
refnum,11,12,,21,22,,10C,11C,20C ",s+="1TUP_C,,,,,,,200,201,230",s+='The first row defines the reference residue numbers, which could be any strings. The 1st cell could be anything. The rest cells are reference residue numbers (e.g., 11, 21, 10C, etc.) or empty cells. Each chain has a separate row. The first cell of the second row is the chain ID "1TUP_A". The rest cells are the corresponding real residue numbers for reference residue numbers in the first row. For example, the reference numbers for residues 100, 101, and 132 in the chain 1TUP_A are 11, 12, and 22, respectively. The fourth row shows another set of reference numners for the chain "1TUP_C". It could be a chain from a different structure.
',s+='To select all residues corresponding to the reference numbers, you can simplay replace ":" with "%" in the
Specification . For example, "%12" selects the residue 101 in 1TUP_A and the residue 111 in 1TUP_B. ".A%12" has the chain "A" filter and selects the residue 101 in 1TUP_A.
',s+="
VAST+ based on VAST : "+e.htmlCls.buttonStr+"reload_align_ori'>All Matching Molecules Superposed"+e.htmlCls.space3+e.htmlCls.buttonStr+"reload_align_refined'>Invariant Substructure SuperposedVAST+ based on TM-align : "+e.htmlCls.buttonStr+"reload_align_tmalign'>All Matching Molecules SuperposedAlphaFold Uniprot IDs: ",s+="All chains will be aligned to the first chain in the comma-separated chain IDs. Each chain ID has the form of PDBID_chain (e.g., 1HHO_A, case sensitive) or UniprotID (e.g., P69905 for AlphaFold structures).Chain IDs : "+e.htmlCls.inputTextStr+"id='"+e.pre+"chainalignids' value='P69905,P01942,1HHO_A' size=50>Align with TM-align "+e.htmlCls.buttonStr+"reload_chainalign_asym' style='margin-left:30px'>Align with VAST
",s+=e.htmlCls.divStr+"dl_chainalign2' class='"+n+"'>",s+=this.addNotebookTitle("dl_chainalign2","Align chains"),s+="",s+="All chains will be aligned to the first chain in the comma-separated chain IDs. Each chain ID has the form of PDBID_chain (e.g., 1HHO_A, case sensitive) or UniprotID (e.g., P69905 for AlphaFold structures).Chain IDs : "+e.htmlCls.inputTextStr+"id='"+e.pre+"chainalignids2' value='P69905,P01942,1HHO_A' size=50>Align by Sequence Alignment
",s+=e.htmlCls.divStr+"dl_chainalign3' class='"+n+"'>",s+=this.addNotebookTitle("dl_chainalign3","Align chains"),s+="",s+=this.getHtmlAlignResidueByResidue("chainalignids3","predefinedres","reload_chainalign_asym3"),s+="
",s+=e.htmlCls.divStr+"dl_realignresbyres' class='"+n+"'>",s+=this.addNotebookTitle("dl_realignresbyres","Realign residue by residue"),s+="",s+="
Option 1 : "+e.htmlCls.buttonStr+"realignSelection'>
Realign Current Selection Residue by Residue ",s+="
Option 2 :
",s+="
"+this.getHtmlAlignResidueByResidue("chainalignids4","predefinedres2","reload_chainalign_asym4")+"
",s+="
",s+='Please specify the mutations with a comma separated mutation list. Each mutation can be specified as "[
uppercase PDB ID or AlphaFold UniProt ID]_[Chain Name]_[Residue Number]_[One Letter Mutant Residue]". E.g., the mutation of N501Y in the E chain of PDB 6M0J can be specified as "6M0J_E_501_Y". For AlphaFold structures, the "Chain ID" is "A".
If you load a custom structure without PDB or UniProt ID, you can open "Seq. & Annotations" window and find the chain ID such as "stru_A". The part before the underscore is the structure ID, which can be used to specify the mutation such as "stru_A_...". Remember to choose "Show Mutation in: Current Page".
',s+="
Mutations:
"+e.htmlCls.inputTextStr+"id='"+e.pre+"mutationids' value='6M0J_E_484_K,6M0J_E_501_Y,6M0J_E_417_N' size=50>
",s+="
ID Type : ",s+='
PDB ID',s+='
AlphaFold UniProt ID
',s+="
Show Mutation in : ",s+='
Current Page',s+='
New Page
',s+=e.htmlCls.buttonStr+"reload_mutation_3d' title='Show the mutations in 3D using the scap program'>3D with scap",s+=e.htmlCls.buttonStr+"reload_mutation_inter' style='margin-left:20px' title='Show the mutations in 3D and the change of interactions'>Interactions",s+=e.htmlCls.buttonStr+"reload_mutation_pdb' style='margin-left:20px' title='Show the mutations in 3D and export the PDB of the mutant within 10 angstrom'>PDB",s+="
",s+=e.htmlCls.optionStr+"'pdb' selected>PDB",s+=e.htmlCls.optionStr+"'mmcif'>mmCIF",s+=e.htmlCls.optionStr+"'mol2'>Mol2",s+=e.htmlCls.optionStr+"'sdf'>SDF",s+=e.htmlCls.optionStr+"'xyz'>XYZ",s+=e.htmlCls.optionStr+"'icn3dpng'>iCn3D PNG",s+=e.htmlCls.optionStr+"'pae'>AlphaFold PAE",s+=" Note : The "biological unit " is the biochemically active form of a biomolecule ,
',s+=e.htmlCls.divStr+"asu_bu' style='display:none;'>",s+='which can range from a monomer (single protein molecule) to an oligomer of 100+ protein molecules.asymmetric unit " is the raw 3D structure data resolved by X-ray crystallography, NMR, or Cryo-electron microscopy. The asymmetric unit is equivalent to the biological unit in approximately 60% of structure records. In the remaining 40% of the records, the asymmetric unit represents a portion of the biological unit that can be reconstructed using crystallographic symmetry, or it represents multiple copies of the biological unit.',s+="",s+=e.htmlCls.divStr+"dl_mmdbafid' class='"+n+"' style='max-width:600px'>",s+=this.addNotebookTitle("dl_mmdbafid","Please input a list of PDB/AlphaFold IDs"),s+="List of PDB, MMDB, or AlphaFold UniProt structures: "+e.htmlCls.inputTextStr+"id='"+e.pre+"mmdbafid' placeholder='e.g., 1HHO,4N7N,P69905,P01942' size=30>
"+e.htmlCls.buttonStr+"reload_mmdbaf' style='width:150px'>Load Biological Unit"+e.htmlCls.buttonStr+"reload_mmdbaf_asym' style='margin-left:30px; width:250px'>Load Asymmetric Unit (All Chains)or
"+e.htmlCls.buttonStr+"reload_mmdbaf_append' style='width:150px'>Append Biological Unit"+e.htmlCls.buttonStr+"reload_mmdbaf_asym_append' style='margin-left:30px; width:250px'>Append Asymmetric Unit (All Chains)Note : The "biological unit " is the biochemically active form of a biomolecule ,
',s+=e.htmlCls.divStr+"asu_bu2' style='display:none;'>",s+='which can range from a monomer (single protein molecule) to an oligomer of 100+ protein molecules.asymmetric unit " is the raw 3D structure data resolved by X-ray crystallography, NMR, or Cryo-electron microscopy. The asymmetric unit is equivalent to the biological unit in approximately 60% of structure records. In the remaining 40% of the records, the asymmetric unit represents a portion of the biological unit that can be reconstructed using crystallographic symmetry, or it represents multiple copies of the biological unit.',s+="",s+=e.htmlCls.divStr+"dl_blast_rep_id' style='max-width:600px;' class='"+n+"'>",s+=this.addNotebookTitle("dl_blast_rep_id","Align sequence to structure"),s+="Enter a Sequence ID (or FASTA sequence) and the aligned protein accession, which can be found using the BLAST search with the Sequence ID or FASTA sequence as input. If the protein accession is not a PDB chain, the corresponding AlphaFold UniProt structure is used.Sequence ID (NCBI protein accession of a sequence): "+e.htmlCls.inputTextStr+"id='"+e.pre+"query_id' value='NP_001108451.1' size=8>NCBI protein accession (or a chain of a PDB): "+e.htmlCls.inputTextStr+"id='"+e.pre+"blast_rep_id' value='1TSR_A' size=8>ESM Metagenomic Atlas . The sequence should be less than 400 characters. For any sequence longer than 400, please see the discussion here .Note : Always load a PDB file before loading map files. 2fofc contour at: ";let a=["0","0.5","1","1.5","2","3","4","5","6","7","8","9","10"];s+=e.htmlCls.setHtmlCls.getOptionHtml(a,3),s+=" σ fofc contour at: ",s+=e.htmlCls.setHtmlCls.getOptionHtml(a,5),s+=" σ Note : Always load a PDB file before loading map files. 2fofc contour at: ",s+=e.htmlCls.setHtmlCls.getOptionHtml(a,3),s+=" σ fofc contour at: ",s+=e.htmlCls.setHtmlCls.getOptionHtml(a,5),s+=" σ ",s+=" "+e.htmlCls.space3,s+=e.htmlCls.buttonStr+"applysymmetry'>Apply"+e.htmlCls.space3,s+=e.htmlCls.buttonStr+"clearsymmetry'>Clear",s+="",s+=e.htmlCls.divStr+"dl_symd' style='max-width:400px' class='"+n+"'>Distance: ",s+=e.htmlCls.setHtmlCls.getOptionHtml(["4","5","6","7","8","9","10"],4),s+=" ",s+="Contact Type: ",s+=e.htmlCls.optionStr+"'calpha' >between C-alpha Atoms",s+=e.htmlCls.optionStr+"'cbeta' selected>between C-beta Atoms",s+=e.htmlCls.optionStr+"'heavyatoms' >between Heavy Atoms",s+=" "+e.htmlCls.buttonStr+"applycontactmap'>Display ",s+=""+e.htmlCls.inputCheckStr+"id='"+e.pre+"analysis_hbond' checked>Hydrogen Bonds "+e.htmlCls.space3+" ",s+="",s+=e.htmlCls.divNowrapStr+" ";let d=["3.2","3.3","3.4","3.5","3.6","3.7","3.8","3.9","4.0","4.1","4.2"];s+=e.htmlCls.setHtmlCls.getOptionHtml(d,6),s+=" Å"+e.htmlCls.space3+" ",s+=""+e.htmlCls.inputCheckStr+"id='"+e.pre+"analysis_saltbridge' checked>Salt Bridge/Ionic "+e.htmlCls.space3+" ",s+="",s+=e.htmlCls.divNowrapStr+" ";let c=["3","4","5","6","7","8"];s+=e.htmlCls.setHtmlCls.getOptionHtml(c,3),s+=" Å"+e.htmlCls.space3+" ",s+=""+e.htmlCls.inputCheckStr+"id='"+e.pre+"analysis_contact' checked>Contacts/Interactions "+e.htmlCls.space3+" ",s+="",s+=e.htmlCls.divNowrapStr+" ",s+=e.htmlCls.setHtmlCls.getOptionHtml(c,1),s+=" Å"+e.htmlCls.space3+" ",s+=" ",s+="",s+=""+e.htmlCls.inputCheckStr+"id='"+e.pre+"analysis_halogen' checked>Halogen Bonds "+e.htmlCls.space3+" ",s+="",s+=e.htmlCls.divNowrapStr+" ",s+=e.htmlCls.setHtmlCls.getOptionHtml(d,6),s+=" Å"+e.htmlCls.space3+" ",s+=""+e.htmlCls.inputCheckStr+"id='"+e.pre+"analysis_pication' checked>π-Cation "+e.htmlCls.space3+" ",s+="",s+=e.htmlCls.divNowrapStr+" ",s+=e.htmlCls.setHtmlCls.getOptionHtml(c,3),s+=" Å"+e.htmlCls.space3+" ",s+=""+e.htmlCls.inputCheckStr+"id='"+e.pre+"analysis_pistacking' checked>π-Stacking "+e.htmlCls.space3+" ",s+="",s+=e.htmlCls.divNowrapStr+" ",s+=e.htmlCls.setHtmlCls.getOptionHtml(["3","4","5"],99),s+=e.htmlCls.optionStr+"'5.5' selected>5.5",s+=e.htmlCls.setHtmlCls.getOptionHtml(["6","7","8"],99),s+=" Å"+e.htmlCls.space3+" ",s+="
",s+=e.htmlCls.divNowrapStr+"2. Select the first set:",s+="",s+="
",s+=" ",s+=e.htmlCls.divNowrapStr+"3. Select the second set:",s+="",s+="
",s+="
",s+="4. "+e.htmlCls.buttonStr+"applyhbonds'>3D Display Interactions
"+e.htmlCls.buttonStr+"hbondWindow'>Highlight Interactions in TableSort Interactions on : "+e.htmlCls.buttonStr+"sortSet1'> Set 1"+e.htmlCls.buttonStr+"sortSet2' style='margin-left:12px'>Set 2
"+e.htmlCls.buttonStr+"hbondLineGraph'>2D Interaction Network "+e.htmlCls.buttonStr+"hbondLineGraph2' style='margin-left:12px'>2D Network with Reference Numbers to show two lines of residue nodes
"+e.htmlCls.buttonStr+"hbondScatterplot'>2D Interaction Map "+e.htmlCls.buttonStr+"hbondScatterplot2' style='margin-left:12px'>2D Map with Reference Numbers to show map
Helix or Sheet'+r+e.pre+'dist_ss" size="4" value="100"> ',s+="Coil or Nucleotide"+r+e.pre+'dist_coil" size="4" value="50"> ',s+="Disulfide Bonds"+r+e.pre+'dist_ssbond" size="4" value="50"> Hydrogen Bonds"+r+e.pre+'dist_hbond" size="4" value="50"> ',s+="Salt Bridge/Ionic"+r+e.pre+'dist_ionic" size="4" value="50"> ',s+="Contacts"+r+e.pre+'dist_inter" size="4" value="25"> Halogen Bonds"+r+e.pre+'dist_halogen" size="4" value="50"> ',s+="π-Cation"+r+e.pre+'dist_pication" size="4" value="50"> ',s+="π-Stacking"+r+e.pre+'dist_pistacking" size="4" value="50">
(Note: you can also adjust thresholds at #1 to add/remove interactions.)
"+e.htmlCls.buttonStr+"areaWindow'>Buried Surface Area
5. "+e.htmlCls.buttonStr+"hbondReset'>Reset and select new sets
",s+="",s+=e.htmlCls.divStr+"dl_realign' class='"+n+"'>",s+=this.addNotebookTitle("dl_realign","Realign by sequence"),s+=e.htmlCls.divNowrapStr+"1. Select sets below ",s+="
2. "+e.htmlCls.buttonStr+"applyRealign'>Realign by Sequence
1 . Select sets below or use your current selection.
",s+="
2 . "+e.htmlCls.buttonStr+"applyRealignByStruct_tmalign'>Realign with TM-align"+e.htmlCls.buttonStr+"applyRealignByStruct' style='margin-left:30px'>Realign with VAST
",s+="
3. "+e.htmlCls.buttonStr+"applyRealignByStruct_vastplus'>VAST+ Alignment based on TM-align
",s+="
",s+="2. "+e.htmlCls.buttonStr+"applyColorSpectrumAcrossSets'>Spectrum Color for Sets
",s+="
",s+="2. "+e.htmlCls.buttonStr+"applyColorSpectrumBySets'>Spectrum Color for Residues in Sets
",s+="
",s+="2. "+e.htmlCls.buttonStr+"applyColorRainbowAcrossSets'>Rainbow Color for Sets
",s+="
",s+="2. "+e.htmlCls.buttonStr+"applyColorRainbowBySets'>Rainbow Color for Residues in Sets
',s+=e.htmlCls.space2+"Hold Ctrl key to select multiple nodes/lines.",s+=e.htmlCls.divStr+"dl_linegraphcolor' style='display:block;'>",s+=e.htmlCls.setHtmlCls.setColorHints(),s+="Scale : ";let h=["0.1","0.2","0.4","0.6","0.8","1","2","4","6","8","10"];s+=e.htmlCls.setHtmlCls.getOptionHtml(h,5),s+="
',s+="",s+=e.htmlCls.divStr+"dl_scatterplot' style='background-color:white' class='"+n+"'>",s+=this.addNotebookTitle("dl_scatterplot","2D Interaction Map"),s+=e.htmlCls.divNowrapStr+"Hold Ctrl key to select multiple nodes."+e.htmlCls.space3,s+='
',s+=e.htmlCls.divStr+"dl_scatterplotcolor' style='display:none;'>",s+=e.htmlCls.setHtmlCls.setColorHints(),s+="",e.scatterplotid=e.pre+"scatterplot",s+=e.htmlCls.divNowrapStr+l+e.scatterplotid+'_svg">SVG'+e.htmlCls.space2,s+=l+e.scatterplotid+'_png">PNG'+e.htmlCls.space2,s+=l+e.scatterplotid+'_json">JSON'+e.htmlCls.space4,s+="Scale : ",s+=e.htmlCls.setHtmlCls.getOptionHtml(h,5),s+="
',s+="",s+=e.htmlCls.divStr+"dl_contactmap' style='background-color:white' class='"+n+"'>",s+=this.addNotebookTitle("dl_contactmap","Contact Map"),s+=e.htmlCls.divNowrapStr+"Hold Ctrl key to select multiple nodes."+e.htmlCls.space3+"",e.contactmapid=e.pre+"contactmap",s+=e.htmlCls.divNowrapStr+l+e.contactmapid+'_svg">SVG'+e.htmlCls.space2,s+=l+e.contactmapid+'_png">PNG'+e.htmlCls.space2,s+=l+e.contactmapid+'_json">JSON'+e.htmlCls.space4,s+="Scale : ";let p=["0.01","0.02","0.04","0.06","0.08","0.1","0.2","0.4","0.6","0.8","1"];s+=e.htmlCls.setHtmlCls.getOptionHtml(p,10),s+="
',s+="",s+=e.htmlCls.divStr+"dl_alignerrormap' style='background-color:white' class='"+n+"'>",s+=this.addNotebookTitle("dl_alignerrormap","PAE Map"),s+=e.htmlCls.divNowrapStr+"Hold Ctrl key to select multiple nodes."+e.htmlCls.space3+"",e.alignerrormapid=e.pre+"alignerrormap",s+=e.htmlCls.divNowrapStr+l+e.alignerrormapid+'_svg">SVG'+e.htmlCls.space2,s+=l+e.alignerrormapid+'_png">PNG (slow)'+e.htmlCls.space2,s+=l+e.alignerrormapid+'_json">JSON'+e.htmlCls.space4,s+='Scale : ',s+=e.htmlCls.setHtmlCls.getOptionHtml(p,2),s+="
",s+="
0 5 10 15 20 25 30 Expected position error (Angstroms)
',s+="",s+=e.htmlCls.divStr+"dl_elecmap2fofc' class='"+n+"'>",s+=this.addNotebookTitle("dl_elecmap2fofc","Electron Density 2F0-Fc Map"),s+="Contour at: ",s+=e.htmlCls.setHtmlCls.getOptionHtml(a,3),s+=" σ "+e.htmlCls.buttonStr+"applymap2fofc'>Display "+e.htmlCls.buttonStr+"elecmapNo2'>Remove Map ",s+="",s+=e.htmlCls.divStr+"dl_elecmapfofc' class='"+n+"'>",s+=this.addNotebookTitle("dl_elecmapfofc","Electron Density F0-Fc Map"),s+="Contour at: ",s+=e.htmlCls.setHtmlCls.getOptionHtml(a,5),s+=" σ "+e.htmlCls.buttonStr+"applymapfofc'>Display "+e.htmlCls.buttonStr+"elecmapNo3'>Remove Map ",s+="",s+=e.htmlCls.divStr+"dl_emmap' class='"+n+"'>",s+=this.addNotebookTitle("dl_emmap","EM Density Map"),s+="Contour at: ",s+=e.htmlCls.setHtmlCls.getOptionHtml(["0","10","20","30","40","50","60","70","80","90","100"],3),s+=" % of maximum EM values "+e.htmlCls.buttonStr+"applyemmap'>Display "+e.htmlCls.buttonStr+"emmapNo2'>Remove EM Map ",s+="",s+=e.htmlCls.divStr+"dl_aroundsphere' class='"+n+"'>",s+=this.addNotebookTitle("dl_aroundsphere","Select a sphere around a set of residues"),s+=e.htmlCls.divNowrapStr+"1. Select the first set:",s+="",s+="
",s+="
"+e.htmlCls.buttonStr+"sphereExport'>Save interacting/contacting residue pairs in a file
",s+="",s+=e.htmlCls.divStr+"dl_adjustmem' class='"+n+"'>",s+=this.addNotebookTitle("dl_adjustmem","Adjust membranes"),s+="Note : The membranes are parallel to the X-Y plane. The center of the membranes is at Z = 0. Note : The membranes are parallel to the X-Y plane. The center of the membranes is at Z = 0. ",s+=e.htmlCls.divNowrapStr+"First set:",s+="",s+="
",s+=" ",s+=e.htmlCls.divNowrapStr+"Second set:",s+="",s+="
",s+="
",s+=e.htmlCls.spanNowrapStr+"2. Color: "+e.htmlCls.inputTextStr+"id='"+e.pre+"distancecolor2' value='"+"#ffff00' size=4>",s+=e.htmlCls.divNowrapStr+"First set:",s+="",s+="
",s+=" ",s+=e.htmlCls.divNowrapStr+"Second set:",s+="",s+="
",s+="
",s+=e.htmlCls.divNowrapStr+"2. Line style: ",s+=e.htmlCls.setHtmlCls.getOptionHtml(["Solid","Dashed"],0),s+=" ",s+=e.htmlCls.setHtmlCls.getOptionHtml(["1.0","0.9","0.8","0.7","0.6","0.5","0.4","0.3","0.2","0.1"],7),s+=" ",s+="
",s+=e.htmlCls.setHtmlCls.getOptionHtml(["Sphere","Cube"],0),s+=" ",s+=e.htmlCls.setHtmlCls.getOptionHtml(["1.0","0.9","0.8","0.7","0.6","0.5","0.4","0.3","0.2","0.1"],7),s+=" ",s+=e.htmlCls.divNowrapStr+"First sets:",s+="",s+="
",s+=" ",s+=e.htmlCls.divNowrapStr+"Second sets:",s+="",s+="
",s+="
",s+=e.htmlCls.spanNowrapStr+"2. "+e.htmlCls.buttonStr+"applydisttable'>Distances in Table",s+="",s+=e.htmlCls.divStr+"dl_stabilizer_rm' class='"+n+"'>",s+=this.addNotebookTitle("dl_stabilizer_rm","Remove a stabilizer"),e.utilsCls.isMobile()?s+=e.htmlCls.spanNowrapStr+"1. Touch TWO atomsNote : The following parameters will be saved in cache. You just need to set them once. Note: The full protein sequences with gaps in MSA are listed one by one. The sequence of the structure is listed at the top. Each sequence has a title line starting with \">\".
Precalculated Multiple Sequence Alignment (MSA) :Position of the first residue in Sequences & Annotations window : "+e.htmlCls.inputTextStr+"id='"+e.pre+"fasta_startpos' value='1' size=2> ",s+=e.htmlCls.optionStr+"'identity' selected>Identity",s+=e.htmlCls.optionStr+"'conservation'>Conservation",s+=" Note: Show exons for all isoforms of the protein in the same gene as specified below.
NCBI Gene IDPosition of the first residue in Sequences & Annotations window : "+e.htmlCls.inputTextStr+"id='"+e.pre+"fasta_startpos2' value='1' size=2> Save Clear URLs Used in Browsers iCn3D GitHub )Commands Used in Jupyter Noteboook Show All Chains Zoom : mouse wheel; "+e.htmlCls.space3+" Move : left button; "+e.htmlCls.space3+" Select Multiple Nodes : Ctrl Key and drag an Area"+e.htmlCls.space3,s+='
',s+=e.htmlCls.divStr+"dl_svgcolor' style='display:none;'>",s+=e.htmlCls.divNowrapStr+'Click "View > H-Bonds & Interactions" to adjust parameters and relaunch the graph ',s+=e.htmlCls.divNowrapStr+'Green : H-Bonds; ',s+='Cyan : Salt Bridge/Ionic; ',s+='Grey : contacts; ',s+='Orange : disulfide bonds',s+=e.htmlCls.divNowrapStr+'Magenta : Halogen Bonds; ',s+='Red : π-Cation; ',s+='Blue : π-Stacking',s+="",s+=e.htmlCls.divNowrapStr+l+e.svgid+'_svg">SVG'+e.htmlCls.space2,s+=l+e.svgid+'_png">PNG'+e.htmlCls.space2,s+=l+e.svgid+'_json">JSON',s+=e.htmlCls.space3+"Force on Nodes : ",s+=e.htmlCls.optionStr+"'0'>No",s+=e.htmlCls.optionStr+"'1'>X-axis",s+=e.htmlCls.optionStr+"'2'>Y-axis",s+=e.htmlCls.optionStr+"'3'>Circle",s+=e.htmlCls.optionStr+"'4' selected>Random",s+="
",s+=e.htmlCls.space3+"Label Size : ",r="icn3d-node-text",s+=e.htmlCls.optionStr+"'"+r+"0'>No",s+=e.htmlCls.optionStr+"'"+r+"4'>4px",s+=e.htmlCls.optionStr+"'"+r+"8' selected>8px",s+=e.htmlCls.optionStr+"'"+r+"12'>12px",s+=e.htmlCls.optionStr+"'"+r+"16'>16px",s+=e.htmlCls.optionStr+"'"+r+"24'>24px",s+=e.htmlCls.optionStr+"'"+r+"32'>32px",s+=" ",s+=e.htmlCls.space3+"Internal Edges : ",s+=e.htmlCls.optionStr+"'1' selected>Hide",s+=e.htmlCls.optionStr+"'0'>Show",s+="
",s+="",s+='EDTSurf algorithm : Toal : "+e.htmlCls.inputTextStr+"id='"+e.pre+"areavalue' value='' size='10'> Å2
",s+="",s+=e.htmlCls.divStr+"dl_colorbyarea' class='"+n+"'>",s+=this.addNotebookTitle("dl_colorbyarea","Color by surface area"),s+="Color each residue based on the percentage of solvent accessilbe surface area. The color ranges from blue, to white, to red for a percentage of 0, 35(variable), and 100, respectively.
Middle Percentage(White) : "+e.htmlCls.inputTextStr+"id='"+e.pre+"midpercent' value='35' size='10'>% Color Select residue based on the percentage of solvent accessilbe surface area. The values are in the range of 0-100.
Min Percentage : "+e.htmlCls.inputTextStr+"id='"+e.pre+"minpercentout' value='0' size='10'>% Max Percentage : "+e.htmlCls.inputTextStr+"id='"+e.pre+"maxpercentout' value='100' size='10'>% Apply Select residue based on B-factor/pLDDT. The values are in the range of 0-100.
Min B-factor/pLDDT : "+e.htmlCls.inputTextStr+"id='"+e.pre+"minbfactor' value='0' size='10'>% Max B-factor/pLDDT : "+e.htmlCls.inputTextStr+"id='"+e.pre+"maxbfactor' value='100' size='10'>% Apply Choose an Ig template for selected residues: ";let u={V:["FAB-HEAVY_5esv_V-n1","FAB-LIGHT_5esv_V-n1","VNAR_1t6vN_shark_V","TCRa_6jxrm_human_V-n1","VISTA_6oilA_human_V","CD8a_1cd8A_human_V","PD1_4zqkB_human_V","ICOS_6x4gA_human_V","CD28_1yjdC_human_V","PDL1_4z18B_human_V-n1","CD2_1hnfA_human_V-n1","LAG3_7tzgD_human_V-n1"],C1:["FAB-LIGHT_5esv_C1-n2","GHR_1axiB_human_FN3-n1","VTCN1_Q7Z7D3_human_V-n2","B2Microglobulin_7phrL_human_C1","FAB-HEAVY_5esv_C1-n2","MHCIa_7phrH_human_C1","TCRa_6jxrm_human_C1-n2"],C2:["CD2_1hnfA_human_C2-n2","Siglec3_5j0bB_human_C2-n2","LAG3_7tzgD_human_C2-n2","Contactin1_3s97C_human_C2-n2"],Iset:["BTLA_2aw2A_human_Iset","Palladin_2dm3A_human_Iset-n1","Titin_4uowM_human_Unk-n152","JAM1_1nbqA_human_VorIset-n2","CD19_6al5A_human_C2orV-n1"],FN3:["InsulinR_8guyE_human_FN3-n1","IL6Rb_1bquB_human_FN3-n3","Sidekick2_1wf5A_human_FN3-n7","InsulinR_8guyE_human_FN3-n2","Contactin1_2ee2A_human_FN3-n9","IL6Rb_1bquB_human_FN3-n2"],Other:["Endo-1,4-BetaXylanase10A_1i8aA_bacteria_n4","CoAtomerGamma1_1r4xA_human","TP34_2o6cA_bacteria","RBPJ_6py8C_human_Unk-n2","TP47_1o75A_bacteria","C3_2qkiD_human_n1","BArrestin1_4jqiA_rat_n1","RBPJ_6py8C_human_Unk-n1","CuZnSuperoxideDismutase_1hl5C_human","TEAD1_3kysC_human","ASF1A_2iijA_human","MPT63_1lmiA_bacteria","NaCaExchanger_2fwuA_dog_n2","ORF7a_1xakA_virus","ECadherin_4zt1A_human_n2","NaKATPaseTransporterBeta_2zxeB_spurdogshark","LaminAC_1ifrA_human","IsdA_2iteA_bacteria"]};for(let t in u){s+="";for(let i=0,n=u[t].length;i"+n+""}s+=" "}return s+=" "+e.htmlCls.buttonStr+"mn6_igrefTpl_apply'>Show Ig Ref. 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i=$(this).attr("resid"),n=$(this).attr("id");$("#"+n).length&&$("#"+n)[0].checked?s.selectionCls.selectOneResid(i):$("#"+n).length&&!$("#"+n)[0].checked&&s.selectionCls.selectOneResid(i,!0),s.hlUpdateCls.updateHlAll()})),$(document).on("click","."+e.pre+"selset",(async function(t){let i=e.icn3d;t.stopImmediatePropagation(),i.bSelOneRes=!1;let n=$("."+e.pre+"seloneres");for(let e=0,t=n.length;e0))return{sequencesHtml:a,maxSeqCnt:d};c[s]=1}let h,p=void 0===t||t;p&&(o.hAtoms={});let m,u,g=0,f=0;for(let t=0,l=e.length;t0?m:l,p&&(o.hAtoms=r.hashUtilsCls.unionHash(o.hAtoms,o.alnChains[l]));let b=[],C="",y=void 0!==o.alnChainsSeq[l]?o.alnChainsSeq[l].length:0;y>d&&(d=y);let v,_,w=u.indexOf("_"),S=u.substr(0,w),A=u.substr(w+1);for(let e=0,t=y;e=0;--e)if("-"!=o.alnChainsSeq[l][e].resn){_=o.alnChainsSeq[l][e].resi;break}C+=""+v+" ",h=!(void 0===e||!c.hasOwnProperty(u));for(let e=0,t=y;e"}""!==a?-1!=o.alnChainsSeq[l][e].resi?C+=""+o.alnChainsSeq[l][e].resn+" ":C+=""+o.alnChainsSeq[l][e].resn+" ":C+=""+o.alnChainsSeq[l][e].resn+" "}C+=""+_+" ";let x=e.length,k=void 0!==o.alnChainsAnno[l]?o.alnChainsAnno[l].length:0;for(let t=0,s=k;t";for(let e=0,i=o.alnChainsAnno[l][t].length;e ':' ';else if("E"==i)if(void 0!==o.alnChainsSeq[s][e]){let i=s+"_"+o.alnChainsSeq[s][e].resi;if(o.residues.hasOwnProperty(i)){o.firstAtomObjCls.getFirstCalphaAtomObj(o.residues[i]).ssend?b[t]+=' ':b[t]+=' '}else b[t]+=' '}else b[t]+=' ';else b[t]+="c"==i?' ':"o"==i?' ':""+i+" "}b[t]+="'+O+'
'+C+" "+t+" "+t+" "}getMenuUrl(e,t,s,i,n){let l=this.icn3dui;return l.icn3d,l.htmlCls.allMenus[e]=s,n&&(l.htmlCls.allMenusSel[e]=n),i&&(l.htmlCls.simpleMenus[e]=1),""+s+" "+t+" "+t+" "}getRadio(e,t,s,i,n,l){let r=this.icn3dui;r.icn3d,r.htmlCls.allMenus[t]=s,l&&(r.htmlCls.allMenusSel[t]=l),n&&(r.htmlCls.simpleMenus[t]=1);let o=i?" checked":"";return""+r.htmlCls.inputRadioStr+"name='"+r.pre+e+"' class='"+r.pre+e+"' v='"+s+"'"+o+">"+s+" "+o.htmlCls.inputRadioStr+"name='"+o.pre+e+"'"+a+">"+o.htmlCls.space3+" "+s+" ",n+="Select: "+t.htmlCls.inputTextStr+"id='"+t.pre+"command"+s+"' placeholder='$[structures].[chains]:[residues]@[atoms]' size='60'> Name: "+t.htmlCls.inputTextStr+"id='"+t.pre+"command_name"+s+"' placeholder='my_selection' size='60'> "+t.htmlCls.space3+t.htmlCls.buttonStr+"command_apply"+s+"'>Save Selection to Defined Sets
",n+='Specification Tips:
Specification: In the selection "$1HHO,4N7N.A,B,C:5-10,LV,3AlaVal,chemicals@CA,C,C*":',n+='"$1HHO,4N7N" uses "$" to indicate structure selection. ".A,B,C" uses "." to indicate chain selection. ":5-10,LV,3LeuVal,chemicals" uses the colon ":" to indicate residue selection. Residue selection could be residue number(5-10), one-letter IUPAC residue name abbreviations(LV), three-letter residue names(AlaVal, "3" indicates each residue name has three letters), or predefined names: "proteins", "nucleotides", "chemicals", "ions", and "water". IUPAC abbreviations can be written either as a contiguous string(e.g., ":LV"), in order to find all instances of that sequence in the structure, or they can be separated by commas(e.g., ":L,V") to select all residues of a given type in the structure(in the latter case, select all Leucine and Valine in the structure). "@CA,C,C*" uses "@" to indicate atom name selection. "C*" selects any atom names starting with "C". Partial definition is allowed, e.g., ":1-10" selects all residue IDs 1-10 in all chains. Different selections can be unioned(with "or ", default), intersected(with "and "), or negated(with "not "). For example, ":1-10 or :K" selects all residues 1-10 and all Lys residues. ":1-10 and :K" selects all Lys residues in the range of residue number 1-10. ":1-10 or not :K" selects all residues 1-10, which are not Lys residues. The wild card character "X" or "x" can be used to represent any character.',n+=" Set Operation: ",n+='Users can select multiple sets in the menu "Select > Defined Sets". Different sets can be unioned(with "or ", default), intersected(with "and "), or negated(with "not "). For example, if the "Defined Sets" menu has four sets ":1-10", ":11-20", ":5-15", and ":7-8", the command "saved atoms :1-10 or :11-20 and :5-15 not :7-8" unions all residues 1-10 and 11-20 to get the residues 1-20, then intersects with the residues 5-15 to get the residues 5-15, then exclude the residues 7-8 to get the final residues 5-6 and 9-15. Full commands in url or command window: ",n+="Select without saving the set: select $1HHO,4N7N.A,B,C:5-10,LV,chemicals@CA,C,C* Select and save: select $1HHO,4N7N.A,B,C:5-10,LV,chemicals@CA,C,C* | name my_name
",n+="",n}getOptionHtml(e,t){let s=this.icn3dui;s.icn3d;let i="";for(let n=0,l=e.length;n"+l+"":s.htmlCls.optionStr+"'"+l+"'>"+l+""}return i}setColorHints(){let e=this.icn3dui;e.icn3d;let t="";return t+=e.htmlCls.divNowrapStr+'Green : H-Bonds; ',t+='Cyan : Salt Bridge/Ionic; ',t+='Grey : contacts',t+=e.htmlCls.divNowrapStr+'Magenta : Halogen Bonds; ',t+='Red : π-Cation; ',t+='Blue : π-Stacking',t}setThicknessHtml(e){let t=this.icn3dui,s=t.icn3d,i="",n="3dprint"==e?"1":"0.1",l="3dprint"==e?"1.2":"0.3",r="3dprint"==e?"0.8":"0.4",o="3dprint"==e?"0.8":"0.4",a="3dprint"==e?"1":"0.4",d="3dprint"==e?"0.6":"0.3",c="3dprint"==e?"1":"0.2",h="3dprint"==e?"2":"1.3",p="3dprint"==e?"1.4":"0.8",m=40,u=.8,g=.4,f=.2,b=0,C=1,y=0;if("style"==e){if(""!=this.getCookie("shininess")&&(m=parseFloat(this.getCookie("shininess"))),""!=this.getCookie("light1")&&(u=parseFloat(this.getCookie("light1")),g=parseFloat(this.getCookie("light2")),f=parseFloat(this.getCookie("light3"))),""!=this.getCookie("lineRadius")){n=parseFloat(this.getCookie("lineRadius")),l=parseFloat(this.getCookie("coilWidth")),r=parseFloat(this.getCookie("cylinderRadius"));let e=this.getCookie("crosslinkRadius");o=isNaN(e)?s.crosslinkRadius:parseFloat(e),a=parseFloat(this.getCookie("traceRadius")),d=parseFloat(this.getCookie("dotSphereScale")),c=parseFloat(this.getCookie("ribbonthickness")),h=parseFloat(this.getCookie("helixSheetWidth")),p=parseFloat(this.getCookie("nucleicAcidWidth"))}""!=this.getCookie("glycan")&&(b=parseFloat(this.getCookie("glycan"))),""!=this.getCookie("membrane")&&(C=parseFloat(this.getCookie("membrane"))),""!=this.getCookie("cmdwindow")&&(y=parseFloat(this.getCookie("cmdwindow"))),i+="Note : The following parameters will be saved in cache. You just need to set them once. 1. Shininess : "+t.htmlCls.inputTextStr+"id='"+t.pre+"shininess' value='"+m+"' size=4>"+t.htmlCls.space3+"(for the shininess of the 3D objects, default 40)2. Three directional lights : Key Light : "+t.htmlCls.inputTextStr+"id='"+t.pre+"light1' value='"+u+"' size=4>"+t.htmlCls.space3+"(for the light strength of the key light, default 0.8)Fill Light : "+t.htmlCls.inputTextStr+"id='"+t.pre+"light2' value='"+g+"' size=4>"+t.htmlCls.space3+"(for the light strength of the fill light, default 0.4)Back Light : "+t.htmlCls.inputTextStr+"id='"+t.pre+"light3' value='"+f+"' size=4>"+t.htmlCls.space3+"(for the light strength of the back light, default 0.2)3. Thickness : Line Radius : "+t.htmlCls.inputTextStr+"id='"+t.pre+"linerad_"+e+"' value='"+n+"' size=4>"+t.htmlCls.space3+"(for stabilizers, hydrogen bonds, distance lines, default 0.1)Coil Radius : "+t.htmlCls.inputTextStr+"id='"+t.pre+"coilrad_"+e+"' value='"+l+"' size=4>"+t.htmlCls.space3+"(for coils, default 0.3)Stick Radius : "+t.htmlCls.inputTextStr+"id='"+t.pre+"stickrad_"+e+"' value='"+r+"' size=4>"+t.htmlCls.space3+"(for sticks, default 0.4)Cross-Linkage Radius : "+t.htmlCls.inputTextStr+"id='"+t.pre+"crosslinkrad_"+e+"' value='"+o+"' size=4>"+t.htmlCls.space3+"(for cross-linkages, default 0.4)Trace Radius : "+t.htmlCls.inputTextStr+"id='"+t.pre+"tracerad_"+e+"' value='"+a+"' size=4>"+t.htmlCls.space3+"(for C alpha trace, O3' trace, default 0.4)Ribbon Thickness : "+t.htmlCls.inputTextStr+"id='"+t.pre+"ribbonthick_"+e+"' value='"+c+"' size=4>"+t.htmlCls.space3+"(for helix and sheet ribbons, nucleotide ribbons, default 0.2)Protein Ribbon Width : "+t.htmlCls.inputTextStr+"id='"+t.pre+"prtribbonwidth_"+e+"' value='"+h+"' size=4>"+t.htmlCls.space3+"(for helix and sheet ribbons, default 1.3)Nucleotide Ribbon Width : "+t.htmlCls.inputTextStr+"id='"+t.pre+"nucleotideribbonwidth_"+e+"' value='"+p+"' size=4>"+t.htmlCls.space3+"(for nucleotide ribbons, default 0.8)Ball Scale : "+t.htmlCls.inputTextStr+"id='"+t.pre+"ballscale_"+e+"' value='"+d+"' size=4>"+t.htmlCls.space3+"(for styles 'Ball and Stick' and 'Dot', default 0.3)4. Show Glycan Cartoon : "+t.htmlCls.inputTextStr+"id='"+t.pre+"glycan' value='"+b+"' size=4>"+t.htmlCls.space3+"(0: hide, 1: show, default 0)5. Show Membrane : "+t.htmlCls.inputTextStr+"id='"+t.pre+"membrane' value='"+C+"' size=4>"+t.htmlCls.space3+"(0: hide, 1: show, default 1)6. Enlarge Command Window : "+t.htmlCls.inputTextStr+"id='"+t.pre+"cmdwindow' value='"+y+"' size=4>"+t.htmlCls.space3+"(0: Regular, 1: Large, default 0)":(n+='
',n+="Selection: Name: "+s.htmlCls.inputTextStr+"id='"+s.pre+"seq_command_name"+e+"' value='seq_"+l+"' size='5'> "+s.htmlCls.space2+"Save Clear
Residue labeling: standard residue with coordinates: UPPER case letter; nonstandard residue with coordinates: the first UPPER case letter plus a period except that water residue uses the letter 'O'; residue missing coordinates: lower case letter."+(s.utilsCls.isMac()&&!s.utilsCls.isMobile()?"Turn on scroll bar: System preferences -> General -> show scroll bars -> check Always":"")+"
',n+="Selection: Name: "+s.htmlCls.inputTextStr+"id='"+s.pre+"alignseq_command_name' value='alseq_"+l+"' size='10'> "+s.htmlCls.space2+"Save Clear
Residue labeling: aligned residue with coordinates: UPPER case letter; non-aligned residue with coordinates: lower case letter which can be highlighted; residue missing coordinates: lower case letter which can NOT be highlighted."+(s.utilsCls.isMac()&&!s.utilsCls.isMobile()?"Turn on scroll bar: System preferences -> General -> show scroll bars -> check Always":"")+"Select Aligned Sequences: touch to select, touch again to deselect, multiple selection is allowed without Ctrl key, click "Save Selection" to save the current selection.Select on 1D sequences: drag to select, drag again to deselect, multiple selection is allowed without Ctrl key, click "Save Selection" to save the current selection.Select on 2D interaction diagram: click on the nodes or lines. The nodes are chains and can be united with the Ctrl key. The lines are interactions and can NOT be united. Each click on the lines selects half of the lines, i.e., select the interacting residues in one of the two chains.Select on 3D structures: "+(e.utilsCls.isMobile()?"use finger to pick":'hold "Alt" and use mouse to pick')+', click the second time to deselect, hold "Ctrl" to union selection, hold "Shift" to select a range, press the up/down arrow to switch among atom/residue/strand/chain/structure, click "Save Selection" to save the current selection.Save the current selection (either on 3D structure, 2D interactions, or 1D sequence): open the menu "Select -> Save Selection", specify the name and description for the selection, and click "Save".Grid Size: ";s+=this.getOptionHtml(["65","97","129"],0),s+=" ",s+="Salt Concentration: ";return s+=this.getOptionHtml(["0","0.15"],1),s+=" M ";return"delphi"==e?s.cfg.cid?i+="
Note : Partial charges(MMFF94) are from PubChem Compound SDF files.
":(i+="
Note : Only the selected residues are used for
DelPhi potential calculation by solving linear Poisson-Boltzmann equation.",i+='
',i+=s.htmlCls.divStr+t+"' style='display:none;'>",i+="
The hydrogens and partial charges of proteins and nucleotides are added using
DelPhiPKa with the Amber charge and size files. The hydrogens of ligands are added using
Open Babel . The partial charges of ligands are calculated using
Antechamber with the Gasteiger charge method. All partial charges are calculated at pH 7.
",i+='Lipids are treated as ligands. Please use "HETATM" instead of "ATOM " for each lipid atom in your PDB file. Each phosphate in lipids is assigned with a charge of -1. You can download PQR and modify it, or prepare your PQR file using other tools. Then load the PQR file at the menu "Analysis > Load PQR/Potential".
',i+="
Note : Always load a PDB file before loading a PQR or DelPhi potential file.",i+='
DelPhi Web Server and be exported as a Cube file. ',"url"==e&&(i+="The PQR or potential file can be accessed in a URL if it is located in the same host as iCn3D."),i+="Potential contour at: ";let d;a+=this.getOptionHtml(["0.5","1","2","3","4","5","6","7","8","9","10"],2),a+=" kT/e(25.6mV at 298K) "+s.htmlCls.buttonStr+n+"mapNo'>Remove Map ",a+=s.htmlCls.divStr+n+"tab1_"+i+"'>",a+=this.addGsizeSalt(i)+"PQR File : "+s.htmlCls.inputFileStr+"id='"+s.pre+i+"file'> Phi File : "+s.htmlCls.inputFileStr+"id='"+s.pre+n+"file'> Cube File : "+s.htmlCls.inputFileStr+"id='"+s.pre+l+"file'> "+s.htmlCls.buttonStr+n+"mapNo'>Remove Map ",a+=s.htmlCls.divStr+n+"tab1_"+i+"2'>",a+=this.addGsizeSalt(i)+"PQR URL in the same host: "+s.htmlCls.inputTextStr+"id='"+s.pre+i+"file'> Phi URL in the same host: "+s.htmlCls.inputTextStr+"id='"+s.pre+n+"file'> Cube URL in the same host: "+s.htmlCls.inputTextStr+"id='"+s.pre+l+"file'> Surface with max potential at: ";a+=this.getOptionHtml(["0.5","1","2","3","4","5","6","7","8","9","10"],2),a+=" kT/e(25.6mV at 298K) Surface : ",a+="Van der Waals ",a+="Molecular Surface ",a+="Solvent Accessible ",a+=" ",a+="Opacity : ";return a+=this.getOptionHtml(["1.0","0.9","0.8","0.7","0.6","0.5","0.4","0.3","0.2","0.1"],0),a+=" Wireframe : ",a+="Yes ",a+="No ",a+=" "+s.htmlCls.buttonStr+n+"mapNo2'>Remove Surface ",a+=s.htmlCls.divStr+n+"tab2_"+i+"'>",a+=this.addGsizeSalt(i+"2")+"PQR File : "+s.htmlCls.inputFileStr+"id='"+s.pre+i+"file2'> Phi File : "+s.htmlCls.inputFileStr+"id='"+s.pre+n+"file2'> Cube File : "+s.htmlCls.inputFileStr+"id='"+s.pre+l+"file2'> "+s.htmlCls.buttonStr+n+"mapNo2'>Remove Surface ",a+=s.htmlCls.divStr+n+"tab2_"+i+"2'>",a+=this.addGsizeSalt(i+"2")+"PQR URL in the same host: "+s.htmlCls.inputTextStr+"id='"+s.pre+i+"file2'> Phi URL in the same host: "+s.htmlCls.inputTextStr+"id='"+s.pre+n+"file2'> Cube URL in the same host: "+s.htmlCls.inputTextStr+"id='"+s.pre+l+"file2'> Save File > iCn3D PNG Image"...');else if(-1!=l){let t=e.substr(l+n.length);s.htmlCls.clickMenuCls.setLogCmd("load iCn3D PNG image "+$("#"+s.pre+"pngimage").val(),!1),window.open(t,"_self")}else if(-1!=o){let n="Start of data file======\n",l=e.indexOf(n);i.bInputfile=-1!=l,i.bInputPNGWithData=i.bInputfile;let a,d=t?t.replace(/;/g,"\n"):"";if(i.bInputfile){let t=e.indexOf("End of data file======\n"),s=e.substr(l+n.length,t-l-n.length);i.InputfileData=i.InputfileData?i.InputfileData+"\nENDMDL\n"+s:s;let c="Start of type file======\n",h=e.indexOf(c),p=e.indexOf("End of type file======\n"),m=e.substr(h+c.length,p-h-c.length-1);i.InputfileType=m;let u=e.indexOf("End of state file======\n");a=e.substr(o+r.length,u-o-r.length),a=decodeURIComponent(a+"\n"+d),"pdb"===m?(await i.pdbParserCls.loadPdbData(s),i.commands=[],i.optsHistory=[]):("mol2"===m?await i.mol2ParserCls.loadMol2Data(s):"sdf"===m?await i.sdfParserCls.loadSdfData(s):"xyz"===m?await i.xyzParserCls.loadXyzData(s):"mmcif"===m&&await i.mmcifParserCls.loadMmcifData(s),i.commands=[],i.optsHistory=[])}else{let t=e.indexOf("End of state file======\n");a=e.substr(o+r.length,t-o-r.length),a=decodeURIComponent(a+"\n"+d),i.commands=[],i.optsHistory=[]}await i.loadScriptCls.loadScript(a,!0),s.htmlCls.clickMenuCls.setLogCmd("load iCn3D PNG image "+$("#"+s.pre+"pngimage").val(),!1)}}fileSupport(){window.File&&window.FileReader&&window.FileList&&window.Blob||alert("The File APIs are not fully supported in this browser.")}getLinkColor(){let e="";return e+=", linkmap: {\n",e+='3: {"type": "peptidebond", "c":""},\n',e+='4: {"type": "ssbond", "c":"FFA500"},\n',e+='5: {"type": "ionic", "c":"0FF"},\n',e+='6: {"type": "ionicInside", "c":"FFF"},\n',e+='11: {"type": "contact", "c":"888"},\n',e+='12: {"type": "contactInside", "c":"FFF"},\n',e+='13: {"type": "hbond", "c":"0F0"},\n',e+='14: {"type": "hbondInside", "c":"FFF"},\n',e+='15: {"type": "clbond", "c":"006400"},\n',e+='17: {"type": "halogen", "c":"F0F"},\n',e+='18: {"type": "halogenInside", "c":"FFF"},\n',e+='19: {"type": "pication", "c":"F00"},\n',e+='20: {"type": "picationInside", "c":"FFF"},\n',e+='21: {"type": "pistacking", "c":"00F"},\n',e+='22: {"type": "pistackingInside", "c":"FFF"}\n',e+="}}\n",', linkmap: {\n3: {"type": "peptidebond", "c":""},\n4: {"type": "ssbond", "c":"FFA500"},\n5: {"type": "ionic", "c":"0FF"},\n6: {"type": "ionicInside", "c":"FFF"},\n11: {"type": "contact", "c":"888"},\n12: {"type": "contactInside", "c":"FFF"},\n13: {"type": "hbond", "c":"0F0"},\n14: {"type": "hbondInside", "c":"FFF"},\n15: {"type": "clbond", "c":"006400"},\n17: {"type": "halogen", "c":"F0F"},\n18: {"type": "halogenInside", "c":"FFF"},\n19: {"type": "pication", "c":"F00"},\n20: {"type": "picationInside", "c":"FFF"},\n21: {"type": "pistacking", "c":"00F"},\n22: {"type": "pistackingInside", "c":"FFF"}\n}}\n'}setCookieForThickness(){let e=this.icn3dui,t=e.icn3d;if(!e.bNode){let e=3650;this.setCookie("lineRadius",t.lineRadius,e),this.setCookie("coilWidth",t.coilWidth,e),this.setCookie("cylinderRadius",t.cylinderRadius,e),this.setCookie("crosslinkRadius",t.crosslinkRadius,e),this.setCookie("traceRadius",t.traceRadius,e),this.setCookie("dotSphereScale",t.dotSphereScale,e),this.setCookie("ribbonthickness",t.ribbonthickness,e),this.setCookie("helixSheetWidth",t.helixSheetWidth,e),this.setCookie("nucleicAcidWidth",t.nucleicAcidWidth,e)}}setLineThickness(e,t){let s=this.icn3dui,i=s.icn3d;if(i.bSetThickness=!0,"style"==e&&(t&&($("#"+s.pre+"shininess").val("40"),$("#"+s.pre+"light1").val("0.8"),$("#"+s.pre+"light2").val("0.4"),$("#"+s.pre+"light3").val("0.2"),$("#"+s.pre+"glycan").val("0"),$("#"+s.pre+"membrane").val("1"),$("#"+s.pre+"cmdwindow").val("0")),i.shininess=parseFloat($("#"+s.pre+"shininess").val()),i.light1=parseFloat($("#"+s.pre+"light1").val()),i.light2=parseFloat($("#"+s.pre+"light2").val()),i.light3=parseFloat($("#"+s.pre+"light3").val()),i.bGlycansCartoon=parseInt($("#"+s.pre+"glycan").val()),i.bMembrane=parseInt($("#"+s.pre+"membrane").val()),i.bCmdWindow=parseInt($("#"+s.pre+"cmdwindow").val())),t&&($("#"+s.pre+"linerad_"+e).val(.1),$("#"+s.pre+"coilrad_"+e).val(.3),$("#"+s.pre+"stickrad_"+e).val(.4),$("#"+s.pre+"crosslinkrad_"+e).val(.4),$("#"+s.pre+"tracerad_"+e).val(.4),$("#"+s.pre+"ballscale_"+e).val(.3),$("#"+s.pre+"ribbonthick_"+e).val(.2),$("#"+s.pre+"prtribbonwidth_"+e).val(1.3),$("#"+s.pre+"nucleotideribbonwidth_"+e).val(.8)),i.lineRadius=parseFloat($("#"+s.pre+"linerad_"+e).val()),i.coilWidth=parseFloat($("#"+s.pre+"coilrad_"+e).val()),i.cylinderRadius=parseFloat($("#"+s.pre+"stickrad_"+e).val()),i.crosslinkRadius=parseFloat($("#"+s.pre+"crosslinkrad_"+e).val()),i.traceRadius=parseFloat($("#"+s.pre+"tracerad_"+e).val()),i.dotSphereScale=parseFloat($("#"+s.pre+"ballscale_"+e).val()),i.ribbonthickness=parseFloat($("#"+s.pre+"ribbonthick_"+e).val()),i.helixSheetWidth=parseFloat($("#"+s.pre+"prtribbonwidth_"+e).val()),i.nucleicAcidWidth=parseFloat($("#"+s.pre+"nucleotideribbonwidth_"+e).val()),!s.bNode){let e=3650;this.setCookie("shininess",i.shininess,e),this.setCookie("light1",i.light1,e),this.setCookie("light2",i.light2,e),this.setCookie("light3",i.light3,e),this.setCookie("glycan",i.bGlycansCartoon,e),this.setCookie("membrane",i.bMembrane,e),this.setCookie("cmdwindow",i.bCmdWindow,e)}if(this.setCookieForThickness(),e=t){let e="reset thickness";s.htmlCls.clickMenuCls.setLogCmd(e,!0),i.bSetThickness=!1,i.threeDPrintCls.resetAfter3Dprint()}else s.htmlCls.clickMenuCls.setLogCmd("set thickness | linerad "+i.lineRadius+" | coilrad "+i.coilWidth+" | stickrad "+i.cylinderRadius+" | crosslinkrad "+i.crosslinkRadius+" | tracerad "+i.traceRadius+" | ribbonthick "+i.ribbonthickness+" | proteinwidth "+i.helixSheetWidth+" | nucleotidewidth "+i.nucleicAcidWidth+" | ballscale "+i.dotSphereScale,!0),s.htmlCls.clickMenuCls.setLogCmd("set glycan "+i.bGlycansCartoon,!0),s.htmlCls.clickMenuCls.setLogCmd("set membrane "+i.bMembrane,!0),s.htmlCls.clickMenuCls.setLogCmd("set cmdwindow "+i.bCmdWindow,!0);i.drawCls.draw()}setCookie(e,t,s){let i=new Date;i.setTime(i.getTime()+24*s*60*60*1e3);let n="expires="+i.toUTCString();document.cookie=e+"="+t+";"+n+";path=/"}updateSurfPara(e){let t=this.icn3dui,s=t.icn3d;s.phisurftype=$("#"+t.pre+e+"surftype").val(),s.phisurfop=$("#"+t.pre+e+"surfop").val(),s.phisurfwf=$("#"+t.pre+e+"surfwf").val()}exportPdb(){let e=this.icn3dui,t=e.icn3d,s="",i=e.hashUtilsCls.intHash(t.dAtoms,t.hAtoms);if(s+=t.saveFileCls.getAtomPDB(i),!e.bNode){let i=Object.keys(e.utilsCls.getHlStructures()).join(",");t.saveFileCls.saveFile(i+"_icn3d.pdb","text",[s])}return s}exportSecondary(){let e=this.icn3dui,t=e.icn3d,s="",i=e.hashUtilsCls.intHash(t.dAtoms,t.hAtoms);if(s+=t.saveFileCls.getSecondary(i),!e.bNode){let i=Object.keys(e.utilsCls.getHlStructures()).join(",");t.saveFileCls.saveFile(i+"_icn3d_ss.txt","text",[s])}return s}}class g{constructor(e){let t=e;this.icn3dui=e,this.cfg=this.icn3dui.cfg,this.opts={},this.opts.background="black",this.allMenus={},this.allMenusSel={},this.simpleMenus={},this.shownMenus={},this.WIDTH=400,this.HEIGHT=400,this.RESIDUE_WIDTH=10,t.utilsCls.isMobile()||this.cfg.mobilemenu?this.MENU_HEIGHT=0:this.MENU_HEIGHT=40,this.LOG_HEIGHT=65,this.MENU_WIDTH=750,this.LESSWIDTH=20,this.LESSWIDTH_RESIZE=20,this.LESSHEIGHT=20,this.width2d=200,this.CMD_HEIGHT=.8*this.LOG_HEIGHT,this.EXTRAHEIGHT=this.MENU_HEIGHT+this.CMD_HEIGHT,null!=this.cfg.showmenu&&0==this.cfg.showmenu&&(this.EXTRAHEIGHT-=this.MENU_HEIGHT),null!=this.cfg.showcommand&&0==this.cfg.showcommand&&(this.EXTRAHEIGHT-=this.CMD_HEIGHT),this.GREY8="#AAAAAA",this.GREYB="#CCCCCC",this.GREYC="#DDDDDD",this.GREYD="#EEEEEE",this.ORANGE="#FFA500",this.themecolor="blue",this.defaultValue=1,this.ssValue=3,this.coilValue=3,this.contactValue=11,this.contactInsideValue=12,this.hbondValue=13,this.hbondInsideValue=14,this.ssbondValue=4,this.ionicValue=5,this.ionicInsideValue=6,this.clbondValue=15,this.halogenValue=17,this.halogenInsideValue=18,this.picationValue=19,this.picationInsideValue=20,this.pistackingValue=21,this.pistackingInsideValue=22,this.contactColor="888",this.contactInsideColor="FFF",this.hbondColor="0F0",this.hbondInsideColor="FFF",this.ssbondColor="FFA500",this.ionicColor="0FF",this.ionicInsideColor="FFF",this.clbondColor="006400",this.halogenColor="F0F",this.halogenInsideColor="FFF",this.picationColor="F00",this.picationInsideColor="FFF",this.pistackingColor="00F",this.pistackingInsideColor="FFF",this.hideedges=1,this.force=4,this.simulation=void 0,this.baseUrl=window&&window.location&&"structure.ncbi.nlm.nih.gov"==window.location.hostname?"https://structure.ncbi.nlm.nih.gov/Structure/":"https://www.ncbi.nlm.nih.gov/Structure/",this.divStr="",this.spanNowrapStr="
",this.inputTextStr="=0&&void 0===r[t]&&console.warn('THREE.GLTFLoader: Unknown extension "'+t+'".')}}a.setExtensions(l),a.setPlugins(r),a.parse(s,i)}parseAsync(e,t){const s=this;return new Promise((function(i,n){s.parse(e,t,i,n)}))}}function b(){let e={};return{get:function(t){return e[t]},add:function(t,s){e[t]=s},remove:function(t){delete e[t]},removeAll:function(){e={}}}}const C={KHR_BINARY_GLTF:"KHR_binary_glTF",KHR_DRACO_MESH_COMPRESSION:"KHR_draco_mesh_compression",KHR_LIGHTS_PUNCTUAL:"KHR_lights_punctual",KHR_MATERIALS_CLEARCOAT:"KHR_materials_clearcoat",KHR_MATERIALS_IOR:"KHR_materials_ior",KHR_MATERIALS_PBR_SPECULAR_GLOSSINESS:"KHR_materials_pbrSpecularGlossiness",KHR_MATERIALS_SHEEN:"KHR_materials_sheen",KHR_MATERIALS_SPECULAR:"KHR_materials_specular",KHR_MATERIALS_TRANSMISSION:"KHR_materials_transmission",KHR_MATERIALS_UNLIT:"KHR_materials_unlit",KHR_MATERIALS_VOLUME:"KHR_materials_volume",KHR_TEXTURE_BASISU:"KHR_texture_basisu",KHR_TEXTURE_TRANSFORM:"KHR_texture_transform",KHR_MESH_QUANTIZATION:"KHR_mesh_quantization",EXT_TEXTURE_WEBP:"EXT_texture_webp",EXT_MESHOPT_COMPRESSION:"EXT_meshopt_compression"};class y{constructor(e){this.parser=e,this.name=C.KHR_LIGHTS_PUNCTUAL,this.cache={refs:{},uses:{}}}_markDefs(){const e=this.parser,t=this.parser.json.nodes||[];for(let s=0,i=t.length;s=0)throw new Error("THREE.GLTFLoader: setKTX2Loader must be called before loading KTX2 textures");return null}return t.loadTextureImage(e,n.source,l)}}class R{constructor(e){this.parser=e,this.name=C.EXT_TEXTURE_WEBP,this.isSupported=null}loadTexture(e){const t=this.name,s=this.parser,i=s.json,n=i.textures[e];if(!n.extensions||!n.extensions[t])return null;const l=n.extensions[t],r=i.images[l.source];let o=s.textureLoader;if(r.uri){const e=s.options.manager.getHandler(r.uri);null!==e&&(o=e)}return this.detectSupport().then((function(n){if(n)return s.loadTextureImage(e,l.source,o);if(i.extensionsRequired&&i.extensionsRequired.indexOf(t)>=0)throw new Error("THREE.GLTFLoader: WebP required by asset but unsupported.");return s.loadTexture(e)}))}detectSupport(){return this.isSupported||(this.isSupported=new Promise((function(e){const t=new Image;t.src="data:image/webp;base64,UklGRiIAAABXRUJQVlA4IBYAAAAwAQCdASoBAAEADsD+JaQAA3AAAAAA",t.onload=t.onerror=function(){e(1===t.height)}}))),this.isSupported}}class I{constructor(e){this.name=C.EXT_MESHOPT_COMPRESSION,this.parser=e}loadBufferView(e){const t=this.parser.json,s=t.bufferViews[e];if(s.extensions&&s.extensions[this.name]){const e=s.extensions[this.name],i=this.parser.getDependency("buffer",e.buffer),n=this.parser.options.meshoptDecoder;if(!n||!n.supported){if(t.extensionsRequired&&t.extensionsRequired.indexOf(this.name)>=0)throw new Error("THREE.GLTFLoader: setMeshoptDecoder must be called before loading compressed files");return null}return Promise.all([i,n.ready]).then((function(t){const s=e.byteOffset||0,i=e.byteLength||0,l=e.count,r=e.byteStride,o=new ArrayBuffer(l*r),a=new Uint8Array(t[0],s,i);return n.decodeGltfBuffer(new Uint8Array(o),l,r,a,e.mode,e.filter),o}))}return null}}const T="glTF",E=1313821514,P=5130562;class M{constructor(e){this.name=C.KHR_BINARY_GLTF,this.content=null,this.body=null;const t=new DataView(e,0,12);if(this.header={magic:THREE.LoaderUtils.decodeText(new Uint8Array(e.slice(0,4))),version:t.getUint32(4,!0),length:t.getUint32(8,!0)},this.header.magic!==T)throw new Error("THREE.GLTFLoader: Unsupported glTF-Binary header.");if(this.header.version<2)throw new Error("THREE.GLTFLoader: Legacy binary file detected.");const s=this.header.length-12,i=new DataView(e,12);let n=0;for(;n",t).replace("#include ",s).replace("#include ",i).replace("#include ",n).replace("#include ",l)},Object.defineProperties(this,{specular:{get:function(){return r.specular.value},set:function(e){r.specular.value=e}},specularMap:{get:function(){return r.specularMap.value},set:function(e){r.specularMap.value=e,e?this.defines.USE_SPECULARMAP="":delete this.defines.USE_SPECULARMAP}},glossiness:{get:function(){return r.glossiness.value},set:function(e){r.glossiness.value=e}},glossinessMap:{get:function(){return r.glossinessMap.value},set:function(e){r.glossinessMap.value=e,e?(this.defines.USE_GLOSSINESSMAP="",this.defines.USE_UV=""):(delete this.defines.USE_GLOSSINESSMAP,delete this.defines.USE_UV)}}}),delete this.metalness,delete this.roughness,delete this.metalnessMap,delete this.roughnessMap,this.setValues(e)}copy(e){return super.copy(e),this.specularMap=e.specularMap,this.specular.copy(e.specular),this.glossinessMap=e.glossinessMap,this.glossiness=e.glossiness,delete this.metalness,delete this.roughness,delete this.metalnessMap,delete this.roughnessMap,this}}class L{constructor(){this.name=C.KHR_MATERIALS_PBR_SPECULAR_GLOSSINESS,this.specularGlossinessParams=["color","map","lightMap","lightMapIntensity","aoMap","aoMapIntensity","emissive","emissiveIntensity","emissiveMap","bumpMap","bumpScale","normalMap","normalMapType","displacementMap","displacementScale","displacementBias","specularMap","specular","glossinessMap","glossiness","alphaMap","envMap","envMapIntensity"]}getMaterialType(){return F}extendParams(e,t,s){const i=t.extensions[this.name];e.color=new Color(1,1,1),e.opacity=1;const n=[];if(Array.isArray(i.diffuseFactor)){const t=i.diffuseFactor;e.color.fromArray(t),e.opacity=t[3]}if(void 0!==i.diffuseTexture&&n.push(s.assignTexture(e,"map",i.diffuseTexture,sRGBEncoding)),e.emissive=new Color(0,0,0),e.glossiness=void 0!==i.glossinessFactor?i.glossinessFactor:1,e.specular=new Color(1,1,1),Array.isArray(i.specularFactor)&&e.specular.fromArray(i.specularFactor),void 0!==i.specularGlossinessTexture){const t=i.specularGlossinessTexture;n.push(s.assignTexture(e,"glossinessMap",t)),n.push(s.assignTexture(e,"specularMap",t,sRGBEncoding))}return Promise.all(n)}createMaterial(e){const t=new F(e);return t.fog=!0,t.color=e.color,t.map=void 0===e.map?null:e.map,t.lightMap=null,t.lightMapIntensity=1,t.aoMap=void 0===e.aoMap?null:e.aoMap,t.aoMapIntensity=1,t.emissive=e.emissive,t.emissiveIntensity=1,t.emissiveMap=void 0===e.emissiveMap?null:e.emissiveMap,t.bumpMap=void 0===e.bumpMap?null:e.bumpMap,t.bumpScale=1,t.normalMap=void 0===e.normalMap?null:e.normalMap,t.normalMapType=TangentSpaceNormalMap,e.normalScale&&(t.normalScale=e.normalScale),t.displacementMap=null,t.displacementScale=1,t.displacementBias=0,t.specularMap=void 0===e.specularMap?null:e.specularMap,t.specular=e.specular,t.glossinessMap=void 0===e.glossinessMap?null:e.glossinessMap,t.glossiness=e.glossiness,t.alphaMap=null,t.envMap=void 0===e.envMap?null:e.envMap,t.envMapIntensity=1,t}}class N{constructor(){this.name=C.KHR_MESH_QUANTIZATION}}class q extends THREE.Interpolant{constructor(e,t,s,i){super(e,t,s,i)}copySampleValue_(e){const t=this.resultBuffer,s=this.sampleValues,i=this.valueSize,n=e*i*3+i;for(let e=0;e!==i;e++)t[e]=s[n+e];return t}}q.prototype.beforeStart_=q.prototype.copySampleValue_,q.prototype.afterEnd_=q.prototype.copySampleValue_,q.prototype.interpolate_=function(e,t,s,i){const n=this.resultBuffer,l=this.sampleValues,r=this.valueSize,o=2*r,a=3*r,d=i-t,c=(s-t)/d,h=c*c,p=h*c,m=e*a,u=m-a,g=-2*p+3*h,f=p-h,b=1-g,C=f-h+c;for(let e=0;e!==r;e++){const t=l[u+e+r],s=l[u+e+o]*d,i=l[m+e+r],a=l[m+e]*d;n[e]=b*t+C*s+g*i+f*a}return n};const U=new THREE.Quaternion;class j extends q{interpolate_(e,t,s,i){const n=super.interpolate_(e,t,s,i);return U.fromArray(n).normalize().toArray(n),n}}const B=0,z=1,G=2,V=3,W=4,Y=5,X=6,K={5120:Int8Array,5121:Uint8Array,5122:Int16Array,5123:Uint16Array,5125:Uint32Array,5126:Float32Array},J={9728:THREE.NearestFilter,9729:THREE.LinearFilter,9984:THREE.NearestMipmapNearestFilter,9985:THREE.LinearMipmapNearestFilter,9986:THREE.NearestMipmapLinearFilter,9987:THREE.LinearMipmapLinearFilter},Q={33071:THREE.ClampToEdgeWrapping,33648:THREE.MirroredRepeatWrapping,10497:THREE.RepeatWrapping},Z={SCALAR:1,VEC2:2,VEC3:3,VEC4:4,MAT2:4,MAT3:9,MAT4:16},ee={POSITION:"position",NORMAL:"normal",TANGENT:"tangent",TEXCOORD_0:"uv",TEXCOORD_1:"uv2",COLOR_0:"color",WEIGHTS_0:"skinWeight",JOINTS_0:"skinIndex"},te={scale:"scale",translation:"position",rotation:"quaternion",weights:"morphTargetInfluences"},se={CUBICSPLINE:void 0,LINEAR:THREE.InterpolateLinear,STEP:THREE.InterpolateDiscrete},ie="OPAQUE",ne="MASK",le="BLEND";function re(e,t,s){for(const i in s.extensions)void 0===e[i]&&(t.userData.gltfExtensions=t.userData.gltfExtensions||{},t.userData.gltfExtensions[i]=s.extensions[i])}function oe(e,t){void 0!==t.extras&&("object"==typeof t.extras?Object.assign(e.userData,t.extras):console.warn("THREE.GLTFLoader: Ignoring primitive type .extras, "+t.extras))}function ae(e,t){if(e.updateMorphTargets(),void 0!==t.weights)for(let s=0,i=t.weights.length;s{const s=this.associations.get(e);null!=s&&this.associations.set(t,s);for(const[s,i]of e.children.entries())n(i,t.children[s])};return n(s,i),i.name+="_instance_"+e.uses[t]++,i}_invokeOne(e){const t=Object.values(this.plugins);t.push(this);for(let s=0;s=2&&m.setY(t,c[e*l+1]),l>=3&&m.setZ(t,c[e*l+2]),l>=4&&m.setW(t,c[e*l+3]),l>=5)throw new Error("THREE.GLTFLoader: Unsupported itemSize in sparse BufferAttribute.")}}return m}))}loadTexture(e){const t=this.json,s=this.options,i=t.textures[e].source,n=t.images[i];let l=this.textureLoader;if(n.uri){const e=s.manager.getHandler(n.uri);null!==e&&(l=e)}return this.loadTextureImage(e,i,l)}loadTextureImage(e,t,s){const i=this,n=this.json,l=n.textures[e],r=n.images[t],o=(r.uri||r.bufferView)+":"+l.sampler;if(this.textureCache[o])return this.textureCache[o];const a=this.loadImageSource(t,s).then((function(t){t.flipY=!1,l.name&&(t.name=l.name);const s=(n.samplers||{})[l.sampler]||{};return t.magFilter=J[s.magFilter]||LinearFilter,t.minFilter=J[s.minFilter]||LinearMipmapLinearFilter,t.wrapS=Q[s.wrapS]||RepeatWrapping,t.wrapT=Q[s.wrapT]||RepeatWrapping,i.associations.set(t,{textures:e}),t})).catch((function(){return null}));return this.textureCache[o]=a,a}loadImageSource(e,t){const s=this,i=this.json,n=this.options;if(void 0!==this.sourceCache[e])return this.sourceCache[e].then((e=>e.clone()));const l=i.images[e],r=self.URL||self.webkitURL;let o=l.uri||"",a=!1;if(void 0!==l.bufferView)o=s.getDependency("bufferView",l.bufferView).then((function(e){a=!0;const t=new Blob([e],{type:l.mimeType});return o=r.createObjectURL(t),o}));else if(void 0===l.uri)throw new Error("THREE.GLTFLoader: Image "+e+" is missing URI and bufferView");const d=Promise.resolve(o).then((function(e){return new Promise((function(s,i){let l=s;!0===t.isImageBitmapLoader&&(l=function(e){const t=new Texture(e);t.needsUpdate=!0,s(t)}),t.load(THREE.LoaderUtils.resolveURL(e,n.path),l,void 0,i)}))})).then((function(e){var t;return!0===a&&r.revokeObjectURL(o),e.userData.mimeType=l.mimeType||((t=l.uri).search(/\.jpe?g($|\?)/i)>0||0===t.search(/^data\:image\/jpeg/)?"image/jpeg":t.search(/\.webp($|\?)/i)>0||0===t.search(/^data\:image\/webp/)?"image/webp":"image/png"),e})).catch((function(e){throw console.error("THREE.GLTFLoader: Couldn't load texture",o),e}));return this.sourceCache[e]=d,d}assignTexture(e,t,s,i){const n=this;return this.getDependency("texture",s.index).then((function(l){if(void 0===s.texCoord||0==s.texCoord||"aoMap"===t&&1==s.texCoord||console.warn("THREE.GLTFLoader: Custom UV set "+s.texCoord+" for texture "+t+" not yet supported."),n.extensions[C.KHR_TEXTURE_TRANSFORM]){const e=void 0!==s.extensions?s.extensions[C.KHR_TEXTURE_TRANSFORM]:void 0;if(e){const t=n.associations.get(l);l=n.extensions[C.KHR_TEXTURE_TRANSFORM].extendTexture(l,e),n.associations.set(l,t)}}return void 0!==i&&(l.encoding=i),e[t]=l,l}))}assignFinalMaterial(e){const t=e.geometry;let s=e.material;const i=void 0===t.attributes.tangent,n=void 0!==t.attributes.color,l=void 0===t.attributes.normal;if(e.isPoints){const e="PointsMaterial:"+s.uuid;let t=this.cache.get(e);t||(t=new PointsMaterial,Material.prototype.copy.call(t,s),t.color.copy(s.color),t.map=s.map,t.sizeAttenuation=!1,this.cache.add(e,t)),s=t}else if(e.isLine){const e="LineBasicMaterial:"+s.uuid;let t=this.cache.get(e);t||(t=new LineBasicMaterial,Material.prototype.copy.call(t,s),t.color.copy(s.color),this.cache.add(e,t)),s=t}if(i||n||l){let e="ClonedMaterial:"+s.uuid+":";s.isGLTFSpecularGlossinessMaterial&&(e+="specular-glossiness:"),i&&(e+="derivative-tangents:"),n&&(e+="vertex-colors:"),l&&(e+="flat-shading:");let t=this.cache.get(e);t||(t=s.clone(),n&&(t.vertexColors=!0),l&&(t.flatShading=!0),i&&(t.normalScale&&(t.normalScale.y*=-1),t.clearcoatNormalScale&&(t.clearcoatNormalScale.y*=-1)),this.cache.add(e,t),this.associations.set(t,this.associations.get(s))),s=t}s.aoMap&&void 0===t.attributes.uv2&&void 0!==t.attributes.uv&&t.setAttribute("uv2",t.attributes.uv),e.material=s}getMaterialType(){return MeshStandardMaterial}loadMaterial(e){const t=this,s=this.json,i=this.extensions,n=s.materials[e];let l;const r={},o=n.extensions||{},a=[];if(o[C.KHR_MATERIALS_PBR_SPECULAR_GLOSSINESS]){const e=i[C.KHR_MATERIALS_PBR_SPECULAR_GLOSSINESS];l=e.getMaterialType(),a.push(e.extendParams(r,n,t))}else if(o[C.KHR_MATERIALS_UNLIT]){const e=i[C.KHR_MATERIALS_UNLIT];l=e.getMaterialType(),a.push(e.extendParams(r,n,t))}else{const s=n.pbrMetallicRoughness||{};if(r.color=new Color(1,1,1),r.opacity=1,Array.isArray(s.baseColorFactor)){const e=s.baseColorFactor;r.color.fromArray(e),r.opacity=e[3]}void 0!==s.baseColorTexture&&a.push(t.assignTexture(r,"map",s.baseColorTexture,sRGBEncoding)),r.metalness=void 0!==s.metallicFactor?s.metallicFactor:1,r.roughness=void 0!==s.roughnessFactor?s.roughnessFactor:1,void 0!==s.metallicRoughnessTexture&&(a.push(t.assignTexture(r,"metalnessMap",s.metallicRoughnessTexture)),a.push(t.assignTexture(r,"roughnessMap",s.metallicRoughnessTexture))),l=this._invokeOne((function(t){return t.getMaterialType&&t.getMaterialType(e)})),a.push(Promise.all(this._invokeAll((function(t){return t.extendMaterialParams&&t.extendMaterialParams(e,r)}))))}!0===n.doubleSided&&(r.side=DoubleSide);const d=n.alphaMode||ie;if(d===le?(r.transparent=!0,r.depthWrite=!1):(r.transparent=!1,d===ne&&(r.alphaTest=void 0!==n.alphaCutoff?n.alphaCutoff:.5)),void 0!==n.normalTexture&&l!==MeshBasicMaterial&&(a.push(t.assignTexture(r,"normalMap",n.normalTexture)),r.normalScale=new Vector2(1,1),void 0!==n.normalTexture.scale)){const e=n.normalTexture.scale;r.normalScale.set(e,e)}return void 0!==n.occlusionTexture&&l!==MeshBasicMaterial&&(a.push(t.assignTexture(r,"aoMap",n.occlusionTexture)),void 0!==n.occlusionTexture.strength&&(r.aoMapIntensity=n.occlusionTexture.strength)),void 0!==n.emissiveFactor&&l!==MeshBasicMaterial&&(r.emissive=(new Color).fromArray(n.emissiveFactor)),void 0!==n.emissiveTexture&&l!==MeshBasicMaterial&&a.push(t.assignTexture(r,"emissiveMap",n.emissiveTexture,sRGBEncoding)),Promise.all(a).then((function(){let s;return s=l===F?i[C.KHR_MATERIALS_PBR_SPECULAR_GLOSSINESS].createMaterial(r):new l(r),n.name&&(s.name=n.name),oe(s,n),t.associations.set(s,{materials:e}),n.extensions&&re(i,s,n),s}))}createUniqueName(e){const t=PropertyBinding.sanitizeNodeName(e||"");let s=t;for(let e=1;this.nodeNamesUsed[s];++e)s=t+"_"+e;return this.nodeNamesUsed[s]=!0,s}loadGeometries(e){const t=this,s=this.extensions,i=this.primitiveCache;function n(e){return s[C.KHR_DRACO_MESH_COMPRESSION].decodePrimitive(e,t).then((function(s){return ue(s,e,t)}))}const l=[];for(let s=0,r=e.length;s0&&ae(h,n),h.name=t.createUniqueName(n.name||"mesh_"+e),oe(h,n),c.extensions&&re(i,h,c),t.assignFinalMaterial(h),a.push(h)}for(let s=0,i=a.length;s1?new Group:1===t.length?t[0]:new Object3D,r!==t[0])for(let e=0,s=t.length;e{const t=new Map;for(const[e,s]of n.associations)(e instanceof Material||e instanceof Texture)&&t.set(e,s);return e.traverse((e=>{const s=n.associations.get(e);null!=s&&t.set(e,s)})),t})(l),l}))}}function me(e,t,s,i){const n=s.nodes[e];return i.getDependency("node",e).then((function(e){if(void 0===n.skin)return e;let t;return i.getDependency("skin",n.skin).then((function(e){t=e;const s=[];for(let e=0,n=t.joints.length;e{const s=n[e];return s&&(l={profileId:e,profilePath:`${t}/${s.path}`,deprecated:!!s.deprecated}),!!l})),!l){if(!s)throw new Error("No matching profile name found");const e=n[s];if(!e)throw new Error(`No matching profile name found and default profile "${s}" missing.`);l={profileId:s,profilePath:`${t}/${e.path}`,deprecated:!!e.deprecated}}const r=await be(l.profilePath);let o;if(i){let t;if(t="any"===e.handedness?r.layouts[Object.keys(r.layouts)[0]]:r.layouts[e.handedness],!t)throw new Error(`No matching handedness, ${e.handedness}, in profile ${l.profileId}`);t.assetPath&&(o=l.profilePath.replace("profile.json",t.assetPath))}return{profile:r,assetPath:o}}const ye={xAxis:0,yAxis:0,button:0,state:fe.ComponentState.DEFAULT};class ve{constructor(e){this.componentProperty=e.componentProperty,this.states=e.states,this.valueNodeName=e.valueNodeName,this.valueNodeProperty=e.valueNodeProperty,this.valueNodeProperty===fe.VisualResponseProperty.TRANSFORM&&(this.minNodeName=e.minNodeName,this.maxNodeName=e.maxNodeName),this.value=0,this.updateFromComponent(ye)}updateFromComponent({xAxis:e,yAxis:t,button:s,state:i}){const{normalizedXAxis:n,normalizedYAxis:l}=function(e=0,t=0){let s=e,i=t;if(Math.sqrt(e*e+t*t)>1){const n=Math.atan2(t,e);s=Math.cos(n),i=Math.sin(n)}return{normalizedXAxis:.5*s+.5,normalizedYAxis:.5*i+.5}}(e,t);switch(this.componentProperty){case fe.ComponentProperty.X_AXIS:this.value=this.states.includes(i)?n:.5;break;case fe.ComponentProperty.Y_AXIS:this.value=this.states.includes(i)?l:.5;break;case fe.ComponentProperty.BUTTON:this.value=this.states.includes(i)?s:0;break;case fe.ComponentProperty.STATE:this.valueNodeProperty===fe.VisualResponseProperty.VISIBILITY?this.value=this.states.includes(i):this.value=this.states.includes(i)?1:0;break;default:throw new Error(`Unexpected visualResponse componentProperty ${this.componentProperty}`)}}}class _e{constructor(e,t){if(!(e&&t&&t.visualResponses&&t.gamepadIndices&&0!==Object.keys(t.gamepadIndices).length))throw new Error("Invalid arguments supplied");this.id=e,this.type=t.type,this.rootNodeName=t.rootNodeName,this.touchPointNodeName=t.touchPointNodeName,this.visualResponses={},Object.keys(t.visualResponses).forEach((e=>{const s=new ve(t.visualResponses[e]);this.visualResponses[e]=s})),this.gamepadIndices=Object.assign({},t.gamepadIndices),this.values={state:fe.ComponentState.DEFAULT,button:void 0!==this.gamepadIndices.button?0:void 0,xAxis:void 0!==this.gamepadIndices.xAxis?0:void 0,yAxis:void 0!==this.gamepadIndices.yAxis?0:void 0}}get data(){return{id:this.id,...this.values}}updateFromGamepad(e){if(this.values.state=fe.ComponentState.DEFAULT,void 0!==this.gamepadIndices.button&&e.buttons.length>this.gamepadIndices.button){const t=e.buttons[this.gamepadIndices.button];this.values.button=t.value,this.values.button=this.values.button<0?0:this.values.button,this.values.button=this.values.button>1?1:this.values.button,t.pressed||1===this.values.button?this.values.state=fe.ComponentState.PRESSED:(t.touched||this.values.button>fe.ButtonTouchThreshold)&&(this.values.state=fe.ComponentState.TOUCHED)}void 0!==this.gamepadIndices.xAxis&&e.axes.length>this.gamepadIndices.xAxis&&(this.values.xAxis=e.axes[this.gamepadIndices.xAxis],this.values.xAxis=this.values.xAxis<-1?-1:this.values.xAxis,this.values.xAxis=this.values.xAxis>1?1:this.values.xAxis,this.values.state===fe.ComponentState.DEFAULT&&Math.abs(this.values.xAxis)>fe.AxisTouchThreshold&&(this.values.state=fe.ComponentState.TOUCHED)),void 0!==this.gamepadIndices.yAxis&&e.axes.length>this.gamepadIndices.yAxis&&(this.values.yAxis=e.axes[this.gamepadIndices.yAxis],this.values.yAxis=this.values.yAxis<-1?-1:this.values.yAxis,this.values.yAxis=this.values.yAxis>1?1:this.values.yAxis,this.values.state===fe.ComponentState.DEFAULT&&Math.abs(this.values.yAxis)>fe.AxisTouchThreshold&&(this.values.state=fe.ComponentState.TOUCHED)),Object.values(this.visualResponses).forEach((e=>{e.updateFromComponent(this.values)}))}}class we{constructor(e,t,s){if(!e)throw new Error("No xrInputSource supplied");if(!t)throw new Error("No profile supplied");this.xrInputSource=e,this.assetUrl=s,this.id=t.profileId,this.layoutDescription=t.layouts[e.handedness],this.components={},Object.keys(this.layoutDescription.components).forEach((e=>{const t=this.layoutDescription.components[e];this.components[e]=new _e(e,t)})),this.updateFromGamepad()}get gripSpace(){return this.xrInputSource.gripSpace}get targetRaySpace(){return this.xrInputSource.targetRaySpace}get data(){const e=[];return Object.values(this.components).forEach((t=>{e.push(t.data)})),e}updateFromGamepad(){Object.values(this.components).forEach((e=>{e.updateFromGamepad(this.xrInputSource.gamepad)}))}}class Se extends THREE.Object3D{constructor(){super(),this.motionController=null,this.envMap=null}setEnvironmentMap(e){return this.envMap==e||(this.envMap=e,this.traverse((e=>{e.isMesh&&(e.material.envMap=this.envMap,e.material.needsUpdate=!0)}))),this}updateMatrixWorld(e){super.updateMatrixWorld(e),this.motionController&&(this.motionController.updateFromGamepad(),Object.values(this.motionController.components).forEach((e=>{Object.values(e.visualResponses).forEach((e=>{const{valueNode:t,minNode:s,maxNode:i,value:n,valueNodeProperty:l}=e;t&&(l===fe.VisualResponseProperty.VISIBILITY?t.visible=n:l===fe.VisualResponseProperty.TRANSFORM&&(t.quaternion.slerpQuaternions(s.quaternion,i.quaternion,n),t.position.lerpVectors(s.position,i.position,n)))}))})))}}function Ae(e,t){!function(e,t){Object.values(e.components).forEach((e=>{const{type:s,touchPointNodeName:i,visualResponses:n}=e;if(s===fe.ComponentType.TOUCHPAD)if(e.touchPointNode=t.getObjectByName(i),e.touchPointNode){const t=new SphereGeometry(.001),s=new MeshBasicMaterial({color:255}),i=new Mesh(t,s);e.touchPointNode.add(i)}else console.warn(`Could not find touch dot, ${e.touchPointNodeName}, in touchpad component ${e.id}`);Object.values(n).forEach((e=>{const{valueNodeName:s,minNodeName:i,maxNodeName:n,valueNodeProperty:l}=e;if(l===fe.VisualResponseProperty.TRANSFORM){if(e.minNode=t.getObjectByName(i),e.maxNode=t.getObjectByName(n),!e.minNode)return void console.warn(`Could not find ${i} in the model`);if(!e.maxNode)return void console.warn(`Could not find ${n} in the model`)}e.valueNode=t.getObjectByName(s),e.valueNode||console.warn(`Could not find ${s} in the model`)}))}))}(e.motionController,t),e.envMap&&t.traverse((t=>{t.isMesh&&(t.material.envMap=e.envMap,t.material.needsUpdate=!0)})),e.add(t)}class xe{constructor(e=null){this.gltfLoader=e,this.path="https://cdn.jsdelivr.net/npm/@webxr-input-profiles/assets@1.0/dist/profiles",this._assetCache={},this.gltfLoader||(this.gltfLoader=new f)}createControllerModel(e){const t=new Se;let s=null;return e.addEventListener("connected",(e=>{const i=e.data;"tracked-pointer"===i.targetRayMode&&i.gamepad&&Ce(i,this.path,"generic-trigger").then((({profile:e,assetPath:n})=>{t.motionController=new we(i,e,n);const l=this._assetCache[t.motionController.assetUrl];if(l)s=l.scene.clone(),Ae(t,s);else{if(!this.gltfLoader)throw new Error("GLTFLoader not set.");this.gltfLoader.setPath(""),this.gltfLoader.load(t.motionController.assetUrl,(e=>{this._assetCache[t.motionController.assetUrl]=e,s=e.scene.clone(),Ae(t,s)}),null,(()=>{throw new Error(`Asset ${t.motionController.assetUrl} missing or malformed.`)}))}})).catch((e=>{console.warn(e)}))})),e.addEventListener("disconnected",(()=>{t.motionController=null,t.remove(s),s=null})),t}}class ke extends THREE.EventDispatcher{constructor(e){if(super(),void 0===e)return void console.error("ControllerGestures must be passed a renderer");const t=new THREE.Clock;this.controller1=e.xr.getController(0),this.controller1.userData.gestures={index:0},this.controller1.userData.selectPressed=!1,this.controller1.addEventListener("selectstart",i),this.controller1.addEventListener("selectend",n),this.controller2=e.xr.getController(1),this.controller2.userData.gestures={index:1},this.controller2.userData.selectPressed=!1,this.controller2.addEventListener("selectstart",i),this.controller2.addEventListener("selectend",n),this.doubleClickLimit=.2,this.pressMinimum=.4,this.right=new THREE.Vector3(1,0,0),this.up=new THREE.Vector3(0,1,0),this.type="unknown",this.prevTap="none",this.clock=t;const s=this;function i(){const e=this.userData.gestures;e.startPosition=void 0,e.startTime=t.getElapsedTime(),-1==s.type.indexOf("tap")&&(e.taps=0),s.type="unknown",this.userData.selectPressed=!0}function n(){const e=this.userData.gestures;e.endTime=t.getElapsedTime();e.endTime-e.startTime.05&&(e.startPosition=this.controller1.position.clone())),this.controller2.userData.selectPressed&&void 0===t.startPosition&&(i=s-t.startTime,i>.05&&(t.startPosition=this.controller2.position.clone())),!this.controller1.userData.selectPressed&&"tap"===this.type&&(i=this.clock.getElapsedTime()-e.endTime,i>this.doubleClickLimit)){switch(e.taps){case 1:self.prevTap="tap";break;case 2:this.dispatchEvent({type:"doubletap",position:this.controller1.position,matrixWorld:this.controller1.matrixWorld}),self.prevTap="doubletap"}this.type="unknown",e.taps=0}if("unknown"===this.type&&this.touch)"doubletap"==self.prevTap?(this.type="pinch",this.startDistance=this.controller1.position.distanceTo(this.controller2.position),this.dispatchEvent({type:"pinch",delta:new THREE.Vector3(0,0,0),scale:1,initialise:!0})):(this.type="pan",this.startPosition=this.controller1.position.clone(),this.dispatchEvent({type:"pan",delta:new THREE.Vector3(0,0,0),initialise:!0}));else if(("pinch"===this.type||"pan"===this.type)&&"doubletap"==self.prevTap&&this.controller2.position){const e=this.controller1.position.distanceTo(this.controller2.position)/this.startDistance,t=this.controller1.position.clone().sub(this.startPosition);this.dispatchEvent({type:"pinch",delta:t,scale:e})}}}class Oe{constructor(e,t){this.config=void 0===t?{panelSize:{width:1,height:1},width:512,height:512,opacity:.7,body:{fontFamily:"Arial",fontSize:30,padding:2,backgroundColor:"#000",fontColor:"#fff",borderRadius:6}}:t,void 0===this.config.width&&(this.config.width=512),void 0===this.config.height&&(this.config.height=512),void 0===this.config.body&&(this.config.body={fontFamily:"Arial",size:30,padding:2,backgroundColor:"#000",fontColor:"#fff",borderRadius:6});const s=this.config.body;void 0===s.borderRadius&&(s.borderRadius=6),void 0===s.fontFamily&&(s.fontFamily="Arial"),void 0===s.padding&&(s.padding=2),void 0===s.fontSize&&(s.fontSize=30),void 0===s.backgroundColor&&(s.backgroundColor="#000"),void 0===s.fontColor&&(s.fontColor="#fff"),Object.entries(this.config).forEach((([e,t])=>{if(!("object"!=typeof t||"panelSize"===e||t instanceof THREE.WebGLRenderer||t instanceof THREE.Scene)){const e=void 0!==t.position?t.position:{x:0,y:0};void 0!==e.left&&void 0===e.x&&(e.x=e.left),void 0!==e.top&&void 0===e.y&&(e.y=e.top);const s=void 0!==t.width?t.width:this.config.width,i=void 0!==t.height?t.height:this.config.height;void 0!==e.right&&void 0===e.x&&(e.x=this.config.width-e.right-s),void 0!==e.bottom&&void 0===e.y&&(e.y=this.config.height-e.bottom-i),void 0===e.x&&(e.x=0),void 0===e.y&&(e.y=0),t.position=e,void 0===t.type&&(t.type="text")}}));const i=this.createOffscreenCanvas(this.config.width,this.config.height);this.context=i.getContext("2d"),this.context.save();const n=void 0!==this.config.opacity?this.config.opacity:.7,l=new THREE.MeshBasicMaterial({transparent:!0,opacity:n});this.panelSize=void 0!==this.config.panelSize?this.config.panelSize:{width:1,height:1};const r=new THREE.PlaneGeometry(this.panelSize.width,this.panelSize.height);this.mesh=new THREE.Mesh(r,l),this.texture=new THREE.CanvasTexture(i),this.mesh.material.map=this.texture,this.scene=this.config.scene;if(Object.values(this.config).filter((e=>"input-text"===e.type)).length>0){this.keyboard=new Re(this.panelSize.width,this.config.renderer);this.keyboard.mesh.position.set(0,-.3,.2),this.mesh.add(this.keyboard.mesh)}if(void 0===e)this.content={body:""},this.config.body.type="text";else{this.content=e;Object.values(t).filter((e=>"button"===e.type||"scroll"===e.overflow||"input-text"===e.type)).length>0&&(void 0===t||void 0===t.renderer?console.warn("CanvasUI: button, scroll or input-text in the config but no renderer"):(this.renderer=t.renderer,this.initControllers()))}this.selectedElements=[void 0,void 0],this.selectPressed=[!1,!1],this.scrollData=[void 0,void 0],this.intersects=[void 0,void 0],this.needsUpdate=!0,this.update()}getIntersectY(e){const t=this.config.height||512,s=this.intersects[e];return void 0===s||void 0===s.uv?0:(1-s.uv.y)*t}initControllers(){this.vec3=new THREE.Vector3,this.mat4=new THREE.Matrix4,this.raycaster=new THREE.Raycaster;const e=this;function t(t){const s=t.target===e.controller?0:1,i=e.selectedElements[s];if(void 0!==i)if("button"==i.type)e.select(s);else if("input-text"==i.type&&e.keyboard)if(e.keyboard.visible)e.keyboard.linkedUI=void 0,e.keyboard.linkedText=void 0,e.keyboard.linkedElement=void 0,e.keyboard.visible=!1;else{let t;e.keyboard.linkedUI=e,Object.entries(e.config).forEach((([e,s])=>{s==i&&(t=e)}));const s=(.5-(i.position.y+i.height+e.config.body.padding)/e.config.height)*e.panelSize.height,n=Math.max(e.panelSize.width,e.panelSize.height)/2;e.keyboard.position.set(0,-n/1.5-s,.1),e.keyboard.linkedText=e.content[t],e.keyboard.linkedName=t,e.keyboard.linkedElement=i,e.keyboard.visible=!0}}function s(t){const s=t.target===e.controller?0:1;if(e.selectPressed[s]=!0,void 0!==e.selectedElements[s]&&"scroll"==e.selectedElements[s].overflow){const t=e.selectedElements[s];e.scrollData[s]={scrollY:t.scrollY,rayY:e.getIntersectY(s)}}}function i(t){const s=t.target===e.controller?0:1;e.selectPressed[s]=!1,void 0!==e.selectedElements[s]&&"scroll"==e.selectedElements[s].overflow&&(e.scrollData[s]=void 0)}if(this.controller=this.renderer.xr.getController(0),this.controller.addEventListener("select",t),this.controller.addEventListener("selectstart",s),this.controller.addEventListener("selectend",i),this.controller1=this.renderer.xr.getController(1),this.controller1.addEventListener("select",t),this.controller1.addEventListener("selectstart",s),this.controller1.addEventListener("selectend",i),this.scene){const e=.015,t=new THREE.IcosahedronBufferGeometry(e),s=new THREE.MeshBasicMaterial({color:170}),i=new THREE.Mesh(t,s);i.visible=!1,this.scene.add(i);const n=new THREE.Mesh(t,s);n.visible=!1,this.scene.add(n),this.intersectMesh=[i,n]}}setClip(e){const t=this.context;if(t.restore(),t.save(),void 0!==e.clipPath){const s=new Path2D(e.clipPath);t.clip(s)}else{const s=void 0!==e.position?e.position:{x:0,y:0},i=e.borderRadius||0,n=e.width||this.config.width,l=e.height||this.config.height;if(t.beginPath(),0!==i){const e=Math.PI/2;t.moveTo(s.x+i,s.y),t.arc(s.x+i,s.y+i,i,e,2*e,!0),t.lineTo(s.x,s.y+l-i),t.arc(s.x+i,s.y+l-i,i,0,e,!0),t.lineTo(s.x+n-i,s.y+l),t.arc(s.x+n-i,s.y+l-i,i,3*e,4*e,!0),t.lineTo(s.x+n,s.y+i),t.arc(s.x+n-i,s.y+i,i,2*e,3*e,!0),t.closePath(),t.clip()}else t.rect(s.x,s.y,n,l),t.clip()}}setPosition(e,t,s){void 0!==this.mesh&&this.mesh.position.set(e,t,s)}setRotation(e,t,s){void 0!==this.mesh&&this.mesh.rotation.set(e,t,s)}updateElement(e,t){let s=this.content[e];void 0!==s?("object"==typeof s?s.content=t:s=t,this.content[e]=s,this.needsUpdate=!0):console.warn(`CanvasGUI.updateElement: No ${e} found`)}get panel(){return this.mesh}getElementAtLocation(e,t){const s=this,i=Object.entries(this.config).filter((([i,n])=>{if(!("object"!=typeof n||"panelSize"===i||"body"===i||n instanceof THREE.WebGLRenderer||n instanceof THREE.Scene)){const i=n.position,l=void 0!==n.width?n.width:s.config.width,r=void 0!==n.height?n.height:s.config.height;return e>=i.x&&e=i.y&&t0?(this.hover(t,s[0].uv),this.intersects[t]=s[0],this.scroll(t)):(this.hover(t),this.intersects[t]=void 0,this.scroll(t))}update(){if(void 0===this.mesh)return;if(this.controller&&this.handleController(this.controller,0),this.controller1&&this.handleController(this.controller1,1),this.keyboard&&this.keyboard.visible&&this.keyboard.update(),!this.needsUpdate)return;let e=this.context;e.clearRect(0,0,this.config.width,this.config.height);const t=this.config.body.backgroundColor?this.config.body.backgroundColor:"#000";!this.config.body.fontFamily||this.config.body.fontFamily;const s=this.config.body.fontColor?this.config.body.fontColor:"#fff";!this.config.body.fontSize||this.config.body.fontSize,this.setClip(this.config.body),e.fillStyle=t,e.fillRect(0,0,this.config.width,this.config.height);const i=this;Object.entries(this.content).forEach((([t,n])=>{const l=void 0!==i.config[t]?i.config[t]:i.config.body;if("none"!==(void 0!==l.display?l.display:"block")){const r=void 0!==l.position?l.position:{x:0,y:0},o=void 0!==l.width?l.width:i.config.width,a=void 0!==l.height?l.height:i.config.height;"button"!=l.type||n.toLowerCase().startsWith("")||(void 0===l.borderRadius&&(l.borderRadius=6),void 0===l.textAlign&&(l.textAlign="center")),i.setClip(l);const d=n.toLowerCase().startsWith(""),c=void 0!==i.selectedElements[0]&&this.selectedElements[0]===l||void 0!==i.selectedElements[1]&&this.selectedElements[1]===l;if(void 0!==l.backgroundColor&&(c&&"button"==l.type&&void 0!==l.hover?e.fillStyle=l.hover:e.fillStyle=l.backgroundColor,e.fillRect(r.x,r.y,o,a)),"text"==l.type||"button"==l.type||"input-text"==l.type){let h=!1;if(c?(d||"button"!=l.type?e.fillStyle=void 0!==l.hover?l.hover:void 0!==l.fontColor?l.fontColor:s:e.fillStyle=void 0!==l.fontColor?l.fontColor:s,h=void 0===l.hover):e.fillStyle=void 0!==l.fontColor?l.fontColor:s,d){const t=n.toUpperCase().substring(6,n.length-7);e.save(),e.translate(r.x,r.y);const s=new Path2D(t);e.fill(s),e.restore()}else i.wrapText(t,n);h&&(e.beginPath(),e.strokeStyle="#fff",e.lineWidth=2,e.rect(r.x,r.y,o,a),e.stroke())}else if("img"==l.type)if(void 0===l.img)this.loadImage(n).then((e=>{console.log(`w: ${e.width} | h: ${e.height}`),l.img=e,i.needsUpdate=!0,i.update()})).catch((e=>console.error(e)));else{const t=o/(l.img.width/l.img.height);e.drawImage(l.img,r.x,r.y,o,t)}}})),this.needsUpdate=!1,this.texture.needsUpdate=!0}loadImage(e){return new Promise(((t,s)=>{const i=new THREE.Image;i.addEventListener("load",(()=>t(i))),i.addEventListener("error",(e=>s(e))),i.src=e}))}createOffscreenCanvas(e,t){const s=document.createElement("canvas");return s.width=e,s.height=t,s}fillRoundedRect(e,t,s,i,n){const l=this.context;l.beginPath(),l.moveTo(e+n,t),l.lineTo(e+s-n,t),l.quadraticCurveTo(e+s,t,e+s,t+n),l.lineTo(e+s,t+i-n),l.quadraticCurveTo(e+s,t+i,e+s-n,t+i),l.lineTo(e+n,t+i),l.quadraticCurveTo(e,t+i,e,t+i-n),l.lineTo(e,t+n),l.quadraticCurveTo(e,t,e+n,t),l.closePath(),l.fill()}lookAt(e){void 0!==this.mesh&&(e instanceof Vector3?this.mesh.lookAt(e):console.error("CanvasUI lookAt called parameter not a THREE.Vector3"))}get visible(){return void 0!==this.mesh&&this.mesh.visible}set visible(e){this.mesh&&(this.mesh.visible=e)}get position(){if(void 0!==this.mesh)return this.mesh.position}set position(e){void 0!==this.mesh&&(e instanceof Vector3?this.mesh.position.copy(e):console.error("CanvasUI trying to set the mesh position using a parameter that is not a THREE.Vector3"))}get quaternion(){if(void 0!==this.mesh)return this.mesh.quaternion}set quaternion(e){void 0!==this.mesh&&(e instanceof QUaternion?this.mesh.quaternion.copy(e):console.error("CanvasUI trying to set the mesh quaternion using a parameter that is not a THREE.Quaternion"))}wrapText(e,t){const s=t.split(" ");let i="";const n=[],l=void 0!==this.config[e]?this.config[e]:this.config.body,r=void 0!==l.width?l.width:this.config.width,o=void 0!==l.height?l.height:this.config.height,a=void 0!==l.position?l.position:{x:0,y:0},d=void 0!==l.padding?l.padding:void 0!==this.config.body.padding?this.config.body.padding:10,c=void 0!==l.paddingTop?l.paddingTop:d,h=void 0!==l.paddingLeft?l.paddingLeft:d,p=void 0!==l.paddingBottom?l.paddingBottom:d,m=void 0!==l.paddingRight?l.paddingRight:d,u={x:a.x+h,y:a.y+c,width:r-h-m,height:o-c-p},g=void 0!==l.textAlign?l.textAlign:void 0!==this.config.body.textAlign?this.config.body.textAlign:"left",f=void 0!==l.fontSize?l.fontSize:void 0!==this.config.body.fontSize?this.config.body.fontSize:30,b=void 0!==l.fontFamily?l.fontFamily:void 0!==this.config.body.fontFamily?this.config.body.fontFamily:"Arial",C=f+(void 0!==l.leading?l.leading:void 0!==this.config.body.leading?this.config.body.leading:8),y=this.context;y.textAlign=g,y.font=`${f}px '${b}'`,s.forEach((function(e){let t=s.length>1?`${i}${e} `:e,l=y.measureText(t);if(l.width>u.width&&e.length>1)if(0==i.length&&l.width>u.width){for(;l.width>u.width;){let s=0;do{s++,t=e.substr(0,s),l=y.measureText(t)}while(l.widthu.height&&"scroll"===l.overflow){void 0===l.scrollY&&(l.scrollY=0);const e=void 0!==l.fontColor?l.fontColor:this.config.body.fontColor;y.fillStyle="#aaa",this.fillRoundedRect(a.x+r-12,a.y,12,o,6),y.fillStyle="#666";const t=u.height/v,s=t*o,i=-l.scrollY*t;this.fillRoundedRect(a.x+r-12,a.y+i,12,s,6),y.fillStyle=e,_=l.scrollY,l.minScrollY=u.height-v}let w,S=_+u.y+f/2;switch(g){case"center":w=u.x+u.width/2;break;case"right":w=u.x+u.width;break;default:w=u.x}n.forEach((e=>{S+C>0&&y.fillText(e,w,S),S+=C}))}}class Re{constructor(e,t,s="EN"){const i=this.getConfig(s);i.panelSize={width:e,height:.5*e},i.height=256,i.body={backgroundColor:"#555"},i.renderer=t;const n=this.getContent(s);this.keyboard=new Oe(n,i),this.keyboard.mesh.visible=!1,this.shift=!1}get mesh(){return this.keyboard.mesh}getConfig(e){const t={};let s=10;const i=39.2,n=49,l="#333",r="#000";let o=s,a=s;for(let e=0;e<10;e++){const d={type:"button",position:{x:a,y:o},width:i,height:n,padding:s,paddingTop:20,backgroundColor:r,borderRadius:6,hover:l,onSelect:this.onSelect.bind(this,e)};t[`btn${e}`]=d,a+=49.2}o+=59,a=s;for(let e=0;e<10;e++){const d={type:"button",position:{x:a,y:o},width:i,height:n,padding:s,paddingTop:20,backgroundColor:r,borderRadius:6,hover:l,onSelect:this.onSelect.bind(this,e+10)};t[`btn${e+10}`]=d,a+=49.2}o+=59,a=s;for(let e=0;e<9;e++){const d=0==e||8==e?1.5*i+5:i,c={type:"button",position:{x:a,y:o},width:d,height:n,padding:s,paddingTop:20,backgroundColor:r,borderRadius:6,hover:l,onSelect:this.onSelect.bind(this,e+20)};t[`btn${e+20}`]=c,a+=d+s}o+=59,a=s;for(let e=0;e<5;e++){const d=0==e||4==e?88.4:2==e?186.8:i,c={type:"button",position:{x:a,y:o},width:d,height:n,padding:s,paddingTop:20,backgroundColor:r,borderRadius:6,hover:l,onSelect:this.onSelect.bind(this,e+30)};0==e&&(c.fontSize=20),t[`btn${e+30}`]=c,a+=d+s}return t}getContent(e,t=0){let s,i={};switch(this.language=e,this.keyboardIndex=t,t){case 0:s=["q","w","e","r","t","y","u","i","o","p","a","s","d","f","g","h","j","k","l","@","⇧","z","x","c","v","b","n","m","⇦","","?123",","," ",".","↲"];for(let e=0;e","_","`","~",":",";","⇦","","abc",","," ",".","↲"];for(let e=0;e=0;e--){let s=t.scene.children[e];t.scene.remove(s)}else t.scene=new THREE.Scene;if(void 0!==t.scene_ghost)for(let e=t.scene_ghost.children.length-1;e>=0;e--){let s=t.scene_ghost.children[e];t.scene_ghost.remove(s)}else t.scene_ghost=new THREE.Scene;if(""!=s.htmlCls.setHtmlCls.getCookie("shininess")){let e=parseFloat(s.htmlCls.setHtmlCls.getCookie("shininess"));t.shininess!=e&&s.htmlCls.clickMenuCls.setLogCmd("set shininess "+e,!0),t.shininess=e}if(!s.bNode&&""!=s.htmlCls.setHtmlCls.getCookie("light1")){let e=parseFloat(s.htmlCls.setHtmlCls.getCookie("light1")),i=parseFloat(s.htmlCls.setHtmlCls.getCookie("light2")),n=parseFloat(s.htmlCls.setHtmlCls.getCookie("light3"));t.light1==e&&t.light2==i&&t.light3==n||s.htmlCls.clickMenuCls.setLogCmd("set light | light1 "+e+" | light2 "+i+" | light3 "+n,!0),t.light1=e,t.light2=i,t.light3=n}t.directionalLight=new THREE.DirectionalLight(16777215,t.light1),t.directionalLight2=new THREE.DirectionalLight(16777215,t.light2),t.directionalLight3=new THREE.DirectionalLight(16777215,t.light3),t.cam_z>0?(t.directionalLight.position.set(-1,1,1),t.directionalLight2.position.set(1,1,1),t.directionalLight3.position.set(1,1,-1),t.lightPos=new THREE.Vector3(-1,1,1),t.lightPos2=new THREE.Vector3(1,1,1),t.lightPos3=new THREE.Vector3(1,1,-1)):(t.directionalLight.position.set(-1,1,-1),t.directionalLight2.position.set(1,1,-1),t.directionalLight3.position.set(1,1,1),t.lightPos=new THREE.Vector3(-1,1,-1),t.lightPos2=new THREE.Vector3(1,1,-1),t.lightPos3=new THREE.Vector3(1,1,1));let i=new THREE.AmbientLight(4210752);if(t.scene.add(t.directionalLight),t.scene.add(i),void 0!==t.mdl)for(let e=t.mdl.children.length-1;e>=0;e--){let s=t.mdl.children[e];s.geometry&&s.geometry.dispose(),s.material&&s.material.dispose(),t.mdl.remove(s)}if(void 0!==t.mdlImpostor){for(let e=t.mdlImpostor.children.length-1;e>=0;e--){let s=t.mdlImpostor.children[e];s.geometry&&s.geometry.dispose(),s.material&&s.material.dispose(),t.mdlImpostor.remove(s)}t.mdlImpostor.children.length=0}s.bNode||t.renderer.renderLists.dispose(),t.mdl=new THREE.Object3D,t.mdlImpostor=new THREE.Object3D,t.scene.add(t.mdl),t.scene.add(t.mdlImpostor),t.mdl_ghost=new THREE.Object3D,t.scene_ghost.add(t.mdl_ghost),t.objects=[],t.objects_ghost=[],t.raycaster=new THREE.Raycaster,t.projector=new THREE.Projector,t.mouse=new THREE.Vector2;let n=s.parasCls.backgroundColors[t.opts.background.toLowerCase()];s.bNode||("transparent"===t.opts.background.toLowerCase()?t.renderer.setClearColor(n,0):t.renderer.setClearColor(n,1)),t.perspectiveCamera=new THREE.PerspectiveCamera(20,t.container.whratio,.1,1e4),t.perspectiveCamera.position.set(0,0,t.cam_z),t.perspectiveCamera.lookAt(new THREE.Vector3(0,0,0)),t.orthographicCamera=new THREE.OrthographicCamera,t.orthographicCamera.position.set(0,0,t.cam_z),t.orthographicCamera.lookAt(new THREE.Vector3(0,0,0)),t.cams={perspective:t.perspectiveCamera,orthographic:t.orthographicCamera}}setVrAr(){let e=this.icn3d;e.icn3dui;let t=this;e.bSetVrAr=!0,e.bVr?(e.canvasUI=this.createUI(),e.raycasterVR=new THREE.Raycaster,e.workingMatrix=new THREE.Matrix4,e.workingVector=new THREE.Vector3,e.origin=new THREE.Vector3,e.dolly=new THREE.Object3D,e.dolly.position.z=5,e.dolly.add(e.cam),e.scene.add(e.dolly),e.dollyId=e.dolly.id,e.dummyCam=new THREE.Object3D,e.cam.add(e.dummyCam),e.clock=new THREE.Clock,e.controllers=this.getControllers(),e.controllers.forEach((s=>{s.addEventListener("connected",(function(e){try{const s={},i="https://cdn.jsdelivr.net/npm/@webxr-input-profiles/assets@1.0/dist/profiles",n="generic-trigger";Ce(e.data,i,n).then((({profile:i,assetPath:n})=>{s.name=i.profileId,s.targetRayMode=e.data.targetRayMode,Object.entries(i.layouts).forEach((([e,t])=>{const i={};Object.values(t.components).forEach((e=>{i[e.rootNodeName]=e.gamepadIndices})),s[e]=i})),t.updateControllers(s)}))}catch(e){}})),s.addEventListener("disconnected",(function(){this.remove(this.children[0]),e.controllers.forEach((e=>{}))}))}))):e.bAr&&(e.gestures=new ke(e.renderer),e.scene.add(e.gestures.controller1),e.scene.add(e.gestures.controller2),e.gestures.addEventListener("doubletap",(e=>{t.positionCenter()})),e.gestures.addEventListener("pinch",(s=>{if(void 0!==s.initialise)t.startPosition=e.mdl.position.clone(),t.startScale=e.mdl.scale.clone();else{let i=1;const n=t.startScale.clone().multiplyScalar(s.scale*i);e.mdl.scale.copy(n)}})))}positionCenter(){let e=this.icn3d;e.icn3dui;const t=e.gestures.controller1;e.mdl.position.set(-.06,0,-.6).applyMatrix4(t.matrixWorld),e.mdl.scale.copy(new THREE.Vector3(.005,.005,.005))}setVrArButtons(){let e=this.icn3d,t=e.icn3dui;e.bSetVrArButtons=!0,t.bNode||($("#"+t.pre+"VRButton").remove(),$("#"+t.pre+"viewer").get(0).appendChild(e.VRButtonCls.createButton(e.renderer)),$("#"+t.pre+"ARButton").remove(),$("#"+t.pre+"viewer").get(0).appendChild(e.ARButtonCls.createButton(e.renderer)))}updateControllers(e){this.icn3d.icn3dui,this.addEventForController(e,"right"),this.addEventForController(e,"left")}addEventForController(e,t){let s=this.icn3d;s.icn3dui;const i="right"==t?s.renderer.xr.getController(0):s.renderer.xr.getController(1),n="right"==t?e.right:e.left;if(i&&void 0!==n){let e=!1,t=!1;Object.keys(n).forEach((i=>{-1!=i.indexOf("trigger")&&(e=!0),-1!=i.indexOf("squeeze")&&(t=!0),-1==i.indexOf("thumbstick")&&-1==i.indexOf("touchpad")||(s.xAxisIndex=n[i].xAxis,s.yAxisIndex=n[i].yAxis)})),e&&(i.addEventListener("selectstart",(function(){this.userData.selectPressed=!0})),i.addEventListener("selectend",(function(){this.userData.selectPressed=!1,this.userData.selected=void 0}))),t&&(i.addEventListener("squeezestart",(function(){this.userData.squeezePressed=!0,s.cam.add(s.canvasUI.mesh)})),i.addEventListener("squeezeend",(function(){this.userData.squeezePressed=!1,s.cam.remove(s.canvasUI.mesh)})))}}createUI(){let e=this.icn3d,t=e.icn3dui,s=94,i=50,n=94,l=34,r=12,o="#1c94c4",a="#ccc",d="#fbcb09",c=20;const h={panelSize:{width:2,height:1.6},height:400,select:{type:"button",paddingTop:c,position:{top:6,left:6},width:s,height:i,fontColor:"#000",fontSize:14,backgroundColor:a},residue:{type:"button",paddingTop:c,position:{top:62,left:6},width:s,height:i,fontColor:o,fontSize:r,backgroundColor:a,hover:d,onSelect:function(){e.pk=2,e.pAtomNum||(e.pAtomNum=0),e.cam.remove(e.canvasUI.mesh)}},secondarySelect:{type:"button",paddingTop:12,position:{top:118,left:6},width:s,height:i,fontColor:o,fontSize:r,backgroundColor:a,hover:d,onSelect:function(){e.pk=3,e.pAtomNum||(e.pAtomNum=0),e.cam.remove(e.canvasUI.mesh)}},chainSelect:{type:"button",paddingTop:c,position:{top:174,left:6},width:s,height:i,fontColor:o,fontSize:r,backgroundColor:a,hover:d,onSelect:function(){e.pk=5,e.pAtomNum||(e.pAtomNum=0),e.cam.remove(e.canvasUI.mesh)}},atom:{type:"button",paddingTop:c,position:{top:230,left:6},width:s,height:i,fontColor:o,fontSize:r,backgroundColor:a,hover:d,onSelect:function(){e.pk=1,e.pAtomNum||(e.pAtomNum=0),e.cam.remove(e.canvasUI.mesh)}},reset:{type:"button",paddingTop:c,position:{top:286,left:6},width:s,height:i,fontColor:o,fontSize:r,backgroundColor:a,hover:d,onSelect:function(){e.viewInterPairsCls.resetInteractionPairs(),e.selectionCls.resetAll(),e.cam.remove(e.canvasUI.mesh)}},togglehl:{type:"button",paddingTop:12,position:{top:342,left:6},width:s,height:i,fontColor:o,fontSize:r,backgroundColor:a,hover:d,onSelect:function(){e.hlUpdateCls.toggleHighlight(),e.cam.remove(e.canvasUI.mesh)}},style:{type:"button",paddingTop:c,position:{top:6,left:106},width:s,height:i,fontColor:"#000",fontSize:14,backgroundColor:a},ribbon:{type:"button",paddingTop:c,position:{top:62,left:106},width:s,height:i,fontColor:o,fontSize:r,backgroundColor:a,hover:d,onSelect:function(){e.setOptionCls.setStyle("proteins","ribbon"),e.setOptionCls.setStyle("nucleotides","nucleotide cartoon"),e.cam.remove(e.canvasUI.mesh)}},schematic:{type:"button",paddingTop:c,position:{top:118,left:106},width:s,height:i,fontColor:o,fontSize:r,backgroundColor:a,hover:d,onSelect:function(){e.setOptionCls.setStyle("proteins","schematic"),e.setOptionCls.setStyle("nucleotides","schematic"),e.cam.remove(e.canvasUI.mesh)}},stick:{type:"button",paddingTop:c,position:{top:174,left:106},width:s,height:i,fontColor:o,fontSize:r,backgroundColor:a,hover:d,onSelect:function(){e.setOptionCls.setStyle("proteins","stick"),e.setOptionCls.setStyle("nucleotides","stick"),e.cam.remove(e.canvasUI.mesh)}},sphere:{type:"button",paddingTop:c,position:{top:230,left:106},width:s,height:i,fontColor:o,fontSize:r,backgroundColor:a,hover:d,onSelect:function(){e.setOptionCls.setStyle("proteins","sphere"),e.setOptionCls.setStyle("nucleotides","sphere"),e.cam.remove(e.canvasUI.mesh)}},surface:{type:"button",paddingTop:c,position:{top:286,left:106},width:s,height:i,fontColor:o,fontSize:r,backgroundColor:a,hover:d,onSelect:function(){e.opts.surface="molecular surface",e.applyMapCls.applySurfaceOptions(),e.cam.remove(e.canvasUI.mesh)}},surfaceTrn:{type:"button",paddingTop:12,position:{top:342,left:106},width:s,height:i,fontColor:o,fontSize:r,backgroundColor:a,hover:d,onSelect:function(){e.opts.surface="molecular surface",e.opts.opacity="0.2",e.applyMapCls.applySurfaceOptions(),e.cam.remove(e.canvasUI.mesh)}},color:{type:"button",paddingTop:c,position:{top:6,left:206},width:s,height:i,fontColor:"#000",fontSize:14,backgroundColor:a},rainbow:{type:"button",paddingTop:c,position:{top:62,left:206},width:s,height:i,fontColor:o,fontSize:r,backgroundColor:a,hover:d,onSelect:function(){e.setOptionCls.setOption("color","rainbow for chains"),e.cam.remove(e.canvasUI.mesh)}},atomColor:{type:"button",paddingTop:c,position:{top:118,left:206},width:s,height:i,fontColor:o,fontSize:r,backgroundColor:a,hover:d,onSelect:function(){e.setOptionCls.setOption("color","atom"),e.cam.remove(e.canvasUI.mesh)}},chainColor:{type:"button",paddingTop:c,position:{top:174,left:206},width:s,height:i,fontColor:o,fontSize:r,backgroundColor:a,hover:d,onSelect:function(){e.setOptionCls.setOption("color","chain"),e.cam.remove(e.canvasUI.mesh)}},secondaryColor:{type:"button",paddingTop:12,position:{top:230,left:206},width:s,height:i,fontColor:o,fontSize:r,backgroundColor:a,hover:d,onSelect:function(){e.setOptionCls.setOption("color","secondary structure green"),e.cam.remove(e.canvasUI.mesh)}},charge:{type:"button",paddingTop:c,position:{top:342,left:206},width:s,height:i,fontColor:o,fontSize:r,backgroundColor:a,hover:d,onSelect:function(){e.setOptionCls.setOption("color","charge"),e.cam.remove(e.canvasUI.mesh)}},AlphaFold:{type:"button",paddingTop:c,position:{top:286,left:206},width:s,height:i,fontColor:o,fontSize:r,backgroundColor:a,hover:d,onSelect:function(){e.setOptionCls.setOption("color","confidence"),e.cam.remove(e.canvasUI.mesh)}},unicolor:{type:"button",paddingTop:c,position:{top:6,left:306},width:s,height:i,fontColor:"#000",fontSize:14,backgroundColor:a},red:{type:"button",position:{top:i,left:300},width:n,height:l,fontColor:"red",hover:d,onSelect:function(){e.setOptionCls.setOption("color","red"),e.cam.remove(e.canvasUI.mesh)}},green:{type:"button",position:{top:78,left:300},width:n,height:l,fontColor:"green",hover:d,onSelect:function(){e.setOptionCls.setOption("color","green"),e.cam.remove(e.canvasUI.mesh)}},blue:{type:"button",position:{top:106,left:300},width:n,height:l,fontColor:"blue",hover:d,onSelect:function(){e.setOptionCls.setOption("color","blue"),e.cam.remove(e.canvasUI.mesh)}},blueviolet:{type:"button",position:{top:134,left:300},width:n,height:l,fontColor:"#8A2BE2",hover:d,onSelect:function(){e.setOptionCls.setOption("color","8A2BE2"),e.cam.remove(e.canvasUI.mesh)}},magenta:{type:"button",position:{top:162,left:300},width:n,height:l,fontColor:"magenta",hover:d,onSelect:function(){e.setOptionCls.setOption("color","magenta"),e.cam.remove(e.canvasUI.mesh)}},yellow:{type:"button",position:{top:190,left:300},width:n,height:l,fontColor:"yellow",hover:d,onSelect:function(){e.setOptionCls.setOption("color","yellow"),e.cam.remove(e.canvasUI.mesh)}},orange:{type:"button",position:{top:218,left:300},width:n,height:l,fontColor:"orange",hover:d,onSelect:function(){e.setOptionCls.setOption("color","FFA500"),e.cam.remove(e.canvasUI.mesh)}},cyan:{type:"button",position:{top:246,left:300},width:n,height:l,fontColor:"cyan",hover:d,onSelect:function(){e.setOptionCls.setOption("color","cyan"),e.cam.remove(e.canvasUI.mesh)}},gray:{type:"button",position:{top:274,left:300},width:n,height:l,fontColor:"gray",hover:d,onSelect:function(){e.setOptionCls.setOption("color","888888"),e.cam.remove(e.canvasUI.mesh)}},white:{type:"button",position:{top:302,left:300},width:n,height:l,fontColor:"white",hover:d,onSelect:function(){e.setOptionCls.setOption("color","white"),e.cam.remove(e.canvasUI.mesh)}},analysis:{type:"button",paddingTop:c,position:{top:6,left:406},width:s,height:i,fontColor:"#000",fontSize:14,backgroundColor:a},distance:{type:"button",paddingTop:c,position:{top:62,left:406},width:s,height:i,fontColor:o,fontSize:r,backgroundColor:a,hover:d,onSelect:function(){try{e.bMeasureDistance=!0;let s=e.pickingCls.getPickedAtomList(e.pk,e.pAtom),i=e.pickingCls.getPickedAtomList(e.pk,e.pAtom2),n=e.applyCenterCls.centerAtoms(t.hashUtilsCls.hash2Atoms(s,e.atoms)).center,l=e.applyCenterCls.centerAtoms(t.hashUtilsCls.hash2Atoms(i,e.atoms)).center,r=0,o=0,a="#FFFF00",d=(n.x+l.x)/2,c=(n.y+l.y)/2,h=(n.z+l.z)/2,p=!0;e.analysisCls.addLine(n.x,n.y,n.z,l.x,l.y,l.z,a,p,"distance");let m=(parseInt(10*n.distanceTo(l))/10).toString()+" A";e.analysisCls.addLabel(m,d,c,h,r,a,o,"distance"),e.drawCls.draw(),e.cam.remove(e.canvasUI.mesh)}catch(e){}}},interaction:{type:"button",paddingTop:c,position:{top:118,left:406},width:s,height:i,fontColor:o,fontSize:r,backgroundColor:a,hover:d,onSelect:function(){try{e.viewInterPairsCls.viewInteractionPairs(["selected"],["non-selected"],!1,"3d",1,1,1,1,1,1),e.cam.remove(e.canvasUI.mesh)}catch(e){}}},delphi:{type:"button",paddingTop:c,position:{top:174,left:406},width:s,height:i,fontColor:o,fontSize:r,backgroundColor:a,hover:d,onSelect:async function(){e.phisurftype=22,e.phisurfop=1,e.phisurfwf="no",await e.delphiCls.CalcPhi(65,.15,2,!0),e.cam.remove(e.canvasUI.mesh)}},removeLabel:{type:"button",paddingTop:c,position:{top:230,left:406},width:s,height:i,fontColor:o,fontSize:r,backgroundColor:a,hover:d,onSelect:function(){for(let t in e.labels)e.labels[t]=[];e.drawCls.draw(),e.cam.remove(e.canvasUI.mesh)}},renderer:e.renderer},p=new Oe({select:"Select",residue:"Residue",secondarySelect:"Secondary Structure",chainSelect:"Chain",atom:"Atom",reset:"Reset",togglehl:"Toggle Highlight",style:"Style",ribbon:"Ribbon",schematic:"Schematic",stick:"Stick",sphere:"Sphere",surface:"Surface",surfaceTrn:"Transparent Surface",color:"Color",rainbow:"Rainbow",atomColor:"Atom",chainColor:"Chain",secondaryColor:"Secondary Structure",AlphaFold:"AlphaFold",charge:"Charge",unicolor:"UniColor",red:"M 100 15 L 15 15 L 15 100 L 100 100 Z",green:"M 100 15 L 15 15 L 15 100 L 100 100 Z",blue:"M 100 15 L 15 15 L 15 100 L 100 100 Z",blueviolet:"M 100 15 L 15 15 L 15 100 L 100 100 Z",magenta:"M 100 15 L 15 15 L 15 100 L 100 100 Z",yellow:"M 100 15 L 15 15 L 15 100 L 100 100 Z",orange:"M 100 15 L 15 15 L 15 100 L 100 100 Z",cyan:"M 100 15 L 15 15 L 15 100 L 100 100 Z",gray:"M 100 15 L 15 15 L 15 100 L 100 100 Z",white:"M 100 15 L 15 15 L 15 100 L 100 100 Z",analysis:"Analysis",distance:"Distance",interaction:"Interaction",delphi:"DelPhi Potential",removeLabel:"Remove Label"},h);return p.mesh.position.set(0,0,-3),p}createUILog(){let e=this.icn3d;e.icn3dui;const t={panelSize:{width:2,height:2},height:512,info:{type:"text",overflow:"scroll",position:{top:6,left:6},width:506,height:506,backgroundColor:"#aaa",fontColor:"#000"},renderer:e.renderer},s=new Oe({info:"Debug info"},t);return s.mesh.position.set(0,-1,-2),s}getControllers(){let e=this.icn3d;e.icn3dui;const t=new xe,s=(new THREE.BufferGeometry).setFromPoints([new THREE.Vector3(0,0,0),new THREE.Vector3(0,0,-1)]),i=new THREE.Line(s);i.name="line",i.scale.z=50;const n=[];for(let s=0;s<=1;s++){const l=e.renderer.xr.getController(s);if(!l)continue;e.dolly.add(l),l.add(i.clone()),l.userData.selectPressed=!1,e.cam.add(l),n.push(l);const r=e.renderer.xr.getControllerGrip(s);r.add(t.createControllerModel(r)),e.scene.add(r)}return n}}class Te{constructor(e){this.icn3d=e}setCamera(){let e=this.icn3d,t=e.icn3dui;if(e.bControlGl&&!t.bNode){window.cam=e.cams[e.opts.camera.toLowerCase()];let s=e.maxD;if(window.cam===e.perspectiveCamera){let i=void 0!==e.biomtMatrices&&e.biomtMatrices.length*e.cnt>e.maxatomcnt;i?window.camMaxDFactor=1:void 0!==window.camMaxDFactorFog?window.camMaxDFactor=window.camMaxDFactorFog:window.camMaxDFactor=3,window.cam_z>0?window.cam.position.z=s*window.camMaxDFactor:window.cam.position.z=-s*window.camMaxDFactor,"yes"===e.opts.slab?i?window.cam.near=.1:void 0!==window.camMaxDFactorFog?window.cam.near=s*window.camMaxDFactorFog-10:window.cam.near=s*window.camMaxDFactor:window.cam.near=.1,window.cam.far=1e4,e.bControlGl&&!t.bNode?window.controls=new THREE.TrackballControls(window.cam,void 0,e):t.bNode?e.controls=new THREE.TrackballControls(e.cam,document,e):e.controls=new THREE.TrackballControls(e.cam,document.getElementById(e.id),e)}else window.cam===e.orthographicCamera&&(void 0!==e.biomtMatrices&&e.biomtMatrices.length*e.cnt>10*e.maxatomcnt?window.cam.right=e.maxD/2*1.5:window.cam.right=e.maxD/2*2.5,window.cam.left=-window.cam.right,window.cam.top=window.cam.right/e.container.whratio,window.cam.bottom=-window.cam.right/e.container.whratio,"yes"===e.opts.slab?window.cam.near=2*e.maxD:window.cam.near=0,window.cam.far=1e4,e.bControlGl&&!t.bNode?window.controls=new THREE.OrthographicTrackballControls(window.cam,void 0,e):t.bNode?e.controls=new THREE.OrthographicTrackballControls(e.cam,document,e):e.controls=new THREE.OrthographicTrackballControls(e.cam,document.getElementById(e.id),e));window.cam.updateProjectionMatrix()}e.cam=e.cams[e.opts.camera.toLowerCase()];let s=e.maxD;if(e.cam===e.perspectiveCamera){let i=void 0!==e.biomtMatrices&&e.biomtMatrices.length*e.cnt>e.maxatomcnt;i?e.camMaxDFactor=1:void 0!==e.camMaxDFactorFog?e.camMaxDFactor=e.camMaxDFactorFog:e.camMaxDFactor=3,e.cam_z>0?e.cam.position.z=s*e.camMaxDFactor:e.cam.position.z=-s*e.camMaxDFactor,"yes"===e.opts.slab?i?e.cam.near=.1:void 0!==e.camMaxDFactorFog?e.cam.near=s*e.camMaxDFactorFog-10:e.cam.near=s*e.camMaxDFactor:e.cam.near=.1,e.cam.far=1e4,e.bControlGl&&!t.bNode?window.controls=new THREE.TrackballControls(e.cam,void 0,e):t.bNode?e.controls=new THREE.TrackballControls(e.cam,document,e):e.controls=new THREE.TrackballControls(e.cam,document.getElementById(e.id),e)}else e.cam===e.orthographicCamera&&(void 0!==e.biomtMatrices&&e.biomtMatrices.length*e.cnt>10*e.maxatomcnt?e.cam.right=e.maxD/2*1.5:e.cam.right=e.maxD/2*2.5,e.cam.left=-e.cam.right,e.cam.top=e.cam.right/e.container.whratio,e.cam.bottom=-e.cam.right/e.container.whratio,"yes"===e.opts.slab?e.cam.near=2*e.maxD:e.cam.near=0,e.cam.far=1e4,e.bControlGl&&!t.bNode?window.controls=new THREE.OrthographicTrackballControls(e.cam,void 0,e):t.bNode?e.controls=new THREE.OrthographicTrackballControls(e.cam,document,e):e.controls=new THREE.OrthographicTrackballControls(e.cam,document.getElementById(e.id),e));e.cam.updateProjectionMatrix()}}class Ee{constructor(e){this.icn3d=e}setFog(e){let t=this.icn3d,s=t.icn3dui.parasCls.backgroundColors[t.opts.background.toLowerCase()];if(e){let e=t.applyCenterCls.centerAtoms(t.hAtoms);t.maxD=e.maxD,t.maxD<25&&(t.maxD=25)}let i=void 0!==t.biomtMatrices&&t.biomtMatrices.length*t.cnt>t.maxatomcnt;if("yes"===t.opts.fog)if("perspective"===t.opts.camera)if(i)t.scene.fog=void 0,t.bSetFog=!1;else{let e=t._zoomFactor>1?1*t._zoomFactor:t._zoomFactor;t.scene.fog=new THREE.Fog(s,2.5*t.maxD*e,4*t.maxD*e),t.bSetFog=!0,t.camMaxDFactorFog=3}else"orthographic"===t.opts.camera&&(t.scene.fog=void 0,t.bSetFog=!1);else t.scene.fog=void 0,t.bSetFog=!1}}class Pe{constructor(e){this.icn3d=e}createBox(e,t,s,i,n,l){let r=this.icn3d,o=r.icn3dui;if(o.bNode)return;void 0===t&&(t=.8),void 0===s&&(s=!1),void 0===i&&(i=.8),l?void 0===n&&(n=r.hColor):void 0===n&&(n=e.color);let a=s?t:(o.parasCls.vdwRadii[e.elem.toUpperCase()]||t)*(i||1);this.createBox_base(e.coord,a,n,l)}createBox_base(e,t,s,i,n,l,r){let o,a=this.icn3d;a.icn3dui.bNode||(void 0===r&&(r=l?.5:1),new THREE.BoxGeometry(1,1,1),o=new THREE.Mesh(a.boxGeometry,new THREE.MeshPhongMaterial({transparent:!0,opacity:r,specular:a.frac,shininess:a.shininess,emissive:a.emissive,color:s})),o.scale.x=o.scale.y=o.scale.z=t,o.position.copy(e),a.mdl.add(o),i?a.prevHighlightObjects.push(o):n?a.prevOtherMesh.push(o):a.objects.push(o))}createBoxRepresentation_P_CA(e,t,s){let i=this.icn3d;if(i.icn3dui.bNode)return;let n=this;i.reprSubCls.createRepresentationSub(e,(function(e){"CA"!==e.name&&"O3'"!==e.name&&"O3*"!==e.name||n.createBox(e,void 0,void 0,t,void 0,s)}))}}class Me{constructor(e){this.icn3d=e}createBrick(e,t,s,i){let n=this.icn3d;if(n.icn3dui.bNode)return;let l=new THREE.CylinderGeometry(1,1,1,4,1),r=new THREE.Mesh(l,new THREE.MeshPhongMaterial({specular:n.frac,shininess:n.shininess,emissive:n.emissive,color:i}));r.position.copy(e).add(t).multiplyScalar(.5),r.matrixAutoUpdate=!1,r.lookAt(t.clone().sub(e)),r.updateMatrix(),r.matrix.multiply((new THREE.Matrix4).makeScale(s,s,e.distanceTo(t))).multiply((new THREE.Matrix4).makeRotationX(.5*Math.PI)),n.mdl.add(r)}}class De{constructor(e){this.icn3d=e}createCurveSubArrow(e,t,s,i,n,l,r,o,a,d,c,h,p,m,u){if(this.icn3d.icn3dui.bNode)return;let g=[],f=[];g.push(e),f.push(o),this.prepareStrand(g,f,t,s,i,void 0,n,l,r,a,d,!1,c,h,p,m,u),g=[],f=[]}createStripArrow(e,t,s,i,n,l,r,o,a,d,c,h,p,m,u,g){if(this.icn3d.icn3dui.bNode)return;let f=[],b=[];f.push(e),f.push(t),b.push(o),b.push(a),this.prepareStrand(f,b,void 0,s,i,n,l,void 0,r,d,c,!0,h,p,m,u,g),f=[],b=[]}prepareStrand(e,t,s,i,n,l,r,o,a,d,c,h,p,m,u,g,f){let b=this.icn3d,C=b.icn3dui;if(1===d.length)return;let y=i,v=!u,_=[];_.push(i[i.length-2]),_.push(i[i.length-1]),n=n||b.axisDIV;let w,S,A,x,k=2/(a-1),O={};for(let e=0,s=t.length;e1)if(void 0!==d){let i,n,l=[];for(let r=0,o=p.length;r0&&i.tubeCls.createTube(a,"CA",i.coilWidth,s),Object.keys(d).length>0&&i.strandCls.createStrand(d,void 0,void 0,!0,0,i.helixSheetWidth,!1,2*i.ribbonthickness,s)):(Object.keys(a).length>0&&i.tubeCls.createTube(a,"CA",i.coilWidth),Object.keys(d).length>0&&i.strandCls.createStrand(d,void 0,void 0,!0,0,i.helixSheetWidth,!1,2*i.ribbonthickness))}createCylinderCurve(e,t,s,i,n){let l=this.icn3d;if(l.icn3dui.bNode)return;let r,o,a,d,c,h,p=null;for(a in e)if(d=e[a],!d.het&&(c=d.structure+"_"+d.chain,h=d.structure+"_"+r,-1!=t.indexOf(d.name))){if(null!==p&&r===d.chain&&l.ParserUtilsCls.getResiNCBI(h,o)+1===l.ParserUtilsCls.getResiNCBI(c,d.resi)&&Math.abs(p.coord.x-d.coord.x)<8&&Math.abs(p.coord.y-d.coord.y)<8&&Math.abs(p.coord.z-d.coord.z)<8){let e=p.coord.clone().add(d.coord).multiplyScalar(.5);if(n)1===n&&(this.createCylinder(p.coord,e,s,p.color,n),this.createCylinder(e,d.coord,s,d.color,n),l.sphereCls.createSphere(d,s,!0,1,n));else if(i){let t=l.lineCls.createSingleLine(p.coord,e,p.color,!1);l.mdl.add(t),l.objects.push(t),t=l.lineCls.createSingleLine(e,d.coord,d.color,!1),l.mdl.add(t),l.objects.push(t)}else this.createCylinder(p.coord,e,s,p.color),this.createCylinder(e,d.coord,s,d.color),l.sphereCls.createSphere(d,s,!0,1,n)}p=d,r=d.chain,o=d.resi,l.sphereCls.createSphere(d,s,!0,1,n),2===n&&l.boxCls.createBox(d,void 0,void 0,void 0,void 0,n)}if(null!==p&&r===d.chain&&l.ParserUtilsCls.getResiNCBI(h,o)+1===l.ParserUtilsCls.getResiNCBI(c,d.resi)&&Math.abs(p.coord.x-d.coord.x)<8&&Math.abs(p.coord.y-d.coord.y)<8&&Math.abs(p.coord.z-d.coord.z)<8){let e=p.coord.add(d.coord).multiplyScalar(.5);if(n)1===n&&(this.createCylinder(p.coord,e,s,p.color,n),this.createCylinder(e,d.coord,s,d.color,n),l.sphereCls.createSphere(d,s,!0,1,n));else if(i){let t=l.lineCls.createSingleLine(p.coord,e,p.color,!1);l.mdl.add(t),l.objects.push(t),t=l.lineCls.createSingleLine(e,d.coord,d.color,!1),l.mdl.add(t),l.objects.push(t)}else this.createCylinder(p.coord,e,s,p.color),this.createCylinder(e,d.coord,s,d.color)}}}class Le{constructor(e){this.icn3d=e}createLineRepresentation(e,t){let s=this.icn3d;if(s.icn3dui.bNode)return;let i=new THREE.BufferGeometry,n=[],l=[],r=0,o=0;s.reprSubCls.createRepresentationSub(e,void 0,(function(e,t){if(e.color===t.color)n[r++]=e.coord.x,n[r++]=e.coord.y,n[r++]=e.coord.z,n[r++]=t.coord.x,n[r++]=t.coord.y,n[r++]=t.coord.z,l[o++]=e.color.r,l[o++]=e.color.g,l[o++]=e.color.b,l[o++]=t.color.r,l[o++]=t.color.g,l[o++]=t.color.b;else{let s=e.coord.clone().add(t.coord).multiplyScalar(.5);n[r++]=e.coord.x,n[r++]=e.coord.y,n[r++]=e.coord.z,n[r++]=s.x,n[r++]=s.y,n[r++]=s.z,n[r++]=t.coord.x,n[r++]=t.coord.y,n[r++]=t.coord.z,n[r++]=s.x,n[r++]=s.y,n[r++]=s.z,l[o++]=e.color.r,l[o++]=e.color.g,l[o++]=e.color.b,l[o++]=e.color.r,l[o++]=e.color.g,l[o++]=e.color.b,l[o++]=t.color.r,l[o++]=t.color.g,l[o++]=t.color.b,l[o++]=t.color.r,l[o++]=t.color.g,l[o++]=t.color.b}}));if(i.setAttribute("position",new THREE.BufferAttribute(new Float32Array(n),3)),i.setAttribute("color",new THREE.BufferAttribute(new Float32Array(l),3)),2!==t){let e;1===t||(e=new THREE.LineSegments(i,new THREE.LineBasicMaterial({linewidth:s.linewidth,vertexColors:!0})),s.mdl.add(e)),1===t?s.prevHighlightObjects.push(e):s.objects.push(e)}else 2===t&&s.boxCls.createBoxRepresentation_P_CA(e,.8,t)}createConnCalphSidechain(e,t){let s=this.icn3d;if(s.icn3dui.bNode)return;let i={};for(let s in e){let n=e[s];if(!n.het&&n.style2===t){i[n.structure+"_"+n.chain+"_"+n.resi]=1}}let n=[],l=[];for(let e in i){let t=s.firstAtomObjCls.getFirstAtomObjByName(s.residues[e],"CA");if(void 0!==t)for(let e=0,i=t.bonds.length;e=t.bonds.length&&e.bonds.length>1)s=e.serial,l=e.bonds[0],d=e.bonds[1];else{if(!(t.bonds.length>=e.bonds.length&&t.bonds.length>1))return void console.log("Double bond was not drawn due to the undefined cross plane");s=t.serial,l=t.bonds[0],d=t.bonds[1]}let i=r.atoms[s].coord.clone();i.sub(r.atoms[l].coord);let n=r.atoms[s].coord.clone();n.sub(r.atoms[d].coord),i.cross(n),0==parseInt(1e4*i.length())&&(i=new THREE.Vector3(.2,.3,.5)),c=t.coord.clone(),c.sub(e.coord),c.cross(i).normalize().multiplyScalar(.2*o),0==parseInt(1e4*c.length())&&(i=new THREE.Vector3(.5,.3,.2),c.cross(i).normalize().multiplyScalar(.2*o))}e.color===t.color?r.dAtoms.hasOwnProperty(e.serial)&&r.dAtoms.hasOwnProperty(t.serial)&&(r.cylinderCls.createCylinder(e.coord.clone().add(c),t.coord.clone().add(c),a,e.color,n),r.cylinderCls.createCylinder(e.coord.clone().sub(c),t.coord.clone().sub(c),a,e.color,n)):r.bImpo?r.dAtoms.hasOwnProperty(e.serial)&&r.dAtoms.hasOwnProperty(t.serial)&&(r.cylinderCls.createCylinder(e.coord.clone().add(c),t.coord.clone().add(c),a,e.color,n,t.color),r.cylinderCls.createCylinder(e.coord.clone().sub(c),t.coord.clone().sub(c),a,e.color,n,t.color)):r.dAtoms.hasOwnProperty(e.serial)&&r.dAtoms.hasOwnProperty(t.serial)&&(r.cylinderCls.createCylinder(e.coord.clone().add(c),i.clone().add(c),a,e.color,n),r.cylinderCls.createCylinder(t.coord.clone().add(c),i.clone().add(c),a,t.color,n),r.cylinderCls.createCylinder(e.coord.clone().sub(c),i.clone().sub(c),a,e.color,n),r.cylinderCls.createCylinder(t.coord.clone().sub(c),i.clone().sub(c),a,t.color,n))}else if(r.aromaticbonds.hasOwnProperty(l)){let s,l,d;if(e.bonds.length>t.bonds.length&&e.bonds.length>1)s=e.serial,l=e.bonds[0],d=e.bonds[1];else{if(!(t.bonds.length>1))return;s=t.serial,l=t.bonds[0],d=t.bonds[1]}let c=r.atoms[s].coord.clone();c.sub(r.atoms[l].coord);let h=r.atoms[s].coord.clone();h.sub(r.atoms[d].coord),c.cross(h);let p=t.coord.clone();p.sub(e.coord),p.cross(c).normalize().multiplyScalar(.2*o);let m=0;for(let s=0,i=e.bondOrder.length;so+1?(s=k.clone(),i=d.atoms[G[G.length-1-o-1]].coord.clone(),i.sub(s)):s=new THREE.Vector3(Math.random(),Math.random(),Math.random()))):d.bCalphaOnly&&"CA"===b.name&&(G.length>o+1?(s=k.clone(),i=d.atoms[G[G.length-1-o-1]].coord.clone(),i.sub(s)):s=new THREE.Vector3(Math.random(),Math.random(),Math.random())),s.normalize(),s.multiplyScalar(f),null!==I&&s.dot(I)<0&&s.negate(),I=s;for(let e=0,s=2/(t-1);e6||c&&Math.abs(S.y-c.y)>6||c&&Math.abs(S.z-c.z)>6;if((u!==b.chain||b.ssbegin||b.ssend||B===j-1||p)&&m[0].length>0){let c="CA",u=[],g=[];if(isNaN(d.atoms[M].resi))u=[];else{let e=d.atoms[M].structure+"_"+d.atoms[M].chain+"_"+(parseInt(d.atoms[M].resi)-1).toString(),t=d.firstAtomObjCls.getAtomCoordFromResi(e,c);u=void 0!==t?[t]:[]}if(!isNaN(d.atoms[M].resi)){let e=d.atoms[M].structure+"_"+d.atoms[M].chain+"_"+(parseInt(d.atoms[M].resi)+1).toString(),t=d.firstAtomObjCls.getAtomCoordFromResi(e,c);void 0!==t&&g.push(t);let s=d.atoms[M].structure+"_"+d.atoms[M].chain+"_"+(parseInt(d.atoms[M].resi)+2).toString(),i=d.firstAtomObjCls.getAtomCoordFromResi(s,c);void 0!==i&&g.push(i)}if(!p){1===a||2===a?w.push(d.hColor):w.push(R),f=b.ssend&&"sheet"===b.ss?0:"coil"===T&&b.ssbegin||E&&b.ssbegin||"coil"===b.ss?n:l;let s,i,o=4;"O"===b.name?(s=A.clone(),s.sub(S)):d.bCalphaOnly&&"CA"===b.name&&(G.length>o?(s=S.clone(),i=d.atoms[G[G.length-1-o]].coord.clone(),i.sub(s)):s=new THREE.Vector3(Math.random(),Math.random(),Math.random())),s.normalize(),s.multiplyScalar(f),null!==I&&s.dot(I)<0&&s.negate(),I=s;for(let e=0,s=2/(t-1);e0){let e="CA",n=[],l=[];if(isNaN(d.atoms[M].resi))n=[];else{let t=d.atoms[M].structure+"_"+d.atoms[M].chain+"_"+(parseInt(d.atoms[M].resi)-1).toString();d.firstAtomObjCls.getAtomCoordFromResi(t,e)}for(let e=0;!i&&e0;--e){let t=a.structure+"_"+a.chain+"_"+e;if(!c.residues.hasOwnProperty(t))break;let s=c.firstAtomObjCls.getFirstCalphaAtomObj(c.residues[t]);if(s.ss===a.ss&&s.ssbegin){g=s.resi;break}}for(let e=g;e0&&(o!==c.chain||Math.abs(c.coord.x-h.coord.x)>6||Math.abs(c.coord.y-h.coord.y)>6||Math.abs(c.coord.z-h.coord.z)>6||r.ParserUtilsCls.getResiNCBI(c.structure+"_"+o,a)+13||Math.abs(c.coord.y-h.coord.y)>3||Math.abs(c.coord.z-h.coord.z)>3))){if(2!==i){if(!isNaN(d.resi)&&!isNaN(h.resi)){let e=d.structure+"_"+d.chain+"_"+(parseInt(d.resi)-1).toString(),i=r.firstAtomObjCls.getAtomCoordFromResi(e,t);g=void 0!==i?[i]:[];let l=h.structure+"_"+h.chain+"_"+(parseInt(h.resi)+1).toString(),o=h.structure+"_"+h.chain+"_"+(parseInt(h.resi)+2).toString(),a=h.structure+"_"+h.chain+"_"+(parseInt(h.resi)+3).toString();if(r.residues.hasOwnProperty(l)){let e=r.firstAtomObjCls.getAtomFromResi(l,t);void 0!==e&&e.ssbegin&&(l=h.structure+"_"+h.chain+"_"+(parseInt(h.resi)+2).toString(),o=h.structure+"_"+h.chain+"_"+(parseInt(h.resi)+3).toString(),p.push(e.coord),n?u.push(this.getCustomtubesize(l)):u.push(this.getRadius(s,e)),m.push(e.color))}if(1==p.length&&r.residues.hasOwnProperty(l)){let e=r.firstAtomObjCls.getAtomFromResi(l,t);if(e){p.push(e.coord),m.push(e.color);let t=this.getRadius(s,c);u.push(t),l=o,o=a}}let b=r.firstAtomObjCls.getAtomCoordFromResi(l,t);void 0!==b&&f.push(b);let C=r.firstAtomObjCls.getAtomCoordFromResi(o,t);void 0!==C&&f.push(C)}C.push({pnts:p,colors:m,radii:u,prevone:g,nexttwo:f})}p=[],m=[],u=[],g=[],f=[],d=c,b=0}if(0==p.length&&!isNaN(c.resi)){let e=c.structure+"_"+c.chain+"_"+(parseInt(c.resi)-1).toString();r.residues.hasOwnProperty(e)&&(h=r.firstAtomObjCls.getAtomFromResi(e,t),void 0!==h&&h.ssend&&(p.push(h.coord),n?u.push(this.getCustomtubesize(e)):u.push(this.getRadius(s,h)),m.push(h.color)))}let e;p.push(c.coord),e=n?this.getCustomtubesize(c.structure+"_"+c.chain+"_"+c.resi):this.getRadius(s,c),u.push(e),m.push(c.color),1===b&&(m[m.length-2]=c.color),o=c.chain,a=c.resi;let l=1.2;2!==i||c.ssbegin||r.boxCls.createBox(c,void 0,void 0,l,void 0,i),++b,h=c}if(2!==i){if(g=[],void 0!==d&&!isNaN(d.resi)){let e=d.structure+"_"+d.chain+"_"+(parseInt(d.resi)-1).toString(),s=r.firstAtomObjCls.getAtomCoordFromResi(e,t);g=void 0!==s?[s]:[]}if(f=[],void 0!==c&&!isNaN(c.resi)){let e=c.structure+"_"+c.chain+"_"+(parseInt(c.resi)+1).toString(),i=c.structure+"_"+c.chain+"_"+(parseInt(c.resi)+2).toString(),n=c.structure+"_"+c.chain+"_"+(parseInt(c.resi)+3).toString();if(1==p.length&&r.residues.hasOwnProperty(e)){let l=r.firstAtomObjCls.getAtomFromResi(e,t);if(l){p.push(l.coord),m.push(l.color);let t=this.getRadius(s,c);u.push(t),e=i,i=n}}let l=r.firstAtomObjCls.getAtomCoordFromResi(e,t);void 0!==l&&f.push(l);let o=r.firstAtomObjCls.getAtomCoordFromResi(i,t);void 0!==o&&f.push(o)}C.push({pnts:p,colors:m,radii:u,prevone:g,nexttwo:f})}for(let e=0,t=C.length;e1?a.parasCls.thr(t[t.length-2]):a.parasCls.thr(t[e]),f[y++]=d.r,f[y++]=d.g,f[y++]=d.b}}let x,k=0;for(let e=0,t=w.length-1;er&&(l=r,e=1);for(let t=0;t0&&t.b<=100?.01*t.b:t.b>100?1:s.coilWidth),i}}class ze{constructor(e){this.icn3d=e}drawCartoonNucleicAcid(e,t,s,i){this.drawStrandNucleicAcid(e,2,t,!0,void 0,s,i)}drawStrandNucleicAcid(e,t,s,i,n,l,r){let o,a,d,c=this.icn3d;if(c.icn3dui.bNode)return;2===r&&(t=void 0,l=void 0),n=n||c.nucleicAcidWidth,s=s||c.axisDIV,t=t||c.nucleicAcidStrandDIV;let h=[];for(d=0;dy?y=C:C=y);let v=.8*b/y;if(g.width=C,g.height=y,f.clearRect(0,0,C,y),h)if(f.fillStyle="rgba("+n.r+","+n.g+","+n.b+","+n.a+")",f.strokeStyle="rgba("+l.r+","+l.g+","+l.b+","+l.a+")",f.lineWidth=r,p){let e=.4*C;this.circle(f,0,0,C,y,e)}else{let e=0;this.roundRect(f,0,0,C,y,e)}f.font="Bold "+a+"px "+o,f.textAlign="center",f.textBaseline="middle",f.fillStyle="rgba("+u.r+", "+u.g+", "+u.b+", 1.0)",f.strokeStyle="rgba("+u.r+", "+u.g+", "+u.b+", 1.0)",f.fillText(e,.5*C,.5*y);let _=new THREE.Texture(g);_.needsUpdate=!0;let w=new THREE.SpriteMaterial({map:_,depthTest:!1,depthWrite:!1});w.map.minFilter=THREE.LinearFilter;let S=new THREE.Sprite(w);return p?S.scale.set(.3*d,.3*d,1):S.scale.set(v*d,d,1),S.renderOrder=1,S}roundRect(e,t,s,i,n,l){e.beginPath(),e.moveTo(t+l,s),e.lineTo(t+i-l,s),e.quadraticCurveTo(t+i,s,t+i,s+l),e.lineTo(t+i,s+n-l),e.quadraticCurveTo(t+i,s+n,t+i-l,s+n),e.lineTo(t+l,s+n),e.quadraticCurveTo(t,s+n,t,s+n-l),e.lineTo(t,s+l),e.quadraticCurveTo(t,s,t+l,s),e.closePath(),e.fill(),e.stroke()}circle(e,t,s,i,n,l){e.beginPath(),e.arc(t+i/2,.9*(s+n/2),l,0,2*Math.PI,!0),e.closePath(),e.fill(),e.stroke()}}class Ve{constructor(e){this.icn3d=e,this.textSpriteCls=new Ge(e)}createLabelRepresentation(e){let t=this.icn3d;t.icn3dui;let s=t.oriMaxD/100;s<.4&&(s=.4);let i=3*s*t.labelScale;for(let s in e){let n=void 0!==e[s]?e[s]:[],l="black"!=t.opts.background?t.colorWhitebkgd:t.colorBlackbkgd;for(let e=0,r=n.length;e.99999)h.set(0,0,0,1);else if(e.y<-.99999)h.set(1,0,0,0);else{let t=new THREE.Vector3;t.set(e.z,0,-e.x).normalize();let s=Math.acos(e.y);h.setFromAxisAngle(t,s)}return c.applyQuaternion(h),c.scale.set(l,n,l),c.position.copy(t),c}setPc1Axes(){let e=this.icn3d,t=e.icn3dui;if(t.bNode)return;let s=t.hashUtilsCls.intHash(e.hAtoms,e.dAtoms),i=[],n=Object.keys(s).length<100;for(let t in s){let s=e.atoms[t],l=s.structure+"_"+s.chain+"_"+s.resi;(n||""!=l)&&i.push(s.coord.clone())}let l=t.rmsdSuprCls.getEigenForSelection(i,i.length),r=new THREE.Vector3(l.h1[0],l.h1[1],l.h1[2]);if(0==l.k&&e.bRender)return void alert("Can't determine the first principal component. Please select a subset and try it again.");let o=e.applyCenterCls.centerAtoms(s),a=o.maxD,d=o.center,c=d.clone().add(r.normalize().multiplyScalar(.4*a)),h=new THREE.Vector3(l.h2[0],l.h2[1],l.h2[2]),p=d.clone().add(h.normalize().multiplyScalar(.3*a)),m=new THREE.Vector3(l.h3[0],l.h3[1],l.h3[2]),u=d.clone().add(m.normalize().multiplyScalar(.3*a));this.buildAxes(void 0,d,c,p,u,!0);let g=[d,c,p,u];return e.axes.push(g),e.drawCls.draw(),g}}class Ye{constructor(e){this.icn3d=e}showGlycans(){let e=this.icn3d,t=e.icn3dui;if(t.bNode)return;let s={},i=e.dAtoms;for(let n in i){let i=e.atoms[n];i.het&&-1!=t.parasCls.glycanHash.hasOwnProperty(i.resn)&&(void 0===s[i.resn]&&(s[i.resn]={}),"Misc"!=i.chain&&(s[i.resn][i.structure+"_"+i.chain+"_"+i.resi]=1))}let n=Object.keys(s);for(let i=0,l=n.length;i>2))+i+((2&t)>>1))*c+n+(1&t)]&this.ISDONE)<=3&&(t.push(t[i]),i=t.length-1,t.push(t[n]),n=t.length-1,t.push(t[l]),l=t.length-1),s.push(i),s.push(n),s.push(l)}}},Xe.prototype.laplacianSmooth=function(e,t,s){let i,n,l,r,o,a=new Array(t.length);for(i=0,n=t.length;ithis.origextent[1][0])&&(!(tthis.origextent[1][1])&&!(sthis.origextent[1][2]))},Ke.prototype.getFacesAndVertices=function(){let e,t,s=this.verts;for(e=0,t=s.length;eh&&(h=this.pmaxy-this.pminy),this.pmaxz-this.pminz>h&&(h=this.pmaxz-this.pminz),this.scaleFactor=(c-1)/h,this.scaleFactor=this.defaultScaleFactor,this.defaultScaleFactor*h>this.threshbox&&(c=Math.floor(this.threshbox),this.scaleFactor=(this.threshbox-1)/h),this.bCalcArea&&(this.scaleFactor=this.defaultScaleFactor),this.pLength=Math.ceil(this.scaleFactor*(this.pmaxx-this.pminx))+1,this.pWidth=Math.ceil(this.scaleFactor*(this.pmaxy-this.pminy))+1,this.pHeight=Math.ceil(this.scaleFactor*(this.pmaxz-this.pminz))+1,this.boundingatom(t),this.cutRadius=this.probeRadius*this.scaleFactor,this.vpBits=new Uint8Array(this.pLength*this.pWidth*this.pHeight),this.vpDistance=new Float64Array(this.pLength*this.pWidth*this.pHeight),this.vpAtomID=new Int32Array(this.pLength*this.pWidth*this.pHeight),this.vpColor=[],this.vpPot=[]},Ke.prototype.boundingatom=function(e){let t,s,i,n,l=[];for(let r in this.vdwRadii){if(!this.vdwRadii.hasOwnProperty(r))continue;let o=this.vdwRadii[r];l[r]=e?(o+this.probeRadius)*this.scaleFactor+.5:o*this.scaleFactor+.5,i=l[r]*l[r],this.widxz[r]=Math.floor(l[r])+1,this.depty[r]=new Int32Array(this.widxz[r]*this.widxz[r]),n=0;for(let e=0;ei?this.depty[r][n]=-1:(s=Math.sqrt(i-t),this.depty[r][n]=Math.floor(s)),n++}},Ke.prototype.fillvoxels=function(e,t){let s,i,n,l;for(s=0,l=this.vpBits.length;sc&&(a=c),C>h&&(C=h),v>p&&(v=p);let _,w=g[o*m+d*u+y],S=g[a*m+d*u+y],A=g[o*m+C*u+y],x=g[o*m+d*u+v],k=g[a*m+C*u+y],O=g[o*m+C*u+v],R=g[a*m+d*u+v],I=g[a*m+C*u+v],T=r.x-o,E=r.y-d,P=r.z-y,M=((w*(1-T)+S*T)*(1-E)+(A*(1-T)+k*T)*E)*(1-P)+((x*(1-T)+R*T)*(1-E)+(O*(1-T)+I*T)*E)*P,D=s*f+i*b+n;this.vpPot[D]=M,M>this.isovalue&&(M=this.isovalue),M<-this.isovalue&&(M=-this.isovalue),M>0?(M/=1*this.isovalue,_=new THREE.Color(1-M,1-M,1)):(M/=-1*this.isovalue,_=new THREE.Color(1,1-M,1-M)),this.vpColor[D]=_}}for(s=0,l=this.vpBits.length;s=this.pLength||g>=this.pWidth||f>=this.pHeight)continue;let h=u*S+g*this.pHeight+f;if(this.vpBits[h]&this.INOUT){let p=t[this.vpAtomID[h]];p.serial!=e.serial&&(l=s+a-Math.floor(.5+this.scaleFactor*(p.x+this.ptranx)),r=i+d-Math.floor(.5+this.scaleFactor*(p.y+this.ptrany)),o=n+c-Math.floor(.5+this.scaleFactor*(p.z+this.ptranz)),a*a+d*d+c*c=this.pLength||p>=this.pWidth||m>=this.pHeight)continue;let u=h*S+p*this.pHeight+m;if(this.vpBits[u]&this.ISDONE){let h=t[this.vpAtomID[u]];h.serial!=e.serial&&(l=s+a-Math.floor(.5+this.scaleFactor*(h.x+this.ptranx)),r=i+d-Math.floor(.5+this.scaleFactor*(h.y+this.ptrany)),o=n+c-Math.floor(.5+this.scaleFactor*(h.z+this.ptranz)),a*a+d*d+c*c-1&&r-1&&a-1&&o=h)||(this.vpBits[n]|=this.ISBOUND))},Ke.prototype.fastoneshell=function(e,t){let s,i,n,l,r,o,a,d,c,h,p,m,u=[];if(0===e.length)return u;let g={ix:-1,iy:-1,iz:-1},f=this.pWidth*this.pHeight;for(a=0,c=e.length;a-1&&g.iy-1&&g.iz-1&&(m=g.ix*f+this.pHeight*g.iy+g.iz,this.vpBits[m]&this.INOUT&&!(this.vpBits[m]&this.ISDONE)?(t.set(g.ix,g.iy,n+this.nb[d][2],p),l=g.ix-p.ix,r=g.iy-p.iy,o=g.iz-p.iz,h=l*l+r*r+o*o,this.vpDistance[m]=h,this.vpBits[m]|=this.ISDONE,this.vpBits[m]|=this.ISBOUND,u.push({ix:g.ix,iy:g.iy,iz:g.iz})):this.vpBits[m]&this.INOUT&&this.vpBits[m]&this.ISDONE&&(l=g.ix-p.ix,r=g.iy-p.iy,o=g.iz-p.iz,h=l*l+r*r+o*o,h-1&&g.iy-1&&g.iz-1&&(m=g.ix*f+this.pHeight*g.iy+g.iz,this.vpBits[m]&this.INOUT&&!(this.vpBits[m]&this.ISDONE)?(t.set(g.ix,g.iy,n+this.nb[d][2],p),l=g.ix-p.ix,r=g.iy-p.iy,o=g.iz-p.iz,h=l*l+r*r+o*o,this.vpDistance[m]=h,this.vpBits[m]|=this.ISDONE,this.vpBits[m]|=this.ISBOUND,u.push({ix:g.ix,iy:g.iy,iz:g.iz})):this.vpBits[m]&this.INOUT&&this.vpBits[m]&this.ISDONE&&(l=g.ix-p.ix,r=g.iy-p.iy,o=g.iz-p.iz,h=l*l+r*r+o*o,h-1&&g.iy-1&&g.iz-1&&(m=g.ix*f+this.pHeight*g.iy+g.iz,this.vpBits[m]&this.INOUT&&!(this.vpBits[m]&this.ISDONE)?(t.set(g.ix,g.iy,n+this.nb[d][2],p),l=g.ix-p.ix,r=g.iy-p.iy,o=g.iz-p.iz,h=l*l+r*r+o*o,this.vpDistance[m]=h,this.vpBits[m]|=this.ISDONE,this.vpBits[m]|=this.ISBOUND,u.push({ix:g.ix,iy:g.iy,iz:g.iz})):this.vpBits[m]&this.INOUT&&this.vpBits[m]&this.ISDONE&&(l=g.ix-p.ix,r=g.iy-p.iy,o=g.iz-p.iz,h=l*l+r*r+o*o,hm&&(m=this.pmaxy-this.pminy),this.pmaxz-this.pminz>m&&(m=this.pmaxz-this.pminz),this.scaleFactor=1,this.pLength=Math.floor(.5+this.scaleFactor*(this.pmaxx-this.pminx))+1,this.pWidth=Math.floor(.5+this.scaleFactor*(this.pmaxy-this.pminy))+1,this.pHeight=Math.floor(.5+this.scaleFactor*(this.pmaxz-this.pminz))+1,this.cutRadius=this.probeRadius*this.scaleFactor,this.vpBits=new Uint8Array(this.pLength*this.pWidth*this.pHeight),this.vpAtomID=new Uint8Array(this.pLength*this.pWidth*this.pHeight)},Je.prototype.transformMemPro=function(e,t,s,i){let n=e.clone();n.sub(s);let l=n.x*t[0]+n.y*t[1]+n.z*t[2]+i.x,r=n.x*t[3]+n.y*t[4]+n.z*t[5]+i.y,o=n.x*t[6]+n.y*t[7]+n.z*t[8]+i.z;return n.x=l,n.y=r,n.z=o,n},Je.prototype.fillvoxels=function(e,t){let s,i,n,l,r,o;for(s=0,l=this.vpBits.length;sthis.pLength&&(o=this.pLength),p>this.pWidth&&(p=this.pWidth),b>this.pHeight&&(b=this.pHeight);let C,y=l[r*a+h*d+f],v=l[o*a+h*d+f],_=l[r*a+p*d+f],w=l[r*a+h*d+b],S=l[o*a+p*d+f],A=l[r*a+p*d+b],x=l[o*a+h*d+b],k=l[o*a+p*d+b],O=n.x-r,R=n.y-h,I=n.z-f,T=((y*(1-O)+v*O)*(1-R)+(_*(1-O)+S*O)*R)*(1-I)+((w*(1-O)+x*O)*(1-R)+(A*(1-O)+k*O)*R)*I;T>this.isovalue&&(T=this.isovalue),T<-this.isovalue&&(T=-this.isovalue),T>0?(T/=1*this.isovalue,C=new THREE.Color(1-T,1-T,1)):(T/=-1*this.isovalue,C=new THREE.Color(1,1-T,1-T)),this.icn3d.atoms[t[s]].color=C,this.icn3d.atomPrevColors[t[s]]=C}}else{for(let p in t){let f,b=e[t[p]];if("DUM"!==b.resn){if(void 0!==this.rmsd_supr&&void 0!==this.rmsd_supr.rot){f=this.transformMemPro(b.coord,g,u,m).applyMatrix4(c)}else f=b.coord.clone().applyMatrix4(c);for(s=Math.floor(f.x)-this.maxdist,l=Math.ceil(f.x)+this.maxdist;s<=l;++s)if(!(s<0||s>this.header.xExtent*this.scaleFactor-1))for(i=Math.floor(f.y)-this.maxdist,r=Math.ceil(f.y)+this.maxdist;i<=r;++i)if(!(i<0||i>this.header.yExtent*this.scaleFactor-1))for(n=Math.floor(f.z)-this.maxdist,o=Math.ceil(f.z)+this.maxdist;n<=o;++n){if(n<0||n>this.header.zExtent*this.scaleFactor-1)continue;let e=s*a+i*d+n;h.push(e)}}}for(s=0,l=h.length;s=this.isovalue?1:0:"fofc"==this.type?(this.vpBits[e]=this.dataArray[e]>=this.isovalue||this.dataArray[e]<=-this.isovalue?1:0,this.vpAtomID[e]=this.dataArray[e]>=0?1:0):"em"==this.type&&(this.vpBits[e]=this.dataArray[e]>=this.isovalue?1:0)}}}else for(s=0;s=this.isovalue||this.dataArray[e]<=-this.isovalue?1:0,this.vpAtomID[t]=this.dataArray[e]>=0?1:0)}for(s=0,l=this.vpBits.length;s-1&&r-1&&a-1&&o1?"Structure ":"",a=Object.keys(i).length>1?"Chain ":"";n+=""+o+a+"Residue Number SASA (Å2 ) Percent Out In/Out ";for(let e in l.resid2area){let d=e.lastIndexOf("_"),c=e.substr(d+1),h=r.utilsCls.getIdArray(e.substr(0,d));o=Object.keys(s).length>1?""+h[0]+" ":"",a=Object.keys(i).length>1?""+h[1]+" ":"";let p="",m="";l.resid2area[e]=(l.resid2area[e]/t).toFixed(2),r.parasCls.residueArea.hasOwnProperty(c)&&(m=parseInt(l.resid2area[e]/r.parasCls.residueArea[c]*100),m>100&&(m=100),m>=50&&(p="out"),m<20&&(p="in")),n+=''+o+a+""+c+' '+h[2]+' '+l.resid2area[e]+' '+m+"% "+p+" "}return n+="
",void(l.areahtml=n)}let p,m,u,g=c.vertices,f=c.faces,b=r.parasCls.thr("#00FFFF"),C=r.parasCls.thr("#00FF00"),y=r.parasCls.thr("#ff0000"),v=r.parasCls.thr("#00FFFF"),_=r.parasCls.thr("#0000FF"),w=r.parasCls.thr("#FF0000");11!=t&&12!=t&&13!=t&&14!=t||void 0===l.rmsd_supr||void 0===l.rmsd_supr.rot||(p=l.rmsd_supr.rot,m=l.rmsd_supr.trans1,u=l.rmsd_supr.trans2);let S=(11==t||12==t||13==t||14==t&&"delphi"!=l.loadPhiFrom)&&void 0!==l.rmsd_supr&&void 0!==l.rmsd_supr.rot;n=new THREE.BufferGeometry;let A,x=[],k=[],O=[],R=0;for(let e=0,s=g.length;e0?-parseInt(C.z):parseInt(C.z),y.onBeforeRender=function(e,t,s,i,n,o){let a,d=new THREE.Vector3(0,0,0),c=i.getAttribute("position").array;for(let e=0,t=c.length;e0?-parseInt(a.z):parseInt(a.z)},l.mdl.add(y),11==t||12==t?l.prevMaps.push(y):13==t?l.prevEmmaps.push(y):14==t?l.prevPhimaps.push(y):l.prevSurfaces.push(y)}}else{let e=new THREE.Mesh(n,new THREE.MeshPhongMaterial({specular:l.frac,shininess:20,emissive:l.emissive,vertexColors:!0,wireframe:s,opacity:i,transparent:!0,depthWrite:10==parseInt(10*i),side:THREE.DoubleSide}));e.renderOrder=-2,l.mdl.add(e),11==t||12==t?l.prevMaps.push(e):13==t?l.prevEmmaps.push(e):14==t?l.prevPhimaps.push(e):l.prevSurfaces.push(e)}c=null,g=null,f=null,n=null}transformMemPro(e,t,s,i,n){this.icn3d.icn3dui;let l=e.clone();l.sub(s),n&&console.log("sub coord: "+JSON.stringify(l));let r=l.x*t[0]+l.y*t[1]+l.z*t[2]+i.x,o=l.x*t[3]+l.y*t[4]+l.z*t[5]+i.y,a=l.x*t[6]+l.y*t[7]+l.z*t[8]+i.z;return l.x=r,l.y=o,l.z=a,n&&console.log("out coord: "+JSON.stringify(l)),l}SetupSurface(e){let t=this.icn3d;t.icn3dui;let s=e.threshbox,i=new Ke(t,s);i.initparm(e.extent,1!==e.type,e.bCalcArea,e.atomsToShow,e.header,e.data,e.matrix,e.isovalue,e.loadPhiFrom),i.fillvoxels(e.allatoms,e.extendedAtoms),i.buildboundary(),2===e.type&&(i.fastdistancemap(),i.boundingatom(!1),i.fillvoxelswaals(e.allatoms,e.extendedAtoms));let n=i.marchingcube();i.vpBits=null,i.vpDistance=null,i.vpAtomID=null;let l=i.getFacesAndVertices(e.atomsToShow);return l.area=n.area,l.serial2area=n.serial2area,l.scaleFactor=n.scaleFactor,i.faces=null,i.verts=null,l}SetupMap(e){let t=this.icn3d;t.icn3dui;let s,i=new Je(t);return i.initparm(e.header,e.data,e.matrix,e.isovalue,e.center,e.maxdist,e.pmin,e.pmax,e.water,e.type,e.rmsd_supr,e.loadPhiFrom,e.icn3d),i.fillvoxels(e.allatoms,e.extendedAtoms),e.header.bSurface||i.buildboundary(),e.header.bSurface||i.marchingcube(),i.vpBits=null,i.vpAtomID=null,e.header.bSurface||(s=i.getFacesAndVertices(e.allatoms,e.atomsToShow)),i.faces=null,i.verts=null,s}}class Ze{constructor(e){this.icn3d=e}applyCenterOptions(e){let t,s=this.icn3d;switch(s.icn3dui,void 0===e&&(e=s.opts),e.rotationcenter.toLowerCase()){case"molecule center":void 0!==s.center&&this.setRotationCenter(s.center);break;case"pick center":void 0!==s.pAtom&&this.setRotationCenter(s.pAtom.coord);break;case"display center":t=this.centerAtoms(s.dAtoms).center,this.setRotationCenter(t);break;case"highlight center":t=this.centerAtoms(s.hAtoms).center,this.setRotationCenter(t)}}setRotationCenter(e){this.icn3d.icn3dui,this.setCenter(e)}setCenter(e){let t=this.icn3d;t.icn3dui,t.mdl.position.set(0,0,0),t.mdlImpostor.position.set(0,0,0),t.mdl_ghost.position.set(0,0,0),t.mdl.position.sub(e),t.mdlImpostor.position.sub(e),t.mdl_ghost.position.sub(e)}centerSelection(e,t){let s=this.icn3d,i=s.icn3dui;if(s.opts.rotationcenter="highlight center",void 0===e&&(e=i.hashUtilsCls.hash2Atoms(s.hAtoms,s.atoms)),t||(s._zoomFactor=1,s.mouseChange=new THREE.Vector2(0,0),s.quaternion=new THREE.Quaternion(0,0,0,1)),Object.keys(e).length>1){let t=this.centerAtoms(e);s.center=t.center,this.setCenter(s.center),s.cameraCls.setCamera()}}centerAtoms(e){let t=this.icn3d;t.icn3dui;let s=new THREE.Vector3(9999,9999,9999),i=new THREE.Vector3(-9999,-9999,-9999),n=new THREE.Vector3;for(let l in e){let e=t.atoms[l].coord;n.add(e),s.min(e),i.max(e)}let l=t.ParserUtilsCls.getGeoCenter(s,i);return{center:l,maxD:t.ParserUtilsCls.getStructureSize(e,s,i,l),pmin:s,pmax:i}}setWidthHeight(e,t){let s=this.icn3d;s.icn3dui,void 0===s.scaleFactor&&(s.scaleFactor=1),s.renderer.setSize(e*s.scaleFactor,t*s.scaleFactor),s.renderer.domElement.style.width=e*s.scaleFactor+"px",s.renderer.domElement.style.height=t*s.scaleFactor+"px",s.renderer.domElement.width=e*s.scaleFactor,s.renderer.domElement.height=t*s.scaleFactor,s.container.whratio=e/t}}class et{constructor(e){this.icn3d=e}applyClbondsOptions(e){let t=this.icn3d,s=t.icn3dui;if(void 0===e&&(e=t.opts),t.bCalcCrossLink||(t.clbondpnts={},t.clbondResid2serial={},this.applyClbondsOptions_base("chemical"),this.applyClbondsOptions_base("all"),t.bCalcCrossLink=!0),"yes"===e.clbonds.toLowerCase()&&"nothing"!==e.chemicals){let e="#006400";if(s.parasCls.thr(25600),t.lines.clbond=[],t.residuesHashClbonds={},t.structures){let i=Object.keys(t.structures);for(let n=0,l=i.length;n1&&"sphere"!==a[Object.keys(a)[0]].style&&"dot"!==a[Object.keys(a)[0]].style){if(void 0===i.bCid||!i.bCid)for(let e in a){let t=a[e],n=1;i.boxCls.createBox(t,void 0,void 0,n,void 0,s)}}else for(let e in o){let l=i.firstAtomObjCls.getFirstCalphaAtomObj(i.residues[e]),r=l,o=r.structure+"_"+r.chain+"_"+(parseInt(r.resi)-1).toString(),a=r.structure+"_"+r.chain+"_"+(parseInt(r.resi)+1).toString();if("cylinder and plate"===r.style&&"helix"===r.ss)for(let t in i.residues[e]){let e=i.atoms[t],n=1;i.boxCls.createBox(e,void 0,void 0,n,void 0,s)}else if("ribbon"===r.style&&"coil"===r.ss||"strand"===r.style&&"coil"===r.ss||"o3 trace"===r.style||"schematic"===r.style||"c alpha trace"===r.style||"b factor tube"===r.style||"cylinder and plate"===r.style&&"helix"!==r.ss){if(void 0!==l&&void 0!==l.style2&&"nothing"!==l.style2)continue;let e=!1;if(!isNaN(r.resi)&&!e&&i.residues.hasOwnProperty(a)){let s=Object.keys(i.residues[a])[0],l=n.hashUtilsCls.hash2Atoms(i.residues[a],i.atoms)[s];if(r.style===l.style&&!l.ssbegin||l.ssbegin){let s=i.residues[a];if(t=n.hashUtilsCls.unionHash(t,s),e=!0,l.ssbegin)for(let e in s)i.atoms[e].notshow=!0}}if(!isNaN(r.resi)&&!e&&i.residues.hasOwnProperty(o)){let s=Object.keys(i.residues[o])[0],l=n.hashUtilsCls.hash2Atoms(i.residues[o],i.atoms)[s];r.style===l.style&&(t=n.hashUtilsCls.unionHash(t,i.residues[o]),e=!0)}}else if("ribbon"===r.style&&"coil"!==r.ss&&r.ssend||"strand"===r.style&&"coil"!==r.ss&&r.ssend){if(void 0!==l&&void 0!==l.style2&&"nothing"!==l.style2)continue;let e=!1;if(!isNaN(r.resi)&&!e&&i.residues.hasOwnProperty(a)){let s=Object.keys(i.residues[a])[0];n.hashUtilsCls.hash2Atoms(i.residues[a],i.atoms)[s],t=n.hashUtilsCls.unionHash(t,i.residues[a]),e=!0}}}a={}}if(i.bInitial){if(""!=n.htmlCls.setHtmlCls.getCookie("membrane")){let e=parseInt(n.htmlCls.setHtmlCls.getCookie("membrane"));i.bMembrane!=e&&n.htmlCls.clickMenuCls.setLogCmd("set membrane "+e,!0),i.bMembrane=isNaN(e)?0:parseInt(e)}i.bMembrane?i.selectionCls.toggleMembrane(!0):i.selectionCls.toggleMembrane(!1)}i.setStyleCls.setStyle2Atoms(t);let d=.5*i.cylinderRadius;void 0!==i.labels&&delete i.labels.schematic;for(let e in i.style2atoms){let t=i.style2atoms[e],l=n.hashUtilsCls.intHash(t,i.nucleotides),r=n.utilsCls.isCalphaPhosOnly(n.hashUtilsCls.hash2Atoms(l,i.atoms));if("ribbon"===e)i.strandCls.createStrand(n.hashUtilsCls.hash2Atoms(t,i.atoms),2,void 0,!0,void 0,void 0,!1,i.ribbonthickness,s);else if("strand"===e)i.strandCls.createStrand(n.hashUtilsCls.hash2Atoms(t,i.atoms),null,null,null,null,null,!1,void 0,s);else if("cylinder and plate"===e)i.cylinderCls.createCylinderHelix(n.hashUtilsCls.hash2Atoms(t,i.atoms),i.cylinderHelixRadius,s);else if("nucleotide cartoon"===e)r?i.cylinderCls.createCylinderCurve(n.hashUtilsCls.hash2Atoms(t,i.atoms),["P"],i.traceRadius,!1,s):(i.cartoonNuclCls.drawCartoonNucleicAcid(n.hashUtilsCls.hash2Atoms(t,i.atoms),null,i.ribbonthickness,s),2!==s&&i.cartoonNuclCls.drawNucleicAcidStick(n.hashUtilsCls.hash2Atoms(t,i.atoms),s));else if("o3 trace"===e)r?i.cylinderCls.createCylinderCurve(n.hashUtilsCls.hash2Atoms(t,i.atoms),["P"],i.traceRadius,!1,s):i.cylinderCls.createCylinderCurve(n.hashUtilsCls.hash2Atoms(t,i.atoms),["O3'","O3*"],i.traceRadius,!1,s);else if("schematic"===e){let e=i.firstAtomObjCls.getFirstAtomObj(t);if(i.chemicals.hasOwnProperty(e.serial)){i.residueLabelsCls.addNonCarbonAtomLabels(n.hashUtilsCls.hash2Atoms(t,i.atoms));let e=!0;i.stickCls.createStickRepresentation(n.hashUtilsCls.hash2Atoms(t,i.atoms),d,d,void 0,s,e)}else i.residueLabelsCls.addResidueLabels(n.hashUtilsCls.hash2Atoms(t,i.atoms),!0),r?i.cylinderCls.createCylinderCurve(n.hashUtilsCls.hash2Atoms(t,i.atoms),["P"],i.traceRadius,!1,s):i.cylinderCls.createCylinderCurve(n.hashUtilsCls.hash2Atoms(t,i.atoms),["O3'","O3*"],i.traceRadius,!1,s),i.cylinderCls.createCylinderCurve(n.hashUtilsCls.hash2Atoms(t,i.atoms),["CA"],i.traceRadius,!1,s)}else"c alpha trace"===e?i.cylinderCls.createCylinderCurve(n.hashUtilsCls.hash2Atoms(t,i.atoms),["CA"],i.traceRadius,!1,s):"b factor tube"===e?i.tubeCls.createTube(n.hashUtilsCls.hash2Atoms(t,i.atoms),"CA",null,s,!1,!0):"custom tube"===e?i.tubeCls.createTube(n.hashUtilsCls.hash2Atoms(t,i.atoms),"CA",null,s,!0,!0):"lines"===e||"lines2"===e?(1===s?i.stickCls.createStickRepresentation(n.hashUtilsCls.hash2Atoms(t,i.atoms),i.hlLineRadius,i.hlLineRadius,void 0,s):i.lineCls.createLineRepresentation(n.hashUtilsCls.hash2Atoms(t,i.atoms),s),i.lineCls.createConnCalphSidechain(n.hashUtilsCls.hash2Atoms(t,i.atoms),e)):"stick"===e||"stick2"===e?(i.stickCls.createStickRepresentation(n.hashUtilsCls.hash2Atoms(t,i.atoms),i.cylinderRadius,i.cylinderRadius,void 0,s,void 0),i.lineCls.createConnCalphSidechain(n.hashUtilsCls.hash2Atoms(t,i.atoms),e)):"backbone"===e?(t=this.selectMainChainSubset(t),i.stickCls.createStickRepresentation(n.hashUtilsCls.hash2Atoms(t,i.atoms),i.cylinderRadius,i.cylinderRadius,void 0,s,void 0)):"ball and stick"===e||"ball and stick2"===e?(i.stickCls.createStickRepresentation(n.hashUtilsCls.hash2Atoms(t,i.atoms),i.cylinderRadius,.5*i.cylinderRadius,i.dotSphereScale,s,void 0),i.lineCls.createConnCalphSidechain(n.hashUtilsCls.hash2Atoms(t,i.atoms),e)):"sphere"===e||"sphere2"===e?i.sphereCls.createSphereRepresentation(n.hashUtilsCls.hash2Atoms(t,i.atoms),i.sphereRadius,void 0,void 0,s):"dot"===e&&i.sphereCls.createSphereRepresentation(n.hashUtilsCls.hash2Atoms(t,i.atoms),i.sphereRadius,!1,i.dotSphereScale,s)}if(i.cnt>i.maxmaxatomcnt&&i.init_base(),void 0!==i.labels&&Object.keys(i.labels).length>0){i.labelCls.hideLabels();for(let e in i.labels)"schematic"!=e&&this.changeLabelColor(i.labels[e]);i.labelCls.createLabelRepresentation(i.labels)}}changeLabelColor(e){let t=this.icn3d;if(t.icn3dui,e)for(let s=0,i=e.length;s0){this.updateStabilizer();let e="#FFFFFF",s=t.stabilizerpnts;t.lines.stabilizer=[];for(let i=0,n=Math.floor(s.length/2);i0)for(let e=0,s=t.distPnts.length;e0&&t.applySymdCls.applySymd(),void 0!==t.prevOtherMesh)for(let e=0,s=t.prevOtherMesh.length;e0&&(e=s.hashUtilsCls.hash2Atoms(t.chemicals,t.atoms));let i=4;if(void 0!==e){let n=t.contactCls.getAtomsWithinAtom(t.atoms,e,i),l=3.5;t.opts.hbonds="yes",Object.keys(n).length>0&&t.hBondCls.calculateChemicalHbonds(e,n,parseFloat(l)),t.bSetFog||t.transformCls.zoominSelection(s.hashUtilsCls.unionHash(e,n))}}else"hide"===e.chemicalbinding&&(t.hBondCls.hideHbonds(),t.showInterCls.hideExtraBonds(),t.bSetFog||t.transformCls.zoominSelection(t.atoms))}updateStabilizer(){let e=this.icn3d;if(e.icn3dui,e.stabilizerpnts=[],void 0!==e.pairArray)for(let t=0,s=e.pairArray.length;t=0;i--){let r=t.ssbondpnts[e][2*i],o=t.ssbondpnts[e][2*i+1],a={};a.color=n,a.dashed=!1;let d=[],c=[],h=[],p=[],m=!1,u=!1;for(let e in t.residues[r])"SG"===t.atoms[e].name&&(h.push(t.atoms[e].coord),d.push(t.atoms[e].serial),m=!0);if(!m)for(let e in t.residues[r])if("CA"===t.atoms[e].name){h.push(t.atoms[e].coord),d.push(t.atoms[e].serial),m=!0,u=!0;break}m=!1;for(let e in t.residues[o])"SG"===t.atoms[e].name&&(p.push(t.atoms[e].coord),c.push(t.atoms[e].serial),m=!0);if(!m)for(let e in t.residues[o])if("CA"===t.atoms[e].name){p.push(t.atoms[e].coord),c.push(t.atoms[e].serial),m=!0,u=!0;break}let g=u?7:3,f=!1;for(let e=0,t=h.length;e1&&(l=!0)}if(t)if(l){let t=Object.keys(r)[0];e=i.chains[t]}else{0==Object.keys(i.hAtoms).length&&(i.hAtoms=n.hashUtilsCls.cloneHash(i.dAtoms));let t,s=parseInt(Object.keys(i.hAtoms).length/u),l=0;for(let n in i.hAtoms)if(e[n]=1,t=n,++l,l>s)break;let r=i.atoms[t].structure+"_"+i.atoms[t].chain+"_"+i.atoms[t].resi;e=n.hashUtilsCls.unionHash(e,i.residues[r])}else{let t=Object.keys(i.structures)[0]+"_"+g;if(i.chains.hasOwnProperty(t)||(t=Object.keys(i.structures)[0]+"_"+g.toLowerCase()),!i.chains.hasOwnProperty(t)){t=Object.keys(i.chains)[0];for(let e in i.chains){let s=Object.keys(i.chains[e])[0];if(i.proteins.hasOwnProperty(s)){t=e;break}}}e=i.chains[t]}let a=s.clone().add(h).multiplyScalar(.5),c=new THREE.Vector3,p=0,f=h.clone().sub(s).normalize(),b=new THREE.Vector3(0,0,1),C=new THREE.Quaternion;C.setFromUnitVectors(f,b);let y=-9999;for(let t in e){let e=i.atoms[t].coord.clone();c.add(e),e.sub(a).applyQuaternion(C);let s=e.x*e.x+e.y*e.y;s>y&&(y=s),++p}let v=i.ParserUtilsCls.getMassCenter(c,p),_=new THREE.Line3(s,h),w=new THREE.Vector3;_.closestPointToPoint(v,!0,w);let S,A,x,k,O=Math.sqrt(y),R=v.clone().sub(w).normalize().multiplyScalar(O),I=a.clone().add(s.clone().sub(a).multiplyScalar(.83)).add(R),T=a.clone().add(h.clone().sub(a).multiplyScalar(.83)).add(R),E=2*Math.PI/o;for(let e=0;et&&(i.sphereCls.createSphereBase(r,colorPolygon,d,1,0),i.cylinderCls.createCylinder(e,r,d,colorPolygon,0),i.cylinderCls.createCylinder(s,r,d,colorPolygon,0),void 0!==n&&i.cylinderCls.createCylinder(c[n],r,d,colorPolygon,0),n=l)}}else if("O"==r)for(let e=0,t=c.length;e0&&(e.mdl.remove(e.prevSurfaces[e.prevSurfaces.length-1]),e.prevSurfaces.slice(e.prevSurfaces.length-1,1))}removeMaps(){let e=this.icn3d;e.icn3dui;for(let t=0,s=e.prevMaps.length;t0&&(e.mdl.remove(e.prevMaps[e.prevMaps.length-1]),e.prevMaps.slice(e.prevMaps.length-1,1))}removeLastEmmap(){let e=this.icn3d;e.icn3dui,e.prevEmmaps.length>0&&(e.mdl.remove(e.prevEmmaps[e.prevEmmaps.length-1]),e.prevEmmaps.slice(e.prevEmmaps.length-1,1))}removeLastPhimap(){let e=this.icn3d;e.icn3dui,e.prevPhimaps.length>0&&(e.mdl.remove(e.prevPhimaps[e.prevPhimaps.length-1]),e.prevPhimaps.slice(e.prevPhimaps.length-1,1))}}class ot{constructor(e){this.icn3d=e}addResidueLabels(e,t,s,i,n){let l=this.icn3d,r=l.icn3dui;if(r.bNode)return;let o=r.hashUtilsCls.intHash(l.hAtoms,e);t?void 0===l.labels.schematic&&(l.labels.schematic=[]):void 0===l.labels.residue&&(l.labels.residue=[]);let a="";for(let e in o){let s=l.atoms[e],o={},d=s.structure+"_"+s.chain+"_"+s.resi;if(!s.het&&("CA"===s.name||"O3'"===s.name||"O3*"===s.name)||l.water.hasOwnProperty(s.serial)||l.ions.hasOwnProperty(s.serial)||l.chemicals.hasOwnProperty(s.serial)&&d!==a){if(o.position=s.coord,o.bSchematic=0,t&&(o.bSchematic=1),o.text=r.utilsCls.residueName2Abbr(s.resn),i)o.text+=s.resi;else if(n){let e=s.structure+"_"+s.chain+"_"+s.resi,t="";l.resid2refnum[e]&&(t=" "==l.resid2refnum[e].substr(0,1)?"":l.resid2refnum[e]),o.text=t}o.size=18,o.factor=.3;let e=s.color.getHexString().toUpperCase();o.color=i?"black"!=l.opts.background?l.colorWhitebkgd:l.colorBlackbkgd:n?"#00FFFF":"CCCCCC"===e||"C8C8C8"===e?"#888888":"#"+e,o.background="#FFFFFF",t?l.labels.schematic.push(o):l.labels.residue.push(o)}a=d}l.hlObjectsCls.removeHlObjects()}addNonCarbonAtomLabels(e){let t=this.icn3d,s=t.icn3dui;if(s.bNode)return;let i=s.hashUtilsCls.intHash(t.hAtoms,e);void 0===t.labels.schematic&&(t.labels.schematic=[]);for(let e in i){let s=t.atoms[e];if(!t.residues.hasOwnProperty(s.structure+"_"+s.chain+"_"+s.resi))continue;if("C"===s.elem)continue;let i={};i.position=s.coord,i.bSchematic=1,i.text=s.elem,i.size=18,i.color="black"!=t.opts.background?t.colorWhitebkgd:s.color.getHexString(),i.background="#FFFFFF",t.labels.schematic.push(i)}t.hlObjectsCls.removeHlObjects()}addAtomLabels(e,t){let s=this.icn3d,i=s.icn3dui;if(i.bNode)return;let n=i.hashUtilsCls.intHash(s.hAtoms,e);n=i.hashUtilsCls.intHash(s.dAtoms,n),void 0===s.labels.residue&&(s.labels.residue=[]);for(let e in n){let i=s.atoms[e],n={};n.position=i.coord,n.bSchematic=0,n.text=t?i.elem:i.name.padEnd(2," "),n.size=18,t&&(n.bSchematic=!0);let l=i.color.getHexString().toUpperCase();n.color="black"!=s.opts.background?s.colorWhitebkgd:s.colorBlackbkgd,t&&(n.color="CCCCCC"===l||"C8C8C8"===l?"#888888":"#"+l),n.background="#FFFFFF",s.labels.residue.push(n)}s.hlObjectsCls.removeHlObjects()}}class at{constructor(e){this.icn3d=e}onBeforeRender(e,t,s,i,n,l){let r=n.uniforms,o=[];if(r.objectId&&(r.objectId.value=SupportsReadPixelsFloat?this.id:this.id/255,o.push("objectId")),(r.modelViewMatrixInverse||r.modelViewMatrixInverseTranspose||r.modelViewProjectionMatrix||r.modelViewProjectionMatrixInverse)&&this.modelViewMatrix.multiplyMatrices(s.matrixWorldInverse,this.matrixWorld),r.modelViewMatrixInverse&&(r.modelViewMatrixInverse.value.copy(this.modelViewMatrix).invert(),o.push("modelViewMatrixInverse")),r.modelViewMatrixInverseTranspose&&(r.modelViewMatrixInverse?r.modelViewMatrixInverseTranspose.value.copy(r.modelViewMatrixInverse.value).transpose():r.modelViewMatrixInverseTranspose.value.copy(this.modelViewMatrix).invert().transpose(),o.push("modelViewMatrixInverseTranspose")),r.modelViewProjectionMatrix&&(s.updateProjectionMatrix(),r.modelViewProjectionMatrix.value.multiplyMatrices(s.projectionMatrix,this.modelViewMatrix),o.push("modelViewProjectionMatrix")),r.modelViewProjectionMatrixInverse){let e=new THREE.Matrix4;r.modelViewProjectionMatrix?(e.copy(r.modelViewProjectionMatrix.value),r.modelViewProjectionMatrixInverse.value.copy(e).invert()):(s.updateProjectionMatrix(),e.multiplyMatrices(s.projectionMatrix,this.modelViewMatrix),r.modelViewProjectionMatrixInverse.value.copy(e).invert()),o.push("modelViewProjectionMatrixInverse")}if(r.projectionMatrix&&(s.updateProjectionMatrix(),r.projectionMatrix.value.copy(s.projectionMatrix),o.push("projectionMatrix")),r.projectionMatrixInverse&&(s.updateProjectionMatrix(),r.projectionMatrixInverse.value.copy(s.projectionMatrix).invert(),o.push("projectionMatrixInverse")),o.length){let t=e.properties.get(n);if(t.program){let s=e.getContext(),i=t.program;s.useProgram(i.program);let n=i.getUniforms();o.forEach((function(e){n.setValue(s,e,r[e].value)}))}}}setParametersForShader(e){let t,s=this.icn3d,i=s.icn3dui.parasCls.backgroundColors[s.opts.background.toLowerCase()],n=2.5*s.maxD,l=4*s.maxD,r=void 0!==s.biomtMatrices&&s.biomtMatrices.length*s.cnt>s.maxatomcnt;"yes"===s.opts.slab?r?t=.1:void 0!==s.camMaxDFactorFog?(t=s.maxD*s.camMaxDFactorFog-10,n=2.5*s.maxD-t<0?0:2.5*s.maxD-t,l=4*s.maxD-t):t=s.maxD*s.camMaxDFactor:t=.1;let o=void 0!==e?e:1,a=s.shininess/100*.5;s.uniforms=THREE.UniformsUtils.merge([THREE.UniformsLib.common,{modelViewMatrix:{value:new THREE.Matrix4},modelViewMatrixInverse:{value:new THREE.Matrix4},modelViewMatrixInverseTranspose:{value:new THREE.Matrix4},modelViewProjectionMatrix:{value:new THREE.Matrix4},modelViewProjectionMatrixInverse:{value:new THREE.Matrix4},projectionMatrix:{value:new THREE.Matrix4},projectionMatrixInverse:{value:new THREE.Matrix4},diffuse:{type:"v3",value:[1,1,1]},emissive:{type:"v3",value:[.06,.06,.06]},roughness:{type:"f",value:.5},metalness:{type:"f",value:a},opacity:{type:"f",value:o},nearClip:{type:"f",value:t},ortho:{type:"f",value:0},shrink:{type:"f",value:.13},fogColor:{type:"v3",value:[i.r,i.g,i.b]},fogNear:{type:"f",value:n},fogFar:{type:"f",value:l},fogDensity:{type:"f",value:2}},THREE.UniformsLib.ambient,THREE.UniformsLib.lights]),s.defines={USE_COLOR:1,NEAR_CLIP:1,CAP:1},"yes"!==s.opts.fog||r||(s.defines.USE_FOG=1,"orthographic"===s.opts.camera&&(s.defines.FOG_EXP2=1)),s.bExtFragDepth&&(s.defines.USE_LOGDEPTHBUF_EXT=1)}drawImpostorShader(){this.icn3d.icn3dui.bNode||(this.setParametersForShader(),this.createImpostorShaderSphere("SphereImpostor"),this.createImpostorShaderCylinder("CylinderImpostor"))}getShader(e){this.icn3d.icn3dui;let t=$NGL_shaderTextHash[e];return t=t.replace(/#include\s+(\S+)/gim,(function(e,t){let s;return THREE.ShaderChunk.hasOwnProperty(t)&&(s=THREE.ShaderChunk[t]),s||""})),t}createImpostorShaderBase(e,t,s,i,n,l,r,o,a){let d=this.icn3d;d.icn3dui;let c=new THREE.ShaderMaterial({defines:d.defines,uniforms:d.uniforms,vertexShader:this.getShader(e+".vert"),fragmentShader:this.getShader(e+".frag"),depthTest:!0,depthWrite:!0,lights:!0});c.extensions.fragDepth=!0,"CylinderImpostor"==e?d.CylinderImpostorMaterial=c:"SphereImpostor"==e&&(d.SphereImpostorMaterial=c);let h,p,m=l*r,u=l*o,g=new(m>65535?Uint32Array:Uint16Array)(u);for(let e=0;e=0;t--){let s=a.children[t];s.onBeforeRender=e.impostorCls.onBeforeRender,s.frustumCulled=!1}l.add(a)}void 0!==e.mdl_ghost&&(a=e.mdl_ghost.clone(),this.applyMat(a,d),r.add(a));let c=e.center.clone();this.applyMat(c,d,!0),s.add(c),++t}e.mdl.add(n),e.mdlImpostor.add(l),e.mdl_ghost.add(r),void 0!==e.bSetInstancing&&e.bSetInstancing?(e.maxD=e.maxDAssembly,e.center=e.centerAssembly.clone(),e.applyCenterCls.setCenter(e.center),e.cameraCls.setCamera()):(e.maxD*=Math.sqrt(t),e.center=e.ParserUtilsCls.getMassCenter(s,t),e.maxDAssembly=e.maxD,e.centerAssembly=e.center.clone(),e.applyCenterCls.setCenter(e.center),e.cameraCls.setCamera()),e.bSetInstancing=!0}createInstancedGeometry(e){let t=this.icn3d,s=t.icn3dui,i=e.geometry,n=new THREE.InstancedBufferGeometry,l=[],r=[],o=[],a=[],d=[],c=[],h=[],p=[];if(t.bImpo&&"Cylinder"==e.type){t.instancedMaterial=this.getInstancedMaterial("CylinderInstancing");let e=s.hashUtilsCls.hashvalue2array(i.attributes.position1.array),r=s.hashUtilsCls.hashvalue2array(i.attributes.color.array),m=s.hashUtilsCls.hashvalue2array(i.attributes.position2.array),u=s.hashUtilsCls.hashvalue2array(i.attributes.color2.array),g=s.hashUtilsCls.hashvalue2array(i.index.array),f=s.hashUtilsCls.hashvalue2array(i.attributes.radius.array),b=s.hashUtilsCls.hashvalue2array(i.attributes.mapping.array);l=l.concat(e),o=o.concat(r),h=h.concat(m),p=p.concat(u),a=a.concat(g),d=d.concat(f),c=c.concat(b),n.setAttribute("position1",new THREE.BufferAttribute(new Float32Array(l),3)),n.setAttribute("color",new THREE.BufferAttribute(new Float32Array(o),3)),n.setAttribute("position2",new THREE.BufferAttribute(new Float32Array(h),3)),n.setAttribute("color2",new THREE.BufferAttribute(new Float32Array(p),3)),n.setAttribute("radius",new THREE.BufferAttribute(new Float32Array(d),1)),n.setAttribute("mapping",new THREE.BufferAttribute(new Float32Array(c),3)),n.setIndex(new THREE.BufferAttribute(new Uint32Array(a),1)),e=null,r=null,m=null,u=null,g=null,f=null,b=null}else if(t.bImpo&&"Sphere"==e.type){t.instancedMaterial=this.getInstancedMaterial("SphereInstancing");let e=s.hashUtilsCls.hashvalue2array(i.attributes.position.array),r=s.hashUtilsCls.hashvalue2array(i.attributes.color.array),h=s.hashUtilsCls.hashvalue2array(i.index.array),p=s.hashUtilsCls.hashvalue2array(i.attributes.radius.array),m=s.hashUtilsCls.hashvalue2array(i.attributes.mapping.array);l=l.concat(e),o=o.concat(r),a=a.concat(h),d=d.concat(p),c=c.concat(m),n.setAttribute("position",new THREE.BufferAttribute(new Float32Array(l),3)),n.setAttribute("color",new THREE.BufferAttribute(new Float32Array(o),3)),n.setAttribute("radius",new THREE.BufferAttribute(new Float32Array(d),1)),n.setAttribute("mapping",new THREE.BufferAttribute(new Float32Array(c),2)),n.setIndex(new THREE.BufferAttribute(new Uint32Array(a),1)),e=null,r=null,h=null,p=null,m=null}else{t.instancedMaterial=this.getInstancedMaterial("Instancing");let e=i.attributes.position?s.hashUtilsCls.hashvalue2array(i.attributes.position.array):[],d=i.attributes.normal?s.hashUtilsCls.hashvalue2array(i.attributes.normal.array):[],c=i.attributes.color?s.hashUtilsCls.hashvalue2array(i.attributes.color.array):[],h=i.index?s.hashUtilsCls.hashvalue2array(i.index.array):[];l=l.concat(e),r=r.concat(d),o=o.concat(c),a=a.concat(h);let p=[],m="CylinderGeometry"==i.type?1:0;for(let e=0,t=l.length/3;e0&&(e.dAtoms=t.hashUtilsCls.cloneHash(s)),e.bShowHighlight=!1}e.applyMapCls.removeSurfaces(),e.applyMapCls.applySurfaceOptions(),e.applyMapCls.removeMaps(),e.applyMapCls.applyMapOptions(),e.applyMapCls.removeEmmaps(),e.applyMapCls.applyEmmapOptions(),e.applyMapCls.removePhimaps(),e.applyMapCls.applyPhimapOptions(),e.applyMapCls.removeSurfaces(),e.applyMapCls.applyphisurfaceOptions(),e.axes=[],e.pc1&&e.axesCls.setPc1Axes(),e.opts.rotationcenter="highlight center",e.drawCls.draw(),e.bShowHighlight=!0}async alternateWrapper(){let e=this.icn3d;e.icn3dui,e.bAlternate=!0,await this.alternateStructures(),e.bAlternate=!1}}class ht{constructor(e){this.icn3d=e}draw(e){let t=this.icn3d,s=t.icn3dui;if(t.impostorCls.clearImpostors(),!t.bRender||t.hAtoms&&0!=Object.keys(t.hAtoms)||(t.hAtoms=s.hashUtilsCls.cloneHash(t.atoms)),t.sceneCls.rebuildScene(),t.bImpo&&t.impostorCls.drawImpostorShader(),t.setColorCls.applyPrevColor(),void 0!==t.biomtMatrices&&t.biomtMatrices.length>1)if(t.bAssembly&&1==Object.keys(t.structures).length&&(void 0===s.cfg.mmdbid&&1==s.cfg.bu||void 0!==s.cfg.mmdbid&&1==s.cfg.bu&&Object.keys(t.atoms).length*t.biomtMatrices.length>t.maxatomcnt))t.instancingCls.drawSymmetryMates();else{let e=!0;t.applyCenterCls.centerSelection(void 0,e)}let i=void 0!==t.hAtoms?Object.keys(t.hAtoms).length:0;if(i>0&&i0){e.children[0].scale.z=t[0].distance,t[0].point.sub(r.mdl.position);let s=r.rayThreshold,i=r.rayCls.getAtomsFromPosition(t[0].point,s);for(;!i&&s<10;)s+=.5,i=r.rayCls.getAtomsFromPosition(t[0].point,s);i&&(r.pAtomNum%2==0?r.pAtom=i:r.pAtom2=i,++r.pAtomNum,this.showPickingVr(r.pk,i))}}}}catch(e){}}showPickingVr(e,t){let s=this.icn3d;s.icn3dui,e||(e=2),s.hAtoms=s.pickingCls.getPickedAtomList(e,t),2===e?s.residueLabelsCls.addResidueLabels(s.hAtoms,void 0,void 0,!0):1===e&&s.residueLabelsCls.addAtomLabels(s.hAtoms),s.setOptionCls.setStyle("proteins",t.style)}render_base(){let e=this.icn3d,t=e.icn3dui,s=this;if(t.bNode)return;let i=e.bControlGl&&!t.bNode?window.cam:e.cam;if(e.directionalLight){let t=new THREE.Quaternion;t.setFromUnitVectors(new THREE.Vector3(0,0,e.cam_z).normalize(),i.position.clone().normalize()),e.directionalLight.position.copy(e.lightPos.clone().applyQuaternion(t).normalize()),e.directionalLight2.position.copy(e.lightPos2.clone().applyQuaternion(t).normalize()),e.directionalLight3.position.copy(e.lightPos3.clone().applyQuaternion(t).normalize())}if(e.bVr||e.renderer.setPixelRatio(window.devicePixelRatio),e.bVr){let t=.04;if(e.controllers){let i=this.updateGamepadState();for(let n=0,l=e.controllers.length;n{const i=e.gamepad.axes;let r=parseInt(1e3*i[t]),o=parseInt(-1e3*i[s]);n.push(r),l.push(o)})),{xArray:n,yArray:l}}return{xArray:[0,0],yArray:[0,0]}}}class pt{constructor(e){this.icn3d=e}getAtomsWithinAtom(e,t,s,i,n,l,r){let o=this.icn3d;o.icn3dui;let a=this.getNeighboringAtoms(e,t,s,r);i&&(o.resid2Residhash={});let d={};for(let e in t){let c,h,p=o.atoms[e],m=p.structure+"_"+p.chain+"_"+p.resi;for(let e in o.residues[m])if(o.atoms[e]&&("CA"===o.atoms[e].name&&"C"===o.atoms[e].elem||"O3'"===o.atoms[e].name||"O3*"===o.atoms[e].name)){c=o.atoms[e];break}void 0===c&&(c=p),i&&(h=p.resn+" $"+p.structure+"."+p.chain+":"+p.resi,void 0===o.resid2Residhash[h]&&(o.resid2Residhash[h]={}));let u=p.structure+"_"+p.chain+"_"+p.resi;for(let e in a){let m=a[e];if(!o.crossstrucinter&&p.structure!=m.structure)continue;if(!r&&m.serial in t)continue;if(o.bOpm&&"DUM"===m.resn)continue;let g=m.coord.distanceTo(p.coord);if(go?r:o,d=Math.sqrt(a),c=(d+s)*(d+s),h={};for(let r in e){let e=n.atoms[r];!i&&t.hasOwnProperty(e.serial)||(this.bOpm&&"DUM"===e.resn||e.coord.xl[1][0]+s||e.coord.yl[1][1]+s||e.coord.zl[1][2]+s||(e.coord.x-l[2][0])*(e.coord.x-l[2][0])+(e.coord.y-l[2][1])*(e.coord.y-l[2][1])+(e.coord.z-l[2][2])*(e.coord.z-l[2][2])e.coord.x?n:e.coord.x,l=l>e.coord.y?l:e.coord.y,r=r>e.coord.z?r:e.coord.z}return[[t,s,i],[n,l,r],[o/c,a/c,d/c]]}hideContact(){let e=this.icn3d;e.icn3dui,e.opts.contact="no",void 0===e.lines&&(e.lines={}),e.lines.contact=[],e.contactpnts=[]}}class mt{constructor(e){this.icn3d=e}isHbondDonorAcceptor(e){let t=this.icn3d;if(t.icn3dui,"N"==e.name&&!e.het||"N"==e.elem&&"Arg"==e.resn||"N"==e.elem&&"Asn"==e.resn||"N"==e.elem&&"Gln"==e.resn||"N"==e.elem&&"Lys"==e.resn||"N"==e.elem&&"Trp"==e.resn)return"donor";if("O"==e.name&&!e.het||"S"==e.elem&&"Met"==e.resn||"O"==e.elem&&"Asn"==e.resn||"O"==e.elem&&"Asp"==e.resn||"O"==e.elem&&"Gln"==e.resn||"O"==e.elem&&"Glu"==e.resn)return"acceptor";if("S"==e.elem&&"Cys"==e.resn||"N"==e.elem&&"His"==e.resn||"O"==e.elem&&"Ser"==e.resn||"O"==e.elem&&"Thr"==e.resn||"O"==e.elem&&"Tyr"==e.resn)return"both";if("Pro"==e.resn)return"none";if("N"==e.elem){if("Asn"==e.resn||"Gln"==e.resn)return"both";let s=0,i=0;for(let i=0,n=e.bonds.length;i1?"ring":"donor":"none"}if("O"==e.elem&&1==e.bonds.length){if("Asn"==e.resn||"Gln"==e.resn)return"both";for(let s=0,i=e.bonds.length;s=2?"acceptor":"both"}if("O"==e.elem&&2==e.bonds.length){for(let s=0,i=e.bonds.length;s1);++t)"H"!=s.atoms[e.bonds[t]].elem&&(i=s.atoms[e.bonds[t]],l[r++].subVectors(s.atoms[e.bonds[t]].coord,e.coord));if(1===r)for(let t=0,n=i.bonds.length;t1);++t)"H"!=s.atoms[i.bonds[t]].elem&&s.atoms[i.bonds[t]].serial!=e.serial&&l[r++].subVectors(s.atoms[i.bonds[t]].coord,e.coord);if(2!==r)return;let o=l[0].cross(l[1]);return Math.abs(Math.PI/2-o.angleTo(n))}isValidHbond(e,t,s){let i=this.icn3d;i.icn3dui;let n,l,r=this.isHbondDonorAcceptor(e),o=this.isHbondDonorAcceptor(t),a=50*Math.PI/180,d=50*Math.PI/180,c=90*Math.PI/180,h=30*Math.PI/180;if("donor"==r&&("acceptor"==o||"both"==o||"ring"==o)||"acceptor"==o&&("donor"==r||"both"==r||"ring"==r))n=e,l=t;else if("acceptor"==r&&("donor"==o||"both"==o||"ring"==o)||"donor"==o&&("acceptor"==r||"both"==r||"ring"==r))l=e,n=t;else{if("both"!=r&&"ring"!=r||"both"!=o&&"ring"!=o)return!1;n=e,l=t,i.nucleotides.hasOwnProperty(e.serial)&&i.nucleotides.hasOwnProperty(t.serial)&&("ring"==r||"ring"==o)||(e.het||t.het)&&"ring"==r&&"ring"==o||(h=90*Math.PI/180)}let p=this.calcAngles(n,l),m=90*Math.PI/180;for(let e=0,t=p.length;ed)return!1;let u=this.calcPlaneAngle(n,l);if(void 0!==u&&u>h)return!1;let g=this.calcAngles(l,n),f=90*Math.PI/180;for(let e=0,t=g.length;ea)return!1;let b=this.calcPlaneAngle(l,n);return!(void 0!==b&&b>c)}calculateChemicalHbonds(e,t,s,i,n,l){let r=this.icn3d,o=r.icn3dui;if(0===Object.keys(e).length||0===Object.keys(t).length)return;r.resid2Residhash={};let a,d,c={},h=s*s;for(let t in e){let s=e[t],n=i?"LYS"===s.resn&&"N"===s.elem&&"N"!==s.name||"ARG"===s.resn&&("NH1"===s.name||"NH2"===s.name)||("GLU"===s.resn||"ASP"===s.resn)&&"O"===s.elem&&"O"!==s.name||s.het&&("N"===s.elem||"O"===s.elem||"S"===s.elem):"N"===s.elem||"O"===s.elem||"S"===s.elem&&(s.het||"Cys"===s.resn||"Met"===s.resn);n=r.bOpm?n&&"DUM"!==s.resn:n,n&&(a=s.structure+"_"+s.chain+"_"+s.resi,d=a+"_"+s.name,c[d]=s)}let p={},m={},u=.5,g=-27.888,f={};for(let e in t){let b=t[e],C=i?"LYS"===b.resn&&"N"===b.elem&&"N"!==b.name||"ARG"===b.resn&&("NH1"===b.name||"NH2"===b.name)||("GLU"===b.resn||"ASP"===b.resn)&&"O"===b.elem&&"O"!==b.name||b.het&&("N"===b.elem||"O"===b.elem||"S"===b.elem):"N"===b.elem||"O"===b.elem||"S"===b.elem&&(b.het||"Cys"===b.resn||"Met"===b.resn);if(C=r.bOpm?C&&"DUM"!==b.resn:C,C){a=b.structure+"_"+b.chain+"_"+b.resi,d=a+"_"+b.name;let e=b.resn+" $"+b.structure+"."+b.chain+":"+b.resi+"@"+b.name;void 0===r.resid2Residhash[e]&&(r.resid2Residhash[e]={});for(let t in c){if(i&&!(("LYS"!==b.resn&&"ARG"!==b.resn||"LYS"!==c[t].resn&&"ARG"!==c[t].resn)&&("GLU"!==b.resn&&"ASP"!==b.resn||"GLU"!==c[t].resn&&"ASP"!==c[t].resn)))continue;if(!r.crossstrucinter&&b.structure!=c[t].structure)continue;if(a==t.substr(0,t.lastIndexOf("_")))continue;let d=Math.abs(b.coord.x-c[t].coord.x);if(d>s)continue;let C=Math.abs(b.coord.y-c[t].coord.y);if(C>s)continue;let y=Math.abs(b.coord.z-c[t].coord.z);if(y>s)continue;let v=d*d+C*C+y*y;if(v>h)continue;if(!r.proteins.hasOwnProperty(b.serial)||!r.proteins.hasOwnProperty(c[t].serial)||"N"!==b.name&&"O"!==b.name||"O"!==c[t].name&&"N"!==c[t].name){if(!this.isValidHbond(b,c[t],s))continue}else{if(b.name===c[t].name)continue;if(b.structure==c[t].structure&&b.chain==c[t].chain&&Math.abs(b.resi-c[t].resi)<=1)continue;let e,i="N"===b.name?b:c[t],n="O"===b.name?b:c[t];if("Pro"===i.resn)continue;if(void 0===i.hcoord){if(!this.isValidHbond(b,c[t],s))continue}else{let s,l=i.hcoord,o=i.coord,a=n.structure+"_"+n.chain+"_"+n.resi;for(let e in r.residues[a])if("C"===r.atoms[e].name){s=r.atoms[e];break}if(!s)continue;let d=s.coord,h=n.coord,p=l.distanceTo(h),m=l.distanceTo(d),f=o.distanceTo(d),C=o.distanceTo(h);e=p2||f[c[t].serial]>2)continue;void 0===f[b.serial]?f[b.serial]=1:++f[b.serial],void 0===f[c[t].serial]?f[c[t].serial]=1:++f[c[t].serial],"graph"!==n&&(i?(r.saltbridgepnts.push({serial:b.serial,coord:b.coord}),r.saltbridgepnts.push({serial:c[t].serial,coord:c[t].coord})):(r.hbondpnts.push({serial:b.serial,coord:b.coord}),r.hbondpnts.push({serial:c[t].serial,coord:c[t].coord})));let _=c[t].structure+"_"+c[t].chain+"_"+c[t].resi;p=o.hashUtilsCls.unionHash(p,r.residues[a]),p=o.hashUtilsCls.unionHash(p,r.residues[_]),m[a]=1,m[_]=1;let w=c[t].resn+" $"+c[t].structure+"."+c[t].chain+":"+c[t].resi+"@"+c[t].name,S=a+"_"+b.resn+","+_+"_"+c[t].resn;void 0!==r.resids2interAll[S]&&void 0!==r.resids2interAll[S].ionic&&r.resids2interAll[S].ionic.hasOwnProperty(e+","+w)||(r.resid2Residhash[e][w]=v.toFixed(1),l||(void 0===r.resids2inter[S]&&(r.resids2inter[S]={}),void 0===r.resids2inter[S].hbond&&(r.resids2inter[S].hbond={}),r.resids2inter[S].hbond[e+","+w]=v.toFixed(1)),void 0===r.resids2interAll[S]&&(r.resids2interAll[S]={}),void 0===r.resids2interAll[S].hbond&&(r.resids2interAll[S].hbond={}),r.resids2interAll[S].hbond[e+","+w]=v.toFixed(1))}}}let b=Object.keys(m);if("graph"!==n)for(let e=0,t=b.length;en)return!1;let c=Math.abs(e.coord.y-t.coord.y);if(c>n)return!1;let h=Math.abs(e.coord.z-t.coord.z);if(h>n)return!1;let p=d*d+c*c+h*h;if(p>l)return!1;"graph"!==s&&("halogen"==i?(a.halogenpnts.push({serial:e.serial,coord:e.coord}),a.halogenpnts.push({serial:t.serial,coord:t.coord})):"pi-cation"==i?(a.picationpnts.push({serial:e.serial,coord:e.coord}),a.picationpnts.push({serial:t.serial,coord:t.coord})):"pi-stacking"==i&&(a.pistackingpnts.push({serial:e.serial,coord:e.coord}),a.pistackingpnts.push({serial:t.serial,coord:t.coord})));let m=t.resn+" $"+t.structure+"."+t.chain+":"+t.resi+"@"+t.name;a.resid2Residhash[r][m]=p.toFixed(1);let u=e.structure+"_"+e.chain+"_"+e.resi+"_"+e.resn+","+t.structure+"_"+t.chain+"_"+t.resi+"_"+t.resn;return o||(void 0===a.resids2inter[u]&&(a.resids2inter[u]={}),void 0===a.resids2inter[u][i]&&(a.resids2inter[u][i]={}),a.resids2inter[u][i][r+","+m]=p.toFixed(1)),void 0===a.resids2interAll[u]&&(a.resids2interAll[u]={}),void 0===a.resids2interAll[u][i]&&(a.resids2interAll[u][i]={}),a.resids2interAll[u][i][r+","+m]=p.toFixed(1),!0}getRingNormal(e){if(this.icn3d.icn3dui,e.length<3)return;let t=e[0].clone().sub(e[1]),s=e[1].clone().sub(e[2]);return t.cross(s).normalize()}getAromaticRings(e,t,s){let i=this.icn3d;i.icn3dui;let n=[],l=[],r=[],o=[];if("nucleotide"==s){let s=new THREE.Vector3,a=new THREE.Vector3;if("A"==e.trim().toUpperCase()||"DA"==e.trim().toUpperCase()||"G"==e.trim().toUpperCase()||"DG"==e.trim().toUpperCase()){for(let e in i.residues[t]){let t=i.atoms[e];"N1"==t.name||"C2"==t.name||"N3"==t.name||"C6"==t.name?(s.add(t.coord),r.push(t.coord)):"C4"==t.name||"C5"==t.name?(s.add(t.coord),a.add(t.coord),r.push(t.coord),o.push(t.coord)):"N7"!=t.name&&"C8"!=t.name&&"N9"!=t.name||(a.add(t.coord),o.push(t.coord))}6==r.length&&(s.multiplyScalar(1/6),n.push(s),l.push(this.getRingNormal(r))),5==o.length&&(a.multiplyScalar(.2),n.push(a),l.push(this.getRingNormal(o)))}else if("C"==e.trim().toUpperCase()||"DC"==e.trim().toUpperCase()||"T"==e.trim().toUpperCase()||"DT"==e.trim().toUpperCase()||"U"==e.trim().toUpperCase()||"DU"==e.trim().toUpperCase()){for(let e in i.residues[t]){let t=i.atoms[e];"N1"==t.name||"C2"==t.name||"N3"==t.name||"C6"==t.name?(s.add(t.coord),r.push(t.coord)):"C4"!=t.name&&"C5"!=t.name||(s.add(t.coord),r.push(t.coord))}6==r.length&&(s.multiplyScalar(1/6),n.push(s),l.push(this.getRingNormal(r)))}}else if("protein"==s){let s=new THREE.Vector3,a=new THREE.Vector3;if("PHE"==e.toUpperCase()||"TYR"==e.toUpperCase()){for(let e in i.residues[t]){let t=i.atoms[e];"CG"!=t.name&&"CD1"!=t.name&&"CE1"!=t.name&&"CZ"!=t.name&&"CE2"!=t.name&&"CD2"!=t.name||(s.add(t.coord),r.push(t.coord))}6==r.length&&(s.multiplyScalar(1/6),n.push(s),l.push(this.getRingNormal(r)))}else if("HIS"==e.toUpperCase()){for(let e in i.residues[t]){let t=i.atoms[e];"CG"!=t.name&&"ND1"!=t.name&&"CE1"!=t.name&&"NE2"!=t.name&&"CD2"!=t.name||(s.add(t.coord),r.push(t.coord))}5==r.length&&(s.multiplyScalar(.2),n.push(s),l.push(this.getRingNormal(r)))}else if("TRP"==e.toUpperCase()){for(let e in i.residues[t]){let t=i.atoms[e];"CZ2"==t.name||"CH2"==t.name||"CZ3"==t.name||"CE3"==t.name?(s.add(t.coord),r.push(t.coord)):"CD2"==t.name||"CE2"==t.name?(s.add(t.coord),a.add(t.coord),r.push(t.coord),o.push(t.coord)):"CG"!=t.name&&"CD1"!=t.name&&"NE1"!=t.name||(a.add(t.coord),o.push(t.coord))}6==r.length&&(s.multiplyScalar(1/6),n.push(s),l.push(this.getRingNormal(r))),5==o.length&&(a.multiplyScalar(.2),n.push(a),l.push(this.getRingNormal(o)))}}return{piPosArray:n,normalArray:l}}dfs_cycle(e,t,s){let i=this.icn3d;if(i.icn3dui,2==i.ring_color[e])return s;if(1==i.ring_color[e]){s++;let n=t;for(i.ring_mark[n]=s;n!=e;)n=i.ring_par[n],i.ring_mark[n]=s;return s}if(i.ring_par[e]=t,i.ring_color[e]=1,void 0!==i.atoms[e])for(let t=0,n=i.atoms[e].bonds.length;t=3&&o<=6&&a[0]&&a[1]&&a[2]&&a[3]){let i=a[0].clone().sub(a[1]).normalize(),r=a[1].clone().sub(a[2]).normalize(),d=a[2].clone().sub(a[3]).normalize(),c=i.cross(r).normalize(),h=c.dot(d);if(Math.abs(h)<.052){l.multiplyScalar(1/o);let i=t.atoms[n];s[e+"_pi"+n]={resn:i.resn,name:"pi"+n,coord:l,serial:i.serial,structure:i.structure,chain:i.chain,resi:i.resi,normal:c}}}}return s}hideHalogenPi(){let e=this.icn3d;e.icn3dui,e.opts.halogen="no",e.opts["pi-cation"]="no",e.opts["pi-stacking"]="no",void 0===e.lines&&(e.lines={}),e.lines.halogen=[],e.lines["pi-cation"]=[],e.lines["pi-stacking"]=[],e.halogenpnts=[],e.picationpnts=[],e.pistackingpnts=[]}}class gt{constructor(e){this.icn3d=e}calculateIonicInteractions(e,t,s,i,n,l){let r=this.icn3d,o=r.icn3dui;if(0===Object.keys(e).length||0===Object.keys(t).length)return;r.resid2Residhash={};let a,d,c={},h={},p=s*s;for(let t in e){let s=e[t];if("ARG"===s.resn&&"NH2"===s.name||"GLU"===s.resn&&"OE2"===s.name||"ASP"===s.resn&&"OD2"===s.name)continue;let i=("LYS"===s.resn||"HIS"===s.resn)&&"N"===s.elem&&"N"!==s.name||"ARG"===s.resn&&("NH1"===s.name||"NH2"===s.name)||s.het&&-1!==o.parasCls.cationsTrimArray.indexOf(s.elem)||s.het&&"N"===s.elem&&1==s.bonds.length,n=this.isAnion(s);i=r.bOpm?i&&"DUM"!==s.resn:i,n=r.bOpm?n&&"DUM"!==s.resn:n,(i||n)&&(a=s.structure+"_"+s.chain+"_"+s.resi,d=a+"_"+s.name,i&&(c[d]=s),n&&(h[d]=s))}let m={},u={};for(let e in t){let i=t[e];if("ARG"===i.resn&&"NH2"===i.name||"GLU"===i.resn&&"OE2"===i.name||"ASP"===i.resn&&"OD2"===i.name)continue;let g=("LYS"===i.resn||"HIS"===i.resn)&&"N"===i.elem&&"N"!==i.name||"ARG"===i.resn&&("NH1"===i.name||"NH2"===i.name)||i.het&&-1!==o.parasCls.cationsTrimArray.indexOf(i.elem),f=this.isAnion(i);if(g=r.bOpm?g&&"DUM"!==i.resn:g,f=r.bOpm?f&&"DUM"!==i.resn:f,g||f){a=i.structure+"_"+i.chain+"_"+i.resi,d=a+"_"+i.name;let e=i.resn+" $"+i.structure+"."+i.chain+":"+i.resi+"@"+i.name;void 0===r.resid2Residhash[e]&&(r.resid2Residhash[e]={});let t={};g?t=h:f&&(t=c);let b,C=i.structure+"_"+i.chain+"_"+i.resi;g&&"ARG"===i.resn&&"NH1"===i.name?b=r.firstAtomObjCls.getFirstAtomObjByName(r.residues[C],"NH2"):f&&"GLU"===i.resn&&"OE1"===i.name?b=r.firstAtomObjCls.getFirstAtomObjByName(r.residues[C],"OE2"):f&&"ASP"===i.resn&&"OD1"===i.name&&(b=r.firstAtomObjCls.getFirstAtomObjByName(r.residues[C],"OD2"));let y=void 0===b?i.coord:i.coord.clone().add(b.coord).multiplyScalar(.5);for(let d in t){if(a==d.substr(0,d.lastIndexOf("_")))continue;if(!r.crossstrucinter&&i.structure!=t[d].structure)continue;let c,h=t[d].structure+"_"+t[d].chain+"_"+t[d].resi;f&&"ARG"===t[d].resn&&"NH1"===t[d].name?c=r.firstAtomObjCls.getFirstAtomObjByName(r.residues[h],"NH2"):g&&"GLU"===t[d].resn&&"OE1"===t[d].name?c=r.firstAtomObjCls.getFirstAtomObjByName(r.residues[h],"OE2"):g&&"ASP"===t[d].resn&&"OD1"===t[d].name&&(c=r.firstAtomObjCls.getFirstAtomObjByName(r.residues[h],"OD2"));let b=void 0===c?t[d].coord:t[d].coord.clone().add(c.coord).multiplyScalar(.5),C=Math.abs(y.x-b.x);if(C>s)continue;let v=Math.abs(y.y-b.y);if(v>s)continue;let _=Math.abs(y.z-b.z);if(_>s)continue;let w=C*C+v*v+_*_;if(w>p)continue;"graph"!==n&&(r.saltbridgepnts.push({serial:i.serial,coord:y}),r.saltbridgepnts.push({serial:t[d].serial,coord:b}));let S=t[d].structure+"_"+t[d].chain+"_"+t[d].resi;m=o.hashUtilsCls.unionHash(m,r.residues[a]),m=o.hashUtilsCls.unionHash(m,r.residues[S]),u[a]=1,u[S]=1;let A=t[d].resn+" $"+t[d].structure+"."+t[d].chain+":"+t[d].resi+"@"+t[d].name;r.resid2Residhash[e][A]=w.toFixed(1);let x=a+"_"+i.resn+","+S+"_"+t[d].resn;l||(void 0===r.resids2inter[x]&&(r.resids2inter[x]={}),void 0===r.resids2inter[x].ionic&&(r.resids2inter[x].ionic={}),r.resids2inter[x].ionic[e+","+A]=w.toFixed(1)),void 0===r.resids2interAll[x]&&(r.resids2interAll[x]={}),void 0===r.resids2interAll[x].ionic&&(r.resids2interAll[x].ionic={}),r.resids2interAll[x].ionic[e+","+A]=w.toFixed(1)}}}let g=Object.keys(u);if("graph"!==n)for(let e=0,t=g.length;e1?1/(n-1):1;for(let n in e){let e=t.atoms[n];e.color=e.het?s.parasCls.atomColors[e.elem]||s.parasCls.defaultAtomColor:s.parasCls.thr().setHSL(3/4*(1-i++*l),1,.45),t.atomPrevColors[n]=e.color}}colorRainbow(e){let t=this.icn3d,s=t.icn3dui,i=0,n=0;e=s.hashUtilsCls.intHash(e,t.hAtoms);for(let s in e){t.atoms[s].het||++n}let l=n>1?1/(n-1):1;for(let n in e){let e=t.atoms[n];e.color=e.het?s.parasCls.atomColors[e.elem]||s.parasCls.defaultAtomColor:s.parasCls.thr().setHSL(3/4*i++*l,1,.45),t.atomPrevColors[n]=e.color}}setColorAcrossSets(e,t){let s=this.icn3d,i=s.icn3dui,n=0,l=e.length,r=l>1?1/(l-1):1;for(let l=0,o=e.length;l0)this.setMmdbChainColor();else{let e=-1,s="",l=n.parasCls.stdChainColors.length;for(let r in t){let t=i.atoms[r];t.chain!=s&&(++e,e%=l),t.het?(t.color=n.parasCls.atomColors[t.elem],i.atomPrevColors[r]=t.color):(t.color=n.parasCls.stdChainColors[e],Object.keys(i.chainsColor).length>0&&this.updateChainsColor(t),i.atomPrevColors[r]=t.color),s=t.chain}}break;case"domain":s=0,l=0;let m=Object.keys(i.tddomains);l=m.length,r=l>1?1/(l-1):1;for(let e=0,t=m.length;e1?1/(l-1):1;for(let e=0;e Defined Sets", and try it again.');break;case"secondary structure green":i.sheetcolor="green";for(let e in t){let t=i.atoms[e];t.color=t.het?n.parasCls.atomColors[t.elem]||n.parasCls.defaultAtomColor:n.parasCls.ssColors[t.ss]||n.parasCls.thr(16711935),i.atomPrevColors[e]=t.color}break;case"secondary structure yellow":case"secondary structure":i.sheetcolor="yellow";for(let e in t){let t=i.atoms[e];t.color=t.het?n.parasCls.atomColors[t.elem]||n.parasCls.defaultAtomColor:n.parasCls.ssColors2[t.ss]||n.parasCls.thr(16711935),i.atomPrevColors[e]=t.color}break;case"secondary structure spectrum":s=0,l=0;let u,g,f=[],b=-9999;for(let e in t){if(!i.proteins.hasOwnProperty(e))continue;let t=i.atoms[e];-9999==b&&(u=parseInt(e)),-9999!=b&&(t.ss!=g.ss||Math.abs(t.resi-g.resi)>1||t.ssbegin&&g.ssend)&&("coil"==g.ss||f.push([u,b]),u=e),b=parseInt(e),g=t}"coil"==g.ss||f.push([u,b]),l=f.length,r=l>1?1/(l-1):1;for(let e=0,t=f.length;e100&&(e=100);let r=(i.middB-e)*i.spanBinv1,o=(e-i.middB)*i.spanBinv2;e=90?t.color=n.parasCls.thr().setRGB(0,.325,.839):e>=70&&e<90?t.color=n.parasCls.thr().setRGB(.396,.572,.953):e>=50&&e<70?t.color=n.parasCls.thr().setRGB(1,.859,.075):e<50&&(t.color=n.parasCls.thr().setRGB(1,.49,.271))}i.atomPrevColors[e]=t.color}break;case"b factor":i.middB=50,i.spanBinv1=.02,i.spanBinv2=.02;for(let e in t){let t=i.atoms[e];if(void 0===t.b||isNaN(t.b)||0==parseInt(1e3*t.b))t.color=n.parasCls.thr().setRGB(0,1,0);else{let e=t.b;e>100&&(e=100),e=t.structure.substr(0,4)!=i.defaultPdbId&&t.structure.length>5?100-e:e;let s=(i.middB-e)*i.spanBinv1,l=(e-i.middB)*i.spanBinv2;t.color=et.b&&(o=t.b),a5?100-t.b:t.b,s=i.bfactorArray.indexOf(e)/C;t.color=s<.5?n.parasCls.thr().setRGB(2*s,2*s,1):n.parasCls.thr().setRGB(1,2*(1-s),2*(1-s))}i.atomPrevColors[e]=t.color}break;case"area":if(void 0===i.resid2area){let e=n.hashUtilsCls.cloneHash(i.hAtoms);i.hAtoms=n.hashUtilsCls.cloneHash(i.atoms),i.bCalcArea=!0,i.opts.surface="solvent accessible surface",i.applyMapCls.applySurfaceOptions(),i.bCalcArea=!1,i.hAtoms=n.hashUtilsCls.cloneHash(e)}let y=void 0!==i.midpercent?i.midpercent:35;i.spanBinv1=.02,i.spanBinv2=.02;for(let e in t){let t=i.atoms[e],s=t.structure+"_"+t.chain+"_"+t.resi+"_"+t.resn,l=n.parasCls.residueArea.hasOwnProperty(t.resn)?i.resid2area[s]/n.parasCls.residueArea[t.resn]*100:y;l>100&&(l=100);let r=(y-l)*i.spanBinv1,o=(l-y)*i.spanBinv2;t.color=l[e,s.parasCls.hydrophobicValues[e]]));l.sort(((e,t)=>parseFloat(e[1])-parseFloat(t[1])));var r=l.map((e=>[e[0],Object.keys(o[e[0]])[0]]));n+="","normalized hydrophobic"==e?(n+="Dark green (W, F, L, I, Y, M, V, C): Hydrophobic
",n+="Light green (P, T, S, A, Q, N, G): Polar
",n+="Grey: Charged, not hydrophobic
"):(n+="Green (W, F, L, I, Y, M, V, C): Hydrophobic
",n+="Yellow (P, T, S, A, Q, N, G): Polar
",n+="Red: Negatively Charged
",n+="Blue: Positively Charged
");let a=0;for(let e of r)s.parasCls.residueAbbrev[e[0]]&&(n+="
",n+="
",n+=s.parasCls.residueAbbrev[e[0]]+"
",a%4==3&&(n+="
"),++a);n+="
B factor quantitates the uncertainty for each atom. A high B factor reflects that the position is less certain.
"+e+" ";for(let e in l[s])n+="
";n+=i.parasCls.atomnames[s.toUpperCase()]+"";let e=Object.keys(s).sort(),i="",n=0;for(let l=0,r=e.length;l
";for(let e in s[o])r+="
";r+=o+" ";for(let e=0,t=r.length;e
",s+="
",s+=t,s+=" ";for(let e in s){t+="
",t+="
",t+=e,t+=" "}return t+="
Protodomain 1 ":"","A Strand":"0000FF","B Strand":"006400","C Strand":"FFD700","C' Strand":"FF8C00","Linker ":"","C'' Strand":"FF0000","Protodomain 2 ":"","D Strand":"0000FF","E Strand":"006400","F Strand":"FFD700","G Strand":"FF8C00","":"",Loop:"CCCCCC"};t+="A protodomain is a supersecondary structure
that by its duplication, symmetry operations
can generate a structural domain.
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',C+=h,y+=v)}else o+="- "}s.seqStartLen&&s.seqStartLen[e]&&(o+=s.showSeqCls.insertMulGap(s.seqEndLen[e],"-")),f=' '+p.toString()+" Residues ",f+=" ",f+="',o+=r,a+=r;let d=s.substr(0,s.indexOf("_"));for(let c in t){let h=t[c],p=[],m=!1;for(let e=0,t=h.length;e5?p.push(e-1):i.UPResi2ResiPosPerChain&&i.UPResi2ResiPosPerChain[s][e]&&p.push(i.UPResi2ResiPosPerChain[s][e]),!m&&i.residues.hasOwnProperty(s+"_"+e)&&(m=!0)}if(0==p.length)continue;let u=p.length,g="ptm"==e?"PTM: "+c:"Transmembrane";g.length>17&&(g=g.substr(0,17)+"...");let f=c,b=''+g+"
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',_+=d,w+=S)}else r+="- ";i.seqStartLen&&i.seqStartLen[s]&&(r+=i.showSeqCls.insertMulGap(i.seqEndLen[s],"-")),y=' '+u.toString()+" Residues ",y+=" ",y+="',a=o,d=o,c=e.indexOf("_"),h=e.substr(c+1);if(h.length>1&&"1"==h.substr(h.length-1)&&(h=h.substr(0,h.length-1)),s)n=e,i=t.domains[e]?t.domains[e].domains:[];else{let e,s=t.moleculeInfor;for(let t in s)if(s[t].chain===h){e=t,n=s[t].name;break}void 0!==e&&void 0!==t.domains[e]&&(i=t.domains[e].domains),void 0===i&&(i=[])}for(let t=0,s=i.length;t17?s.substr(0,17)+"...":s,h=i[t].intervals,p={},m={},u=[],g=[],f={},b=0;for(let e=0,t=h.length;e'+c+" ",y=''+b.toString()+" Res ";d+=C+y+"';o+=C+y+v,a+=C+y+v;let _="domain3d"+t.toString();l.seqStartLen&&l.seqStartLen[e]&&(o+=l.showSeqCls.insertMulGap(l.seqStartLen[e],"-"));for(let t=0,s=l.giSeq[e].length;t1&&(n=i[0]+"..");let r=s;o+=''+i+" "}else o+="- "}l.seqStartLen&&l.seqStartLen[e]&&(o+=l.showSeqCls.insertMulGap(l.seqEndLen[e],"-"));let w=l.firstAtomObjCls.getFirstCalphaAtomObj(l.chains[e]),S=void 0===w.color||"FFFFFF"===w.color.getHexString()?"DDDDDD":w.color.getHexString(),A=void 0!==w.color?S:"CCCCCC";if(l.seqStartLen&&l.seqStartLen[e]&&(a+=l.showSeqCls.insertMulGapOverview(e,l.seqStartLen[e])),r.cfg.blast_rep_id!=e)for(let i=0,n=u.length;i ',a+='3D domain '+(t+1).toString()+"
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"}else if(2==e&&m){let e=b.utilsCls.isMobile()?"none":"button";C+='< ClinVar
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"),$("#"+p.pre+"ov_custom_"+e+"_"+f).width(b),$("#"+p.pre+"tt_custom_"+e).append("
"),$("#"+p.pre+"tt_custom_"+e+"_"+f).width(b);let C='',y=C,v=C,_=C,w=C,S=parseInt(10*Math.random()),A='
'+f+"
",x='
Exons
',k='
'+g.toString()+" Pos ";_+=A+k+"
",w+=x+k+"
";let O='
';C+=A+k+O,y+=x+k+O,v+=A+k+O;let R=e.indexOf("_"),I="cst"+e.substr(R+1),T=0,E=0,P=(void 0===l||"seq"===l||"custom"===l)&&-1==s.indexOf("cannot-be-aligned")&&-1==s.indexOf("cannot be aligned"),M="identity"===l&&-1==s.indexOf("cannot-be-aligned")&&-1==s.indexOf("cannot be aligned"),D={},H=0;A="";let F={},L={},N={},q=0;if(h)for(let e=0,t=h.length;e"+d+" ";let g='style="background-color:'+F[q]+'"';y+='
";for(let t in p.residues[e+"_"+u]){let e=p.atoms[t];e.color=m.parasCls.thr(F[q]),p.atomPrevColors[t]=e.color}A+=p.showSeqCls.insertGapOverview(e,t);let f=Math.round(p.seqAnnWidth*t/(p.maxAnnoLength+p.nTotalGap)-T-E);f<0&&(f=0),A+='
',s=void 0!==i&&""!=i[t]?i[t]:r?"rgb("+r+")":P?"#"+c:"#333",A+='
',T+=f,E+=1,++q}else u?C+="
"+d+" ":(C+="
- ",y+="
")}if(void 0!==a){A="";let s=[],i=[];for(let e=0,t=a.length;e
=i&&c<=n&&(t={exonIndex:e,rangeStart:i,rangeEnd:n,from:c,genomeRange:h[e].genomeRange}),p>=i&&p<=n&&(s={exonIndex:e,rangeStart:i,rangeEnd:n,to:p,genomeRange:h[e].genomeRange})}if(t&&s&&t.exonIndex==s.exonIndex)i=this.getExonColor(t.rangeStart,t.rangeEnd,c),r=this.getExonColor(t.rangeStart,t.rangeEnd,p),o=i+" 0%, #FFF 50%, "+r+" 100%",A+=this.getExonHtml(t.exonIndex,o,t.from,s.to,t.genomeRange,e,f);else if(t&&(i=this.getExonColor(t.rangeStart,t.rangeEnd,c),o=i+" 0%, #FFF 50%, #00F 100%",A+=this.getExonHtml(t.exonIndex,o,t.from,t.rangeEnd,t.genomeRange,e,f)),t&&s){for(let i=t.exonIndex+1;i'+t+""}}O=''+g.toString()+" Pos ",O+="",O+="1e-200&&(h=parseFloat(h).toExponential()),n.scores.bit_score;let p=t.targets[l].seqdata,m=i.seqdata,u=n.segs;for(let e=0,t=u.length;e0&&(l=n+"H"+d.toString().padStart(2,"0")+")","coil"==t&&(s.selectionCls.selectResidueList(r,l,l,o,a),o||(o=!0)),r={})),n=e+"_H"+d.toString().padStart(2,"0"),r[p]=1,i.ssend&&(h=e+"_C(H"+d.toString().padStart(2,"0"),"helix"==t&&(s.selectionCls.selectResidueList(r,n,n,o,a),o||(o=!0)),r={})):"E"==m?(i.ssbegin&&(++c,Object.keys(r).length>0&&(l=n+"S"+c.toString().padStart(2,"0")+")","coil"==t&&(s.selectionCls.selectResidueList(r,l,l,o,a),o||(o=!0)),r={})),n=e+"_S"+c.toString().padStart(2,"0"),r[p]=1,i.ssend&&(h=e+"_C(S"+c.toString().padStart(2,"0"),"sheet"==t&&(s.selectionCls.selectResidueList(r,n,n,o,a),o||(o=!0)),r={})):(n=h+"-",r[p]=1)}}Object.keys(r).length>0&&(l=n+"Cterm)","coil"==t&&s.selectionCls.selectResidueList(r,l,l,o,a))}defineIgstrand(e,t){let s=this.icn3d,i=s.icn3dui;$("#"+s.pre+"dl_definedsets").hasClass("ui-dialog-content")&&$("#"+s.pre+"dl_definedsets").dialog("isOpen")||(i.htmlCls.dialogCls.openDlg("dl_definedsets","Select sets"),$("#"+s.pre+"atomsCustom").resizable());let n,l,r,o,a,d={},c=!1,h=!0,p=0,m=0,u="NT";s.hAtoms={};let g=!1;for(let i=0,f=s.chainsSeq[e].length;i0&&("igstrand"==a?(++p,n="Strand-"+r+"-"+e+"-"+p.toString().padStart(3,"0"),n=n.replace(/'/g,"`"),"igstrand"==t&&(s.selectionCls.selectResidueList(d,n,n,c,h),c||(c=!0)),u=r):"igloop"==a&&(++m,n="Loop-"+u+"_"+l+"-"+e+"-"+m.toString().padStart(3,"0"),n=n.replace(/'/g,"`"),"igloop"==t&&(s.selectionCls.selectResidueList(d,n,n,c,h),c||(c=!0))),d={}),d[C]=1,r=l,a=o,g=!0))}"igstrand"==a?(++p,n="Strand-"+r+"-"+e+"-"+p.toString().padStart(3,"0"),n=n.replace(/'/g,"`"),"igstrand"==t&&s.selectionCls.selectResidueList(d,n,n,c,h)):"igloop"==a&&(++m,l="CT",n="Loop-"+u+"_"+l+"-"+e+"-"+m.toString().padStart(3,"0"),n=n.replace(/'/g,"`"),"igloop"==t&&s.selectionCls.selectResidueList(d,n,n,c,h))}simplifyText(e){this.icn3d.icn3dui;let t,s,i="",n=!1,l=-1;for(t=0,s=(e=e.replace(/undefined/g," ")).length;t20)return!1;if(void 0!==o.giSeq&&void 0!==o.giSeq[e]){let r=this.getFullText(s);return s=r.text,this.showNewTrack(e,t,s,void 0,void 0,i,n,l),!1}setTimeout((function(){a.checkGiSeq(e,t,s,i,n,l,r+1)}),100)}getFullText(e){this.icn3d.icn3dui;let t="",s=[],i=[],n=e.split(","),l=-1;for(let e=0,r=n.length;ep?t+=c.substr(0,p):t+=c;for(let e=0;ed&&(d=t.length,c=h),++h}o=n.htmlCls.baseUrl+"pwaln/pwaln.fcgi?from=msa";let p=e.split(","),m={};m[t]=0;for(let e=0,t=p.length;e0&&(g+=","+p.join(","));let f={targets:u,queries:g},b=await n.getAjaxPostPromise(o,f);if(!b.data)return void console.log("The protein accessions "+u+","+g+" can not be aligned...");let C=[];i.qt_start_end={};let y=[],v=[],_=Object.keys(b.targets)[0],w=b.targets[_].seqdata;p.splice(0,0,t);for(let e=0,s=p.length;eA&&(A=e)}let x=S,k=w.length-(A+1),O=[],R=[];for(let e=0,t=p.length;ea&&(a=t.length,d=c),++c}s.qt_start_end={};let m="genomeRes",u={};for(let e=0,i=h.length;ef&&(f=e)}for(let e=0,t=h.length;e0&&(d=h,o.targetGapHash[a+o.startposGiSeq]={from:a+o.startposGiSeq,to:d+m-1+o.startposGiSeq}),c=t[s],h=p,"-"!=t[s]?(++p,f=s,o.seqEndLen[e]=b-1-f,u||(g=s,o.seqStartLen[e]=g,u=!0)):++m;o.maxAnnoLength0&&(C+=" "),C+=e+"_"+o.targetGapHash[e].from+"_"+o.targetGapHash[e].to,++y;let v={};for(let a=0,d=i.length;a5?(l.uniprot2acc&&l.uniprot2acc[y]&&(y=l.uniprot2acc[y]),f=y):f=e,y.length>5){let e="";for(let t=0,s=l.chainsSeq.length;t"),d=a[1].indexOf("\n");n=a[1].substr(d+1).replace(/\n/g,"");for(let e=2,t=a.length;e0&&($("#"+e.pre+"anno_cdd")[0].checked?(this.setAnnoTabCdd(),t.htmlCls.clickMenuCls.setLogCmd("set annotation cdd",!0)):(this.hideAnnoTabCdd(),t.htmlCls.clickMenuCls.setLogCmd("hide annotation cdd",!0)))}showAnnoSelectedChains(){let e=this.icn3d,t=e.icn3dui,s={};for(let t in e.hAtoms){let i=e.atoms[t];s[i.structure+"_"+i.chain]=1}$("#"+e.pre+"dl_annotations > .icn3d-annotation").hide();for(let i in s){$("#"+e.pre+"anno_"+i).length&&$("#"+e.pre+"anno_"+i).show();let s=e.firstAtomObjCls.getFirstCalphaAtomObj(e.chains[i]);if(void 0!==s.resn){let i=t.utilsCls.residueName2Abbr(s.resn.substr(0,3));$("#"+e.pre+"anno_"+i).show()}}}showAnnoAllChains(){let e=this.icn3d;e.icn3dui,$("#"+e.pre+"dl_annotations > .icn3d-annotation").show()}setAnnoView(e){let t=this.icn3d;t.icn3dui.bNode||("detailed view"===e?(t.view="detailed view",$("#"+t.pre+"dl_anno_view_tabs").tabs("option","active",1)):(t.view="overview",$("#"+t.pre+"dl_anno_view_tabs").tabs("option","active",0)))}setAnnoDisplay(e,t){let s=this.icn3d;s.icn3dui;let i=["giseq","custom","site","ptm","snp","clinvar","cdd","domain","interaction","ssbond","crosslink","transmem"];for(let n in i){let l=i[n];$("[id^="+s.pre+t+"_"+l+"]").attr("style",e)}}showFixedTitle(){this.icn3d.icn3dui;this.setAnnoDisplay("display:block;","tt")}hideFixedTitle(){this.icn3d.icn3dui;this.setAnnoDisplay("display:none!important;","tt")}setAnnoViewAndDisplay(e){let t=this.icn3d;if(t.icn3dui,"detailed view"===e){this.setAnnoView("detailed view");let e="display:block;";this.setAnnoDisplay(e,"dt"),$("#"+t.pre+"seqguide_wrapper").attr("style",e),e="display:none;",this.setAnnoDisplay(e,"ov")}else{this.setAnnoView("overview"),this.hideFixedTitle();let e="display:none;";this.setAnnoDisplay(e,"dt"),$("#"+t.pre+"seqguide_wrapper").attr("style",e),e="display:block;",this.setAnnoDisplay(e,"ov")}}async updateClinvar(){let e=this.icn3d;if(e.icn3dui,void 0===e.bClinvarShown||!e.bClinvarShown)for(let t in e.protein_chainid){let s=e.protein_chainid[t];await e.annoSnpClinVarCls.showClinvar(t,s)}e.bClinvarShown=!0}async updateSnp(){let e=this.icn3d;if(e.icn3dui,void 0===e.bSnpShown||!e.bSnpShown)for(let t in e.protein_chainid){let s=e.protein_chainid[t];await e.annoSnpClinVarCls.showSnp(t,s)}e.bSnpShown=!0}updateDomain(){let e=this.icn3d;e.icn3dui,void 0!==e.bDomainShown&&e.bDomainShown||e.annoDomainCls.showDomainAll(),e.bDomainShown=!0}updateInteraction(){let e=this.icn3d;if(e.icn3dui,void 0===e.bInteractionShown||!e.bInteractionShown)for(let t in e.interactChainbase){let s=e.interactChainbase[t];e.annoContactCls.showInteraction(t,s)}e.bInteractionShown=!0}async updatePTM(){let e=this.icn3d;if(e.icn3dui,void 0===e.bPTMShown||!e.bPTMShown)for(let t in e.PTMChainbase){let s=e.PTMChainbase[t];await e.annoPTMCls.showPTM(t,s,"ptm")}e.bPTMShown=!0}updateSsbond(){let e=this.icn3d;if(e.icn3dui,void 0===e.bSSbondShown||!e.bSSbondShown)for(let t in e.ssbondChainbase){let s=e.ssbondChainbase[t];e.annoSsbondCls.showSsbond(t,s)}e.bSSbondShown=!0}updateCrosslink(){let e=this.icn3d;if(e.icn3dui,void 0===e.bCrosslinkShown||!e.bCrosslinkShown)for(let t in e.crosslinkChainbase){let s=e.crosslinkChainbase[t];e.annoCrossLinkCls.showCrosslink(t,s)}e.bCrosslinkShown=!0}async updateTransmem(){let e=this.icn3d,t=e.icn3dui;if(void 0===e.bTranememShown||!e.bTranememShown)for(let s in e.protein_chainid){let i=e.protein_chainid[s];if(void 0!==t.cfg.opmid)e.annoTransMemCls.showTransmem(s,i);else if(e.bAfMem&&e.afmem_start_end){let t=e.afmem_start_end[0],n=e.afmem_start_end[1];await e.annoPTMCls.showPTM(s,i,"afmem",t,n)}else await e.annoPTMCls.showPTM(s,i,"transmem")}e.bTranememShown=!0}}class Et{constructor(e){this.icn3d=e}showAnnotations_part1(){let e=this.icn3d,t=e.icn3dui;if(t.htmlCls.dialogCls.openDlg("dl_selectannotations","Sequences and Annotations"),(void 0===e.bAssemblyNote||!e.bAssemblyNote)&&void 0!==e.asuCnt){let t=" Assembly Tips: Only the asymmetric unit is shown in the sequence window."+e.asuCnt+" asymmetric unit).
";$("#"+e.pre+"dl_annotations_tabs").append(t),e.bAssemblyNote=!0}e.bResetAnno&&(e.giSeq={},e.currClin={},e.resi2disease_nonempty={},e.baseResi={},e.matchedPos={},$("#"+t.pre+"dl_annotations").empty(),e.annotationCls.setAnnoView("overview"));let s={},i={},n={};if(void 0===e.bAnnoShown||!e.bAnnoShown||e.bResetAnno){e.protein_chainid={};let l,r=Object.keys(e.chains);void 0===e.giSeq&&(e.giSeq={}),void 0===e.currClin&&(e.currClin={}),void 0===e.resi2disease_nonempty&&(e.resi2disease_nonempty={}),void 0===e.baseResi&&(e.baseResi={}),void 0===e.matchedPos&&(e.matchedPos={}),l=t.bNode?500:t.cfg.notebook?t.htmlCls.WIDTH/2:$("#"+e.pre+"dl_selectannotations").dialog("option","width"),e.seqAnnWidth=l-120-60-50;for(let l=0,o=r.length;l1&&"1"==d.substr(d.length-1)?(d=d.substr(0,d.length-1),a=r[l].substr(0,r[l].indexOf("_"))+"_"+d):a=r[l],e.proteins.hasOwnProperty(o.serial)&&e.chainsSeq[r[l]].length>1)e.protein_chainid[r[l]]=a;else if(e.nucleotides.hasOwnProperty(o.serial)&&e.chainsSeq[r[l]].length>1)s[r[l]]=a;else if(e.chainsSeq[r[l]].length>1)i[r[l]]=a;else{let t=e.chainsSeq[r[l]][0].name,s=r[l]+"_"+e.chainsSeq[r[l]][0].resi;void 0===n[t]&&(n[t]=[]),n[t].push(s)}if((void 0!==t.cfg.pdbid||void 0!==t.cfg.opmid||void 0!==t.cfg.mmcifid||void 0!==t.cfg.mmtfid)&&(e.proteins.hasOwnProperty(o.serial)||e.nucleotides.hasOwnProperty(o.serial)))for(let t=0,s=e.chainsSeq[r[l]].length;te.maxAnnoLengthOri&&(e.protein_chainid.hasOwnProperty(t)||s.hasOwnProperty(t))&&(e.maxAnnoLengthOri=e.chainsSeq[t].length);e.maxAnnoLength=e.maxAnnoLengthOri}return{nucleotide_chainid:s,chemical_chainid:i,chemical_set:n}}async showAnnotations(){let e=this.icn3d,t=e.icn3dui,s=this,i=this.showAnnotations_part1(),n=i.nucleotide_chainid,l=i.chemical_chainid,r=i.chemical_set;if(!e.bAnnoShown||e.bResetAnno)if(e.bAnnoShown=!0,void 0===t.cfg.blast_rep_id){if(e.bFullUi){if(void 0!==t.cfg.mmtfid){let t=Object.keys(e.structures)[0];await e.mmcifParserCls.downloadMmcifSymmetry(t,"mmtfid")}await this.showAnnoSeqData(n,l,r)}}else if(void 0===t.cfg.blast_rep_id||e.bSmithwm||e.bLocalSmithwm){if(void 0!==t.cfg.blast_rep_id&&(e.bSmithwm||e.bLocalSmithwm)){let i,o,a=[t.cfg.blast_rep_id];if(-1!=t.cfg.query_id.indexOf(">")?o=t.cfg.query_id.substr(t.cfg.query_id.indexOf("\n")+1):!/\d/.test(t.cfg.query_id)||t.cfg.query_id.length>50?o=t.cfg.query_id:a.push(t.cfg.query_id),e.blastAcxn){let s=t.cfg.afid+"_A",n="";for(let t=0,i=e.chainsSeq[s].length;t5){let n;e.uniprot2acc&&e.uniprot2acc[i]?e.uniprot2acc[i]:e.uniprot2acc={},n="https://rest.uniprot.org/uniprotkb/search?format=json&fields=xref_geneid,gene_names&query="+i;let l=await t.getAjaxPromise(n,"json"),r=l.results[0]&&l.results[0].uniProtKBCrossReferences&&l.results[0].uniProtKBCrossReferences[0]?l.results[0].uniProtKBCrossReferences[0].id:void 0,o=l.results[0]&&l.results[0].genes&&l.results[0].genes[0]&&l.results[0].genes[0].geneName?l.results[0].genes[0].geneName.value:"ID "+r;e.chainsGene[s]={geneId:r,geneSymbol:o}}}for(let s in e.protein_chainid){let i=t.utilsCls.isMobile()?"none":"button",l=e.showSeqCls.getProteinName(s),r=l,o=0==n?"Proteins : "+e.chainsGene[s].geneSymbol+" )":"",d=s.substr(0,s.indexOf("_")),c=d.length>5?''+s+" ":s,h=""+o+"
Annotations of "+c+" :
"+r+" "+a+" "+this.addButton(s,"icn3d-addtrack","Add Track","Add a custom track",60,i)+" ";h+=this.addButton(s,"icn3d-customcolor","Custom Color/Tube","Use a custom file to define the colors or tubes in 3D structure",110,i)+" ",h+=this.addButton(s,"icn3d-helixsets","Helix Sets",'Define sets for each helix in this chain and add them to the menu of "Defined Sets"',60,i)+" "+this.addButton(s,"icn3d-sheetsets","Sheet Sets",'Define sets for each sheet in this chain and add them to the menu of "Defined Sets"',60,i)+" "+this.addButton(s,"icn3d-coilsets","Coil Sets",'Define sets for each coil in this chain and add them to the menu of "Defined Sets"',60,i),e.bShowRefnum&&e.chainid2refpdbname.hasOwnProperty(s)&&e.chainid2refpdbname[s].length>0&&(h+=" "+this.addButton(s,"icn3d-igstrandsets","Ig Strand Sets",'Define sets for each Ig strand in this chain and add them to the menu of "Defined Sets"',80,i)+" "+this.addButton(s,"icn3d-igloopsets","Ig Loop Sets",'Define sets for each Ig loop in this chain and add them to the menu of "Defined Sets"',80,i)),$("#"+e.pre+"dl_annotations").append(h);let p=["giseq","cdd","clinvar","snp","site","ptm","ssbond","crosslink","transmem","domain","custom","interaction"];for(let t in p){let i=p[t];$("#"+e.pre+"anno_"+s).append(this.getAnDiv(s,i))}$("#"+e.pre+"anno_"+s).append("
"),++n}if(t.bNode||e.annoCddSiteCls.setToolTip(),void 0!==e.chainid_seq)await this.processSeqData(e.chainid_seq);else try{let n=[],l=[];for(let e=0,t=i.length;e
=6?l.push(i[e]):n.push(i[e])}if(n.length>0){let s=t.htmlCls.baseUrl+"/vastdyn/vastdyn.cgi?chainlist="+n;e.chainid_seq=await t.getAjaxPromise(s,"jsonp")}else e.chainid_seq={};for(let t=0,s=l.length;t40&&(r=r.substr(0,40)+"...");let o="";0==i&&("protein"==s?o="Proteins : Nucleotides : Chemicals/Ions/Water : "+o+""+e+" : "+r+"
"),$("#"+n.pre+"anno_"+e).append(this.getAnDiv(e,"giseq")),$("#"+n.pre+"anno_"+e).append(this.getAnDiv(e,"interaction")),$("#"+n.pre+"anno_"+e).append("Chemicals/Ions/Water : "+e+" ":""+e+" ",$("#"+n.pre+"dl_annotations").append(""+r+i+"
"),$("#"+n.pre+"anno_"+e).append(""),$("#"+n.pre+"anno_"+e).append("';c+='
Chem. '+e+"
",c+='
Count: '+t.length+" ",c+='
';let h=c,p=c;for(let s=0,i=t.length;s3&&(l=i.substr(0,3)),s'+l+" "}let m=l.htmlCls.GREY8,u=Math.round(n.seqAnnWidth*t.length/n.maxAnnoLength);u<1&&(u=1),p+='
',c="",c+="
",c+="
14?"Query: "+o.substr(0,6)+"...":isNaN(s.cfg.query_id)?"Query: "+o:"Query: gi "+o;let a="cannot be aligned";t.queryStart="",t.queryEnd="",t.bRender&&alert("The sequence can NOT be aligned to the structure"),t.showSeqCls.showSeq(i,n,void 0,e,l,a,r)}else if(s.cfg.blast_rep_id==i&&(void 0!==t.seqStructAlignData||void 0!==t.seqStructAlignDataSmithwm)){let e,l,r,o,a,d=s.cfg.oriQuery_id?s.cfg.oriQuery_id:s.cfg.query_id;if(e=d.length>14?"Query: "+d.substr(0,6)+"...":isNaN(s.cfg.query_id)?"Query: "+d:"Query: gi "+d,void 0!==t.seqStructAlignData){let e,s,i=t.seqStructAlignData;if(void 0!==i.data){e=i.data[0].query;let t=Object.keys(i.data[0].targets);s=i.data[0].targets[t[0]],s=void 0!==s&&s.hsps.length>0?s.hsps[0]:void 0}if(void 0!==e&&void 0!==s){l=s.scores.e_value.toPrecision(2),l>1e-200&&(l=parseFloat(l).toExponential()),s.scores.bit_score;let t=Object.keys(i.targets);r=i.targets[t[0]].seqdata,o=e.seqdata,a=s.segs}}else{let e=t.seqStructAlignDataSmithwm;l=e.score,r=e.target.replace(/-/g,""),o=e.query.replace(/-/g,""),a=[];let s=-1,i=-1,n=!1,d={};for(let t=0,l=e.target.length;t0)if(i.orifrom-ni.from-l)for(let t=n+1;t
"+i+"
"+i+"
"+s+"
"}addSnpButton(e,t,s,i,n,l){let r=this.icn3d;return r.icn3dui,""+s+"
"}conservativeReplacement(e,t){let s=this.icn3d.icn3dui,i=-1!==s.parasCls.b62ResArray.indexOf(e)?s.parasCls.b62ResArray.indexOf(e):s.parasCls.b62ResArray.length-1,n=-1!==s.parasCls.b62ResArray.indexOf(t)?s.parasCls.b62ResArray.indexOf(t):s.parasCls.b62ResArray.length-1;return s.parasCls.b62Matrix[i][n]>0}getColorhexFromBlosum62(e,t){let s=this.icn3d.icn3dui,i="333333";if(!e||!t)return i;e=e.toUpperCase(),t=t.toUpperCase();let n=-1!==s.parasCls.b62ResArray.indexOf(e)?s.parasCls.b62ResArray.indexOf(e):s.parasCls.b62ResArray.length-1,l=-1!==s.parasCls.b62ResArray.indexOf(t)?s.parasCls.b62ResArray.indexOf(t):s.parasCls.b62ResArray.length-1,r=s.parasCls.b62Matrix[n][l];if(void 0===r)return"333333";if(r>0){let e=221-parseInt(r/11*221),t=e<10?"0"+e.toString(16):e.toString(16);i="DD"+t+t}else{let e=221-parseInt(-1*r/4*221),t=e<10?"0"+e.toString(16):e.toString(16);i=t+t+"DD"}return i}}class Pt{constructor(e){this.icn3d=e}showSeq(e,t,s,i,n,l,r){let o,a=this.icn3d,d=a.icn3dui,c=!1;if(void 0===d.cfg.mmdbid&&void 0===d.cfg.gi&&void 0===d.cfg.blast_rep_id&&void 0===d.cfg.align&&void 0===d.cfg.chainalign&&void 0===d.cfg.mmdbafid){c=!0,o=[];for(let t=0;t10){u='';let t=a.firstAtomObjCls.getFirstCalphaAtomObj(a.chains[e]);void 0===d.cfg.mmdbid&&void 0===d.cfg.gi&&void 0===d.cfg.blast_rep_id&&void 0===d.cfg.align&&void 0===d.cfg.chainalign&&void 0===d.cfg.mmdbafid||void 0===t.resi_ori||t.resi_ori==t.resi||-1!=e.indexOf("Misc")?u+='
':u+='
NCBI Residue Numbers
',u+='
',b+=u+"
",g+=u+'
';let s=0,i=0,n="";a.seqStartLen&&a.seqStartLen[e]&&(g+=this.insertMulGap(a.seqStartLen[e]," "));for(let t=0,l=o.length;t",l%10==0&&(g+=l);let r=e+"_"+l,o=l%10!=0&&l%10!=1&&l%10!=9;if(a.residues.hasOwnProperty(r)){let e=a.firstAtomObjCls.getFirstCalphaAtomObj(a.residues[r]);"H"==a.secondaries[r]&&e.ssbegin?(++s,n='H'+s+" ",o&&(g+=n,n="")):"E"==a.secondaries[r]&&e.ssbegin?(++i,"green"==a.sheetcolor?n='S'+i+" ":"yellow"==a.sheetcolor&&(n='S'+i+" "),o&&(g+=n,n="")):e.ssend&&(n=""),""!=n&&o&&(g+=n,n="")}g+=" "}a.seqStartLen&&a.seqStartLen[e]&&(g+=this.insertMulGap(a.seqEndLen[e]," ")),g+='
',g+="",g+="
",g+="
',u+='
',u+='
',b+=u+"
",g+=u+'
',a.seqStartLen&&a.seqStartLen[e]&&(g+=this.insertMulGap(a.seqStartLen[e],"-"));for(let t=0,s=o.length;t':'',g+=" ";else if("E"==a.secondaries[s]){a.firstAtomObjCls.getFirstCalphaAtomObj(a.residues[s]).ssend?"green"==a.sheetcolor?g+='':"yellow"==a.sheetcolor&&(g+=''):"green"==a.sheetcolor?g+='':"yellow"==a.sheetcolor&&(g+=''),g+=" "}else"c"==a.secondaries[s]?g+=' ':"o"==a.secondaries[s]&&(g+=' ');else g+="- "}a.seqStartLen&&a.seqStartLen[e]&&(g+=this.insertMulGap(a.seqEndLen[e],"-")),g+=' ",g+=" ':'
';let C="Protein",y="Protein";void 0!==s&&("nucleotide"==s?(C="Nucl.",y="Nucleotide"):"chemical"==s&&(C="Chem.",y="Chemical")),u+='
'+C+" "+e+"
",u+='
'+(a.baseResi[e]+1).toString()+" ",b+=u+"
";let v='
';g+=u+v,f+=u+v;let _,w=0;a.seqStartLen&&a.seqStartLen[e]&&(g+=this.insertMulGap(a.seqStartLen[e],"-"));for(let t=0,s=o.length;t1&&(i=s[0]+".."),_=a.ParserUtilsCls.getResi(e,t),a.residues.hasOwnProperty(e+"_"+_)){let n="333333";if(d.cfg.blast_rep_id==e&&void 0!==a.fullpos2ConsTargetpos&&void 0!==a.fullpos2ConsTargetpos[t+w])n=a.fullpos2ConsTargetpos[t+w].color;else{let t=a.firstAtomObjCls.getFirstCalphaAtomObj(a.residues[e+"_"+_]),s=void 0===t.color||"FFFFFF"===t.color.getHexString().toUpperCase()||"FFF"===t.color.getHexString().toUpperCase()?"DDDDDD":t.color.getHexString();n=void 0!==t.color?s:"CCCCCC"}g+=''+i+" "}else i=i.toLowerCase(),g+=''+i+" "}a.seqStartLen&&a.seqStartLen[e]&&(g+=this.insertMulGap(a.seqEndLen[e],"-")),d.cfg.blast_rep_id==e&&(a.opts.color=a.blastAcxn?"confidence":"conservation",a.setColorCls.setColorByOptions(a.opts,a.atoms));let S=a.firstAtomObjCls.getFirstCalphaAtomObj(a.chains[e]),A=S.color?S.color.getHexString():"CCCCCC",x=Math.round(a.seqAnnWidth*o.length/(a.maxAnnoLength+a.nTotalGap));if(x<1&&(x=1),a.seqStartLen&&a.seqStartLen[e]&&(f+=this.insertMulGapOverview(e,a.seqStartLen[e])),d.cfg.blast_rep_id!=e)f+=''+e+"
";else{let t=[],s=[];t.push(0);for(let e=0,i=o.length;e';for(let i=0,n=t.length;i'+e+" ";f+="
'+_+" ",u+="",u+="'+n+"
",u+='';g+=u+t,f+=u+t;let s=0,i=0,l=1;a.queryStart;for(let t=0,n=r.length;t- ";else if(" "==n)g+=" ";else{let r=a.fullpos2ConsTargetpos[t].pos;if(a.residues.hasOwnProperty(e+"_"+r)){let s=a.fullpos2ConsTargetpos[t].color;g+=''+n+" "}else n=n.toLowerCase(),g+=''+n+" ";f+=this.insertGapOverview(e,t);let o=Math.round(a.seqAnnWidth*t/(a.maxAnnoLength+a.nTotalGap)-s-i);o>=0&&(f+='
',f+='
',s+=o,i+=l)}}u=''+i+"
",u+=''+a.queryStart+" ",b+=u+"';g+=u+t,f+=u+t;let s=a.queryStart;for(let t=0,i=l.length;t- ":(void 0===a.fullpos2ConsTargetpos||void 0===a.fullpos2ConsTargetpos[t]||a.residues.hasOwnProperty(e+"_"+a.fullpos2ConsTargetpos[t].pos)||(i=i.toLowerCase()),g+=''+i+" ",++s)}let o=a.firstAtomObjCls.getFirstCalphaAtomObj(a.chains[e]),d=void 0===o.color||"FFFFFF"===o.color.getHexString()?"DDDDDD":o.color.getHexString(),c=void 0!==o.color?d:"CCCCCC",h=[],p=[],m="-";for(let e=0,t=l.length;e ',f+=''+i+"
"}u=''+a.queryEnd+" ",u+="",u+="',u+='
',u+='
PDB Residue Numbers
',u+='
',b+=u+"
",g+=u+'
',a.seqStartLen&&a.seqStartLen[e]&&(g+=this.insertMulGap(a.seqStartLen[e],"-"));for(let t=0,s=o.length;t",e%10==0&&(g+=e+" "),g+=" "}else g+="
"}a.seqStartLen&&a.seqStartLen[e]&&(g+=this.insertMulGap(a.seqEndLen[e],"-")),g+='
',g+="",g+="
",g+="
",g+="
';p+='
',p+=i?'
Custom Ref. No.
':1==s?'
Kabat Ref. No.
':2==s?'
IMGT Ref. No.
':'
IgStRAnD Ref. No.
',p+='
',o+=p+"
",r+=p+'
';let m=!1;for(let s=0,l=e.length;s0){m=!0;break}}if(1==s&&!m)return{html:"",html3:""};let u=!1;for(let s=0,l=e.length;s0){u=!0;break}}if(2==s&&!u)return{html:"",html3:""};let g,f,b,C,y,v,_,w,S=!1,A="",x="",k=!1,O=!1,R=1,I=!1;if(!i&&!s&&!l.bNode){let e=l.hashUtilsCls.intHash(n.chains[t],n.hAtoms),s=n.firstAtomObjCls.getResiduesFromAtoms(e);for(let e in s)delete n.residIgLoop[e]}let T,E=[],P={},M=0,D=0,H=0,F=0;if(!i&&!s){for(let s=0,i=e.length;s=0;--t)"G"!=E[t].strand.substr(0,1)&&E[t].endRefnum-E[t].startRefnum+1<3&&(t!=e-1&&(E[t+1].loopResCnt+=E[t].loopResCnt+parseInt(E[t].endResi)-parseInt(E[t].startResi)+1),E.splice(t,1));M=0;let s,i,l=0,r=!0,o=!0,a=0;I=!1;let d=0;if(E.length>0)for(let c=0,h=e.length;cE[M].endResi:parseInt(e)>parseInt(E[M].endResi),c=!t&&!p,t)if(n.residIgLoop[h]=1,r)I?(i=E[M].startRefnum-E[M].loopResCnt+l,s=E[M].strand+i,g=s+E[M].strandPostfix):(s=void 0,g=void 0);else if(a>=0&&"G"==E[a].strand.substr(0,1))o?I&&n.resid2refnum[h]?(o=!0,i=E[a].endRefnum+l,s=E[a].strand+i,g=s+E[a].strandPostfix):(I=!1,r=!0,o=!1,s=void 0,g=void 0):(s=void 0,g=void 0);else{o=!0;let e=E[M].loopResCnt;l<=parseInt(e/2+.5)?(i=E[a].endRefnum+l,s=E[a].strand+i,g=s+E[a].strandPostfix):(i=E[M].startRefnum-e+l-1,s=E[M].strand+i,g=s+E[M].strandPostfix)}else c?(r=!1,E[M].anchorRefnum&&(e==E[M].startResi?(d=E[M].anchorRefnum-E[M].resCntBfAnchor,E[M].startRefnum=d):e==E[M].endResi&&(E[M].endRefnum=d),s=E[M].strand+d,g=s+E[M].strandPostfix),e==E[M].endResi&&(++M,l=0,E[M]||--M)):p&&(n.residIgLoop[h]=1,o?n.resid2refnum[h]?(o=!0,i=E[M].endRefnum+l,s=E[M].strand+i,g=s+E[M].strandPostfix):(o=!1,s=void 0,g=void 0):(s=void 0,g=void 0))}else g=void 0;x=A,a=M-1,n.resid2refnum[h]=g,b=n.refnumCls.rmStrandFromRefnumlabel(g),n.refnum2residArray.hasOwnProperty(b)?n.refnum2residArray[b].push(h):n.refnum2residArray[b]=[h],n.chainsMapping.hasOwnProperty(t)||(n.chainsMapping[t]={}),n.chainsMapping[t][h]=s}}for(let l=0,o=e.length;l'+b+" ":'
'}else r+="
";else if(1==s||2==s)if(b){let e=parseInt(b).toString(),t='style="color:'+this.getRefnumColor(A,!0)+'"';r+=parseInt(e.substr(e.length-2,2))%2==0?"
'+b+" ":"
'}else r+="
";else" "!=A?(S=n.residIgLoop[e],r+=this.getRefnumHtml(e,b,f,g,A,S,a)):r+="
";else r+="
";x=T}return r+='
',r+="",r+="
",r+="
",r+="
'+g+" "):b+=" ':(o.hAtomsRefnum=a.hashUtilsCls.unionHash(o.hAtomsRefnum,o.residues[e]),b+="'+i.substr(0,1)+" "+i.substr(1)+""+t+"";return i}insertGapOverview(e,t){let s=this.icn3d;s.icn3dui;let i="";return void 0!==s.targetGapHash&&s.targetGapHash.hasOwnProperty(t)&&(i+=this.insertMulGapOverview(e,s.targetGapHash[t].to-s.targetGapHash[t].from+1)),i}insertMulGapOverview(e,t){let s=this.icn3d;s.icn3dui;let i="",n=s.seqAnnWidth*t/(s.maxAnnoLength+s.nTotalGap);return n=parseInt(n),i+='
',i}setAlternativeSeq(e,t){let s=this.icn3d;s.icn3dui;let i=s.chainsSeq[e];s.giSeq[e]=[];for(let t=0,n=i.length;t1&&s.htmlCls.clickMenuCls.setLogCmd("select sets "+e,!0)}else{let o={};if(void 0!==$(e).attr("domain")||void 0!==$(e).attr("feat")||void 0!==$(e).attr("3ddomain")||void 0!==$(e).attr("custom")){t.hlUpdateCls.hlSummaryDomain3ddomain(e);let a,d,c,h=$(e).attr("from").split(","),p=$(e).attr("to").split(",");r.substr(0,r.indexOf("_"));for(let s=0,i=h.length;s1&&s.htmlCls.clickMenuCls.setLogCmd("select sets "+c,!0)}}else{t.bCtrl||t.bShift?(t.currSelectedSets.push(i),t.selectionCls.selectAChain(r,i,!0,!0)):(t.currSelectedSets=[i],t.selectionCls.selectAChain(r,i,t.bAlignSeq)),t.bAlignSeq?s.htmlCls.clickMenuCls.setLogCmd("select alignChain "+r,!0):s.htmlCls.clickMenuCls.setLogCmd("select chain "+r,!0);let e=t.currSelectedSets.join(" or ");t.currSelectedSets.length>1&&s.htmlCls.clickMenuCls.setLogCmd("select sets "+e,!0)}else t.hlObjectsCls.removeHlObjects(),t.hlUpdateCls.removeHl2D(),$("#"+t.pre+"atomsCustom").val("")}}selectResidues(e,t){let s=this.icn3d,i=s.icn3dui;if(!i.bNode&&(!1!==s.bSelectResidue||s.bShift||s.bCtrl||s.selectionCls.removeSelection(),void 0!==e&&""!==e)){e=e.substr(e.indexOf("_")+1),s.bSelectResidue=!0,$(t).toggleClass("icn3d-highlightSeq");let n=e.substr(e.indexOf("_")+1);if(s.residues.hasOwnProperty(n))if($(t).hasClass("icn3d-highlightSeq")){for(let e in s.residues[n])s.hAtoms[e]=1;if(s.selectedResidues[n]=1,s.bAnnotations&&void 0!==$(t).attr("disease")){let e=$(t).attr("disease"),l=s.applyCenterCls.centerAtoms(i.hashUtilsCls.hash2Atoms(s.residues[n],s.atoms)),r=15;e.length>r&&(e=e.substr(0,r)+"...");let o=s.LABELSIZE,a=i.htmlCls.GREYD;s.analysisCls.addLabel(e,l.center.x,l.center.y,l.center.z,o,a,void 0,"custom")}}else{for(let e in s.residues[n])delete s.hAtoms[e];delete s.selectedResidues[n],s.hlObjectsCls.removeHlObjects()}}}}class Dt{constructor(e){this.icn3d=e}update2DdgmContent(){let e=this.icn3d,t=e.icn3dui,s="";void 0!==t.cfg.mmdbid||void 0!==t.cfg.gi?(s+=e.diagram2dCls.draw2Ddgm(e.interactionData,e.inputid,void 0,!0),s+=e.diagram2dCls.set2DdgmNote(),$("#"+e.pre+"dl_2ddgm_html").html(s)):e.mmdbidArray&&(void 0!==t.cfg.align||void 0!==t.cfg.chainalign||e.bRealign)&&(s+=e.diagram2dCls.draw2Ddgm(e.interactionData1,e.mmdbidArray[0].toUpperCase(),0,!0),void 0!==e.mmdbid_q&&e.mmdbid_q===e.mmdbid_t?s+=e.diagram2dCls.draw2Ddgm(e.interactionData2,e.mmdbidArray[0].toUpperCase(),1,!0):s+=e.diagram2dCls.draw2Ddgm(e.interactionData2,e.mmdbidArray[1].toUpperCase(),1,!0),s+=e.diagram2dCls.set2DdgmNote(!0),$("#"+e.pre+"dl_2ddgm_html").html(s))}changeSeqColor(e){let t=this.icn3d,s=t.icn3dui;for(let i=0,n=e.length;i0&&($("#"+e.pre+"dl_2ddgm svg line").attr("stroke","#000000"),$("#"+e.pre+"dl_2ddgm line").attr("stroke-width",1))}removeHlMenus(){let e=this.icn3d;e.icn3dui,$("#"+e.pre+"atomsCustom").val(""),$("#"+e.pre+"atomsCustom")[0].blur()}updateHlAll(e,t,s,i){let n=this.icn3d,l=n.icn3dui;n.prevHighlightAtoms=l.hashUtilsCls.cloneHash(n.hAtoms),this.updateHlObjects(i),void 0!==e?this.updateHlSeqInChain(e,s):this.updateHlSeq(void 0,void 0,s),this.updateHl2D(),(void 0===t||t)&&this.updateHlMenus(e)}updateHlObjects(e){let t=this.icn3d;t.icn3dui,t.hlObjectsCls.removeHlObjects(),(t.hAtoms&&t.atoms&&Object.keys(t.hAtoms).length0&&(e=s.defNames2Residues[i]);let t={};if(void 0!==s.defNames2Atoms[i]&&s.defNames2Atoms[i].length>0){for(let e=0,n=s.defNames2Atoms[i].length;e0&&(r=t.firstAtomObjCls.getFirstCalphaAtomObj(l))}let o=void 0!==r&&void 0!==r.color?"#"+r.color.getHexString():"#FFFFFF",a=$("#"+t.pre+"dl_2ddgm g[chainid="+e[i]+"] rect[class='icn3d-hlnode']"),d=$("#"+t.pre+"dl_2ddgm g[chainid="+e[i]+"] rect[class='icn3d-basenode']");void 0!==a&&(t.diagram2dCls.highlightNode("rect",a,d,l),$(a).attr("fill",o)),a=$("#"+t.pre+"dl_2ddgm g[chainid="+e[i]+"] circle[class='icn3d-hlnode']"),d=$("#"+t.pre+"dl_2ddgm g[chainid="+e[i]+"] circle[class='icn3d-basenode']"),void 0!==a&&(t.diagram2dCls.highlightNode("circle",a,d,l),$(a).attr("fill",o)),a=$("#"+t.pre+"dl_2ddgm g[chainid="+e[i]+"] ellipse[class='icn3d-hlnode']"),void 0!==a&&t.diagram2dCls.highlightNode("ellipse",a,void 0,l),a=$("#"+t.pre+"dl_2ddgm g[chainid="+e[i]+"] polygon[class='icn3d-hlnode']"),d=$("#"+t.pre+"dl_2ddgm g[chainid="+e[i]+"] polygon[class='icn3d-basenode']"),void 0!==a&&(t.diagram2dCls.highlightNode("polygon",a,d,l),$(a).attr("fill",o))}if(void 0!==t.lineArray2d)for(let e=0,i=t.lineArray2d.length;e1){let e={},l=[],o=[],a=[],c=[],h=[],m=[],u=[],g=[],f=[],b=[],C=[],y=[],v={},_={};for(let t=0,s=p.length;t0&&(T=1,t=i.getGraphCls.getNodeTopBottom(c[e],d,void 0,T,g[e]),h[e]=t.nodeArray1,m[e]=t.nodeArray2,d=n.hashUtilsCls.unionHash(d,t.name2node),T=2,t=i.getGraphCls.getNodeTopBottom(c[e],d,void 0,T,y[e]),f[e]=t.nodeArray1,b[e]=t.nodeArray2,d=n.hashUtilsCls.unionHash(d,t.name2node)),k[e]=l[e].length,O[e]=o[e].length,R=Math.max(R,O[e]),I.push(p[e])}let E,P,M,D,H,F=1,L=3*F,N=7*F,q=10,U=10,$=30,j=20;t?(M=(n.utilsCls.sumArray(k)+2*I.length)*(L+N)+4*U+2*$+j*I.length,P=(R+2)*(L+N)+2*q+$):(E=110+j,M=E*I.length,P=(R+2)*(L+N)+2*q,P+=20),Object.keys(i.chainsMapping).length>0&&(M*=3),t?(i.scatterplotWidth=2*P,H=i.scatterplotWidth,D=n.scatterplotid):(i.linegraphWidth=2*P,H=i.linegraphWidth,D=n.linegraphid),s=0==I.length?"No interactions found for each structure"+I+' . There are three sections: "Interactions", "Common interactions", and "Different interactions". Each section has '+I.length+" graphs.";let B,z=0;T=0,B=this.drawGraphPerType(T,p,t,l,o,a,d,z,E,j,k,L,N,U),z=B.heightFinal,s+=B.html,Object.keys(i.chainsMapping).length>0&&(T=1,B=this.drawGraphPerType(T,p,t,h,m,u,d,z,E,j,k,L,N,U),z=B.heightFinal,s+=B.html,T=2,B=this.drawGraphPerType(T,p,t,f,b,C,d,z,E,j,k,L,N,U),z=B.heightFinal,s+=B.html),s+=" "}else if(t){let e,t,l,c,h=p[0],m=o.length,u=a.length,g=1,f=3*g,b=7*g,C=30;t=(m+2)*(f+b)+2*10+C,e=(u+2)*(f+b)+2*10+C,i.scatterplotWidth=2*e,c=i.scatterplotWidth,l=n.scatterplotid,s=r.length>0?"":"No interactions found for these two sets",s+=this.drawScatterplot_base(o,a,r,d,0),i.lineGraphStr+=i.getGraphCls.updateGraphJson(h,1,o,a,r),s+=" "}else{let e=p[0],t=o.length,l=a.length,c=1,h=3*c,m=7*c,u=110,g=10,f=t>l?t*(h+m)+2*g:l*(h+m)+2*g;i.linegraphWidth=2*f,s=r.length>0?"":"No interactions found for these two sets",s+=this.drawLineGraph_base(o,a,r,d,0),i.lineGraphStr+=i.getGraphCls.updateGraphJson(e,1,o,a,r),s+=" "}return i.lineGraphStr+="}\n",i.scatterplotStr=i.lineGraphStr,t?$("#"+i.pre+"scatterplotDiv").html(s):$("#"+i.pre+"linegraphDiv").html(s),s}drawGraphPerType(e,t,s,i,n,l,r,o,a,d,c,h,p,m){let u=this.icn3d;u.icn3dui;let g,f,b="",C=2==t.length&&"2"==t[1].replace(t[0],"");0==e?(g="Interactions in ",f=""):1==e?(g="Common interactions in ",f="_common"):2==e&&(g="Different interactions in ",f="_diff");for(let y=0,v=t.length;y0&&(u.lineGraphStr+=", \n"):u.lineGraphStr+=", \n",u.lineGraphStr+=u.getGraphCls.updateGraphJson(t[y],y+f,i[y],n[y],l[y])}return{heightFinal:o,html:b}}getIdArrayFromNode(e){let t=this.icn3d.icn3dui,s=[];s.push(""),s.push("");let i=e.r.substr(4);return s=s.concat(t.utilsCls.getIdArray(i)),s}drawLineGraph_base(e,t,s,i,n,l,r){let o,a,d=this.icn3d,c=d.icn3dui,h="",p=e.length,m=t.length;p>m?(o=10,a=10*Math.abs(p-m)*.5+10):(a=10,o=10*Math.abs(p-m)*.5+10),l&&(h+=""+l+" ");let u=30+n,g=80+n,f="",b={},C={};for(let t=0;t";let u=1==t.n?"Interaction":t.n+" interactions";t.n>1&&(h+=""+u+" of residue "+n.id+" with residue "+l.id+" "),h+=" "}return h+=f,h}drawScatterplot_base(e,t,s,i,n,l,r,o,a){let d=this.icn3d;d.icn3dui;let c="",h=e.length,p=t.length,m=l?3:7,u=(h+1)*(3+m)+30+40;r&&(c+=""+r+" ");let g=n+u-(50+(3+m)),f=40+(3+m),b="",C={},y={};for(let t=0;t";let i=1==e.n?"Interaction":e.n+" interactions";e.n>1&&(h+=""+i+" of residue "+t.id+" with residue "+s.id+" "),h+=l?" "}return h}copyStylesInline(e,t){this.icn3d.icn3dui;let s=["svg","g"];for(let i=0;ii.domainid2score[a])&&(i.domainid2score[a]=e,i.domainid2refpdbname[a]=d,r[a]=o[0].segs,i.domainid2ig2kabat[a]=o[0].ig2kabat,i.domainid2ig2imgt[a]=o[0].ig2imgt)}else console.log("domainid: "+a),(!i.domainid2score.hasOwnProperty(a)||o[0].score>=i.domainid2score[a])&&(i.domainid2score[a]=o[0].score,i.domainid2refpdbname[a]=d,r[a]=o[0].segs,i.domainid2ig2kabat[a]=o[0].ig2kabat,i.domainid2ig2imgt[a]=o[0].ig2imgt)}if(s){n.bNode||console.log("Start round 2 alignment with the reference culsters "+JSON.stringify(i.domainid2refpdbname));let e=[],t=[],s=n.htmlCls.baseUrl+"tmalign/tmalign.cgi";for(let l in i.domainid2refpdbname){let r=[],o=i.domainid2refpdbname[l],a=l.substr(0,l.indexOf(","));if(i.refpdbHash.hasOwnProperty(a)&&(o=a,n.bNode||console.log("Adjusted refpdbname for domainid "+l+": "+o)),!i.refpdbHash[o])continue;for(let e=0,t=i.refpdbHash[o].length;e0){if(i.bShowRefnum=!0,i.hAtomsRefnum={},i.bAnnoShown)for(let e in i.protein_chainid){let t=i.protein_chainid[e];i.showSeqCls.showSeq(e,t,"protein")}else await i.showAnnoCls.showAnnotations();i.annotationCls.setAnnoViewAndDisplay("detailed view")}else alert("No Ig reference numbers are assigned based on the reference structures in iCn3D...")}getLabelFromRefnum(e,t,s){this.icn3d.icn3dui;let i=parseInt(e);return i<1e3?void 0:i>=1200&&i<1290?"A---"+e:i>=1320&&i<1390?"A--"+e:i>=1420&&i<1490?"A-"+e:i>=1520&&i<1590?"A"+e:i>=1620&&i<1690?"A+"+e:i>=1820&&i<1890?"A'"+e:i>=2e3&&i<2900?"B"+e:i>=3300&&i<3390?"C--"+e:i>=3420&&i<3490?"C-"+e:i>=3520&&i<3590?"C"+e:i>=4e3&&i<4900?"C'"+e:i>=5e3&&i<5900?"C''"+e:i>=6e3&&i<6900?"D"+e:i>=7500&&i<7590?"E"+e:i>=7620&&i<7900?"E+"+e:i>=8e3&&i<8900?"F"+e:i>=9500&&i<9590?"G"+e:i>=9620&&i<9690?"G+"+e:i>=9720&&i<9790?"G++"+e:i>9900?void 0:" "+e}async parseCustomRefFile(e){let t=this.icn3d;t.icn3dui,t.bShowCustomRefnum=!0;let s=e.split("\n");t.resid2refnum||(t.resid2refnum={}),t.refnum2residArray||(t.refnum2residArray={}),t.chainsMapping||(t.chainsMapping={});let i=[];for(let e=0,t=s.length;e",C=e.id;return c.resid2refnum[p]&&(C+="=>"+c.resid2refnum[p]),b+=""+C+" ",o?(b+=""+g+" "):(b+=""+g+" "),b+="",b}getNodeTopBottom(e,t,s,i,n){let l=this.icn3d.icn3dui,r=this,o=[],a=[],d={};for(let s in e){let e=t[s];if(e){if(1==i||2==i){if(e=l.hashUtilsCls.cloneHash(e),1==i){let t=n[s]?n[s]:"-";e.id+="=>"+t}else{let t=n[s]?n[s]:"--";e.id+="==>"+t}d[e.id]=e}"a"==e.s?o.push(e):"b"==e.s?a.push(e):"ab"==e.s&&(o.push(e),a.push(e))}}return o.sort((function(e,t){return r.compNode(e,t)})),a.sort((function(e,t){return r.compNode(e,t,s)})),{nodeArray1:o,nodeArray2:a,name2node:d}}updateGraphJson(e,t,s,i,n){let l=this.icn3d.icn3dui,r="";return r+='"structure'+t+'": {"id": "'+e+'", "nodes1":[',r+=l.utilsCls.getJSONFromArray(s),r+='], \n"nodes2":[',r+=l.utilsCls.getJSONFromArray(i),r+='], \n"links":[',r+=l.utilsCls.getJSONFromArray(n),r+="]}",r}updateGraphColor(){let e=this.icn3d,t=e.icn3dui;if(void 0!==e.graphStr){let s=JSON.parse(e.graphStr),i={};for(let t in e.residues){let s=e.firstAtomObjCls.getFirstAtomObj(e.residues[t]);i[t]=s.color.getHexString().toUpperCase()}let n={};for(let e=0,l=s.nodes.length;e0&&c==e.chain&&(n.resid2ncbi[e.resi]==n.resid2ncbi[p]+1||n.resid2ncbi[e.resi]==n.resid2ncbi[p])&&(o.push('{"source": "'+h+'", "target": "'+u+'", "v": '+d+', "c": "'+f+'"}'),e.ssbegin&&(d=l.htmlCls.ssValue),e.ssend&&(d=l.htmlCls.coilValue)),c=e.chain,h=u,p=e.resi,++a}}return{node:r,link:o}}getHbondLinksForSet(e,t){let s=this.icn3d,i=s.icn3dui,n={},l=parseFloat($("#"+s.pre+"hbondthreshold").val()),r=e,o=r;if(Object.keys(o).length>0&&Object.keys(r).length>0){let e=!1;s.hBondCls.calculateChemicalHbonds(i.hashUtilsCls.hash2Atoms(o,s.atoms),i.hashUtilsCls.hash2Atoms(r,s.atoms),parseFloat(l),e,"graph",!0),n=i.hashUtilsCls.cloneHash(s.resid2Residhash)}return this.getGraphLinks(n,n,i.htmlCls.hbondInsideColor,t,i.htmlCls.hbondInsideValue)}getIonicLinksForSet(e,t){let s=this.icn3d,i=s.icn3dui,n={},l=parseFloat($("#"+s.pre+"saltbridgethreshold").val()),r=e,o=r;if(Object.keys(o).length>0&&Object.keys(r).length>0){let e=!1;s.saltbridgeCls.calculateIonicInteractions(i.hashUtilsCls.hash2Atoms(o,s.atoms),i.hashUtilsCls.hash2Atoms(r,s.atoms),parseFloat(l),e,"graph",!0),n=i.hashUtilsCls.cloneHash(s.resid2Residhash)}return this.getGraphLinks(n,n,i.htmlCls.ionicInsideColor,t,i.htmlCls.ionicInsideValue)}getHalogenPiLinksForSet(e,t){let s,i=this.icn3d,n=i.icn3dui,l={},r=e,o=r,a="";return s=parseFloat($("#"+i.pre+"halogenthreshold").val()),Object.keys(o).length>0&&Object.keys(r).length>0&&(i.piHalogenCls.calculateHalogenPiInteractions(n.hashUtilsCls.hash2Atoms(r,i.atoms),n.hashUtilsCls.hash2Atoms(o,i.atoms),parseFloat(s),"graph","halogen",!0),l=n.hashUtilsCls.cloneHash(i.resid2Residhash)),a+=this.getGraphLinks(l,l,n.htmlCls.halogenInsideColor,t,n.htmlCls.halogenInsideValue),s=parseFloat($("#"+i.pre+"picationthreshold").val()),Object.keys(o).length>0&&Object.keys(r).length>0&&(i.piHalogenCls.calculateHalogenPiInteractions(n.hashUtilsCls.hash2Atoms(r,i.atoms),n.hashUtilsCls.hash2Atoms(o,i.atoms),parseFloat(s),"graph","pi-cation",!0),l=n.hashUtilsCls.cloneHash(i.resid2Residhash)),a+=this.getGraphLinks(l,l,n.htmlCls.picationInsideColor,t,n.htmlCls.picationInsideValue),s=parseFloat($("#"+i.pre+"pistackingthreshold").val()),Object.keys(o).length>0&&Object.keys(r).length>0&&(i.piHalogenCls.calculateHalogenPiInteractions(n.hashUtilsCls.hash2Atoms(r,i.atoms),n.hashUtilsCls.hash2Atoms(o,i.atoms),parseFloat(s),"graph","pi-stacking",!0),l=n.hashUtilsCls.cloneHash(i.resid2Residhash)),a+=this.getGraphLinks(l,l,n.htmlCls.pistackingInsideColor,t,n.htmlCls.pistackingInsideValue),a}getContactLinksForSet(e,t,s){let i=this.icn3d;i.icn3dui;let n=[],l="",r="",o={};for(let t in e){let e=i.atoms[t];e.ss==l&&e.chain==r||(Object.keys(o).length>0&&n.push(o),o={}),o[e.serial]=1,l=e.ss,r=e.chain}Object.keys(o).length>0&&n.push(o);let a=n.length,d="";for(let e=0;ed?s?-1:1:ah?1:c0&&Object.keys(a).length>0)){let t,s=c.hBondCls.calculateChemicalHbonds(h.hashUtilsCls.hash2Atoms(d,c.atoms),h.hashUtilsCls.hash2Atoms(a,c.atoms),parseFloat(e),n);n?(c.resid2ResidhashSaltbridge=h.hashUtilsCls.cloneHash(c.resid2Residhash),t="all atoms that have salt bridges with the selected atoms"):(c.resid2ResidhashHbond=h.hashUtilsCls.cloneHash(c.resid2Residhash),t="all atoms that are hydrogen-bonded with the selected atoms");let i={};for(let e in s){i[c.atoms[e].structure+"_"+c.atoms[e].chain+"_"+c.atoms[e].resi]=1}c.hAtoms={};for(let e in i)for(let t in c.residues[e])c.hAtoms[t]=1,c.atoms[t].style2="stick";let l=r+"_auto";c.selectionCls.addCustomSelection(Object.keys(i),l,t,o,!0),c.selectionCls.saveSelectionIfSelected(),c.drawCls.draw()}}showHydrogens(){let e=this.icn3d;if(void 0!==e.icn3dui.cfg.cid)for(let t in e.hAtoms){let s=e.atoms[t];if("H"!==s.elem.substr(0,1)){e.atoms[s.serial].bonds=e.atoms[s.serial].bonds2.concat(),e.atoms[s.serial].bondOrder=e.atoms[s.serial].bondOrder2.concat();for(let t=0,i=e.atoms[s.serial].bonds.length;t0){let i=e.atoms[t].bonds[0];e.atoms[i].bonds.push(s.serial),e.atoms[i].bondOrder&&e.atoms[i].bondOrder.push(1)}e.dAtoms[t]=1}}e.bShowHighlight=!1}hideHydrogens(){let e=this.icn3d;e.icn3dui;for(let t in e.hAtoms){let s=e.atoms[t];if("H"===s.elem.substr(0,1)){if(e.atoms[s.serial].bonds.length>0){let t=e.atoms[s.serial].bonds[0],i=e.atoms[t].bonds?e.atoms[t].bonds.indexOf(s.serial):-1;-1!==i&&(e.atoms[t].bonds.splice(i,1),e.atoms[t].bondOrder&&e.atoms[t].bondOrder.splice(i,1))}delete e.dAtoms[s.serial],delete e.hAtoms[s.serial]}}}hideExtraBonds(){let e=this.icn3d;e.icn3dui;for(let t in e.atoms)e.atoms[t].style2="nothing";for(let t in e.sidec)e.hAtoms.hasOwnProperty(t)&&(e.atoms[t].style2=e.opts.sidec);for(let t in e.water)e.hAtoms.hasOwnProperty(t)&&(e.atoms[t].style=e.opts.water)}hideHbondsContacts(){let e=this.icn3d,t=e.icn3dui,s="set hbonds off";t.htmlCls.clickMenuCls.setLogCmd(s,!0),e.hBondCls.hideHbonds(),s="set salt bridge off",t.htmlCls.clickMenuCls.setLogCmd(s,!0),e.saltbridgeCls.hideSaltbridge(),s="set contact off",t.htmlCls.clickMenuCls.setLogCmd(s,!0),e.contactCls.hideContact(),s="set halogen pi off",t.htmlCls.clickMenuCls.setLogCmd(s,!0),e.piHalogenCls.hideHalogenPi(),this.hideExtraBonds()}showIonicInteractions(e,t,s,i,n,l){let r,o,a,d,c=this.icn3d,h=c.icn3dui;if(!i&&(r="saltbridge",o="salt bridge "+e+" | sets "+t+" "+s+" | "+i,c.opts.saltbridge="yes",a=c.definedSetsCls.getAtomsFromNameArray(t),d=c.definedSetsCls.getAtomsFromNameArray(s),c.firstAtomObjCls.getFirstAtomObj(a),Object.keys(d).length>0&&Object.keys(a).length>0)){let t,s=c.saltbridgeCls.calculateIonicInteractions(h.hashUtilsCls.hash2Atoms(d,c.atoms),h.hashUtilsCls.hash2Atoms(a,c.atoms),parseFloat(e),n);c.resid2ResidhashSaltbridge=h.hashUtilsCls.cloneHash(c.resid2Residhash),t="all atoms that have ionic interactions with the selected atoms";let i={};for(let e in s){i[c.atoms[e].structure+"_"+c.atoms[e].chain+"_"+c.atoms[e].resi]=1}c.hAtoms={};for(let e in i)for(let t in c.residues[e])c.hAtoms[t]=1,c.atoms[t].style2="stick",c.ions.hasOwnProperty(t)&&(c.atoms[t].style2="sphere");let l="saltbridge_auto";c.selectionCls.addCustomSelection(Object.keys(i),l,t,o,!0),c.selectionCls.saveSelectionIfSelected(),c.drawCls.draw()}}showHalogenPi(e,t,s,i,n,l){let r=this.icn3d,o=r.icn3dui;if(i)return;let a,d,c=l+" "+e+" | sets "+t+" "+s+" | "+i;if(r.opts[l]="yes",a=r.definedSetsCls.getAtomsFromNameArray(t),d=r.definedSetsCls.getAtomsFromNameArray(s),r.firstAtomObjCls.getFirstAtomObj(a),Object.keys(d).length>0&&Object.keys(a).length>0){let t,s=r.piHalogenCls.calculateHalogenPiInteractions(o.hashUtilsCls.hash2Atoms(a,r.atoms),o.hashUtilsCls.hash2Atoms(d,r.atoms),parseFloat(e),n,l);"halogen"==l?(r.resid2ResidhashHalogen=o.hashUtilsCls.cloneHash(r.resid2Residhash),t="all atoms that have halogen bonds with the selected atoms"):"pi-cation"==l?(r.resid2ResidhashPication=o.hashUtilsCls.cloneHash(r.resid2Residhash),t="all atoms that have pi-cation interactions with the selected atoms"):"pi-stacking"==l&&(r.resid2ResidhashPistacking=o.hashUtilsCls.cloneHash(r.resid2Residhash),t="all atoms that have pi-stacking with the selected atoms");let i={};for(let e in s){i[r.atoms[e].structure+"_"+r.atoms[e].chain+"_"+r.atoms[e].resi]=1}r.hAtoms={};for(let e in i)for(let t in r.residues[e])r.hAtoms[t]=1,r.atoms[t].style2="stick",r.ions.hasOwnProperty(t)&&(r.atoms[t].style2="sphere");let h=l+"_auto";r.selectionCls.addCustomSelection(Object.keys(i),h,t,c,!0),r.selectionCls.saveSelectionIfSelected(),r.drawCls.draw()}}showClbonds(){let e=this.icn3d,t=e.icn3dui;e.opts.clbonds="yes";let s=e.applyClbondsCls.applyClbondsOptions();for(let i in s)e.hAtoms=t.hashUtilsCls.unionHash(e.hAtoms,e.residues[i]);if(Object.keys(s).length>0){let t="clbonds",i="all atoms that have cross-linkages";e.selectionCls.addCustomSelection(Object.keys(s),t,i,"cross linkage",!0),e.selectionCls.saveSelectionIfSelected(),e.drawCls.draw()}}showSsbonds(){let e=this.icn3d,t=e.icn3dui;e.opts.ssbonds="yes";let s={},i=Object.keys(e.structures);for(let n=0,l=i.length;n0){let t="ssbonds",i="all atoms that have disulfide bonds";e.selectionCls.addCustomSelection(Object.keys(s),t,i,"disulfide bonds",!0),e.selectionCls.saveSelectionIfSelected(),e.drawCls.draw()}}pickCustomSphere(e,t,s,i,n,l){let r=this.icn3d,o=r.icn3dui;if(i)return;let a,d,c="select zone cutoff "+e+" | sets "+t+" "+s+" | "+i;n&&(c="interactions "+e+" | sets "+t+" "+s+" | "+i,r.opts.contact="yes"),a=r.definedSetsCls.getAtomsFromNameArray(t),d=r.definedSetsCls.getAtomsFromNameArray(s);let h,p,m=this.pickCustomSphere_base(e,a,d,i,n,l,c,!0),u=Object.keys(m.residues);r.hAtoms={};for(let e=0,t=u.length;e1?"structure":v>1?"chain":"residue";let w=[];if(n&&w.push("hbonds"),l&&w.push("salt bridge"),r&&w.push("interactions"),o&&w.push("halogen"),a&&w.push("pi-cation"),d&&w.push("pi-stacking"),s||(p.resids2inter={},p.resids2interAll={}),l){let n=parseFloat($("#"+p.pre+"saltbridgethreshold").val());n&&!isNaN(n)||(n=p.tsIonic),s||(p.hAtoms=m.hashUtilsCls.cloneHash(f),p.showInterCls.showIonicInteractions(n,e,t,s,!0,i)),g=m.hashUtilsCls.unionHash(g,p.hAtoms)}if(n){let n=parseFloat($("#"+p.pre+"hbondthreshold").val());n&&!isNaN(n)||(n=p.tsHbond),s||(p.hAtoms=m.hashUtilsCls.cloneHash(f),p.showInterCls.showHbonds(n,e,t,s,void 0,i)),g=m.hashUtilsCls.unionHash(g,p.hAtoms)}let S,A,x,k,O="";if(n&&(O+=this.exportHbondPairs(i,u)),l&&(O+=this.exportSaltbridgePairs(i,u)),o){let n=parseFloat($("#"+p.pre+"halogenthreshold").val());n&&!isNaN(n)||(n=p.tsHalogen),s||(p.hAtoms=m.hashUtilsCls.cloneHash(f),p.showInterCls.showHalogenPi(n,e,t,s,i,"halogen")),g=m.hashUtilsCls.unionHash(g,p.hAtoms),O+=this.exportHalogenPiPairs(i,u,"halogen")}if(a){let n=parseFloat($("#"+p.pre+"picationthreshold").val());n&&!isNaN(n)||(n=p.tsPication),s||(p.hAtoms=m.hashUtilsCls.cloneHash(f),p.showInterCls.showHalogenPi(n,e,t,s,i,"pi-cation")),g=m.hashUtilsCls.unionHash(g,p.hAtoms),O+=this.exportHalogenPiPairs(i,u,"pi-cation")}if(d){let n=parseFloat($("#"+p.pre+"pistackingthreshold").val());n&&!isNaN(n)||(n=p.tsPistacking),s||(p.hAtoms=m.hashUtilsCls.cloneHash(f),p.showInterCls.showHalogenPi(n,e,t,s,i,"pi-stacking")),g=m.hashUtilsCls.unionHash(g,p.hAtoms),O+=this.exportHalogenPiPairs(i,u,"pi-stacking")}if(r){let n=b?c:parseFloat($("#"+p.pre+"contactthreshold").val());if(n&&!isNaN(n)||(n=p.tsContact),1!=e.length||1!=t.length||e[0]!=t[0])s||(p.hAtoms=m.hashUtilsCls.cloneHash(f),p.showInterCls.pickCustomSphere(n,e,t,s,!0,i)),g=m.hashUtilsCls.unionHash(g,p.hAtoms),O+=this.exportSpherePairs(!0,i,u);else{if(!s){let l={},o={};if(b){let e=!0,t=p.showInterCls.pickCustomSphere_base(n,C,y,s,!0,void 0,void 0,!0,e);l=m.hashUtilsCls.unionHash(l,t.residues);for(let e in t.resid2Residhash)o[e]=m.hashUtilsCls.unionHash(o[e],t.resid2Residhash[e])}else{let r=[],a="",d="",c={};for(let e in C){let t=p.atoms[e];t.ss==a&&t.chain==d||(Object.keys(c).length>0&&r.push(c),c={}),c[t.serial]=1,a=t.ss,d=t.chain}Object.keys(c).length>0&&r.push(c);let h=r.length;A="interactions "+n+" | sets "+e+" "+t+" | true",p.opts.contact="yes";for(let e=0;eHighlight in 3D Highlight in 3D The interfaces are: Highlight in 3D Highlight in 3D
',T+='Note : Each checkbox below selects the corresponding residue. You can click "Save Selection" in the "Select" menu to save the selection and click on "Highlight" button to clear the checkboxes.
Interactions Sorted on '+e+' : Show Count Only Show Details
';let t=this.getAllInteractionTable(i);T+=t.html,h=t.bondCnt,$("#"+p.pre+"dl_interactionsorted_html").html(T),m.htmlCls.dialogCls.openDlg("dl_interactionsorted","Show sorted interactions")}else if("view"==i)$("#"+p.pre+"dl_allinteraction_html").html(T),m.htmlCls.dialogCls.openDlg("dl_allinteraction","Show interactions");else if("linegraph"==i){m.htmlCls.dialogCls.openDlg("dl_linegraph","Show interactions between two lines of residue nodes"),p.graphStr=p.getGraphCls.getGraphData(C,y,e,t,T,u),p.bLinegraph=!0;let s=p.lineGraphCls.drawLineGraph(p.graphStr);$("#"+p.pre+"linegraphDiv").html(s)}else if("scatterplot"==i){m.htmlCls.dialogCls.openDlg("dl_scatterplot","Show interactions as scatterplot"),p.graphStr=p.getGraphCls.getGraphData(C,y,e,t,T,u),p.bScatterplot=!0;let s=p.lineGraphCls.drawLineGraph(p.graphStr,!0);$("#"+p.pre+"scatterplotDiv").html(s)}else if(b){m.htmlCls.dialogCls.openDlg("dl_contactmap","Show contact map");let s=!0,i=p.getGraphCls.getGraphData(C,y,e,t,T,u,s);p.bContactMap=!0;let n=p.contactMapCls.drawContactMap(i);$("#"+p.pre+"contactmapDiv").html(n)}else if("graph"==i){if(p.graphStr=p.getGraphCls.getGraphData(C,y,e,t,T,u),p.bGraph=!0,Object.keys(y).length+Object.keys(C).length>Object.keys(p.dAtoms).length&&(p.graphStr=p.selectionCls.getGraphDataForDisplayed()),void 0===p.bD3){let e="https://www.ncbi.nlm.nih.gov/Structure/icn3d/script/d3v4-force-all.min.js";await m.getAjaxPromise(e,"script"),p.bD3=!0}$("#"+m.svgid).empty(),m.htmlCls.dialogCls.openDlg("dl_graph","Force-directed graph"),p.drawGraphCls.drawGraph(p.graphStr,p.pre+"dl_graph")}return{interactionTypes:w.toString(),bondCnt:h}}clearInteractions(){let e=this.icn3d;e.icn3dui,e.lines.hbond=[],e.hbondpnts=[],e.lines.saltbridge=[],e.saltbridgepnts=[],e.lines.contact=[],e.contactpnts=[],e.lines.halogen=[],e.lines["pi-cation"]=[],e.lines["pi-stacking"]=[],e.halogenpnts=[],e.picationpnts=[],e.pistackingpnts=[]}resetInteractionPairs(){let e=this.icn3d;e.icn3dui,e.bHbondCalc=!1,e.showInterCls.hideHbondsContacts(),e.hlUpdateCls.clearHighlight(),e.resids2inter={},e.resids2interAll={}}async retrieveInteractionData(){let e=this.icn3d,t=e.icn3dui;if(!e.b2DShown)if(void 0!==t.cfg.align){let s=Object.keys(e.structures);if(2==t.cfg.atype){let t=!0;await e.alignParserCls.downloadAlignment(s[0]+","+s[1],t)}await e.ParserUtilsCls.set2DDiagramsForAlign(s[0].toUpperCase(),s[1].toUpperCase())}else void 0!==t.cfg.chainalign?(Object.keys(e.structures),await e.ParserUtilsCls.set2DDiagramsForChainalign(e.chainidArray)):e.ParserUtilsCls.download2Ddgm(e.inputid.toUpperCase())}getAllInteractionTable(e){let t=this.icn3d,s=t.icn3dui,i=[],n=Object.keys(t.resids2inter);("save1"==e||"save2"==e)&&n.sort((function(t,i){return s.utilsCls.compResid(t,i,e)}));let l,r,o="",a="",d="",c="",h="",p="",m="",u="",g="",f=0,b=0,C=0,y=0,v=0,_=0,w="";for(let s=0,S=n.length;s0&&l!=a&&(i.push({res1:a,res2:w,cntHbond:f,cntIonic:b,cntContact:C,cntHalegen:y,cntPication:v,cntPistacking:_}),o+=this.getInteractionPerResidue(d,c,h,p,m,u,g,f,b,C,y,v,_),c="",h="",p="",m="",u="",g="",f=0,b=0,C=0,y=0,v=0,_=0,w=""),x=t.resids2inter[S].hbond,k=this.getInteractionPairDetails(x,e,"hbond"),c+=k.html,f+=k.cnt,k.cnt>0&&(w+=r+":hbond_"+k.cnt+" "),x=t.resids2inter[S].ionic,k=this.getInteractionPairDetails(x,e,"ionic"),h+=k.html,b+=k.cnt,k.cnt>0&&(w+=r+":ionic_"+k.cnt+" "),x=t.resids2inter[S].contact,k=this.getContactPairDetails(x,e,"contact"),p+=k.html,C+=k.cnt,k.cnt>0&&(w+=r+":contact_"+k.cnt+" "),x=t.resids2inter[S].halogen,k=this.getInteractionPairDetails(x,e,"halogen"),m+=k.html,y+=k.cnt,k.cnt>0&&(w+=r+":halogen_"+k.cnt+" "),x=t.resids2inter[S]["pi-cation"],k=this.getInteractionPairDetails(x,e,"pi-cation"),u+=k.html,v+=k.cnt,k.cnt>0&&(w+=r+":pi-cation_"+k.cnt+" "),x=t.resids2inter[S]["pi-stacking"],k=this.getInteractionPairDetails(x,e,"pi-stacking"),g+=k.html,_+=k.cnt,k.cnt>0&&(w+=r+":pi-stacking_"+k.cnt+" "),a=l,d=O}i.push({res1:a,res2:w,cntHbond:f,cntIonic:b,cntContact:C,cntHalegen:y,cntPication:v,cntPistacking:_}),o+=this.getInteractionPerResidue(d,c,h,p,m,u,g,f,b,C,y,v,_);let S="";if(n.length>0){S+='',S+="Residue # Hydrogen # Salt Bridge # Contact ",S+="# Halogen # π-Cation # π-Stacking ",S+="Hydrogen Bond (backbone atoms: @CA, @N, @C, @O) Salt Bridge/Ionic Interaction Contact ",S+="Halogen Bond π-Cation π-Stacking ";let e='Atom1 Atom2 Distance(Å) Highlight in 3D
Atom1 Atom2 # Contacts Min Distance(Å) C-alpha Distance(Å) Highlight in 3D
",S+=" ",S+=o,S+="
'+e[3]+e[2]+" "+o+" "+a+" "+d+" "+c+" "+h+" "+p+" ";let u=[t,s,i,n,l,r];for(let e in u){m+=' ';if(void 0!==e)for(let a in e){let d=a.split(","),c="save1"==t?d[0]:d[1],h="save1"==t?d[1]:d[0],p=i.getGraphCls.convertLabel2Resid(c),m=i.firstAtomObjCls.getFirstAtomObj(i.residues[p]),u=m.color?m.color.getHexString():"",g=i.getGraphCls.convertLabel2Resid(h),f=i.firstAtomObjCls.getFirstAtomObj(i.residues[g]),b=f.color?f.color.getHexString():"",C=Math.sqrt(e[a]).toFixed(1);n+=''+C+" ",n+='Highlight ';if(void 0!==e)for(let o in e){let a=o.split(","),d="save1"==t?a[0]:a[1],c="save1"==t?a[1]:a[0],h=s.getGraphCls.convertLabel2Resid(d),p=s.firstAtomObjCls.getFirstAtomObj(s.residues[h]),m=p.color?p.color.getHexString():"",u=s.getGraphCls.convertLabel2Resid(c),g=s.firstAtomObjCls.getFirstAtomObj(s.residues[u]),f=g.color?g.color.getHexString():"",b=e[o].split("_"),C=b[0],y=b[1],v=b[2],_=b[3],w=b[4];i+=''+w+' '+C+' '+y+" ",i+='Highlight Interacting residues :
Base Chain: Residues Interacting Chain "+t+": ",s+=e.resid2specCls.residueids2spec(e.chainname2residues[t][i]),s+=" "+n+"
"+n[e]+" Cys "+n[e+1]+" Cys ",++i}}let n=''+i+" disulfide pairs :
Residue ID 1 Residue ID 2
"+r+" "+t.resn+" "+o+" "+n.resn+" ",++i}n[r+"_"+o]=1,n[o+"_"+r]=1}}let l=''+i+" cross-linkage pairs :
Residue ID 1 Residue ID 2
';for(let t in s.resid2ResidhashHbond){let i=s.getGraphCls.convertLabel2Resid(t),a=s.firstAtomObjCls.getFirstAtomObj(s.residues[i]),d=a.color?a.color.getHexString():"";for(let i in s.resid2ResidhashHbond[t]){let a=s.getGraphCls.convertLabel2Resid(i),c=s.firstAtomObjCls.getFirstAtomObj(s.residues[a]),h=c.color?c.color.getHexString():"",p=Math.sqrt(s.resid2ResidhashHbond[t][i]).toFixed(1);n+=''+p+" ","view"==e&&(n+='Highlight '+l+" hydrogen bond pairs (backbone atoms: @CA, @N, @C, @O):
Atom 1 Atom 2 Distance(Å) ","view"==e&&(a+='Highlight in 3D '),a+="
';for(let t in s.resid2ResidhashSaltbridge){let i=s.getGraphCls.convertLabel2Resid(t),a=s.firstAtomObjCls.getFirstAtomObj(s.residues[i]),d=a.color?a.color.getHexString():"";for(let i in s.resid2ResidhashSaltbridge[t]){let a=s.getGraphCls.convertLabel2Resid(i),c=s.firstAtomObjCls.getFirstAtomObj(s.residues[a]),h=c.color?c.color.getHexString():"",p=Math.sqrt(s.resid2ResidhashSaltbridge[t][i]).toFixed(1);n+=''+p+" ","view"==e&&(n+='Highlight '+l+" salt bridge/ionic interaction pairs :
Atom 1 Atom 2 Distance(Å) ","view"==e&&(a+='Highlight in 3D '),a+="
';"halogen"==s?(l=i.resid2ResidhashHalogen,r=n.htmlCls.halogenColor,o=n.htmlCls.halogenValue):"pi-cation"==s?(l=i.resid2ResidhashPication,r=n.htmlCls.picationColor,o=n.htmlCls.picationValue):"pi-stacking"==s&&(l=i.resid2ResidhashPistacking,r=n.htmlCls.pistackingColor,o=n.htmlCls.pistackingValue);for(let t in l){let n=i.getGraphCls.convertLabel2Resid(t),r=i.firstAtomObjCls.getFirstAtomObj(i.residues[n]),o=r.color?r.color.getHexString():"";for(let n in l[t]){let r=i.getGraphCls.convertLabel2Resid(n),p=i.firstAtomObjCls.getFirstAtomObj(i.residues[r]),m=p.color?p.color.getHexString():"",u=Math.sqrt(l[t][n]).toFixed(1);a+=''+u+" ","view"==e&&(a+='Highlight '+d+" "+s+" pairs :
Atom 1 Atom 2 Distance(Å) ","view"==e&&(p+='Highlight in 3D '),p+="
';for(let s in o){let n=i.getGraphCls.convertLabel2Resid(s),c=i.firstAtomObjCls.getFirstAtomObj(i.residues[n]),h=c.color?c.color.getHexString():"";for(let n in o[s]){let p=i.getGraphCls.convertLabel2Resid(n),m=i.firstAtomObjCls.getFirstAtomObj(i.residues[p]),u=m.color?m.color.getHexString():"",g=o[s][n].split("_"),f=g[0],b=g[1];c=g[2],m=g[3];let C=g[4];e?(l+=''+C+' '+f+' '+b+" ","view"==t&&(l+='Highlight "+s+" "+n+' '+C+' '+f+' '+b+" '+r+" residue pairs in "+(e?"the contacts":"sphere")+" :
Residue 1 Residue 2 Num Contacts Min Distance(Å) C-alpha Distance(Å) ',"view"==t&&(c+='Highlight in 3D '),c+="Residue 1 Residue 2 Num Contacts Min Distance(Å) C-alpha Distance(Å)
0?n.structures[0]:n.defaultPdbId;p=10*(a.length+2)+20+30,h=10*(d.length+2)+20+30,t?(n.alignerrormapWidth=2*h,u=n.alignerrormapWidth,m=l.alignerrormapid):(n.contactmapWidth=2*h,u=n.contactmapWidth,m=l.contactmapid),i=o.length>0?"":"No interactions found for these two sets";if(t){n.hex2id={};let e=29/s;n.hex2skip={};let t=1e3;for(let s=0;se&&(n.hex2skip[d]=c)}}if(i+=n.lineGraphCls.drawScatterplot_base(a,d,o,c,0,!0,void 0,void 0,t),g+=n.getGraphCls.updateGraphJson(f,1,a,d,o),i+=" ",g+="}\n",t){n.alignerrormapStr=g,$("#"+n.pre+"alignerrormapDiv").html(i);let e=$("#"+l.alignerrormapid+"_scale").val();$("#"+l.alignerrormapid).attr("width",(n.alignerrormapWidth*parseFloat(e)).toString()+"px")}else n.contactmapStr=g,$("#"+n.pre+"contactmapDiv").html(i);return i}}class Bt{constructor(e){this.icn3d=e}async downloadAlignment(e,t){let s=this.icn3d,i=s.icn3dui,n=this;s.opts.proteins="c alpha trace";let l=e.split(","),r="ids="+e,o=i.htmlCls.baseUrl+"vastplus/vastplus.cgi?v=3&cmd=c&b=1&s=1&w3d&"+r;void 0!==i.cfg.inpara&&(o+=i.cfg.inpara),s.pdbid_chain2title={},void 0===s.chainids2resids&&(s.chainids2resids={});let a={},d="These two MMDB IDs "+l+' do not have 3D alignment data in the VAST+ database. You can try the VAST alignment by visiting the VAST+ page https://www.ncbi.nlm.nih.gov/Structure/vastplus/vastplus.cgi?uid=[PDB ID] (e.g., uid=1KQ2), and clicking "Original VAST"',c=await i.getAjaxPromise(o,"jsonp",!0,d);if(a=c.seqalign,void 0===a)return alert(d),!1;s.pdbid_molid2chain={},s.chainsColor={};for(let e=0,t=2;e5){let t=!1,s=!0;d=await r.pdbParserCls.loadPdbData(e,n,!1,t,"target",h,s)}else{let t=!0;d=await r.mmdbParserCls.parseMmdbData(e,"target",i[0],0,h,t)}for(let e=0,s=t.length;e5){let s=!0,i=!0;c=await r.pdbParserCls.loadPdbData(t[e],l,!1,s,"query",h,i)}else{let s=!0;c=await r.mmdbParserCls.parseMmdbData(t[e],"query",i[e+1],e,h,s)}d=o.hashUtilsCls.unionHash(d,c)}if(o.cfg.resnum)await r.realignParserCls.realignChainOnSeqAlign(s,i);else if(o.cfg.resdef)await r.realignParserCls.realignChainOnSeqAlign(s,i,void 0,!0);else{await r.pdbParserCls.applyCommandDssp(!0);for(let e in r.pdbChainIndexHash){let t=r.pdbChainIndexHash[e].split("_");l=t[0],t[1],n=t[2],t[3],a.transformStructure(l,e-1,"query")}let e=[],t=[],c=[],h=o.htmlCls.baseUrl+"vastdyn/vastdyn.cgi",p=o.htmlCls.baseUrl+"tmalign/tmalign.cgi";for(let s in r.afChainIndexHash){let i=r.afChainIndexHash[s].split("_");l=i[0];let a=i[1];n=i[2];let d,m=i[3];if("tmalign"!=o.cfg.aligntool){let e={domains1:r.domain3dCls.getDomainJsonForAlign(r.chains[l+"_"+a]),domains2:r.domain3dCls.getDomainJsonForAlign(r.chains[n+"_"+m])};d=o.getAjaxPostPromise(h,e)}else{let e={pdb_query:r.saveFileCls.getAtomPDB(r.chains[l+"_"+a]),pdb_target:r.saveFileCls.getAtomPDB(r.chains[n+"_"+m])};d=o.getAjaxPostPromise(p,e)}e.push(d),t.push(s-1),c.push(l)}let m=Promise.allSettled(e),u=await m;await a.downloadChainalignmentPart2b(s,i,d,u,t,n,c)}}async downloadChainalignmentPart2b(e,t,s,i,n,l,r){let o=this.icn3d,a=o.icn3dui;for(let e=0,t=i.length;ec&&(c=l[t[0]],a=t[0]),l[t[1]]>c&&(c=l[t[1]],a=t[1])}let h={},p={},m={},u={};for(let e in r){let t,s,i=e.split("_"),n=r[e].split(","),l=n[2];a==i[0]?(t=i[0],s=i[1]):a==i[1]?(t=i[1],s=i[0]):(t=i[0],s=i[1]),m[t]=1,m.hasOwnProperty(s)||(m[s]=1,u[e]=r[e],d="target",this.transformStructure(t,l,d),d="query",this.transformStructure(s,l,d),h[n[0]]=1,h[n[1]]=1)}for(let e in u)if(void 0!==i.q_rotation){let t=u[e].split(","),s=[t[1],t[0],t[2]],l=i.setSeqAlignCls.setSeqAlignChain(void 0,void 0,s);p=n.hashUtilsCls.unionHash(p,l);let r=!1,o=n.htmlCls.alignSeqCls.getAlignSequencesAnnotations(Object.keys(i.alnChains),void 0,void 0,!1,void 0,r),a=$("#"+i.pre+"dl_sequence2").html();$("#"+i.pre+"dl_sequence2").html(a+o.sequencesHtml),$("#"+i.pre+"dl_sequence2").width(n.htmlCls.RESIDUE_WIDTH*o.maxSeqCnt+200)}i.dAtoms=n.hashUtilsCls.cloneHash(p),i.hAtoms=n.hashUtilsCls.cloneHash(p);let g="protein_aligned";i.selectionCls.saveSelection(g,g),i.opts.color="identity",i.setColorCls.setColorByOptions(i.opts,i.hAtoms),n.htmlCls.dialogCls.openDlg("dl_alignment","Select residues in aligned sequences"),i.drawCls.draw(),i.transformCls.zoominSelection(),i.hlUpdateCls.updateHlAll()}transformStructure(e,t,s,i){let n=this.icn3d,l=n.icn3dui,r=n.structures[e];for(let e=0,o=r.length;e2){let e=i.firstAtomObjCls.getResiduesFromAtoms(s),t="protein_aligned",n="protein aligned",l="select "+i.resid2specCls.residueids2spec(Object.keys(e));i.selectionCls.addCustomSelection(Object.keys(e),t,n,l,!0)}i.hlUpdateCls.updateHlAll(),n.htmlCls.dialogCls.openDlg("dl_alignment","Select residues in aligned sequences"),void 0!==n.cfg.rotate&&i.resizeCanvasCls.rotStruc(n.cfg.rotate,!0),i.html2ddgm="",n.cfg.show2d&&i.bFullUi&&(n.htmlCls.dialogCls.openDlg("dl_2ddgm","Interactions"),i.bFullUi&&(i.bChainAlign?await i.ParserUtilsCls.set2DDiagramsForChainalign(t):i.ParserUtilsCls.download2Ddgm(i.inputid.toUpperCase())))}addPostfixForChainids(e){this.icn3d.icn3dui;let t={};for(let s=0,i=e.length;s5?(d="https://alphafold.ebi.ac.uk/files/AF-"+i.mmdbid_t+"-F1-model_"+i.AFUniprotVersion+".pdb",a=n.getAjaxPromise(d,"text")):(d=n.htmlCls.baseUrl+"mmdb/mmdb_strview.cgi?v=2&program=icn3d&b=1&s=1&ft=1&bu="+n.cfg.bu+"&uid="+i.mmdbid_t,void 0!==n.cfg.inpara&&(d+=n.cfg.inpara),a=n.getAjaxPromise(d,"jsonp")),c.push(a),i.ParserUtilsCls.setYourNote(e.toUpperCase()+" in iCn3D"),i.pdbid_chain2title={},void 0===i.chainids2resids&&(i.chainids2resids={}),i.afChainIndexHash={},i.pdbChainIndexHash={};for(let e=1,t=l.length;e5?(t="https://alphafold.ebi.ac.uk/files/AF-"+i.mmdbid_q+"-F1-model_"+i.AFUniprotVersion+".pdb",s=n.getAjaxPromise(t,"text")):(t=n.htmlCls.baseUrl+"mmdb/mmdb_strview.cgi?v=2&program=icn3d&b=1&s=1&ft=1&bu="+n.cfg.bu+"&uid="+i.mmdbid_q,void 0!==n.cfg.inpara&&(t+=n.cfg.inpara),s=n.getAjaxPromise(t,"jsonp")),c.push(s)}for(let e=1,t=l.length;e0?r[e]+","+r[0]:void 0;if("tmalign"!=n.cfg.aligntool&&4==i.mmdbid_t.length&&4==i.mmdbid_q.length){let o;o=r.length>0?n.htmlCls.baseUrl+"vastdyn/vastdyn.cgi?domainpairs="+l:n.htmlCls.baseUrl+"vastdyn/vastdyn.cgi?chainpairs="+t;let a=n.getAjaxPromise(o,"jsonp");c.push(a),i.pdbChainIndexHash[e]=s+"_"+i.chain_q+"_"+i.mmdbid_t+"_"+i.chain_t}else i.afChainIndexHash[e]=i.mmdbid_q+"_"+i.chain_q+"_"+i.mmdbid_t+"_"+i.chain_t}}let h=Promise.allSettled(c),p=await h;await this.parseChainAlignData(p,l,i.mmdbid_t,i.chain_t)}async parseChainAlignData(e,t,s,i){let n=this.icn3d,l=n.icn3dui,r=e[0].value,o="HEADER "+s+"\n";isNaN(s)&&s.length>5&&(r=o+r),n.t_trans_add=[],n.q_trans_sub=[],"tmalign"==l.cfg.aligntool&&(n.q_trans_add=[]),n.q_rotation=[],n.qt_start_end=[],n.mmdbidArray=[],n.mmdbidArray.push(s);let a=[];for(let s=1,i=t.length;s5&&(i=o+i),void 0===i||-1!==JSON.stringify(i).indexOf("Oops there was a problem"))return void alert("The coordinate data can NOT be retrieved for the structure "+r+"...");n.mmdbidArray.push(r),a.push(i)}let d=0;for(let r=1,o=t.length;r";"tmalign"==o.cfg.aligntool&&(n+="TM-score : "+e[0].score.toPrecision(4)+"5)t="https://alphafold.ebi.ac.uk/files/AF-"+l+"-F1-model_"+i.AFUniprotVersion+".pdb",s=n.getAjaxPromise(t,"text");else{let e=l;5==l.length&&(e=l.substr(0,4)),t=n.htmlCls.baseUrl+"mmdb/mmdb_strview.cgi?v=2&program=icn3d&b=1&s=1&ft=1&bu="+n.cfg.bu+"&uid="+e,void 0!==n.cfg.inpara&&(t+=n.cfg.inpara),s=n.getAjaxPromise(t,"jsonp")}o.push(s)}i.ParserUtilsCls.setYourNote(i.structArray+" in iCn3D"),i.ParserUtilsCls.showLoading();let a=Promise.allSettled(o),d=await a;await this.parseMMdbAfData(d,r,t,s),void 0===s&&i.ParserUtilsCls.hideLoading()}async parseMMdbAfData(e,t,s,i){let n=this.icn3d,l=n.icn3dui,r=[];for(let s=0,i=t.length;s5&&(i=n+i),void 0===i||-1!==JSON.stringify(i).indexOf("Oops there was a problem"))return void alert("The coordinate data can NOT be retrieved for the structure "+t[s]+"...");r.push(i)}let o={},a={},d=!1;n.opts.color=n.structArray.length>1?"structure":t[0].length>5?"confidence":"chain";for(let e=0,i=t.length;e5){let s=!1;a=await n.pdbParserCls.loadPdbData(r[e],t[e],!1,c,i,d,s)}else{let s=!0,l=t[e];a=await n.mmdbParserCls.parseMmdbData(r[e],i,void 0,void 0,d,s,l)}o=l.hashUtilsCls.unionHash(o,a)}if(n.structArray.length>1&&(n.opts.color="structure"),n.setColorCls.setColorByOptions(n.opts,n.atoms),await n.ParserUtilsCls.renderStructure(),void 0!==l.cfg.rotate&&n.resizeCanvasCls.rotStruc(l.cfg.rotate,!0),s&&l.cfg.matchedchains){let e=!0,t=!0;await n.realignParserCls.realignChainOnSeqAlign(void 0,n.chainidArray,e,t),$("#"+n.pre+"dl_annotations").html(""),n.bAnnoShown=!1,$("#"+l.pre+"dl_selectannotations").hasClass("ui-dialog-content")&&$("#"+n.pre+"dl_selectannotations").dialog("isOpen")&&$("#"+n.pre+"dl_selectannotations").dialog("close")}else if(void 0!==i){let e=Object.keys(n.structures);await n.vastplusCls.vastplusAlign(e,i)}}}class Gt{constructor(e){this.icn3d=e}async dsn6Parser(e,t,s){this.icn3d.icn3dui;let i="https://edmaps.rcsb.org/maps/"+e.toLowerCase()+"_"+t+".dsn6";await this.dsn6ParserBase(i,t,s)}async dsn6ParserBase(e,t,s){let i=this.icn3d,n=i.icn3dui,l=this;if("2fofc"==t&&i.bAjax2fofc)i.mapData.sigma2=s,i.setOptionCls.setOption("map",t);else if("fofc"==t&&i.bAjaxfofc)i.mapData.sigma=s,i.setOptionCls.setOption("map",t);else{let r=await n.getXMLHttpRqstPromise(e,"GET","arraybuffer","rcsbEdmaps");l.loadDsn6Data(r,t,s),"2fofc"==t?i.bAjax2fofc=!0:"fofc"==t&&(i.bAjaxfofc=!0),i.setOptionCls.setOption("map",t)}}loadDsn6Data(e,t,s){let i=this.icn3d;i.icn3dui;let n,l,r={},o=e.buffer&&e.buffer instanceof ArrayBuffer?e.buffer:e,a=new Int16Array(o),d=new Uint8Array(o),c=String.fromCharCode.apply(null,d.subarray(0,512));if(0==c.indexOf(":-)"))r.xStart=parseInt(c.substr(10,5)),r.yStart=parseInt(c.substr(15,5)),r.zStart=parseInt(c.substr(20,5)),r.xExtent=parseInt(c.substr(32,5)),r.yExtent=parseInt(c.substr(38,5)),r.zExtent=parseInt(c.substr(42,5)),r.xRate=parseInt(c.substr(52,5)),r.yRate=parseInt(c.substr(58,5)),r.zRate=parseInt(c.substr(62,5)),r.xlen=1*parseFloat(c.substr(73,10)),r.ylen=1*parseFloat(c.substr(83,10)),r.zlen=1*parseFloat(c.substr(93,10)),r.alpha=parseFloat(c.substr(103,10)),r.beta=parseFloat(c.substr(113,10)),r.gamma=parseFloat(c.substr(123,10)),n=parseFloat(c.substr(138,12))/100,l=parseInt(c.substr(155,8)),r.sigma=100*parseFloat(c.substr(170,12));else{if(100!==a[18])for(let e=0,t=a.length;e>8&255}r.zStart=a[2],r.xStart=a[0],r.yStart=a[1],r.xExtent=a[3],r.yExtent=a[4],r.zExtent=a[5],r.xRate=a[6],r.yRate=a[7],r.zRate=a[8];let e=1/a[17],t=1*e;r.xlen=a[9]*t,r.ylen=a[10]*t,r.zlen=a[11]*t,r.alpha=a[12]*e,r.beta=a[13]*e,r.gamma=a[14]*e,n=a[15]/a[18],l=a[16]}let h=new Float32Array(r.xExtent*r.yExtent*r.zExtent),p=512,m=Math.ceil(r.xExtent/8),u=Math.ceil(r.yExtent/8),g=Math.ceil(r.zExtent/8);for(let e=0;es.maxatomcnt&&(s.bAssembly=!0)}if("mmtfid"===t&&void 0!==o.missingseq){let t=0,n="";for(let l=0,r=o.missingseq.length;lt)&&(s.chainMissingResidueArray[c].push(h),t=d,n=a)}s.loadPDBCls.adjustSeq(s.chainMissingResidueArray)}}async loadMmcifData(e,t){let s=this.icn3d;if(s.icn3dui,t||(t=e.mmcif),t||(t=s.defaultPdbId),void 0===e.atoms)return!1;s.init(),void 0!==e.emd&&(s.emd=e.emd),void 0!==e.organism&&(s.organism=e.organism),void 0!==s.emd?($("#"+s.pre+"mapWrapper1").hide(),$("#"+s.pre+"mapWrapper2").hide(),$("#"+s.pre+"mapWrapper3").hide()):($("#"+s.pre+"emmapWrapper1").hide(),$("#"+s.pre+"emmapWrapper2").hide(),$("#"+s.pre+"emmapWrapper3").hide()),await s.opmParserCls.loadOpmData(e,t,void 0,"mmcif")}}class Wt{constructor(e){this.icn3d=e}async downloadMmdb(e,t){let s,i=this.icn3d,n=i.icn3dui;try{if(s=await this.loadMmdbPrms(e,t),!s||s.error)return void this.getNoData(e,t)}catch(s){return void this.getNoData(e,t)}if(0!=Object.keys(s.atoms).length)if(n.utilsCls.isCalphaPhosOnly(s.atoms)||s.atomCount<=i.maxatomcnt)await this.parseMmdbData(s);else{let s;try{s=await this.loadMmdbPrms(e,t,!0)}catch(s){return void this.getNoData(e,t)}await this.parseMmdbData(s)}else{let e=s.pdbId;await i.mmtfParserCls.downloadMmtf(e)}}async downloadGi(e){let t=this.icn3d;t.icn3dui,t.bCid=void 0;await this.downloadMmdb(e,!0)}async downloadBlast_rep_id(e){let t=this.icn3d,s=t.icn3dui,i=e.split(",");s.cfg.query_id=i[0],s.cfg.blast_rep_id=i[1];let n=s.cfg.blast_rep_id.split("_")[0];4==n.length?await this.downloadMmdb(n):(t.blastAcxn=s.cfg.blast_rep_id.split(".")[0],await this.downloadRefseq(t.blastAcxn,!0))}async downloadRefseq(e,t){let s=this.icn3d,i=s.icn3dui,n=i.htmlCls.baseUrl+"vastdyn/vastdyn.cgi?refseq2uniprot="+e;i.cfg.refseqid=e;let l=await i.getAjaxPromise(n,"jsonp",!1,"The protein accession "+e+" can not be mapped to AlphaFold UniProt ID...");if(!l||!l.uniprot)return void alert("The accession "+e+" can not be mapped to AlphaFold UniProt ID. It will be treated as a UniProt ID instead.");i.cfg.afid=l.uniprot,s.uniprot2acc||(s.uniprot2acc={}),s.uniprot2acc[l.uniprot]=e,t&&(i.cfg.blast_rep_id=i.cfg.afid+"_A");await s.pdbParserCls.downloadPdb(i.cfg.afid,!0)}async downloadProteinname(e){let t=this.icn3d,s=t.icn3dui;s.icn3d.bCid=void 0;let i=s.htmlCls.baseUrl+"vastdyn/vastdyn.cgi?protein2acc="+e,n=(await s.getAjaxPromise(i,"jsonp")).acc;if(0==n.length)return void(s.bNode||alert("The protein/gene name "+e+" can not be mapped to RefSeq proteins..."));let l=[];for(let e=0,t=n.length;e=20231001||!i.cfg.date&&parseInt(i.utilsCls.getDateDigitStr())>=20231001)&&(h=h.replace(/_/g,"")),void 0===d[h]?d[h]=1:++d[h];let p=n+"_"+(1===d[h]?h:h+d[h].toString());r[e]=c,o[p]=e,a[e]=p,s.chainsColor[p]=void 0===t||i.cfg.mmdbafid?i.parasCls.thr(c):i.parasCls.thr(i.htmlCls.GREY8);let m=void 0===l[e].geneId?"":l[e].geneId,u=void 0===l[e].geneSymbol?"":l[e].geneSymbol,g=void 0===l[e].geneDesc?"":l[e].geneDesc;s.chainsGene[p]={geneId:m,geneSymbol:u,geneDesc:g}}s.molid2chain=a,$("#"+s.pre+"accordion5").show()}loadMmdbPrms(e,t,s){let i,n=this.icn3d,l=n.icn3dui;return i=t?l.htmlCls.baseUrl+"mmdb/mmdb_strview.cgi?v=2&program=icn3d&b=1&s=1&ft=1&bu="+l.cfg.bu+"&simple=1&gi="+e:l.htmlCls.baseUrl+"mmdb/mmdb_strview.cgi?v=2&program=icn3d&b=1&s=1&ft=1&bu="+l.cfg.bu+"&simple=1&uid="+e,void 0!==l.cfg.blast_rep_id&&(i+="&bu=0"),void 0!==l.cfg.inpara&&(i+=l.cfg.inpara),s&&(i+="&complexity=2"),void 0===n.chainids2resids&&(n.chainids2resids={}),l.getAjaxPromise(i,"jsonp",!0)}}class Yt{constructor(e){this.icn3d=e}async downloadMmtf(e){let t=this.icn3d,s=t.icn3dui;t.ParserUtilsCls.setYourNote(e.toUpperCase()+"(MMTF) in iCn3D");let i=await s.getMmtfReducedPromise(e);if(10*i.numAtoms>t.maxatomcnt){let s=!1;if(0==Object.keys(i).length)return void alert("This PDB structure is not found at RCSB...");await t.opmParserCls.loadOpmData(i,e,s,"mmtf")}else{let i=await s.getMmtfPromise(e),n=!0;if(0==Object.keys(i).length)return void alert("This PDB structure is not found at RCSB...");await t.opmParserCls.loadOpmData(i,e,n,"mmtf")}}async parseMmtfData(e,t,s){let i=this.icn3d,n=i.icn3dui;e.numAtoms,i.init();let l=new THREE.Vector3(9999,9999,9999),r=new THREE.Vector3(-9999,-9999,-9999),o=new THREE.Vector3,a=e.structureId;if(i.molTitle=e.title,void 0!==e.bioAssemblyList&&void 0!==e.bioAssemblyList[0]&&e.bioAssemblyList[0].transformList.length>1){i.biomtMatrices=[];for(let t=0,s=e.bioAssemblyList[0].transformList.length;t1&&($("#"+i.pre+"assemblyWrapper").show(),i.asuCnt=i.biomtMatrices.length);let d,c,h,p,m,u,g,f,b,C,y,v,_,w,S,A,x,k,O,R={},I=[],T="coil",E="",P=0,M=0,D={onModel:function(e){d=0===e.modelIndex?a:a+(e.modelIndex+1).toString()},onChain:function(e){c=e.chainName;let t=d+"_"+c;void 0===i.structures[d]&&(i.structures[d]=[]),i.structures[d].push(t)},onGroup:function(e){h=e.groupName,p=e.groupId;let t=d+"_"+c+"_"+p;m=0===e.secStruct||2===e.secStruct||4===e.secStruct?"helix":3===e.secStruct?"sheet":-1===e.secStruct?"other":"coil";let s=!1;if(c!==E){if(x=void 0,O=void 0,"coil"!==m&&"other"!==m?(u=!0,g=!1):(u=!1,g=!1),"coil"!==T&&"other"!==T){let e=d+"_"+E+"_"+P.toString();for(let t in i.residues[e])i.atoms[t].ssbegin=!1,i.atoms[t].ssend=!0}}else x=A,O=k,m!==T?"coil"===T||"other"===T?(u=!0,g=!1):"coil"===m||"other"===m?(s=!0,u=!1,g=!1):("sheet"===T&&"helix"===m||"helix"===T&&"sheet"===m)&&(s=!0,u=!0,g=!1):(u=!1,g=!1);if(s&&!isNaN(p)){let e=d+"_"+c+"_"+(p-1).toString();for(let t in i.residues[e])i.atoms[t].ssbegin=!1,i.atoms[t].ssend=!0}T=m,E=c,P=p,f=!1,b=!1,C=!1,"non-polymer"===e.chemCompType.toLowerCase()||"other"===e.chemCompType.toLowerCase()||-1!==e.chemCompType.toLowerCase().indexOf("saccharide")?f=!0:-1!==e.chemCompType.toLowerCase().indexOf("peptide")?b=!0:-1!==e.chemCompType.toLowerCase().indexOf("dna")||-1!==e.chemCompType.toLowerCase().indexOf("rna")?C=!0:b=!0;let l=d+"_"+c,r={};r.resi=p,r.name=n.utilsCls.residueName2Abbr(h),i.residueId2Name[t]=r.name,r.resi%10==0&&r.resi.toString();let o="-";"helix"===m?o="H":"sheet"===m?o="E":"coil"===m?o="c":"other"===m&&(o="o"),void 0===i.chainsSeq[l]&&(i.chainsSeq[l]=[]),i.bFullUi&&i.chainsSeq[l].push(r),i.secondaries[t]=o},onAtom:function(e){if(y=e.element,v=e.atomName,_=new THREE.Vector3(e.xCoord,e.yCoord,e.zCoord),w=e.bFactor,S=e.altLoc,"\0"===e.altLoc&&(S=""),""===S||"A"===S){++M,"SG"===v&&I.push(M),R[e.atomIndex]=M;let t={het:f,serial:M,name:v,alt:S,resn:h,structure:d,chain:c,resi:p,coord:_,b:w,elem:y,bonds:[],bondOrder:[],ss:m,ssbegin:u,ssend:g};if(t.het||"C"!==t.name||(A=M),t.het||"O"!==t.name||(k=M),!t.het&&"N"===t.name&&void 0!==x&&void 0!==O){let e=i.atoms[x].coord.distanceTo(i.atoms[O].coord),s=t.coord.x+(i.atoms[x].coord.x-i.atoms[O].coord.x)/e,n=t.coord.y+(i.atoms[x].coord.y-i.atoms[O].coord.y)/e,l=t.coord.z+(i.atoms[x].coord.z-i.atoms[O].coord.z)/e;t.hcoord=new THREE.Vector3(s,n,l)}i.atoms[M]=t,l.min(_),r.max(_),o.add(_);let a=d+"_"+c,T=a+"_"+p;void 0===i.chains[a]&&(i.chains[a]={}),i.chains[a][M]=1,void 0===i.residues[T]&&(i.residues[T]={}),i.residues[T][M]=1,b?(i.proteins[M]=1,"CA"===v&&(i.calphas[M]=1),"N"!==v&&"H"!==v&&"CA"!==v&&"HA"!==v&&"C"!==v&&"O"!==v&&(i.sidec[M]=1)):C?(i.nucleotides[M]=1,(!s||"O3'"!=v&&"O3*"!=v)&&(s||"P"!=v)||(i.nucleotidesO3[M]=1),-1===n.parasCls.nuclMainArray.indexOf(v)&&(i.ntbase[M]=1)):y.toLowerCase()===h.toLowerCase()?i.ions[M]=1:"HOH"===h||"WAT"===h||"SQL"===h||"H2O"===h||"W"===h||"DOD"===h||"D3O"===h?i.water[M]=1:i.chemicals[M]=1,i.dAtoms[M]=1,i.hAtoms[M]=1}},onBond:function(e){let t=R[e.atomIndex1],s=R[e.atomIndex2];if(R.hasOwnProperty(e.atomIndex1)&&R.hasOwnProperty(e.atomIndex2)&&(i.atoms[t].bonds.push(s),i.atoms[s].bonds.push(t),f)){let n=e.bondOrder;i.atoms[t].bondOrder.push(n),i.atoms[s].bondOrder.push(n),2===n?(i.doublebonds[t+"_"+s]=1,i.doublebonds[s+"_"+t]=1):3===n&&(i.triplebonds[t+"_"+s]=1,i.triplebonds[s+"_"+t]=1)}}};MMTF.traverse(e,D),i.loadPDBCls.setResidMapping();for(let e=0,t=I.length;ei.maxatomcnt||void 0!==i.biomtMatrices&&i.biomtMatrices.length*i.cnt>10*i.maxatomcnt)&&(i.opts.proteins="c alpha trace",i.opts.nucleotides="o3 trace"),i.pmin=l,i.pmax=r,i.center=i.ParserUtilsCls.getGeoCenter(i.pmin,i.pmax),i.maxD=i.ParserUtilsCls.getStructureSize(i.atoms,i.pmin,i.pmax,i.center),i.maxD<5&&(i.maxD=5),i.oriMaxD=i.maxD,i.oriCenter=i.center.clone(),i.ParserUtilsCls.transformToOpmOri(t),void 0===n.cfg.align&&1==Object.keys(i.structures).length&&$("#"+i.pre+"alternateWrapper").hide(),i.setStyleCls.setAtomStyleByOptions(i.opts),i.setColorCls.setColorByOptions(i.opts,i.atoms),await i.ParserUtilsCls.renderStructure(),i.saveFileCls.showTitle(),void 0!==n.cfg.rotate&&i.resizeCanvasCls.rotStruc(n.cfg.rotate,!0)}}class Xt{constructor(e){this.icn3d=e}async loadMol2Data(e){let t=this.icn3d,s=t.icn3dui,i=this.loadMol2AtomData(e);void 0===s.cfg.align&&1==Object.keys(t.structures).length&&$("#"+t.pre+"alternateWrapper").hide(),i?(t.setStyleCls.setAtomStyleByOptions(t.opts),t.setColorCls.setColorByOptions(t.opts,t.atoms),await t.ParserUtilsCls.renderStructure(),void 0!==s.cfg.rotate&&t.resizeCanvasCls.rotStruc(s.cfg.rotate,!0)):alert("The Mol2 file has the wrong format...")}loadMol2AtomData(e){let t=this.icn3d;t.icn3dui;let s=e.split(/\r?\n|\r/);if(s.length<4)return!1;t.init();let i,n,l="LIG",r={},o="1_A",a=0,d=0,c=1,h=!1,p=!1,m={},u={};for(let e=0,o=s.length;eMOLECULE"==o){t.molTitle=s[e+1].trim();let l=s[e+2].trim().replace(/\s+/g," ").split(" ");i=l[0],n=l[1],e+=4}else"@ATOM"==o?(c=1,h=!0,++e):"@BOND"==o?(p=!0,h=!1,++e):"@SUBSTRUCTURE"==o&&(p=!1,++e);if(o=s[e].trim(),""!==o&&"#"!==o.substr(0,1)){if(h&&a1&&($("#"+l.pre+"assemblyWrapper").show(),l.asuCnt=l.biomtMatrices.length),l.setStyleCls.setAtomStyleByOptions(l.opts),l.setColorCls.setColorByOptions(l.opts,l.atoms),await l.ParserUtilsCls.renderStructure(),void 0!==r.cfg.rotate&&l.resizeCanvasCls.rotStruc(r.cfg.rotate,!0)}else"pdb"===i?await l.pdbParserCls.loadPdbData(e,t):"align"===i&&(l.bOpm?await l.alignParserCls.downloadAlignmentPart2(t):void 0!==n?await this.loadOpmData(e,n,s,i):await l.alignParserCls.downloadAlignmentPart2(t))}}class Jt{constructor(e){this.icn3d=e}async downloadPdb(e,t){let s,i=this.icn3d,n=i.icn3dui;t?(s="https://alphafold.ebi.ac.uk/files/AF-"+e+"-F1-model_"+i.AFUniprotVersion+".pdb",n.cfg.refseqid?i.ParserUtilsCls.setYourNote(n.cfg.refseqid.toUpperCase()+"(NCBI Protein Acc.) in iCn3D"):n.cfg.protein?i.ParserUtilsCls.setYourNote(n.cfg.protein+"(NCBI Protein/Gene) in iCn3D"):i.ParserUtilsCls.setYourNote(e.toUpperCase()+"(AlphaFold) in iCn3D")):(s="https://files.rcsb.org/view/"+e+".pdb",e=e.toUpperCase(),i.ParserUtilsCls.setYourNote(e+"(PDB) in iCn3D"));let l=await n.getAjaxPromise(s,"text",!0,"The ID "+e+" can not be found in the server "+s+"...");if(t){l="HEADER "+e+"\n"+l,await i.opmParserCls.parseAtomData(l,e,void 0,"pdb",void 0)}else await i.opmParserCls.loadOpmData(l,e,void 0,"pdb")}async downloadUrl(e,t,s){let i=this.icn3d,n=i.icn3dui,l=e.lastIndexOf("/");if(-1!=l){let t=e.lastIndexOf(".");i.filename=e.substr(l+1,t-l-1)}else{let t=e.lastIndexOf(".");i.filename=e.substr(0,t)}let r=await n.getAjaxPromise(e,"text",!0);if(i.InputfileData=i.InputfileData?i.InputfileData+"\nENDMDL\n"+r:r,i.InputfileType=t,"pdb"===t)await this.loadPdbData(r);else if("mmcif"===t){let e=n.htmlCls.baseUrl+"mmcifparser/mmcifparser.cgi",t={mmciffile:r},s=await n.getAjaxPostPromise(e,t,!0);await i.mmcifParserCls.loadMmcifData(s,void 0)}else if("mol2"===t)await i.mol2ParserCls.loadMol2Data(r);else if("sdf"===t)await i.sdfParserCls.loadSdfData(r);else if("xyz"===t)await i.xyzParserCls.loadXyzData(r);else if("mmcif"===t)await i.mmcifParserCls.loadMmcifData(r);else if("icn3dpng"===t)await n.htmlCls.setHtmlCls.loadPng(r,s);else if("pae"===t){n.htmlCls.dialogCls.openDlg("dl_alignerrormap","Show Predicted Aligned Error (PAE) map");let e=!0;i.contactMapCls.processAfErrorMap(JSON.parse(r),e)}}async loadPdbData(e,t,s,i,n,l,r,o){let a=this.icn3d,d=a.icn3dui;if(!i&&(void 0===n||"target"===n)){let e=!!a.bCommandLoad;a.bStatefile||a.init(e)}let c=a.loadPDBCls.loadPDB(e,t,s,void 0,void 0,i,n,o);void 0===d.cfg.opmid&&a.ParserUtilsCls.transformToOpmOri(t),void 0!==a.biomtMatrices&&a.biomtMatrices.length>1&&(d.bNode||$("#"+a.pre+"assemblyWrapper").show(),a.asuCnt=a.biomtMatrices.length),d.bNode||(void 0!==a.emd?($("#"+a.pre+"mapWrapper1").hide(),$("#"+a.pre+"mapWrapper2").hide(),$("#"+a.pre+"mapWrapper3").hide()):($("#"+a.pre+"emmapWrapper1").hide(),$("#"+a.pre+"emmapWrapper2").hide(),$("#"+a.pre+"emmapWrapper3").hide()));let h=!1;return a.bSecondaryStructure&&1==Object.keys(a.structures).length?h=!1:d.cfg.mmtfid||d.cfg.pdbid||d.cfg.opmid||d.cfg.mmdbid||d.cfg.gi||d.cfg.uniprotid||d.cfg.blast_rep_id||d.cfg.cid||d.cfg.mmcifid||d.cfg.align||d.cfg.chainalign||(h=!0),(!a.bSecondaryStructure||h)&&Object.keys(a.proteins).length>0&&!r?await this.applyCommandDssp(i):(await this.loadPdbDataRender(i),d.bNode||await a.ParserUtilsCls.checkMemProteinAndRotate()),c}async applyCommandDssp(e){let t=this.icn3d,s=t.icn3dui,i=s.utilsCls.isCalphaPhosOnly(s.hashUtilsCls.hash2Atoms(t.proteins,t.atoms));await t.dsspCls.applyDssp(i,e)}async loadPdbDataRender(e){let t=this.icn3d,s=t.icn3dui;void 0===s.cfg.align&&1==Object.keys(t.structures).length&&$("#"+t.pre+"alternateWrapper").hide(),(s.cfg.afid&&!t.bAfMem||t.bEsmfold)&&(t.opts.color="confidence"),t.setStyleCls.setAtomStyleByOptions(t.opts),t.setColorCls.setColorByOptions(t.opts,t.hAtoms),await t.ParserUtilsCls.renderStructure(),t.saveFileCls.showTitle(),void 0!==s.cfg.rotate&&t.resizeCanvasCls.rotStruc(s.cfg.rotate,!0),e&&!s.bNode&&t.definedSetsCls.setModeAndDisplay("all")}}class Qt{constructor(e){this.icn3d=e}async downloadCid(e){let t=this.icn3d,s=t.icn3dui;t.ParserUtilsCls.setYourNote("PubChem CID "+e+" in iCn3D"),t.bCid=!0;let i="https://pubchem.ncbi.nlm.nih.gov/rest/pug/compound/cid/"+t.inputid+"/cids/JSONP?cids_type=parent",n="https://pubchem.ncbi.nlm.nih.gov/rest/pug/compound/cid/"+(await s.getAjaxPromise(i,"jsonp",!0,"Can not retrieve the parant CID...")).IdentifierList.CID[0]+"/record/SDF/?record_type=3d&response_type=display",l=await s.getAjaxPromise(n,"text",!0,"This CID may not have 3D structure..."),r=this.loadSdfAtomData(l,e);void 0===s.cfg.align&&1==Object.keys(t.structures).length&&$("#"+t.pre+"alternateWrapper").hide(),r?(t.setStyleCls.setAtomStyleByOptions(t.opts),t.setColorCls.setColorByOptions(t.opts,t.atoms),await t.ParserUtilsCls.renderStructure(),void 0!==s.cfg.rotate&&t.resizeCanvasCls.rotStruc(s.cfg.rotate,!0)):alert("The SDF of CID "+e+" has the wrong format...")}async loadSdfData(e){let t=this.icn3d,s=t.icn3dui,i=this.loadSdfAtomData(e);void 0===s.cfg.align&&1==Object.keys(t.structures).length&&$("#"+t.pre+"alternateWrapper").hide(),i?(t.setStyleCls.setAtomStyleByOptions(t.opts),t.setColorCls.setColorByOptions(t.opts,t.atoms),await t.ParserUtilsCls.renderStructure(),void 0!==s.cfg.rotate&&t.resizeCanvasCls.rotStruc(s.cfg.rotate,!0)):alert("The SDF file has the wrong format...")}loadSdfAtomData(e,t){let s=this.icn3d;s.icn3dui;let i=e.split(/\r?\n|\r/);if(i.length<4)return!1;s.init();let n=t||1,l="LIG",r=n,o=n+"_A",a=o+"_1",d=parseInt(i[3].substr(0,3));if(isNaN(d)||d<=0)return!1;let c=parseInt(i[3].substr(3,3)),h=4;if(i.lengthr||(Math.abs(t.coord.y-i.coord.y)>r||Math.abs(t.coord.z-i.coord.z)>r||l.utilsCls.hasCovalentBond(t,i)&&(n.atoms[o[e]].bonds.push(o[s]),n.atoms[o[s]].bonds.push(o[e])))}}}loadXyzAtomData(e){let t=this.icn3d;t.icn3dui;let s=e.split(/\r?\n|\r/);if(s.length<3)return!1;t.init();let i,n,l,r={},o=0,a=1;t.molTitle="";for(let e=0,d=s.length;e1&&(t.molTitle+="; "),t.molTitle+=s[e+1].trim(),e+=2),d=s[e].trim(),""===d)continue;let c=d.replace(/,/," ").replace(/\s+/g," ").split(" "),h=c[0],p=parseFloat(c[1]),m=parseFloat(c[2]),u=parseFloat(c[3]),g={het:!0,serial:a,name:h,resn:"LIG",structure:l,chain:"A",resi:1,coord:new THREE.Vector3(p,m,u),b:0,elem:h,bonds:[],ss:"coil",ssbegin:!1,ssend:!1,bondOrder:[]};t.atoms[a]=g,r[a]=1,++a}return this.setXyzAtomSeq(r,o,i,n),t.ParserUtilsCls.setMaxD(),t.saveFileCls.showTitle(),!0}}class es{constructor(e){this.icn3d=e}realign(){let e=this.icn3d,t=e.icn3dui;e.selectionCls.saveSelectionPrep();let s="alseq_"+Object.keys(e.defNames2Atoms).length;e.selectionCls.saveSelection(s,s),t.htmlCls.clickMenuCls.setLogCmd("realign",!0);let i={},n={};e.realignResid={};let l="";for(let s in e.hAtoms){let r=e.atoms[s],o=r.structure+"_"+r.chain;if(e.proteins.hasOwnProperty(s)&&"CA"==r.name||e.nucleotides.hasOwnProperty(s)&&("O3'"==r.name||"O3*"==r.name)){if(r.structure+"_"+r.resi==l)continue;i.hasOwnProperty(r.structure)||(i[r.structure]=[]),i[r.structure].push(r.coord.clone()),e.realignResid.hasOwnProperty(o)||(e.realignResid[o]=[]),e.realignResid[o].push({resid:o+"_"+r.resi,resn:t.utilsCls.residueName2Abbr(r.resn.substr(0,3)).substr(0,1)}),n[r.structure]=r.structure+"_"+r.chain,l=r.structure+"_"+r.resi}}let r=Object.keys(i),o=r[0],a=[];e.qt_start_end=[],a.push(n[o]);for(let t=1,s=r.length;t5){let e=r.cfg.chainalign.split(",");e.length>0&&(l.hAtoms=l.definedSetsCls.getAtomsFromNameArray(e)),r.cfg.aligntool="tmalign",await l.realignParserCls.realignOnStructAlign()}else l.hAtoms=l.chainalignParserCls.setMsa(e),l.transformCls.zoominSelection(),await l.chainalignParserCls.downloadChainalignmentPart3(void 0,e,l.hAtoms)}async parseChainRealignData(e,t,s,i,n,l,r){let o=this.icn3d,a=o.icn3dui,d=s[0].substr(0,s[0].indexOf("_"));r||(d=d.toUpperCase());let c={};o.realignResid={},o.opts.color="grey",o.setColorCls.setColorByOptions(o.opts,o.dAtoms),o.qt_start_end=[];for(let t=0,h=e.length;t=6&&C.length>=6&&!a.cfg.command&&o.bRender&&alert("These sequences can not be aligned to each other")):o.bRender&&alert("Please do not align residues in the same structure")}if(r){o.hAtoms=o.chainalignParserCls.setMsa(s);let e="protein_aligned";if(o.selectionCls.saveSelection(e,e),o.bAfMem?(o.selectionCls.selectAll_base(),o.opts.chemicals="stick",o.opts.color="confidence",o.setColorCls.setColorByOptions(o.opts,o.atoms)):(o.transformCls.zoominSelection(),o.dAtoms=a.hashUtilsCls.cloneHash(o.hAtoms),o.opts.color="identity",o.setColorCls.setColorByOptions(o.opts,o.hAtoms)),o.drawCls.draw(),o.hlUpdateCls.updateHlAll(),o.bAfMem){let e=new THREE.Vector3(1,0,0),t=-.5*Math.PI;o.transformCls.setRotation(e,t)}}else o.hAtoms=o.chainalignParserCls.setMsa(s),o.transformCls.zoominSelection(),await o.chainalignParserCls.downloadChainalignmentPart3(t,s,o.hAtoms)}async realignOnSeqAlign(e){let t=this.icn3d;t.icn3dui;let s=t.firstAtomObjCls.getChainsFromAtoms(t.hAtoms),i=Object.keys(s),n=[],l="";for(let e=0,t=i.length;ei){n[e][o]=a;break}}}let l=[],r=[],o=s.htmlCls.baseUrl+"vastdyn/vastdyn.cgi",a=s.htmlCls.baseUrl+"tmalign/tmalign.cgi",d=Object.keys(n);e&&(d=d.reverse());for(let e=0,i=d.length;ei){n[r]=o;break}}let l=[],r=[],o=[],a=s.htmlCls.baseUrl+"vastdyn/vastdyn.cgi",d=s.htmlCls.baseUrl+"tmalign/tmalign.cgi",c=e[0],h=c.substr(0,c.indexOf("_")),p=t.domain3dCls.getDomainJsonForAlign(n[c]);for(let i=1,m=e.length;if&&(f=s)}}}return{data:n,min:g,max:f}}(e.getCategory("_volume_data_3d").getColumn("values"),o,n.sampleCount,l);return{name:n.name,spacegroup:function(e,t,s){let i=Math.PI/180*s[0],n=Math.PI/180*s[1],l=Math.PI/180*s[2],r=t[0],o=t[1],a=t[2],d=Math.cos(n),c=(Math.cos(i)-Math.cos(n)*Math.cos(l))/Math.sin(l),h=Math.sqrt(1-d*d-c*c);return{number:e,size:t,angles:s,basis:{x:[r,0,0],y:[Math.cos(l)*o,Math.sin(l)*o,0],z:[d*a,c*a,h*a]}}}(n.spacegroupNumber,n.cellSize,n.cellAngles),box:{origin:r(n.origin),dimensions:r(n.dimensions),sampleCount:o},data:a.data,valuesInfo:{min:a.min,max:a.max,mean:n.mean,sigma:n.sigma}}}BinaryParse(e){this.icn3d.icn3dui;let t=new Uint8Array(e),s=this.MessagePackParse({buffer:t,offset:0,dataView:new DataView(t.buffer)}),i=function(){function e(e){this.additionalData={},this.header=e.header,this.categoryList=e.categories.map((function(e){return new n(e)})),this.categoryMap=new Map;for(let e=0,t=this.categoryList;e=0;s--)t=c(t,e.encoding[s]);return t}function p(e){if(!e.data.data)return _UndefinedColumn;let t,s=h(e.data);return e.mask&&(t=h(e.mask)),s.buffer&&s.byteLength&&s.BYTES_PER_ELEMENT?t?new f(s,t):new g(s):t?new C(s,t):new b(s)}function m(e,t,s){let i=0,n=1;for(45===e.charCodeAt(t)&&(n=-1,t++);t9||s<0)return n*i|0;i=10*i+s|0}return n*i}function u(e,t,s){let i=1,n=0,l=0,r=1;for(45===e.charCodeAt(t)&&(i=-1,++t);t=0&&o<10)){if(-2===o){for(++t;t=0&&o<10))return 53===o||21===o?parseScientific(i*(n+l/r),e,t+1,s):i*(n+l/r);l=10*l+o,r*=10,++t}return i*(n+l/r)}if(53===o||21===o)return parseScientific(i*n,e,t+1,s);break}n=10*n+o,++t}return i*n}let g=function(){function e(e){this.data=e,this.isDefined=!0}return e.prototype.getString=function(e){return""+this.data[e]},e.prototype.getInteger=function(e){return 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i(e)}))}return e.prototype.toJSON=function(){return this.dataBlocks.map((function(e){return e.toJSON()}))},e}();return new y(s)}MessagePackParse(e){this.icn3d.icn3dui;let t=this;function s(e,s){let i={};for(let n=0;n0&&(i[i.length]=l.slice(0,a).join(""));return i.join("")}(e.buffer,e.offset,t);return e.offset+=t,s}let r=function(){let e=[];for(let t=0;t<1024;t++)e[t]=String.fromCharCode(t);return e}();let o,a,d=e.buffer[e.offset];if(0==(128&d))return e.offset++,d;if(128==(240&d))return a=15&d,e.offset++,s(e,a);if(144==(240&d))return a=15&d,e.offset++,n(e,a);if(160==(224&d))return a=31&d,e.offset++,l(e,a);if(224==(224&d))return o=e.dataView.getInt8(e.offset),e.offset++,o;switch(d){case 192:return e.offset++,null;case 194:return e.offset++,!1;case 195:return e.offset++,!0;case 196:return a=e.dataView.getUint8(e.offset+1),e.offset+=2,i(e,a);case 197:return a=e.dataView.getUint16(e.offset+1),e.offset+=3,i(e,a);case 198:return a=e.dataView.getUint32(e.offset+1),e.offset+=5,i(e,a);case 202:return o=e.dataView.getFloat32(e.offset+1),e.offset+=5,o;case 203:return o=e.dataView.getFloat64(e.offset+1),e.offset+=9,o;case 204:return o=e.buffer[e.offset+1],e.offset+=2,o;case 205:return o=e.dataView.getUint16(e.offset+1),e.offset+=3,o;case 206:return o=e.dataView.getUint32(e.offset+1),e.offset+=5,o;case 208:return o=e.dataView.getInt8(e.offset+1),e.offset+=2,o;case 209:return o=e.dataView.getInt16(e.offset+1),e.offset+=3,o;case 210:return o=e.dataView.getInt32(e.offset+1),e.offset+=5,o;case 217:return a=e.dataView.getUint8(e.offset+1),e.offset+=2,l(e,a);case 218:return a=e.dataView.getUint16(e.offset+1),e.offset+=3,l(e,a);case 219:return a=e.dataView.getUint32(e.offset+1),e.offset+=5,l(e,a);case 220:return a=e.dataView.getUint16(e.offset+1),e.offset+=3,n(e,a);case 221:return a=e.dataView.getUint32(e.offset+1),e.offset+=5,n(e,a);case 222:return a=e.dataView.getUint16(e.offset+1),e.offset+=3,s(e,a);case 223:return a=e.dataView.getUint32(e.offset+1),e.offset+=5,s(e,a)}}}class ss{constructor(e){this.icn3d=e}alignCoords(e,t,s,i,n,l,r,o){let a,d=this.icn3d,c=d.icn3dui,h=e.length=4&&(d.bAfMem?d.rmsd_suprTmp=c.rmsdSuprCls.getRmsdSuprCls(t,e,h):d.rmsd_suprTmp=c.rmsdSuprCls.getRmsdSuprCls(e,t,h),void 0!==d.rmsd_suprTmp.rot)){let e=d.rmsd_suprTmp.rot;null===e[0]&&alert("Please select more residues in each structure...");let t=d.rmsd_suprTmp.trans1,i=d.rmsd_suprTmp.trans2;if(a=d.rmsd_suprTmp.rmsd,a){c.htmlCls.clickMenuCls.setLogCmd("realignment RMSD: "+a.toPrecision(4),!1);let e="Realignment RMSD : "+a.toPrecision(4)+" Å"+s.diagram2dCls.set2DdgmNote(!0),$("#"+s.pre+"dl_2ddgm_html").html(s.html2ddgm),s.b2DShown=!0}async set2DDiagramsForChainalign(e){let t=this.icn3d.icn3dui,s=this;t.htmlCls.dialogCls.openDlg("dl_2ddgm","Interactions");let i=[];for(let s=0,n=e.length;s"+s.diagram2dCls.set2DdgmNote(!0),s.b2DShown=!0,$("#"+s.pre+"dl_2ddgm_html").html(s.html2ddgm),i.cfg.show2d&&i.htmlCls.dialogCls.openDlg("dl_2ddgm","Interactions")}download2Ddgm(e,t){this.set2DDiagrams(e)}set2DDiagrams(e){let t=this.icn3d;t.icn3dui.htmlCls.dialogCls.openDlg("dl_2ddgm","Interactions"),void 0!==t.b2DShown&&t.b2DShown||(t.html2ddgm="",t.diagram2dCls.draw2Ddgm(t.interactionData,e),t.html2ddgm+="=4)if(i.rmsd_supr=n.rmsdSuprCls.getRmsdSuprCls(o,a,d),void 0!==i.rmsd_supr.rot&&i.rmsd_supr.rmsd<.1){let s=i.rmsd_supr.rot,l=i.rmsd_supr.trans1,r=i.rmsd_supr.trans2,o=i.rmsd_supr.rmsd;n.htmlCls.clickMenuCls.setLogCmd("RMSD of alignment to OPM: "+o.toPrecision(4),!1);let a=0;for(let e in i.atoms){let t=i.atoms[e];t.coord=i.surfaceCls.transformMemPro(t.coord,s,l,r);let n=t.coord.x*t.coord.x+t.coord.y*t.coord.y;Math.abs(t.coord.z)<=25&&n>a&&(a=n)}i.center=t.center,i.oriCenter=i.center.clone(),this.addMemAtoms(i.halfBilayerSize,e,Math.sqrt(a)),i.bStopRotate=!0,i.bOpm=!0,$("#"+i.pre+"togglememli").show(),$("#"+i.pre+"adjustmemli").show(),$("#"+i.pre+"selectplaneli").show()}else i.bOpm=!1;else i.bOpm=!1}}addOneDumAtom(e,t,s,i,n,l){let r=this.icn3d,o=r.icn3dui,a={het:!0,serial:++l,name:t,alt:void 0,resn:"DUM",structure:e,chain:"MEM",resi:1,coord:new THREE.Vector3(s,i,n),b:void 0,elem:t,bonds:[],ss:"",ssbegin:!1,ssend:!1,color:o.parasCls.atomColors[t]};return r.atoms[l]=a,r.chains[e+"_MEM"][l]=1,r.residues[e+"_MEM_1"][l]=1,r.chemicals[l]=1,r.dAtoms[l]=1,r.hAtoms[l]=1,l}addMemAtoms(e,t,s){let i=this.icn3d;if(i.icn3dui,!t)return;t=t?t.toUpperCase():i.defaultPdbId,i.structures[t].push(t+"_MEM"),i.chains[t+"_MEM"]={},i.residues[t+"_MEM_1"]={},i.chainsSeq[t+"_MEM"]=[{name:"DUM",resi:1}];let n=Object.keys(i.atoms).length;for(let e=0;e<1e3;++e)if(!i.atoms.hasOwnProperty(n+e)){n=n+e-1;break}for(let i=0;i<81;++i)for(let l=0;l<81;++l){let r=2*i-80,o=2*l-80;if(Math.sqrt(r*r+o*o)=2?$("#"+e.pre+"mn2_alternateWrap").show():$("#"+e.pre+"mn2_alternateWrap").hide(),setTimeout((async function(){if(e.bInitial){if(void 0!==t.cfg.align||void 0!==t.cfg.chainalign){let s=e.pre+"selection";if($("#"+s).show(),$("#"+s+"_expand").hide(),$("#"+s+"_shrink").show(),void 0!==t.cfg.align&&2!=t.cfg.atype){let s=!1,i=t.htmlCls.alignSeqCls.getAlignSequencesAnnotations(Object.keys(e.alnChains),void 0,void 0,s);$("#"+e.pre+"dl_sequence2").html(i.sequencesHtml),$("#"+e.pre+"dl_sequence2").width(t.htmlCls.RESIDUE_WIDTH*i.maxSeqCnt+200)}}if(t.cfg.showanno){let s="view annotations";t.htmlCls.clickMenuCls.setLogCmd(s,!0),await e.showAnnoCls.showAnnotations()}(t.cfg.closepopup||t.cfg.imageonly)&&e.resizeCanvasCls.closeDialogs()}else e.hlUpdateCls.updateHlAll();$("#"+e.pre+"atomsCustom").length>0&&$("#"+e.pre+"atomsCustom")[0].blur(),e.bInitial=!1,t.cfg.imageonly&&e.saveFileCls.saveFile(void 0,"png",void 0,!0)}),0)}processCommand(){let e=this.icn3d,t=e.icn3dui;if(1==Object.keys(e.structures).length){let s=Object.keys(e.structures)[0];t.cfg.command=t.cfg.command.replace(new RegExp("!","g"),s+"_")}}getMassCenter(e,t){return this.icn3d.icn3dui,e.multiplyScalar(1/t)}getGeoCenter(e,t){return this.icn3d.icn3dui,e.clone().add(t).multiplyScalar(.5)}getStructureSize(e,t,s,i){let n=this.icn3d;n.icn3dui;let l=0;for(let r in e){let e=n.atoms[r].coord;if(Math.round(t.x)==Math.round(e.x)||Math.round(t.y)==Math.round(e.y)||Math.round(t.z)==Math.round(e.z)||Math.round(s.x)==Math.round(e.x)||Math.round(s.y)==Math.round(e.y)||Math.round(s.z)==Math.round(e.z)){let t=2*e.distanceTo(i);t>l&&(l=t)}}return l}async checkMemProteinAndRotate(){let e=this.icn3d,t=e.icn3dui;if(!e.bCheckMemProtein){e.bCheckMemProtein=!0;let s=t.cfg.afid?t.cfg.afid:t.cfg.mmdbafid;if(await e.ParserUtilsCls.checkMemProtein(s),t.cfg.url&&-1!=t.cfg.url.indexOf("membranome")){let t=new THREE.Vector3(1,0,0),s=-.5*Math.PI;e.transformCls.setRotation(t,s)}}}async checkMemProtein(e){let t=this.icn3d,s=t.icn3dui;try{let i=s.htmlCls.baseUrl+"vastdyn/vastdyn.cgi?afid2mem="+e,n=await s.getAjaxPromise(i,"jsonp");if(n&&n.pdbid){let e='This is a single-spanning (bitopic) transmembrane protein according to the Membranome database. Do you want to align the protein with the model from Membranome? If you click "OK", you can press the letter "a" to alternate the structures.';if("off"==s.cfg.afmem);else if("on"==s.cfg.afmem||confirm(e))try{let e="https://storage.googleapis.com/membranome-assets/pdb_files/proteins/"+n.pdbid+".pdb",i=await s.getAjaxPromise(e,"text");t.bAfMem=!0,s.bNode||$("#"+s.pre+"togglememli").show();let l=n.pdbid.substr(0,n.pdbid.indexOf("_")),r=!0,o=!0;await t.pdbParserCls.loadPdbData(i,l,r,o),o&&(t.bSetChainsAdvancedMenu&&t.definedSetsCls.showSets(),t.bAnnoShown&&await t.showAnnoCls.showAnnotations());let a=n.segment.replace(/ /gi,"").split("(")[0];t.afmem_start_end=a.split("-"),t.hAtoms={},t.dAtoms={};for(let e in t.atoms)t.atoms[e].structure!=l&&(t.hAtoms[e]=1),t.dAtoms[e]=1;for(let e=parseInt(t.afmem_start_end[0]);e<=parseInt(t.afmem_start_end[1]);++e)t.hAtoms=s.hashUtilsCls.unionHash(t.hAtoms,t.residues[l+"_A_"+e]);await t.realignParserCls.realignOnSeqAlign(l)}catch(e){return void console.log("Error in retrieving matched PDB from Membranome...")}}}catch(e){return void console.log("Error in finding matched PDB in Membranome...")}}getResi(e,t){let s=this.icn3d;s.icn3dui;let i=s.ncbi2resid[e+"_"+(t+1).toString()];return i?i.substr(i.lastIndexOf("_")+1):""}getResiNCBI(e,t){let s=this.icn3d;s.icn3dui;let i=s.resid2ncbi[e+"_"+t];return i?parseInt(i.substr(i.lastIndexOf("_")+1)):0}}class is{constructor(e){this.icn3d=e}loadAtomDataIn(e,t,s,i,n,l,r,o,a){let d=this.icn3d,c=d.icn3dui;d.pmin=new THREE.Vector3(9999,9999,9999),d.pmax=new THREE.Vector3(-9999,-9999,-9999),d.psum=new THREE.Vector3;let h=e.atoms,p=d.atoms?Object.keys(d.atoms).length:0,m={},u={};d.pmid=e.pubmedId,void 0===d.chainid2title&&(d.chainid2title={}),void 0===d.chainid2sid&&(d.chainid2sid={});let g={},f={};if("align"===s){d.pmid="",d.molTitle="",c.cfg.inpara&&-1!==c.cfg.inpara.indexOf("atype=1")?d.molTitle="Invariant Core Structure Alignment (VAST) of ":c.cfg.inpara&&-1!==c.cfg.inpara.indexOf("atype=2")?d.molTitle="Structure Alignment (TM-align) of ":d.molTitle="Structure Alignment (VAST) of ";let t=!1;for(let s=0,i=e.alignedStructures[0].length;s'+i.pdbId.toUpperCase()+"",void 0!==i.descr&&(d.pmid+=i.descr.pubmedid),0===s&&(d.molTitle+=" and ",void 0!==i.descr&&(d.pmid+="_")),t=!0}d.molTitle+=" from VAST+",t||(d.molTitle="")}else if(void 0!==e.descr&&(d.molTitle+=e.descr.name),"mmdbid"===s){let s=isNaN(t)?t:e.pdbId,i={};void 0===d.alignmolid2color&&(d.alignmolid2color=[]);let n=1;for(let t in e.moleculeInfor){if(0===Object.keys(e.moleculeInfor[t]).length)continue;let l=e.moleculeInfor[t].chain.trim();(parseInt(c.cfg.date)>=20231001||!c.cfg.date&&parseInt(c.utilsCls.getDateDigitStr())>=20231001)&&(l=l.replace(/_/g,""));let r=s+"_"+l;i.hasOwnProperty(l)?(++i[l],r+=i[l]):i[l]=1,void 0!==d.mmdbid_q&&(d.mmdbid_q,d.mmdbid_t);let o=e.moleculeInfor[t].kind,a=e.moleculeInfor[t].color,h=e.moleculeInfor[t].sid;if(g[r]=o,f[r]=a,"protein"==o&&(d.organism=e.moleculeInfor[t].taxonomyName.toLowerCase()),void 0!==h&&(d.chainid2sid[r]=h),void 0===d.pdbid_chain2title&&(d.pdbid_chain2title={}),d.pdbid_chain2title[r]=e.moleculeInfor[t].name,l==r.substr(r.lastIndexOf("_"))){let e={};e[t]=n.toString(),d.alignmolid2color.push(e)}++n}}"mmdbid"===s&&(d.molTitleHash||(d.molTitleHash={}),d.molTitleHash[t]=d.molTitle);let b,C,y,v,_,w={},S="",A="",x="",k="",O="",R="",I=0,T=0,E="",P=!0,M=!1,D="",H=c.utilsCls.isCalphaPhosOnly(h),F=0,L={};for(let e in h){++p,w[e]=p;let i,n=h[e];n.serial=p,"mmdbid"===s||"mmcifid"===s?i=t:"align"===s&&(i=m[p]);let l=!1;if(void 0!==n.chain||"mmdbid"!==s&&"align"!==s)n.chain=""===n.chain?"Misc":n.chain;else if("mmdbid"===s)if(b=n.ids.m,void 0!==d.molid2chain[b]){let e=d.molid2chain[b].indexOf("_");n.chain=d.molid2chain[b].substr(e+1)}else{let e="Misc";("protein"===g[O]&&"nucleotide"===g[O]&&n.resi!=T||"protein"!==g[O]&&"nucleotide"!==g[O]&&(n.resn.substr(0,3)!=E.substr(0,3)||n.resi!=T||"solvent"===g[O]||"HOH"===n.resn))&&++F,n.resi_ori=n.resi,n.resi=F,l=!0,n.chain=e}else if("align"===s)if(b=n.ids.m,void 0!==d.pdbid_molid2chain[i+"_"+b])n.chain=d.pdbid_molid2chain[i+"_"+b];else{let e="Misc";("protein"===g[O]&&"nucleotide"===g[O]&&n.resi!=T||"protein"!==g[O]&&"nucleotide"!==g[O]&&(n.resn.substr(0,3)!=E.substr(0,3)||n.resi!=T||"solvent"===g[O]||"HOH"===n.resn))&&(++F,n.resi_ori=n.resi,n.resi=F,l=!0),n.chain=e}if(n.chain=n.chain.trim(),(parseInt(c.cfg.date)>=20231001||!c.cfg.date&&parseInt(c.utilsCls.getDateDigitStr())>=20231001)&&(n.chain=n.chain.replace(/_/g,"")),"mmdbid"!==s&&"align"!==s||(n.structure=i,"mmdbid"===s&&void 0!==d.mmdbid_q&&(d.mmdbid_q,d.mmdbid_t)),k=n.structure,O=k+"_"+n.chain,"mmdbid"===s||"align"===s){l||(n.resi_ori=n.resi,d.bUsePdbNum?n.resi=n.resi_ori:n.resi=n.ids.r);let e=n.resn.indexOf(" ");-1!==e&&0!=e&&(n.resn=n.resn.substr(0,e))}O!==A&&(I=0),n.resi!==I&&(O!==A?(y=void 0,_=void 0):(y=C,_=v)),n.coord="mmdbid"===s?new THREE.Vector3(n.coord[0],n.coord[1],n.coord[2]):new THREE.Vector3(n.coord.x,n.coord.y,n.coord.z);let r=c.utilsCls.residueName2Abbr(n.resn.substr(0,3));"mmdbid"!==s&&"align"!==s||!d.bFullUi||(void 0===d.mmdbMolidResid2mmdbChainResi&&(d.mmdbMolidResid2mmdbChainResi={}),d.mmdbMolidResid2mmdbChainResi[i+"_"+n.ids.m+"_"+n.ids.r]=i+"_"+n.chain+"_"+n.resi),d.pmin.min(n.coord),d.pmax.max(n.coord),d.psum.add(n.coord);let o=void 0===c.cfg.mmcifid&&"mmcif"!=d.InputfileType?"protein"===g[O]:"p"===n.mt,a=void 0===c.cfg.mmcifid&&"mmcif"!=d.InputfileType?"nucleotide"===g[O]:"n"===n.mt,u=void 0===c.cfg.mmcifid&&"mmcif"!=d.InputfileType?"solvent"===g[O]:"s"===n.mt,N=void 0===c.cfg.mmcifid&&"mmcif"!=d.InputfileType?"ligand"===g[O]||void 0!==g[O]&&-1!==g[O].indexOf("other")||void 0===g[O]:"l"===n.mt;if("Misc"!==n.chain&&"other"!==g[O]||"protein"===L[O]||"nucleotide"===L[O]||("CA"===n.name&&"C"===n.elem?L[O]="protein":"P"===n.name&&"P"===n.elem?L[O]="nucleotide":L[O]="chemical"),o||a?(o?(d.proteins[p]=1,"CA"===n.name&&(d.calphas[p]=1),"N"!==n.name&&"H"!==n.name&&"CA"!==n.name&&"HA"!==n.name&&"C"!==n.name&&"O"!==n.name&&(d.sidec[p]=1)):a&&(d.nucleotides[p]=1,("O3'"==n.name||"O3*"==n.name||H&&"P"==n.name)&&(d.nucleotidesO3[p]=1),-1===c.parasCls.nuclMainArray.indexOf(n.name)&&(d.ntbase[p]=1)),n.het=!1):u?(d.water[p]=1,n.het=!0):N&&("HOH"===n.resn||"O"===n.resn?d.water[p]=1:n.elem===n.resn?d.ions[p]=1:d.chemicals[p]=1,n.het=!0),"mmdbid"===s?n.het?n.color=c.parasCls.atomColors[n.elem]||c.parasCls.defaultAtomColor:n.color=void 0!==f[O]?c.parasCls.thr(f[O]):c.parasCls.chargeColors[n.resn]:void 0!==n.color&&(n.color=c.parasCls.thr(n.color))," "!==n.resn.charAt(0)&&" "===n.resn.charAt(1)&&(n.resn=n.resn.charAt(0)),n.het||"C"!==n.name||(C=p),n.het||"O"!==n.name||(v=p),!n.het&&"N"===n.name&&void 0!==y&&void 0!==_){let e=d.atoms[y].coord.distanceTo(d.atoms[_].coord),t=n.coord.x+(d.atoms[y].coord.x-d.atoms[_].coord.x)/e,s=n.coord.y+(d.atoms[y].coord.y-d.atoms[_].coord.y)/e,i=n.coord.z+(d.atoms[y].coord.z-d.atoms[_].coord.z)/e;n.hcoord=new THREE.Vector3(t,s,i)}"HOH"==n.resn&&(d.water[p]=1),d.atoms[p]=n,d.dAtoms[p]=1,d.hAtoms[p]=1;let q=n.structure+"_"+n.chain;void 0===d.chains[q]&&(d.chains[q]={}),d.chains[q][p]=1;let U=q+"_"+n.resi;void 0===d.residues[U]&&(d.residues[U]={}),d.residues[U][p]=1,R=O+"_"+n.resi,R!==x&&O!==A&&(P=!0,""!==S&&(void 0===d.structures[S]&&(d.structures[S]=[]),d.structures[S].push(A))),d.residueId2Name[U]=r;let $="-";if("helix"===n.ss?$="H":"sheet"===n.ss?$="E":n.het||a?$="o":(!n.het&&c.parasCls.residueColors.hasOwnProperty(n.resn.toUpperCase())||"coil"===n.ss)&&($="c"),d.secondaries[n.structure+"_"+n.chain+"_"+n.resi]=$,(n.resi!=I||b!=D)&&d.bFullUi&&(void 0===d.chainsSeq[q]&&(d.chainsSeq[q]=[],P=!1),!isNaN(n.resi)))if(P&&!M&&void 0!==d.chainsSeq[q][n.resi-1])d.chainsSeq[q][n.resi-1].name=r;else if(!P||!d.chainsSeq[q].hasOwnProperty(n.resi-1)){let e={};e.resi=n.resi,e.name=r,n.resi%10==0&&n.resi.toString(),d.chainsSeq[q].push(e),M=!0}I=n.resi,T=n.resi_ori,E=n.resn,S=k,A=O,x=R,D=b}for(let e in d.chemicals){let t=d.atoms[e];if("P"==t.elem&&t.bonds.length>=4)for(let e=t.bonds.length-1;e>=0;--e){"P"==d.atoms[t.bonds[e]].elem&&t.bonds.splice(e,1)}}for(let e in L)if(!(Object.keys(d.chains[e]).length<10)&&"chemical"!==L[e])for(let t in d.chains[e]){let s=d.atoms[t];delete d.chemicals[t],s.het=!1,"protein"===L[e]?(d.proteins[t]=1,"CA"===s.name&&(d.calphas[t]=1),"N"!==s.name&&"H"!==s.name&&"CA"!==s.name&&"HA"!==s.name&&"C"!==s.name&&"O"!==s.name&&(d.sidec[t]=1)):"nucleotide"===L[e]&&(d.nucleotides[t]=1,("O3'"==s.name||"O3*"==s.name||H&&"P"==s.name)&&(d.nucleotidesO3[t]=1),-1===c.parasCls.nuclMainArray.indexOf(s.name)&&(d.ntbase[t]=1))}if(void 0===d.structures[k]&&(d.structures[k]=[]),d.structures[k].push(O),d.bFullUi)if("mmdbid"===s||"mmcifid"===s)for(let i in e.sequences){let n=e.sequences[i],l=t+"_"+i;void 0!==d.mmdbid_q&&(d.mmdbid_q,d.mmdbid_t),d.ParserUtilsCls.getMissingResidues(n,s,l)}else if("align"===s)for(let e in d.chainid2seq){let t=d.chainid2seq[e];d.ParserUtilsCls.getMissingResidues(t,s,e)}if(d.loadPDBCls.setResidMapping(),"mmcifid"!==s)for(let e in h){let t=w[e],s=void 0===d.atoms[t].bonds?0:d.atoms[t].bonds.length;for(let e=0;ed.maxatomcnt||void 0!==d.biomtMatrices&&d.biomtMatrices.length*d.cnt>10*d.maxatomcnt)&&(d.opts.proteins="c alpha trace",d.opts.nucleotides="o3 trace"),d.center=d.ParserUtilsCls.getGeoCenter(d.pmin,d.pmax),d.maxD=d.ParserUtilsCls.getStructureSize(d.atoms,d.pmin,d.pmax,d.center),d.maxD<5&&(d.maxD=5),d.oriMaxD=d.maxD,("align"===s||o)&&(d.ssbondpnts={},d.loadPDBCls.setSsbond()),"mmdbid"===s&&1==Object.keys(d.structures).length){let t=e.disulfides;if(void 0!==t)for(let e=0,s=t.length;ep&&(p=e)),c[e]={resi:t,resn:i,aligned:n}}r=e[t][1];let u=r.moleculeId,g=s.pdbid_molid2chain[l+"_"+u],f=l+"_"+g;void 0===s.alnChainsAnTtl[d]&&(s.alnChainsAnTtl[d]=[]),void 0===s.alnChainsAnTtl[d][0]&&(s.alnChainsAnTtl[d][0]=[]),void 0===s.alnChainsAnTtl[d][1]&&(s.alnChainsAnTtl[d][1]=[]),void 0===s.alnChainsAnTtl[d][2]&&(s.alnChainsAnTtl[d][2]=[]),void 0===s.alnChainsAnTtl[d][3]&&(s.alnChainsAnTtl[d][3]=[]),void 0===s.alnChainsAnTtl[d][4]&&(s.alnChainsAnTtl[d][4]=[]),void 0===s.alnChainsAnTtl[d][5]&&(s.alnChainsAnTtl[d][5]=[]),void 0===s.alnChainsAnTtl[d][6]&&(s.alnChainsAnTtl[d][6]=[]),s.alnChainsAnTtl[d][0].push(f),s.alnChainsAnTtl[d][1].push(d),s.alnChainsAnTtl[d][2].push(""),s.alnChainsAnTtl[d][3].push(""),s.alnChainsAnTtl[d][4].push(f),s.alnChainsAnTtl[d][5].push(d),s.alnChainsAnTtl[d][6].push("");let b=1;s.chainsMapping[d]||(s.chainsMapping[d]={}),s.chainsMapping[f]||(s.chainsMapping[f]={});for(let e=h;e<=p;++e){let t,o,p,m=s.bUsePdbNum?s.ParserUtilsCls.getResi(f,r.sequence[e][0]-1):r.sequence[e][0],u="~"===r.sequence[e][2]?"-":r.sequence[e][2],C=r.sequence[e][3]?1:0,y=c[e].aligned+C;2===y?(c[e].resn===u?(t="#FF0000",p="icn3d-cons",s.consHash1[d+"_"+c[e].resi]=1,s.consHash2[f+"_"+m]=1):(t="#0000FF",p="icn3d-ncons",s.nconsHash1[d+"_"+c[e].resi]=1,s.nconsHash2[f+"_"+m]=1),s.chainsMapping[d][d+"_"+c[e].resi]=c[e].resn+c[e].resi,s.chainsMapping[f][f+"_"+m]=c[e].resn+c[e].resi,o="#"+s.showAnnoCls.getColorhexFromBlosum62(c[e].resn,u)):(t=i.htmlCls.GREY8,p="icn3d-nalign",s.nalignHash1[d+"_"+c[e].resi]=1,s.nalignHash2[f+"_"+m]=1),void 0===s.alnChainsSeq[d]&&(s.alnChainsSeq[d]=[]);let v={};v.mmdbid=n,v.chain=a,v.resi=c[e].resi,v.resn=""===v.resi||"icn3d-nalign"===p?c[e].resn.toLowerCase():c[e].resn,v.aligned=y,v.color=""===v.resi?i.htmlCls.GREYC:t,v.color2=""===v.resi?i.htmlCls.GREYC:o,v.class=p,s.alnChainsSeq[d].push(v),""!==c[e].resi&&(void 0===s.alnChains[d]&&(s.alnChains[d]={}),$.extend(s.alnChains[d],s.residues[d+"_"+c[e].resi])),void 0===s.alnChainsSeq[f]&&(s.alnChainsSeq[f]=[]),v={},v.mmdbid=l,v.chain=g,v.resi=m,v.resn=""===v.resi||"icn3d-nalign"===p?u.toLowerCase():u,v.aligned=y,v.color=""===v.resi?i.htmlCls.GREYC:t,v.color2=""===v.resi?i.htmlCls.GREYC:o,v.class=p,s.alnChainsSeq[f].push(v),""!==v.resi&&(void 0===s.alnChains[f]&&(s.alnChains[f]={}),$.extend(s.alnChains[f],s.residues[f+"_"+m])),void 0===s.alnChainsAnno[d]&&(s.alnChainsAnno[d]=[]),void 0===s.alnChainsAnno[d][0]&&(s.alnChainsAnno[d][0]=[]),void 0===s.alnChainsAnno[d][1]&&(s.alnChainsAnno[d][1]=[]),void 0===s.alnChainsAnno[d][2]&&(s.alnChainsAnno[d][2]=[]),void 0===s.alnChainsAnno[d][3]&&(s.alnChainsAnno[d][3]=[]),e===h&&(void 0===s.alnChainsAnno[d][4]&&(s.alnChainsAnno[d][4]=[]),void 0===s.alnChainsAnno[d][5]&&(s.alnChainsAnno[d][5]=[]),void 0===s.alnChainsAnno[d][6]&&(s.alnChainsAnno[d][6]=[]),s.alnChainsAnno[d][4].push(s.pdbid_chain2title[f]),s.alnChainsAnno[d][5].push(s.pdbid_chain2title[d]),s.alnChainsAnno[d][6].push(""));let _=d+"_"+c[e].resi,w=f+"_"+m,S=s.secondaries[_],A=s.secondaries[w];A?s.alnChainsAnno[d][0].push(A):s.alnChainsAnno[d][0].push("-"),S?s.alnChainsAnno[d][1].push(S):s.alnChainsAnno[d][1].push("-");let x=".";b%5==0&&(x="*"),b%10==0&&(x="|"),s.alnChainsAnno[d][2].push(x);let k="";b%10==0&&(k=b.toString()),s.alnChainsAnno[d][3].push(k),++b}}e={}}getPosFromResi(e,t){let s=this.icn3d;s.icn3dui;let i,n=s.resid2ncbi[e+"_"+t];if(n){i=n.substr(n.lastIndexOf("_")+1)-1}return i}getResnFromResi(e,t){let s=this.icn3d;s.icn3dui;let i=e+"_"+t,n=s.residueId2Name[i];return n||(n="?"),n}getResiAferAlign(e,t,s){let i,n=this.icn3d,l=n.icn3dui;if(t&&"tmalign"==l.cfg.aligntool)i=s;else if(n.posid2resid){let t=n.posid2resid[e+"_"+s];i=t.substr(t.lastIndexOf("_")+1)}else i=n.chainsSeq[e][s].resi;return i}setSeqAlignChain(e,t,s){let i,n,l,r,o,a,d,c,h,p,m,u=this.icn3d,g=u.icn3dui,f={},b=!!s;if(b){if(o=s[1],a=s[0],t=s[2],d=o.indexOf("_"),c=a.indexOf("_"),i=o.substr(0,d).toUpperCase(),n=a.substr(0,c).toUpperCase(),l=o.substr(d+1),r=a.substr(d+1),i==n&&l==r){let e=u.chainsSeq[n+"_"+r].length;u.qt_start_end[t]={q_start:1,q_end:e,t_start:1,t_end:e}}}else{let d=s[0].indexOf("_"),c=e.indexOf("_");if(i=u.mmdbid_t,n=e.substr(0,c).toUpperCase(),l=s[0].substr(d+1),r=e.substr(c+1),i==n&&l==r){let e=u.chainsSeq[u.mmdbid_q+"_"+u.chain_q].length;u.qt_start_end[t]={q_start:1,q_end:e,t_start:1,t_end:e}}o=i+"_"+l,a=n+"_"+r,void 0!==n&&u.mmdbid_t}u.conservedName1=o+"_cons",u.nonConservedName1=o+"_ncons",u.notAlignedName1=o+"_nalign",u.conservedName2=a+"_cons",u.nonConservedName2=a+"_ncons",u.notAlignedName2=a+"_nalign",u.consHash1={},u.nconsHash1={},u.nalignHash1={},u.consHash2={},u.nconsHash2={},u.nalignHash2={},u.alnChains={},u.alnChainsSeq[o]=[],u.alnChains[o]={},u.alnChainsSeq[a]=[],u.alnChains[a]={},u.alnChainsAnno[o]=[],u.alnChainsAnTtl[o]=[],void 0===u.alnChainsAnTtl[o]&&(u.alnChainsAnTtl[o]=[]);for(let e=0;e<7;++e)void 0===u.alnChainsAnTtl[o][e]&&(u.alnChainsAnTtl[o][e]=[]);u.alnChainsAnTtl[o][0].push(a),u.alnChainsAnTtl[o][1].push(o),u.alnChainsAnTtl[o][2].push(""),u.alnChainsAnTtl[o][3].push(""),u.alnChainsAnTtl[o][4].push(a),u.alnChainsAnTtl[o][5].push(o),u.alnChainsAnTtl[o][6].push("");let C=0,y=0;if(void 0===u.qt_start_end[t])return;let v=1;u.chainsMapping[o]||(u.chainsMapping[o]={}),u.chainsMapping[a]||(u.chainsMapping[a]={});let _={},w={};for(let e=0,s=u.qt_start_end[t].length;e0){let e=v;for(let t=C+1,i=s;tc&&(c=t)}}}"tmalign"==n.cfg.aligntool&&(s=!0);let p=Object.keys(a);p.sort((function(e,t){return parseInt(e)-parseInt(t)}));let m=-999,u=0,g=0,f=[],b=0;for(let e=0,t=p.length;e0&&i.resid2ncbi[t]!=i.resid2ncbi[m]+1&&i.resid2ncbi[t]!=i.resid2ncbi[m]){g=m;for(let e=0,t=f.length;ec)continue;let o={},p=r.indexOf("_");o.mmdbid=r.substr(0,p),o.chain=r.substr(p+1),o.resi=t,o.resn=a[t]?i.chainsSeq[r][e].name.toUpperCase():i.chainsSeq[r][e].name.toLowerCase(),o.aligned=!!a[t],o.color=a[t]?"#FF0000":n.htmlCls.GREYC,o.color2=a[t]?"#FF0000":n.htmlCls.GREYC,o.class=a[t]?"icn3d-align":"icn3d-nalign",i.alnChainsSeq[r].push(o),a[t]&&($.extend(i.alnChains[r],i.residues[r+"_"+o.resi]),l=n.hashUtilsCls.unionHash(l,i.residues[r+"_"+o.resi]))}let C=[0];for(let i=0,r=t.length;in)for(let e=0,t=u-m;e=n)for(let e=0,s=t-n;en)for(let e=0,t=d-a;e=n)for(let t=0,s=e-n;t0?void 0!==n?p.alnChainsAnno[t][0].push(n):p.alnChainsAnno[t][0].push("-"):console.log("Error: ic.alnChainsAnno[chainid1] is undefined")}}}class ls{constructor(e){this.icn3d=e}getStructureId(e,t,s){let i=this.icn3d;i.icn3dui;let n=e;return(e==i.defaultPdbId||s||i.structures.hasOwnProperty(e))&&(n=1===t?e:e+t.toString()),n}loadPDB(e,t,s,i,n,l,r,o){let a,d,c=this.icn3d,h=c.icn3dui,p={},m=!1,u=e.split("\n"),g={},f={};c.atoms||(l=!1),n||l?(c.oriNStru=c.structures?Object.keys(c.structures).length:0,d=c.oriNStru+1,a=c.atoms?Object.keys(c.atoms).length:0):(c.init(),d=1,a=0);let b,C,y,v,_,w,S,A=[],x=[],k=[],O=[],R=[],I=[],T="",E="",P="",M={},D=t||c.defaultPdbId,H=D,F="",L=!1,N=!0;for(let e in u){let r=u[e],q=r.substr(0,6);if("HEADER"!==q||L||t)if("TITLE "===q){let e=r.substr(10).replace(/ALPHAFOLD MONOMER V2.0 PREDICTION FOR /gi,"");c.molTitle+=e.trim()+" ",o&&c.esmTitle&&(c.molTitle=c.esmTitle),c.molTitleHash||(c.molTitleHash={}),c.molTitleHash[H]=c.molTitle}else if("HELIX "===q){c.bSecondaryStructure=!0;let e=""==r.substr(18,2).trim()?"A":r.substr(18,2).trim(),t=parseInt(r.substr(21,4)),s=parseInt(r.substr(33,4));for(let i=t;i<=s;++i){let n=H+"_"+e+"_"+i;O.push(n),i===t&&R.push(n),i===s&&I.push(n)}}else if("SHEET "===q){void 0!==s&&s||(c.bSecondaryStructure=!0);let e=""==r.substr(20,2).trim()?"A":r.substr(20,2).trim(),t=parseInt(r.substr(22,4)),i=parseInt(r.substr(33,4));for(let s=t;s<=i;++s){let n=H+"_"+e+"_"+s;A.push(n),s===t&&x.push(n),s===i&&k.push(n)}}else if("HBOND "===q)void 0!==s&&s||(c.bSecondaryStructure=!0);else if("SSBOND"===q){c.bSsbondProvided=!0;let e=D+"_"+(" "==r.substr(15,1)?"A":r.substr(15,1))+"_"+r.substr(17,4).trim(),t=D+"_"+(" "==r.substr(29,1)?"A":r.substr(29,1))+"_"+r.substr(31,4).trim();void 0===c.ssbondpnts[D]&&(c.ssbondpnts[D]=[]),c.ssbondpnts[D].push(e),c.ssbondpnts[D].push(t)}else if("REMARK"===q){let e=parseInt(r.substr(7,3));if(-1!==r.indexOf("1/2 of bilayer thickness:"))c.halfBilayerSize=parseFloat(r.substr(r.indexOf(":")+1).trim());else if(210==e)"EXPERIMENT TYPE"==r.substr(11,32).trim()&&"NMR"==r.substr(45).trim()&&(m=!0);else if(350==e&&"BIOMT"==r.substr(13,5)){let e=parseInt(r[18])-1,t=parseInt(r.substr(21,2))-1;null==c.biomtMatrices[t]&&(c.biomtMatrices[t]=(new THREE.Matrix4).identity()),c.biomtMatrices[t].elements[e]=parseFloat(r.substr(24,9)),c.biomtMatrices[t].elements[e+4]=parseFloat(r.substr(34,9)),c.biomtMatrices[t].elements[e+8]=parseFloat(r.substr(44,9)),c.biomtMatrices[t].elements[e+12]=parseFloat(r.substr(54,14))}else if(465==e&&" "==r.substr(18,1)&&" "==r.substr(20,1)&&"S"!=r.substr(21,1)){let e=r.substr(15,3),t=r.substr(18,2).trim(),s=r.substr(21,5).trim(),i=D+"_"+t;void 0===c.chainMissingResidueArray[i]&&(c.chainMissingResidueArray[i]=[]);let n={};n.resi=s,n.name=h.utilsCls.residueName2Abbr(e).toLowerCase(),""!=F&&t==F&&t!=F||(c.chainMissingResidueArray[i].push(n),F=t)}else 900==e&&void 0===c.emd&&"RELATED DB: EMDB"==r.substr(34).trim()&&(c.emd=r.substr(23,11).trim())}else if("SOURCE"===q&&void 0===c.organism&&"ORGANISM_COMMON"==r.substr(11,15).trim())c.organism=r.substr(28).toLowerCase().trim(),c.organism=c.organism.substr(0,c.organism.length-1);else if("ENDMDL"===q)++d,D=c.defaultPdbId,H=this.getStructureId(D,d,n),m||(A=[],x=[],k=[],O=[],R=[],I=[]),L=!1;else if("JRNL "===q)"PMID"===r.substr(12,4)&&(c.pmid=r.substr(19).trim());else if("ATOM "===q||"HETATM"===q){N&&(H=this.getStructureId(D,d,n),N=!1);let e=r.substr(16,1);++a,M[parseInt(r.substr(6,5))]=a;let t=r.substr(76,2).trim();""===t&&(t=r.substr(12,2).trim());let l=r.substr(12,4).trim(),u=r.substr(17,3),F=r.substr(20,2).trim();""===F&&(F="A");let L=r.substr(22,5).trim(),U=L;if(s&&"DUM"===u&&(t=l,F="MEM",U=1,L=1),i&&"DUM"===u)break;b=H+"_"+F,y=b+"_"+L,C=b+"_"+U;let $=parseFloat(r.substr(30,8)),j=parseFloat(r.substr(38,8)),B=parseFloat(r.substr(46,8)),z=new THREE.Vector3($,j,B),G=parseFloat(r.substr(60,8));o&&(G*=100);let V={het:"H"===q[0],serial:a,name:l,alt:e,resn:u,structure:H,chain:F,resi:U,coord:z,b:G,elem:t,bonds:[],ss:"coil",ssbegin:!1,ssend:!1};if(V.het||"C"!==V.name||(v=a),V.het||"O"!==V.name||(w=a),!V.het&&"N"===V.name&&void 0!==_&&void 0!==S){let e=c.atoms[_].coord.distanceTo(c.atoms[S].coord),t=V.coord.x+(c.atoms[_].coord.x-c.atoms[S].coord.x)/e,s=V.coord.y+(c.atoms[_].coord.y-c.atoms[S].coord.y)/e,i=V.coord.z+(c.atoms[_].coord.z-c.atoms[S].coord.z)/e;V.hcoord=new THREE.Vector3(t,s,i)}c.atoms[a]=V,c.dAtoms[a]=1,c.hAtoms[a]=1,p[a]=1,this.isSecondary(C,A,m)?(c.atoms[a].ss="sheet",this.isSecondary(C,x,m)&&(c.atoms[a].ssbegin=!0),this.isSecondary(C,k,m)&&(c.atoms[a].ssend=!0)):this.isSecondary(C,O,m)&&(c.atoms[a].ss="helix",this.isSecondary(C,R,m)&&(c.atoms[a].ssbegin=!0),this.isSecondary(C,I,m)&&(c.atoms[a].ssend=!0));let W="-";if(W="helix"===c.atoms[a].ss?"H":"sheet"===c.atoms[a].ss?"E":!c.atoms[a].het&&h.parasCls.residueColors.hasOwnProperty(c.atoms[a].resn.toUpperCase())?"c":"o",c.secondaries[C]=W,y!==P){let e=h.utilsCls.residueName2Abbr(u);if(c.residueId2Name[C]=e,1!==a&&""!==E&&(c.residues[E]=f),C!==E&&(f={}),b!==T){_=void 0,S=void 0,1!==a&&""!==T&&(void 0===c.chains[T]&&(c.chains[T]={}),c.chains[T]=h.hashUtilsCls.unionHash(c.chains[T],g)),g={},void 0===c.structures[H.toString()]&&(c.structures[H.toString()]=[]),c.structures[H.toString()].includes(b)||c.structures[H.toString()].push(b),void 0===c.chainsSeq[b]&&(c.chainsSeq[b]=[]);let t={};t.resi=U,t.name=e,c.chainsSeq[b].push(t)}else{_=v,S=w;let t={};t.resi=U,t.name=e,c.chainsSeq[b].push(t)}}g[a]=1,f[a]=1,T=b,E=C,P=y}else if("CONECT"===q){let e=parseInt(r.substr(6,5));for(let t=0;t<4;++t){let s=parseInt(r.substr([11,16,21,26][t],5));isNaN(s)||void 0!==c.atoms[M[e]]&&c.atoms[M[e]].bonds.push(M[s])}}else q.substr(0,3);else D=r.substr(62).trim(),""==D&&(D=l?c.defaultPdbId:c.inputid&&-1==c.inputid.indexOf("/")?c.inputid.substr(0,10):c.defaultPdbId),H=this.getStructureId(D,d,n),c.molTitle="",c.molTitleHash={},L=!0}c.residues[C]=f,void 0===c.chains[b]&&(c.chains[b]={}),c.chains[b]=h.hashUtilsCls.unionHash2Atoms(c.chains[b],g,c.atoms),this.adjustSeq(c.chainMissingResidueArray);let q=Object.keys(c.structures);for(let e=0,t=q.length;e=l?n:l,o=new Array(s+i),a=0,d=0,c=0,h=!1;for(;ar&&i>r&&(h=!0),s<=r&&i>r?s>i||h?(o[c]=t[d],d++):(o[c]=e[a],a++):s>r&&i<=r?s<=i||h?(o[c]=e[a],a++):(o[c]=t[d],d++):s<=i?(o[c]=e[a],a++):(o[c]=t[d],d++),c++}if(a4||Math.abs(l.y-r.y)>4||Math.abs(l.z-r.z)>4||(l.x-r.x)*(l.x-r.x)+(l.y-r.y)*(l.y-r.y)+(l.z-r.z)*(l.z-r.z)<16&&(void 0===t.ssbondpnts[e]&&(t.ssbondpnts[e]=[]),t.ssbondpnts[e].push(o),t.ssbondpnts[e].push(a)))}}}getChainCalpha(e,t,s,i){let n=this.icn3d,l=n.icn3dui,r={};for(let o in e){if(void 0!==i){if(o.split("_")[0]!==i)continue}let a=Object.keys(e[o]),d=[],c=0,h=0;for(let e=0,i=a.length;e3?i.resn.trim().substr(0,3):i.resn.trim();if(!l.parasCls.chargeColors.hasOwnProperty(e))continue;s?i.resi_ori:i.resi,d.push(i.coord.clone()),++c,h=i.resi}}if(c>0){r[t[a[0]].chain]=d}}return{chainresiCalphaHash:r,center:n.center.clone()}}isSecondary(e,t,s){if(this.icn3d.icn3dui,s){let s=e.substr(e.indexOf("_")+1),i=!1;for(let e=0,n=t.length;e0&&(d=!0);for(let n=0,l=t.length;na&&(a=l),s.push(l)}o.push(s)}if(!d)return void(n.bRender&&alert("These structures can not be aligned..."));a<1e-6&&(a=1);for(let e=0,s=t.length;ep[e]=4&&(n.rmsd_suprTmp=l.rmsdSuprCls.getRmsdSuprCls(c,a,p),void 0!==n.rmsd_suprTmp.rot))){let e=n.rmsd_suprTmp.rot;if(null===e[0])continue;let i=n.rmsd_suprTmp.trans1,r=n.rmsd_suprTmp.trans2,a=n.rmsd_suprTmp.rmsd;if(aRealignment RMSD : "+a.toPrecision(4)+" Å8)return s;let g=[];g[0]=n[0]*r[0]+n[1]*r[1]+n[2]*r[2],g[1]=n[3]*r[0]+n[4]*r[1]+n[5]*r[2],g[2]=n[6]*r[0]+n[7]*r[1]+n[8]*r[2],g[0]-=n[0]*a[0]+n[1]*a[1]+n[2]*a[2],g[1]-=n[3]*a[0]+n[4]*a[1]+n[5]*a[2],g[2]-=n[6]*a[0]+n[7]*a[1]+n[8]*a[2];let f=0;return f=c[0]*g[0],f+=c[1]*g[1],f+=c[2]*g[2],f/=p*m,f<.866?s:(g[0]=l[0]*r[0]+l[1]*r[1]+l[2]*r[2],g[1]=l[3]*r[0]+l[4]*r[1]+l[5]*r[2],g[2]=l[6]*r[0]+l[7]*r[1]+l[8]*r[2],g[0]-=l[0]*a[0]+l[1]*a[1]+l[2]*a[2],g[1]-=l[3]*a[0]+l[4]*a[1]+l[5]*a[2],g[2]-=l[6]*a[0]+l[7]*a[1]+l[8]*a[2],f=c[0]*g[0],f+=c[1]*g[1],f+=c[2]*g[2],f/=p*m,f<.866?s:(u=0,u+=Math.pow(e.q_rotation.x1-t.q_rotation.x1,2),u+=Math.pow(e.q_rotation.y1-t.q_rotation.y1,2),u+=Math.pow(e.q_rotation.z1-t.q_rotation.z1,2),u+=Math.pow(e.q_rotation.x2-t.q_rotation.x2,2),u+=Math.pow(e.q_rotation.y2-t.q_rotation.y2,2),u+=Math.pow(e.q_rotation.z2-t.q_rotation.z2,2),u+=Math.pow(e.q_rotation.x3-t.q_rotation.x3,2),u+=Math.pow(e.q_rotation.y3-t.q_rotation.y3,2),u+=Math.pow(e.q_rotation.z3-t.q_rotation.z3,2),Math.sqrt(u)))}GetRotMatrix(e,t,s){this.icn3d.icn3dui;let i=[];return i&&(i[0]=e.q_rotation.x1/t,i[1]=e.q_rotation.y1/t,i[2]=e.q_rotation.z1/t,i[3]=e.q_rotation.x2/t,i[4]=e.q_rotation.y2/t,i[5]=e.q_rotation.z2/t,i[6]=e.q_rotation.x3/t,i[7]=e.q_rotation.y3/t,i[8]=e.q_rotation.z3/t,2!=s?(i[9]=e.t_trans_add.x/t,i[10]=e.t_trans_add.y/t,i[11]=e.t_trans_add.z/t,i[12]=-e.q_trans_sub.x/t,i[13]=-e.q_trans_sub.y/t,i[14]=-e.q_trans_sub.z/t):(i[9]=-e.q_trans_add.x/t,i[10]=-e.q_trans_add.y/t,i[11]=-e.q_trans_add.z/t,i[12]=0,i[13]=0,i[14]=0)),i}cbu_dist(e,t,s){return er&&(s.push(e[n].leaves),i.push(e[n].dist));return{clusters:s,scores:i}}}class os{constructor(e){this.icn3d=e}async applyCommand(e){let t=this.icn3d,s=t.icn3dui;t.bAddCommands=!1;let i=e.split("|||")[0].split("%7C%7C%7C")[0].replace(/\s+/g," ").trim(),n=i.toLowerCase();if("share link"==n)await t.shareLinkCls.shareLink();else if("export state file"==n);else if(0==n.indexOf("export canvas"))setTimeout((async function(){let e=n.substr(13).trim();t.scaleFactor=""===e?1:parseInt(e);let s=""!==e;await t.shareLinkCls.shareLink(!0,s)}),500);else if("export interactions"==n)t.viewInterPairsCls.exportInteractions();else if("export stl file"==n)setTimeout((function(){t.export3DCls.exportStlFile("")}),500);else if("export vrml file"==n)setTimeout((function(){t.export3DCls.exportVrmlFile("")}),500);else if("export stl stabilizer file"==n)setTimeout((function(){t.threeDPrintCls.hideStabilizer(),t.threeDPrintCls.resetAfter3Dprint(),t.threeDPrintCls.addStabilizer(),t.export3DCls.exportStlFile("_stab")}),500);else if("export vrml stabilizer file"==n)setTimeout((function(){t.threeDPrintCls.hideStabilizer(),t.threeDPrintCls.resetAfter3Dprint(),t.threeDPrintCls.addStabilizer(),t.export3DCls.exportVrmlFile("_stab")}),500);else if("export pdb"==n)s.htmlCls.setHtmlCls.exportPdb();else if("export pdb missing atoms"==n)await t.scapCls.exportPdbProfix(!1);else if("export pdb hydrogen"==n)await t.scapCls.exportPdbProfix(!0);else if(-1!=n.indexOf("export refnum ")){let e=n.substr(14);t.refnumCls.exportRefnum(e)}else if("export secondary structure"==n)s.htmlCls.setHtmlCls.exportSecondary();else if("select all"==n)t.selectionCls.selectAll();else if("show all"==n)t.selectionCls.showAll();else if("select complement"==n)t.resid2specCls.selectComplement();else if("set pk atom"==n)t.pk=1,t.opts.pk="atom";else if("set pk off"==n)t.pk=0,t.opts.pk="no",t.drawCls.draw(),t.hlObjectsCls.removeHlObjects();else if("set pk residue"==n)t.pk=2,t.opts.pk="residue";else if("set pk strand"==n)t.pk=3,t.opts.pk="strand";else if("set pk domain"==n)t.pk=4,t.opts.pk="domain";else if("set pk chain"==n)t.pk=5,t.opts.pk="chain";else if("set surface wireframe on"==n)t.opts.wireframe="yes",t.applyMapCls.applySurfaceOptions();else if("set surface wireframe off"==n)t.opts.wireframe="no",t.applyMapCls.applySurfaceOptions();else if("set map wireframe on"==n)t.opts.mapwireframe="yes",t.applyMapCls.applyMapOptions();else if("set map wireframe off"==n)t.opts.mapwireframe="no",t.applyMapCls.applyMapOptions();else if("set emmap wireframe on"==n)t.opts.emmapwireframe="yes",t.applyMapCls.applyEmmapOptions();else if("set emmap wireframe off"==n)t.opts.emmapwireframe="no",t.applyMapCls.applyEmmapOptions();else if("set surface neighbors on"==n)t.bConsiderNeighbors=!0,t.applyMapCls.applySurfaceOptions();else if("set surface neighbors off"==n)t.bConsiderNeighbors=!1,t.applyMapCls.applySurfaceOptions();else if("set axis on"==n)t.opts.axis="yes";else if("set pc1 axis"==n)t.pc1=!0,t.axesCls.setPc1Axes();else if("set axis off"==n)t.opts.axis="no",t.pc1=!1;else if("set fog on"==n)t.opts.fog="yes",t.fogCls.setFog(!0);else if("set fog off"==n)t.opts.fog="no",t.fogCls.setFog(!0);else if("set slab on"==n)t.opts.slab="yes";else if("set slab off"==n)t.opts.slab="no";else if("set assembly on"==n)t.bAssembly=!0;else if("set assembly off"==n)t.bAssembly=!1;else if("set chemicalbinding show"==n)t.setOptionCls.setOption("chemicalbinding","show");else if("set chemicalbinding hide"==n)t.setOptionCls.setOption("chemicalbinding","hide");else if("set hbonds off"==n)t.hBondCls.hideHbonds(),t.showInterCls.hideExtraBonds(),t.drawCls.draw();else if("set salt bridge off"==n)t.saltbridgeCls.hideSaltbridge(),t.showInterCls.hideExtraBonds(),t.drawCls.draw();else if("set contact off"==n)t.contactCls.hideContact(),t.showInterCls.hideExtraBonds(),t.drawCls.draw();else if("set halogen pi off"==n)t.piHalogenCls.hideHalogenPi(),t.showInterCls.hideExtraBonds(),t.drawCls.draw();else if("hydrogens"==n)t.showInterCls.showHydrogens(),t.drawCls.draw();else if("set hydrogens off"==n)t.showInterCls.hideHydrogens(),t.drawCls.draw();else if("close popup"==n)t.resizeCanvasCls.closeDialogs();else if("set stabilizer off"==n)t.threeDPrintCls.hideStabilizer(),t.drawCls.draw();else if("set disulfide bonds off"==n)t.opts.ssbonds="no",t.drawCls.draw();else if("set cross linkage off"==n)t.opts.clbonds="no",t.drawCls.draw();else if("set lines off"==n)t.labels.distance=[],t.lines.distance=[],t.drawCls.draw();else if("set labels off"==n){for(let e in t.labels)t.labels[e]=[];t.drawCls.draw()}else if("set mode all"==n)t.definedSetsCls.setModeAndDisplay("all");else if("set mode selection"==n)t.definedSetsCls.setModeAndDisplay("selection");else if("set view detailed view"==n)t.annotationCls.setAnnoViewAndDisplay("detailed view");else if("set view overview"==n)t.annotationCls.setAnnoViewAndDisplay("overview");else if("set annotation custom"==n)t.annotationCls.setAnnoTabCustom();else if("set annotation interaction"==n)t.annotationCls.setAnnoTabInteraction();else if("set annotation ptm"==n)await t.annotationCls.setAnnoTabPTM();else if("set annotation cdd"==n)t.annotationCls.setAnnoTabCdd();else if("set annotation site"==n)t.annotationCls.setAnnoTabSite();else if("set annotation ssbond"==n)t.annotationCls.setAnnoTabSsbond();else if("set annotation crosslink"==n)t.annotationCls.setAnnoTabCrosslink();else if("set annotation transmembrane"==n)await t.annotationCls.setAnnoTabTransmem();else if("highlight level up"==n)t.resid2specCls.switchHighlightLevelUp();else if("highlight level down"==n)t.resid2specCls.switchHighlightLevelDown();else if(0==n.indexOf("hide annotation")){let e=n.lastIndexOf(" "),s=n.substr(e+1);"all"==s?t.annotationCls.hideAnnoTabAll():"custom"==s?t.annotationCls.hideAnnoTabCustom():"clinvar"==s?t.annotationCls.hideAnnoTabClinvar():"snp"==s?t.annotationCls.hideAnnoTabSnp():"cdd"==s?t.annotationCls.hideAnnoTabCdd():"3ddomain"==s?t.annotationCls.hideAnnoTab3ddomain():"site"==s?t.annotationCls.hideAnnoTabSite():"ptm"==s?t.annotationCls.hideAnnoTabPTM():"interaction"==s?t.annotationCls.hideAnnoTabInteraction():"ssbond"==s?t.annotationCls.hideAnnoTabSsbond():"crosslink"==s?t.annotationCls.hideAnnoTabCrosslink():"transmembrane"==s&&t.annotationCls.hideAnnoTabTransmem()}else if("add residue labels"==n)t.residueLabelsCls.addResidueLabels(t.hAtoms),t.drawCls.draw();else if("add residue number labels"==n)t.residueLabelsCls.addResidueLabels(t.hAtoms,void 0,void 0,!0),t.drawCls.draw();else if("add reference number labels"==n)t.residueLabelsCls.addResidueLabels(t.hAtoms,void 0,void 0,void 0,!0),t.drawCls.draw();else if("add atom labels"==n)t.residueLabelsCls.addAtomLabels(t.hAtoms),t.drawCls.draw();else if("add element labels"==n)t.residueLabelsCls.addAtomLabels(t.hAtoms,!0),t.drawCls.draw();else if("add chain labels"==n)t.analysisCls.addChainLabels(t.hAtoms),t.drawCls.draw();else if("add terminal labels"==n)t.analysisCls.addTerminiLabels(t.hAtoms),t.drawCls.draw();else if("rotate left"==n)t.bStopRotate=!1,t.ROT_DIR="left",t.transformCls.rotateCountMax=6e3,t.resizeCanvasCls.rotStruc("left");else if("rotate right"==n)t.bStopRotate=!1,t.ROT_DIR="right",t.transformCls.rotateCountMax=6e3,t.resizeCanvasCls.rotStruc("right");else if("rotate up"==n)t.bStopRotate=!1,t.ROT_DIR="up",t.transformCls.rotateCountMax=6e3,t.resizeCanvasCls.rotStruc("up");else if("rotate down"==n)t.bStopRotate=!1,t.ROT_DIR="down",t.transformCls.rotateCountMax=6e3,t.resizeCanvasCls.rotStruc("down");else if("rotate x"==n){let e=new THREE.Vector3(1,0,0),s=.5*Math.PI;t.transformCls.setRotation(e,s)}else if("rotate y"==n){let e=new THREE.Vector3(0,1,0),s=.5*Math.PI;t.transformCls.setRotation(e,s)}else if("rotate z"==n){let e=new THREE.Vector3(0,0,1),s=.5*Math.PI;t.transformCls.setRotation(e,s)}else if("reset"===n)t.selectionCls.resetAll();else if("reset orientation"===n)t.transformCls.resetOrientation(),t.drawCls.draw();else if("reset thickness"==n)t.threeDPrintCls.resetAfter3Dprint(),t.drawCls.draw();else if("clear selection"==n)t.hlObjectsCls.removeHlObjects(),t.hlUpdateCls.removeHl2D(),t.bShowHighlight=!1,t.bSelectResidue=!1;else if("zoom selection"==n)t.transformCls.zoominSelection(),t.drawCls.draw();else if("center selection"==n)t.applyCenterCls.centerSelection(),t.drawCls.draw();else if("show selection"==n)t.selectionCls.showSelection();else if("hide selection"==n)t.selectionCls.hideSelection();else if("output selection"==n)t.threeDPrintCls.outputSelection();else if("toggle selection"==n)t.selectionCls.toggleSelection();else if("toggle highlight"==n)t.hlUpdateCls.toggleHighlight();else if("stabilizer"==n)t.threeDPrintCls.addStabilizer(),t.threeDPrintCls.prepareFor3Dprint();else if("disulfide bonds"==n)t.showInterCls.showSsbonds();else if("cross linkage"==n)t.showInterCls.showClbonds();else if("back"==n)await t.resizeCanvasCls.back();else if("forward"==n)await t.resizeCanvasCls.forward();else if("clear all"==n)t.selectionCls.selectAll();else if("defined sets"==n)t.definedSetsCls.showSets();else if("delete selected sets"==n)t.definedSetsCls.deleteSelectedSets();else if("view interactions"==n)void 0===s.cfg.mmdbid&&void 0===s.cfg.gi||t.ParserUtilsCls.set2DDiagrams(t.inputid);else if("show annotations all chains"==n)t.annotationCls.showAnnoAllChains();else if("save color"==n)t.setOptionCls.saveColor();else if("apply saved color"==n)t.setOptionCls.applySavedColor();else if("save style"==n)t.setOptionCls.saveStyle();else if("apply saved style"==n)t.setOptionCls.applySavedStyle();else if("select main chains"==n)t.selectionCls.selectMainChains();else if("select side chains"==n)t.selectionCls.selectSideChains();else if("select main side chains"==n)t.selectionCls.selectMainSideChains();else if("realign"==n)t.realignParserCls.realign();else if(-1!=n.indexOf("realign predefined ")){let e="realign predefined ",n=i.substr(e.length),l=n.indexOf(" "),r=n.substr(0,l).split(",");s.cfg.resdef=n.substr(l+1).replace(/:/gi,";"),await t.realignParserCls.realignChainOnSeqAlign(void 0,r,!0,!0)}else if("area"==n)t.analysisCls.calculateArea();else if("table inter count only"==n)$(".icn3d-border").hide();else if("table inter details"==n)$(".icn3d-border").show();else if("setoption map nothing"==n)t.setOptionCls.setOption("map","nothing");else if("setoption emmap nothing"==n)t.setOptionCls.setOption("emmap","nothing");else if("setoption phimap nothing"==n)t.setOptionCls.setOption("phimap","nothing");else if("setoption phisurface nothing"==n)t.setOptionCls.setOption("phisurface","nothing");else if("clear symd symmetry"==n)t.symdArray=[];else if("show axis"==n)t.bAxisOnly=!0;else if(0==i.indexOf("define helix sets")){let e=i.split(" | ")[1].split(" ")[1];t.addTrackCls.defineSecondary(e,"helix")}else if(0==i.indexOf("define sheet sets")){let e=i.split(" | ")[1].split(" ")[1];t.addTrackCls.defineSecondary(e,"sheet")}else if(0==i.indexOf("define coil sets")){let e=i.split(" | ")[1].split(" ")[1];t.addTrackCls.defineSecondary(e,"coil")}else if(0==i.indexOf("define igstrand sets")){let e=i.split(" | ")[1].split(" ")[1];t.addTrackCls.defineIgstrand(e,"igstrand")}else if(0==i.indexOf("define igloop sets")){let e=i.split(" | ")[1].split(" ")[1];t.addTrackCls.defineIgstrand(e,"igloop")}else if(0==i.indexOf("select interaction")){let e=i.substr(i.lastIndexOf(" ")+1).split(",");if(null!==e){let s=e[0].split("_")[0];t.b2DShown||t.ParserUtilsCls.download2Ddgm(s.toUpperCase()),t.diagram2dCls.selectInteraction(e[0],e[1])}}else if(0==i.indexOf("select saved atoms")||0==i.indexOf("select sets")){i=i.replace(/aligned_protein/g,"protein_aligned");let e=i.split(" | "),s=e[0].replace(/,/g," or "),n=19;0==i.indexOf("select sets")&&(n=12);let l=s.substr(n),r=l;2==e.length&&(r=e[1].substr(5)),t.definedSetsCls.selectCombinedSets(l,r)}else if(-1!==i.indexOf("select chain")){let e=i.substr(i.lastIndexOf(" ")+1).split(",");for(let s=0,i=e.length;s6?e[6].substr(e[6].lastIndexOf(" ")+1):0,d=e.length>7?e[7].substr(e[7].lastIndexOf(" ")+1):1;t.analysisCls.addLine(parseFloat(s[1]),parseFloat(s[3]),parseFloat(s[5]),parseFloat(i[1]),parseFloat(i[3]),parseFloat(i[5]),l,r,o,parseFloat(a),parseFloat(d)),t.drawCls.draw()}else if(0==n.indexOf("add sphere"))this.addShape(n,"sphere");else if(0==n.indexOf("add cube"))this.addShape(n,"cube");else if(0==n.indexOf("clear shape"))t.shapeCmdHash={};else if(0==n.indexOf("clear line between sets"))t.lines.cylinder=[];else if(0==i.indexOf("add label")){let e,n,l,r,o,a,d,c=i.split(" | "),h=c[0].substr("add label".length+1),p=!1;for(let t=1,s=c.length;t=5&&(e=l[4].substr(5)),l.length>=6&&(s=l[5].substr(6)),l.length>=7&&(n=l[6].substr(4)),$("#"+t.pre+"anno_custom")[0]&&($("#"+t.pre+"anno_custom")[0].checked=!0),$("[id^="+t.pre+"custom]").show(),"0"==s&&(s=void 0),t.addTrackCls.checkGiSeq(r,o,a,e,s,n,0)}else if(0==n.indexOf("remove one stabilizer")){let e=n.split(" | ")[1].split(" "),s=[];s.push(parseInt(e[0])),s.push(parseInt(e[1])),t.threeDPrintCls.removeOneStabilizer(s),t.drawCls.draw()}else if(0==n.indexOf("add one stabilizer")){let e=n.split(" | ")[1].split(" ");void 0===t.pairArray&&(t.pairArray=[]),t.pairArray.push(parseInt(e[0])),t.pairArray.push(parseInt(e[1])),t.drawCls.draw()}else if(0==n.indexOf("select planes z-axis")){let e=n.split(" ");if(5==e.length){let s=parseFloat(e[3]),i=parseFloat(e[4]);t.selectionCls.selectBtwPlanes(s,i)}}else if(0==n.indexOf("adjust membrane z-axis")){let e=n.split(" ");if(5==e.length){let s=parseFloat(e[3]),i=parseFloat(e[4]);t.selectionCls.adjustMembrane(s,i)}}else if(0==n.indexOf("toggle membrane"))t.selectionCls.toggleMembrane();else if(0==i.indexOf("calc buried surface")){let e=i.split(" | ");if(2==e.length){let s=e[1].split(" ");if(2==s.length){let e=s[0].split(","),i=s[1].split(",");t.analysisCls.calcBuriedSurface(e,i)}}}else if(0==i.indexOf("dist ")){let e=i.split(" | ");if(2==e.length){let s=e[1].split(" ");if(2==s.length){let e=s[0].split(","),i=s[1].split(",");t.analysisCls.measureDistTwoSets(e,i)}}}else if(0==i.indexOf("disttable")){let e=i.split(" | ");if(2==e.length){let i=e[1].split(" ");if(2==i.length){let e=i[0].split(","),n=i[1].split(",");t.analysisCls.measureDistManySets(e,n),s.htmlCls.dialogCls.openDlg("dl_disttable","Distance among the sets")}}}else if(0==i.indexOf("display interaction 3d")||0==i.indexOf("view interaction pairs")||0==i.indexOf("save1 interaction pairs")||0==i.indexOf("save2 interaction pairs")||0==i.indexOf("line graph interaction pairs")||0==i.indexOf("scatterplot interaction pairs")){let e=i.split(" | ");if(e.length>=3){let s=e[1].split(" ");if(2==s.length){let n,l,r=s[0].split(","),o=s[1].split(","),a=-1!==e[2].indexOf("hbonds"),d=-1!==e[2].indexOf("salt bridge"),c=-1!==e[2].indexOf("interactions"),h=-1!==e[2].indexOf("halogen"),p=-1!==e[2].indexOf("pi-cation"),m=-1!==e[2].indexOf("pi-stacking");if(e.length>=4&&(n="true"==e[3]),e.length>=5){let s=e[4].split(" ");s.length>=4&&($("#"+t.pre+"hbondthreshold").val(s[1]),$("#"+t.pre+"saltbridgethreshold").val(s[2]),$("#"+t.pre+"contactthreshold").val(s[3]),7==s.length&&($("#"+t.pre+"halogenthreshold").val(s[4]),$("#"+t.pre+"picationthreshold").val(s[5]),$("#"+t.pre+"pistackingthreshold").val(s[6])))}0==i.indexOf("display interaction 3d")?l="3d":0==i.indexOf("view interaction pairs")?l="view":0==i.indexOf("save1 interaction pairs")?l="save1":0==i.indexOf("save2 interaction pairs")?l="save2":0==i.indexOf("line graph interaction pairs")?l="linegraph":0==i.indexOf("scatterplot interaction pairs")&&(l="scatterplot"),await t.viewInterPairsCls.viewInteractionPairs(r,o,n,l,a,d,c,h,p,m)}}}else if(0==i.indexOf("export pairs")){let e=i.split(" | ");if(3==e.length){let i=e[1].split(" ");if(2==i.length){let n=i[0].split(","),l=i[1].split(","),r=e[2].split(" ")[1];t.showInterCls.pickCustomSphere(r,n,l,t.bSphereCalc),t.bSphereCalc=!0;let o=t.viewInterPairsCls.exportSpherePairs(),a=Object.keys(s.utilsCls.getHlStructures()).join(",");t.saveFileCls.saveFile(a+"_sphere_pairs.html","html",o)}}}else if(0==n.indexOf("graph label")){let e=n.lastIndexOf(" "),t=n.substr(e+1);$("#"+s.svgid+"_label").val(t),$("#"+s.svgid+" text").removeClass(),$("#"+s.svgid+" text").addClass(t)}else if(0==n.indexOf("cartoon label")){let e=n.lastIndexOf(" "),t=n.substr(e+1);$("#"+s.svgid_ct+"_label").val(t),$("#"+s.svgid_ct+" text").removeClass(),$("#"+s.svgid_ct+" text").addClass(t)}else if(0==n.indexOf("line graph scale")){let e=n.lastIndexOf(" "),i=n.substr(e+1);$("#"+s.linegraphid+"_scale").val(i),$("#"+s.linegraphid).attr("width",(t.linegraphWidth*parseFloat(i)).toString()+"px")}else if(0==n.indexOf("scatterplot scale")){let e=n.lastIndexOf(" "),i=n.substr(e+1);$("#"+s.scatterplotid+"_scale").val(i),$("#"+s.scatterplotid).attr("width",(t.scatterplotWidth*parseFloat(i)).toString()+"px")}else if(0==n.indexOf("contactmap scale")){let e=n.lastIndexOf(" "),i=n.substr(e+1);$("#"+s.contactmapid+"_scale").val(i),$("#"+s.contactmapid).attr("width",(t.contactmapWidth*parseFloat(i)).toString()+"px")}else if(0==n.indexOf("alignerrormap scale")){let e=n.lastIndexOf(" "),i=n.substr(e+1);$("#"+s.alignerrormapid+"_scale").val(i),$("#"+s.alignerrormapid).attr("width",(t.alignerrormapWidth*parseFloat(i)).toString()+"px")}else if(0==n.indexOf("graph force")){let e=n.lastIndexOf(" ");s.htmlCls.force=parseInt(n.substr(e+1)),$("#"+s.svgid+"_force").val(s.htmlCls.force),t.getGraphCls.handleForce()}else if(0==n.indexOf("hide edges")){let e=n.lastIndexOf(" ");s.htmlCls.hideedges=parseInt(n.substr(e+1)),$("#"+s.svgid+"_hideedges").val(s.htmlCls.hideedges),s.htmlCls.hideedges?(s.htmlCls.contactInsideColor="FFF",s.htmlCls.hbondInsideColor="FFF",s.htmlCls.ionicInsideColor="FFF"):(s.htmlCls.contactInsideColor="DDD",s.htmlCls.hbondInsideColor="AFA",s.htmlCls.ionicInsideColor="8FF"),void 0!==t.graphStr&&t.bRender&&s.htmlCls.force&&t.drawGraphCls.drawGraph(t.graphStr,t.pre+"dl_graph")}else if(0==n.indexOf("reset interaction pairs"))t.viewInterPairsCls.resetInteractionPairs();else if(0==n.indexOf("side by side")){let e=n.split(" | ")[1],t="_blank";window.open(e,t)}else if(0==i.indexOf("your note")){let e=i.split(" | ");t.yournote=e[1],$("#"+t.pre+"yournote").val(t.yournote),s.cfg.shownote&&(document.title=t.yournote)}else if(0==n.indexOf("cross structure interaction"))t.crossstrucinter=parseInt(n.substr(n.lastIndexOf(" ")+1)),$("#"+t.pre+"crossstrucinter").val(t.crossstrucinter);else if("replay on"==n)await t.resizeCanvasCls.replayon();else if("replay off"==n)await t.resizeCanvasCls.replayoff();else if(0==n.indexOf("contact map")){let e=n.split(" | ");if(3===e.length){let s=parseFloat(e[1].split(" ")[1]),i=e[2].split(" ")[1];await t.contactMapCls.contactMap(s,i)}}else if(0==n.indexOf("pickatom")){let e=parseInt(n.substr(n.lastIndexOf(" ")+1));t.pAtom=t.atoms[e],t.pickingCls.showPicking(t.pAtom)}else if(0==i.indexOf("set color spectrum")){let e=i.split(" | ");if(2==e.length){let s=e[1].split(","),i=!0;t.setColorCls.setColorAcrossSets(s,i)}}else if(0==i.indexOf("set residues color spectrum")){let e=i.split(" | ");if(2==e.length){let s=e[1].split(","),i=!0;t.setColorCls.setColorBySets(s,i)}}else if(0==i.indexOf("set color rainbow")){let e=i.split(" | ");if(2==e.length){let s=e[1].split(","),i=!1;t.setColorCls.setColorAcrossSets(s,i)}}else if(0==i.indexOf("set residues color rainbow")){let e=i.split(" | ");if(2==e.length){let s=e[1].split(","),i=!1;t.setColorCls.setColorBySets(s,i)}}else if(0==i.indexOf("color")){let e=i.split(" | "),n=e[0].substr(e[0].indexOf(" ")+1);if(t.opts.color=n,"residue custom"==n&&2==e.length){t.customResidueColors=JSON.parse(e[1]);for(let e in t.customResidueColors)t.customResidueColors[e.toUpperCase()]=s.parasCls.thr("#"+t.customResidueColors[e])}else if("align custom"==n&&3==e.length){let s=e[1],i=e[2].split(", ");t.queryresi2score={},t.queryresi2score[s]={};for(let e=0,n=i.length;e=4?this.setQueryresi2score(e):"area"==n&&2==e.length&&(t.midpercent=e[1],$("#"+t.pre+"midpercent").val(t.midpercent));t.setColorCls.setColorByOptions(t.opts,t.hAtoms),t.hlUpdateCls.updateHlAll(),t.getGraphCls.updateGraphColor()}else if(0==i.indexOf("remove legend"))$("#"+s.pre+"legend").hide();else if(0==i.indexOf("custom tube")){let e=i.split(" | ");this.setQueryresi2score(e),t.setOptionCls.setStyle("proteins","custom tube")}else if(0==n.indexOf("style")){let e=n.substr(n.indexOf(" ")+1),s=e.substr(0,e.indexOf(" ")),i=e.substr(e.indexOf(" ")+1);t.setOptionCls.setStyle(s,i)}else if(0==n.indexOf("window")){let e=n.substr(n.indexOf(" ")+1);setTimeout((function(){"aligned sequences"==e?s.htmlCls.dialogCls.openDlg("dl_alignment","Select residues in aligned sequences"):"interaction table"==e?s.htmlCls.dialogCls.openDlg("dl_allinteraction","Show interactions"):"interaction graph"==e?s.htmlCls.dialogCls.openDlg("dl_linegraph","Show interactions between two lines of residue nodes"):"interaction scatterplot"==e?s.htmlCls.dialogCls.openDlg("dl_scatterplot","Show interactions as scatterplot"):"force-directed graph"==e&&s.htmlCls.dialogCls.openDlg("dl_graph","Force-directed graph")}),1e3)}else if(0==n.indexOf("set theme")){let e=n.substr(n.lastIndexOf(" ")+1);s.htmlCls.setMenuCls.setTheme(e)}else if(0==n.indexOf("set double color")){let e=n.substr(n.lastIndexOf(" ")+1);"on"==e?(t.bDoublecolor=!0,t.setOptionCls.setStyle("proteins","ribbon")):"off"==e&&(t.bDoublecolor=!1)}else if(0==n.indexOf("adjust dialog")){let e=n.substr(n.lastIndexOf(" ")+1);t.scapCls.adjust2DWidth(e)}else if(0==n.indexOf("glycans cartoon")){let e=n.substr(n.lastIndexOf(" ")+1);t.bGlycansCartoon="yes"==e}else if(0==n.indexOf("save html")){let e=n.substr(n.lastIndexOf(" ")+1);s.htmlCls.eventsCls.saveHtml(e)}else if(0==n.indexOf("resdef"))s.cfg.resdef=n.substr(n.indexOf(" ")+1);else if(0==n.indexOf("vast_search_chainid")){t.chainidArray=i.substr(i.indexOf(" ")+1).split(",");let e=!0,s=!0;await t.realignParserCls.realignChainOnSeqAlign(void 0,t.chainidArray,e,s)}else if(0==n.indexOf("ig refnum off"))await t.refnumCls.hideIgRefNum();else if(0==n.indexOf("custom refnum")){let e=i.split(" | ")[1].replace(/\\n/g,"\n");await t.refnumCls.parseCustomRefFile(e)}else if(0==n.indexOf("show ref number"))t.bShownRefnum=!0;else if(0==n.indexOf("hide ref number"))t.bShownRefnum=!1;else if(-1!==n.indexOf("select displayed set"))t.hAtoms=s.hashUtilsCls.cloneHash(t.viewSelectionAtoms),t.hlUpdateCls.updateHlAll();else if(-1!==n.indexOf("select prop")){let e,s,n=i.split(" | "),l=n[0].substr("select prop".length+1);if(2==n.length){let t=n[1].split("_");e=t[0],s=t[1]}t.resid2specCls.selectProperty(l,e,s)}else if(-1!==n.indexOf("select each residue"))t.selectionCls.saveEachResiInSel();else if(0==n.indexOf("select")&&-1!==n.indexOf("name")){let e=i.split(" | "),s="",n="",l="";for(let t=0,i=e.length;t1&&(n=e[1].substr(e[1].indexOf(" ")+1)),e.length>2&&(l=e[2].substr(e[2].indexOf(" ")+1)),-1!==s.indexOf(" or ")?await t.selByCommCls.selectByCommand(s,n,l):await t.selByCommCls.selectBySpec(s,n,l)}s.htmlCls.clickMenuCls.setLogCmd(i,!1),t.bAddCommands=!0}setStrengthPara(e){let t=this.icn3d;if(t.icn3dui,e.length>=5){let s=e[4].split(" ");s.length>=4&&($("#"+t.pre+"hbondthreshold").val(s[1]),$("#"+t.pre+"saltbridgethreshold").val(s[2]),$("#"+t.pre+"contactthreshold").val(s[3]),s.length>=7&&($("#"+t.pre+"halogenthreshold").val(s[4]),$("#"+t.pre+"picationthreshold").val(s[5]),$("#"+t.pre+"pistackingthreshold").val(s[6])))}if(6==e.length){let s=e[5].split(" 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e=parseInt(n[0]),s=0;e<=parseInt(n[1]);++e,++s)"_"!=l[s]&&(t.queryresi2score[i][e]=11.11111111111111*parseInt(l[s]));if(e.length>4){let i=e[4].split(" ");t.startColor=i[1],t.midColor=i[2],t.endColor=i[3];let n=s.htmlCls.clickMenuCls.setLegendHtml();$("#"+s.pre+"dl_legend_html").html(n),s.htmlCls.dialogCls.openDlg("dl_legend","Color Range")}}addShape(e,t){let s=this.icn3d,i=s.icn3dui;s.shapeCmdHash[e]=1;let n=e.split(" | "),l=n[1].split(" "),r=n[2].substr(n[2].lastIndexOf(" ")+1),o=n[3].substr(n[3].lastIndexOf(" ")+1),a=n[4].substr(n[4].lastIndexOf(" ")+1);r="#"+r.replace(/\#/g,"");let d=i.parasCls.thr(r),c=new THREE.Vector3(parseFloat(l[1]),parseFloat(l[3]),parseFloat(l[5]));"sphere"==t?s.sphereCls.createSphereBase(c,d,parseFloat(a),void 0,void 0,void 0,parseFloat(o)):s.boxCls.createBox_base(c,parseFloat(a),d,void 0,void 0,void 0,parseFloat(o))}getMenuFromCmd(e){this.icn3d.icn3dui;let t="Windows > View Sequences & Annotations",s="Analysis > Interactions",i=s+" > 2D Graph(Force-Directed)",n="View > Rotate > Auto Rotation > Rotate ",l="View > Rotate > Rotate 90 deg > ",r="Select > Select on 3D > ",o="Analysis > Label > ",a="File > 3D Printing > ";return 0==(e=e.trim()).indexOf("load")?"File > Retrieve by ID, Align":0==e.indexOf("set map")&&-1==e.indexOf("set map wireframe")?"Style > Electron Density":0==e.indexOf("set emmap")&&-1==e.indexOf("set emmap wireframe")?"Style > EM Density Map":0==e.indexOf("set phi")?"Analysis > Load Potential > URL(CORS) Phi/Cube":0==e.indexOf("set delphi")?"Analysis > DelPhi Potential":0==e.indexOf("setoption map")?"Style > Remove Map":0==e.indexOf("setoption emmap")?"Style > Remove EM Map":0==e.indexOf("view annotations")?t:0==e.indexOf("set annotation all")?t+': "All" checkbox':0==e.indexOf("set annotation clinvar")?t+': "ClinVar" checkbox':0==e.indexOf("set annotation snp")?t+': "SNP" checkbox':0==e.indexOf("set annotation 3ddomain")?t+': "3D Domains" checkbox':0==e.indexOf("view interactions")?"Windows > View 2D Diagram":0==e.indexOf("symmetry")?"Analysis > Symmetry":0==e.indexOf("realign on seq align")?"File > Realign Selection > on Sequence Alignment":0==e.indexOf("realign")?"File > Realign Selection > Residue by Residue":0==e.indexOf("graph interaction pairs")?s+" > 2D Graph(Force-Directed)":0==e.indexOf("export canvas")?"File > Save File > iCn3D PNG Image":"export stl file"==e?a+"STL":"export vrml file"==e?a+"VRML(Color)":"export stl stabilizer file"==e?a+"STL W/ Stabilizers":"export vrml stabilizer file"==e?a+"VRML(Color, W/ Stabilizers)":"select all"==e?'Select > All; or Toggle to "All"(next to "Help")':"show all"==e?"View > View Full Structure":"select complement"==e?"Select > Inverse":"set pk atom"==e?r+"Atom":"set pk residue"==e?r+"Residue":"set pk strand"==e?r+"Strand/Helix":"set pk domain"==e?r+"3D Domain":"set pk chain"==e?r+"Chain":"set surface wireframe on"==e?"Style > Surface Wireframe > Yes":"set surface wireframe off"==e?"Style > Surface Wireframe > No":"set map wireframe on"==e?"Style > Map Wireframe > Yes":"set map wireframe off"==e?"Style > Map Wireframe > No":"set emmap wireframe on"==e?"Style > EM Map Wireframe > Yes":"set emmap wireframe off"==e?"Style > EM Map Wireframe > No":"set surface neighbors on"==e?"Style > Surface Type > ... with Context":"set axis on"==e?"View > XYZ-axes > Show":"set axis off"==e?"View > XYZ-axes > Hide":"set fog on"==e?"View > Fog for Selection > On":"set fog off"==e?"View > Fog for Selection > Off":"set slab on"==e?"View > Slab for Selection > On":"set slab off"==e?"View > Slab for Selection > Off":"set assembly on"==e?"Analysis > Assembly > Biological Assembly":"set assembly off"==e?"Analysis > Assembly > Asymmetric Unit":"set chemicalbinding show"==e?"Analysis > Chem. Binding > Show":"set chemicalbinding hide"==e?"Analysis > Chem. Binding > Hide":"set hbonds off"==e||"set salt bridge off"==e||"set contact off"==e||"set halogen pi off"==e?s+" > Reset":"hydrogens"==e?"Style > Hydrogens > Show":"set hydrogens off"==e?"Style > Hydrogens > Hide":"set stabilizer off"==e?"File > 3D Printing > Remove All Stabilizers":"set disulfide bonds off"==e?"Analysis > Disulfide Bonds > Hide":"set cross linkage off"==e?"Analysis > Cross-Linkages > Hide":"set lines off"==e?"Analysis > Distance > Hide":"set labels off"==e?"Analysis > Label > Remove":"set mode all"==e?'Toggle to "All"(next to "Help")':"set mode selection"==e?'Toggle to "Selection"(next to "Help")':"set view detailed view"==e?t+': "Details" tab':"set view overview"==e?t+': "Summary" tab':"set annotation custom"==e?t+': "Custom" checkbox':"set annotation interaction"==e?t+': "Interactions" checkbox':"set annotation ptm"==e?t+': "PTM" checkbox':"set annotation cdd"==e?t+': "Conserved Domains" checkbox':"set annotation site"==e?t+': "Functional Sites" checkbox':"set annotation ssbond"==e?t+': "Disulfide Bonds" checkbox':"set annotation crosslink"==e?t+': "Cross-Linkages" checkbox':"set annotation transmembrane"==e?t+': "Transmembrane" checkbox':"highlight level up"==e?"Keyboard Arrow Up":"highlight level down"==e?"Keyboard Arrow Down":0==e.indexOf("hide annotation")?t+": checkboxes off":"add residue labels"==e?o+"per Residue":"add residue number labels"==e?o+"per Residue & Number":"add atom labels"==e?o+"per Atom":"add chain labels"==e?o+"per Chain":"add terminal labels"==e?o+"N- & C- Termini":"rotate left"==e?n+"Left; or Key l":"rotate right"==e?n+"Right; or Key j":"rotate up"==e?n+"Up; or Key i":"rotate down"==e?n+"Down; or Key m":"rotate x"==e?l+"X-axis":"rotate y"==e?l+"Y-axis":"rotate z"==e?l+"Z-axis":"reset"==e?"View > Reset > All":"reset orientation"==e?"View > Reset > Orientation":"clear selection"==e?"Select > Clear Selection":"zoom selection"==e?"Select > Zoom in Selection":"center selection"==e?"Select > Center Selection":"show selection"==e?"Select > View Only Selection":"hide selection"==e?"Select > Hide Selection":"output selection"==e?"Select > Clear Selection":"toggle highlight"==e?"Select > Toggle Highlight":"stabilizer"==e?"File > 3D Printing > Add all Stabilizers":"disulfide bonds"==e?"Analysis > Disulfide Bonds > Show":"cross linkage"==e?"Analysis > Cross-Linkages > Show":"back"==e?"View > Undo":"forward"==e?"View > Redo":"clear all"==e?"Select > Clear Selection":"defined sets"==e?"Windows > Defined Sets":"delete selected sets"==e?'Windows > Defined Sets: "Delete Selected Sets" button':"view interactions"==e?"Windows > View Interactions":"show annotations all chains"==e?t+': "Show All Chains" button':"save color"==e?"Color > Save Color":"apply saved color"==e?"Color > Apply Saved Color":"save style"==e?"Style > Save Style":"apply saved style"==e?"Style > Apply Saved Style":"select main chains"==e?"Select > Main Chains":"select side chains"==e?"Select > Side Chains":"select main side chains"==e?"Select > Main & Side Chains":"area"==e?"View > Surface Area":"table inter count only"==e?s+': "Set 1" button: "Show Count Only" button':"table inter details"==e?s+': "Set 1" button: "Show Details" button':0==e.indexOf("define helix sets")?t+': "Helix Sets" button':0==e.indexOf("define sheet sets")?t+': "Sheet Sets" button':0==e.indexOf("define coil sets")?t+': "Coil Sets" button':0==e.indexOf("select interaction")?"Windows > View 2D Diagram: click on edges":0==e.indexOf("select saved atoms")||0==e.indexOf("select sets")?"Windows > Defined Sets: select in menu":-1!==e.indexOf("select chain")?t+": click on chain names":-1!==e.indexOf("select alignChain")?"Windows > View Aligned Sequences: click on chain names":0==e.indexOf("select zone cutoff")?"Select > by Distance":0==e.indexOf("set surface opacity")?"Style > Surface Opacity":0==e.indexOf("set label scale")?"View > Label Scale":0==e.indexOf("set surface")?"Style > Surface Type":0==e.indexOf("set camera")?"View > Camera":0==e.indexOf("set background")?"Style > Background":0==e.indexOf("set thickness")?"File > 3D Printing > Set Thickness":0==e.indexOf("set highlight color")?"Select > Highlight Color":0==e.indexOf("set highlight style")?"Select > Highlight Style":0==e.indexOf("add line")||0==e.indexOf("add label")?"Analysis > Distance > between Two Atoms":0==e.indexOf("dist")?"Analysis > Distance > between Two Sets":0==e.indexOf("msa")?t+': "Add Track" button: "FASTA Alignment" button':0==e.indexOf("add track")?t+': "Add Track" button':0==e.indexOf("remove one stabilizer")?"File > 3D Printing > Remove One Stablizer":0==e.indexOf("add one stabilizer")?"File > 3D Printing > Add One Stablizer":0==e.indexOf("select planes z-axis")?"View > Select between Two X-Y Planes":0==e.indexOf("adjust membrane z-axis")?"View > Adjust Membrane":0==e.indexOf("toggle membrane")?"View > Toggle Membrane":0==e.indexOf("calc buried surface")?s+': "Buried Surface Area" button':0==e.indexOf("display interaction 3d")?s+': "3D Display Interactions" button':0==e.indexOf("view interaction pairs")?s+': "Highlight Interactions in Table" button':0==e.indexOf("save1 interaction pairs")?s+': "Set 1" button':0==e.indexOf("save2 interaction pairs")?s+': "Set 2" button':0==e.indexOf("line graph interaction pairs")?s+': "2D Interaction Network" button':0==e.indexOf("scatterplot interaction pairs")?s+': "2D Interaction Map" button':0==e.indexOf("graph label")?i+': "Label Size" menu':0==e.indexOf("graph force")?i+': "Force on Nodes" menu':0==e.indexOf("hide edges")?i+': "Internal Edges" menu':0==e.indexOf("reset interaction pairs")?s+" > Reset":0==e.indexOf("side by side")?"View > Side by Side":0==e.indexOf("your note")?"Windows > Your Notes / Window Title":0==e.indexOf("pickatom")?"Hold Alt key and click on 3D structure":0==e.indexOf("color")?"Color menu":0==e.indexOf("custom tube")?t+': "Custom Color/Tube" button: "Custom Tube" button':0==e.indexOf("style")?"Style menu":-1!==e.indexOf("select displayed set")?"Select > Displayed Set":-1!==e.indexOf("select prop")?"Select > by Property":0==e.indexOf("select")&&-1!==e.indexOf("name")?t+": drag on residues to select":-1!==e.indexOf("select $")||-1!==e.indexOf("select .")||-1!==e.indexOf("select :")||-1!==e.indexOf("select @")?"Select > Advanced; or other selection":-1!==e.indexOf("replay on")?"File > Replay Each Step > On":-1!==e.indexOf("replay off")?"File > Replay Each Step > Off":-1!==e.indexOf("set theme")?"Style > Theme Color":-1!==e.indexOf("set double color")?"Style > Two-color Helix":""}}class as{constructor(e){this.icn3d=e}setProtNuclLigInMenu(){let e=this.icn3d;if(e.icn3dui,Object.keys(e.proteins).length>0&&(e.defNames2Residues.proteins=Object.keys(e.firstAtomObjCls.getResiduesFromAtoms(e.proteins)),e.defNames2Descr.proteins="proteins",e.defNames2Command.proteins="select :proteins"),Object.keys(e.nucleotides).length>0&&(e.defNames2Residues.nucleotides=Object.keys(e.firstAtomObjCls.getResiduesFromAtoms(e.nucleotides)),e.defNames2Descr.nucleotides="nucleotides",e.defNames2Command.nucleotides="select :nucleotides"),Object.keys(e.chemicals).length>0)if(e.bOpm){let t={},s={};for(let i in e.chemicals){let n=e.atoms[i],l=n.structure+"_"+n.chain+"_"+n.resi;"DUM"===n.resn?s[l]=1:t[l]=1}Object.keys(t).length>0&&(e.defNames2Residues.chemicals=Object.keys(t),e.defNames2Descr.chemicals="chemicals",e.defNames2Command.chemicals="select :chemicals"),Object.keys(s).length>0&&(e.defNames2Residues.membrane=Object.keys(s),e.defNames2Descr.membrane="membrane",e.defNames2Command.membrane="select :membrane")}else e.defNames2Residues.chemicals=Object.keys(e.firstAtomObjCls.getResiduesFromAtoms(e.chemicals)),e.defNames2Descr.chemicals="chemicals",e.defNames2Command.chemicals="select :chemicals";Object.keys(e.ions).length>0&&(e.defNames2Residues.ions=Object.keys(e.firstAtomObjCls.getResiduesFromAtoms(e.ions)),e.defNames2Descr.ions="ions",e.defNames2Command.ions="select :ions"),Object.keys(e.water).length>0&&(e.defNames2Residues.water=Object.keys(e.firstAtomObjCls.getResiduesFromAtoms(e.water)),e.defNames2Descr.water="water",e.defNames2Command.water="select :water"),this.setTransmemInMenu(e.halfBilayerSize,-e.halfBilayerSize)}setPredefinedInMenu(){let e=this.icn3d,t=e.icn3dui;if(this.setChainsInMenu(),this.setProtNuclLigInMenu(),void 0!==t.cfg.mmdbid||void 0!==t.cfg.gi||void 0!==t.cfg.chainalign||void 0!==t.cfg.mmdbafid)for(let t in e.tddomains)e.selectionCls.selectResidueList(e.tddomains[t],t,t,!1,!1);if((void 0!==t.cfg.align||void 0!==t.cfg.chainalign&&2==e.chainidArray.length)&&e.bFullUi){e.selectionCls.selectResidueList(e.consHash1,e.conservedName1,e.conservedName1,!1,!1),e.selectionCls.selectResidueList(e.consHash2,e.conservedName2,e.conservedName2,!1,!1),e.selectionCls.selectResidueList(e.nconsHash1,e.nonConservedName1,e.nonConservedName1,!1,!1),e.selectionCls.selectResidueList(e.nconsHash2,e.nonConservedName2,e.nonConservedName2,!1,!1),e.selectionCls.selectResidueList(e.nalignHash1,e.notAlignedName1,e.notAlignedName1,!1,!1),e.selectionCls.selectResidueList(e.nalignHash2,e.notAlignedName2,e.notAlignedName2,!1,!1);let s={};for(let i in e.alnChains)s=t.hashUtilsCls.unionHash(s,e.alnChains[i]);let i=e.firstAtomObjCls.getResiduesFromAtoms(s),n="protein_aligned",l="aligned protein and nucleotides",r="select "+e.resid2specCls.residueids2spec(Object.keys(i));e.selectionCls.addCustomSelection(Object.keys(i),n,l,r,!0)}}setAtomMenu(e){let t=this.icn3d;t.icn3dui;let s="",i=void 0!==t.defNames2Residues?Object.keys(t.defNames2Residues):[],n=void 0!==t.defNames2Atoms?Object.keys(t.defNames2Atoms):[],l=i.concat(n).sort(),r=[];l.forEach((e=>{-1===$.inArray(e,r)&&r.push(e)}));for(let i=0,n=r.length;i0&&(n=t.atoms[e[0]])}else if(void 0!==t.defNames2Residues&&t.defNames2Residues.hasOwnProperty(o)){let e=t.defNames2Residues[o];e.length>0&&(l=t.residues[e[0]],l&&(n=t.atoms[Object.keys(l)[0]]))}let a=void 0===n||void 0===n.color||"FFFFFF"===n.color.getHexString().toUpperCase()?"DDDDDD":n.color.getHexString(),d=void 0!==n&&void 0!==n.color?a:"000000";-1!=e.indexOf(o)?s+=""+o+" ":s+=""+o+" "}return s}setChainsInMenu(){let e=this.icn3d;e.icn3dui;for(let t in e.chains)if(e.chainsSeq[t]&&e.chainsSeq[t].length>1){e.defNames2Residues[t]=Object.keys(e.firstAtomObjCls.getResiduesFromAtoms(e.chains[t])),e.defNames2Descr[t]=t;let s=t.indexOf("_"),i=t.substr(0,s),n=t.substr(s+1);e.defNames2Command[t]="select $"+i+"."+n}if(1==Object.keys(e.structures)){let t=Object.keys(e.structures)[0];e.defNames2Residues[t]=Object.keys(e.residues),e.defNames2Descr[t]=t,e.defNames2Command[t]="select $"+t}else{let t=Object.keys(e.residues),s={};for(let e=0,i=t.length;ee?l[a]=1:o.coord.z0&&(i.defNames2Residues["transmembrane"+o]=Object.keys(n),i.defNames2Descr["transmembrane"+o]="transmembrane"+o,i.defNames2Command["transmembrane"+o]="select :transmembrane"+o),Object.keys(l).length>0&&(i.defNames2Residues["extracellular"+o]=Object.keys(l),i.defNames2Descr["extracellular"+o]="extracellular"+o,i.defNames2Command["extracellular"+o]="select :extracellular"+o),Object.keys(r).length>0&&(i.defNames2Residues["intracellular"+o]=Object.keys(r),i.defNames2Descr["intracellular"+o]="intracellular"+o,i.defNames2Command["intracellular"+o]="select :intracellular"+o)}}showSets(){let e=this.icn3d,t=e.icn3dui;t.bNode||(t.htmlCls.dialogCls.openDlg("dl_definedsets","Select sets"),$("#"+e.pre+"dl_setsmenu").show(),$("#"+e.pre+"dl_setoperations").show(),$("#"+e.pre+"dl_command").hide(),$("#"+e.pre+"atomsCustom").resizable());let s=t.hashUtilsCls.cloneHash(e.hAtoms),i=t.hashUtilsCls.cloneHash(e.dAtoms);void 0!==e.bSetChainsAdvancedMenu&&e.bSetChainsAdvancedMenu&&!e.bResetSets||(this.setPredefinedInMenu(),e.bSetChainsAdvancedMenu=!0),e.hAtoms=t.hashUtilsCls.cloneHash(s),e.dAtoms=t.hashUtilsCls.cloneHash(i),e.hlUpdateCls.updateHlMenus()}clickCustomAtoms(){let e=this.icn3d,t=e.icn3dui,s=this;$("#"+e.pre+"atomsCustom").change((function(e){let i=s.icn3d,n=$(this).val();if(i.nameArray=n,null!==n){let e=!1;s.changeCustomAtoms(n,e),t.htmlCls.clickMenuCls.setLogCmd("select sets "+n.join(" "+i.setOperation+" "),!0),i.bSelectResidue=!1}})),t.myEventCls.onIds("#"+e.pre+"atomsCustom","focus",(function(e){let i=s.icn3d;t.utilsCls.isMobile()&&$("#"+i.pre+"atomsCustom").val("")}))}deleteSelectedSets(){let e=this.icn3d;e.icn3dui;let t=$("#"+e.pre+"atomsCustom").val();for(let s=0;s0)for(let n=0,l=t.defNames2Residues[e].length;n0)for(let s=0,n=t.defNames2Atoms[e].length;s0&&(n[0]=i.commands[0]);let l=e.trim().split("\n");i.commands=l;let r=l[0].indexOf("command=");if(t&&-1!=r){let e=l[0].substr(0,r-1);i.commands.splice(0,1,e)}i.STATENUMBER=i.commands.length,i.commands=n.concat(i.commands),i.STATENUMBER=i.commands.length,i.CURRENTNUMBER=0,i.bReplay?await this.replayFirstStep(i.CURRENTNUMBER):await this.execCommands(i.CURRENTNUMBER,i.STATENUMBER-1,i.STATENUMBER,s)}async execCommands(e,t,s,i){let n=this.icn3d;n.icn3dui,n.bRender=!1,i||n.reinitAfterLoad(),await this.execCommandsBase(e,t,s)}getNameArray(e){let t=this.icn3d;t.icn3dui;let s=e.split(" | "),i=[];return 2==s.length&&(i=s[1].split(","),t.hAtoms=t.definedSetsCls.getAtomsFromNameArray(i)),i}async execCommandsBase(e,t,s,i){let n,l=this.icn3d,r=l.icn3dui,o=this;for(n=e;n<=t;++n){let i=n===s-1;if(!l.commands[n].trim())continue;if(0==(l.atoms?Object.keys(l.atoms).length:0)&&-1==l.commands[n].indexOf("load"))continue;let a=l.commands[n].split("|||"),d=a[0].trim();if(l.inputid&&(l.bNotLoadStructure=!0),-1!==d.indexOf("load")){if(0===t&&e===t)return void(l.bNotLoadStructure?(l.hAtoms=r.hashUtilsCls.cloneHash(l.atoms),1===l.commands.length&&(l.bAddCommands=!0),i&&this.renderFinalStep(s)):(await o.applyCommandLoad(l.commands[n]),1===l.commands.length&&(l.bAddCommands=!0),i&&o.renderFinalStep(s)));l.bNotLoadStructure?(l.hAtoms=r.hashUtilsCls.cloneHash(l.atoms),l.backForward&&this.renderFinalStep(1)):(await o.applyCommandLoad(l.commands[n]),l.backForward&&o.renderFinalStep(1))}else if(0==d.indexOf("set map")&&-1==d.indexOf("set map wireframe")){let e=a[0].trim().split(" | ")[0].substr(8).split(" ");3==e.length&&"sigma"==e[1]&&(e[2],e[0],await o.applyCommandMap(a[0].trim()))}else if(0==d.indexOf("set emmap")&&-1==d.indexOf("set emmap wireframe")){let e=a[0].trim().substr(10).split(" ");2==e.length&&"percentage"==e[0]&&(e[1],await o.applyCommandEmmap(a[0].trim()))}else if(0==d.indexOf("set phi"))await l.delphiCls.applyCommandPhi(a[0].trim());else if(0==d.indexOf("set delphi"))await l.delphiCls.applyCommandDelphi(a[0].trim());else if(0==d.indexOf("view annotations"))Object.keys(l.proteins).length>0&&await o.applyCommandAnnotationsAndCddSite(a[0].trim());else if(0==d.indexOf("set annotation clinvar"))Object.keys(l.proteins).length>0&&await o.applyCommandClinvar(a[0].trim());else if(0==d.indexOf("set annotation snp"))Object.keys(l.proteins).length>0&&await o.applyCommandSnp(a[0].trim());else if(0==d.indexOf("set annotation ptm"))Object.keys(l.proteins).length>0&&await o.applyCommandPTM(a[0].trim());else if(0==d.indexOf("ig refnum on"))await l.refnumCls.showIgRefNum();else if(0==d.indexOf("ig template")){let e=d.substr(d.lastIndexOf(" ")+1);await l.refnumCls.showIgRefNum(e)}else if(0==d.indexOf("set annotation 3ddomain"))Object.keys(l.proteins).length>0&&o.applyCommand3ddomain(a[0].trim());else if(0==d.indexOf("set annotation all"))Object.keys(l.proteins).length>0&&(await o.applyCommandClinvar(a[0].trim()),await o.applyCommandSnp(a[0].trim()),o.applyCommand3ddomain(a[0].trim())),await l.annotationCls.setAnnoTabAll();else if(0==d.indexOf("view interactions")&&void 0!==r.cfg.align)await o.applyCommandViewinteraction(a[0].trim());else if(0==d.indexOf("symmetry")){l.bAxisOnly=!1;let e=d.substr(d.indexOf(" ")+1);l.symmetrytitle="none"===e?void 0:e,"none"!==e&&await l.symdCls.retrieveSymmetry(Object.keys(l.structures)[0]),l.drawCls.draw()}else if(0==d.indexOf("symd symmetry"))l.bAxisOnly=!1,await l.symdCls.applyCommandSymd(d),l.drawCls.draw();else if(0==d.indexOf("scap"))await l.scapCls.applyCommandScap(d);else if(0==d.indexOf("realign on seq align"))this.getNameArray(d),await o.applyCommandRealign(d);else if(0==d.indexOf("realign on structure align msa")){let e=this.getNameArray(d);r.cfg.aligntool="vast",await l.realignParserCls.realignOnStructAlignMsa(e)}else if(0==d.indexOf("realign on structure align"))this.getNameArray(d),r.cfg.aligntool="vast",await l.realignParserCls.realignOnStructAlign();else if(0==d.indexOf("realign on tmalign msa")){let e=this.getNameArray(d);r.cfg.aligntool="tmalign",await l.realignParserCls.realignOnStructAlignMsa(e)}else if(0==d.indexOf("realign on tmalign"))this.getNameArray(d),r.cfg.aligntool="tmalign",await l.realignParserCls.realignOnStructAlign();else if(0==d.indexOf("realign on vastplus"))o.getHAtoms(l.commands[n]),await l.vastplusCls.realignOnVastplus();else if(0==d.indexOf("graph interaction pairs"))await o.applyCommandGraphinteraction(d);else if(0==d.indexOf("cartoon 2d domain"))await o.applyCommandCartoon2d(d);else if(0==d.indexOf("set half pae map"))await o.applyCommandAfmap(d);else if(0==d.indexOf("set full pae map"))await o.applyCommandAfmap(d,!0);else if(0==d.indexOf("export pqr"))await r.htmlCls.setHtmlCls.exportPqr();else if(0==d.indexOf("cartoon 2d chain")||0==d.indexOf("cartoon 2d secondary")){let e=d.lastIndexOf(" "),t=d.substr(e+1);await l.cartoon2dCls.draw2Dcartoon(t)}else if(0==d.indexOf("add msa track")){let e=d.split(" | "),t=e[1].substr(8),s=e[2].substr(9),i=e[3].substr(5),n=e[4].substr(10);$("#"+l.pre+"anno_custom")[0]&&($("#"+l.pre+"anno_custom")[0].checked=!0),$("[id^="+l.pre+"custom]").show(),await l.addTrackCls.addMsaTracks(t,s,i,n)}else if(0==d.indexOf("add exon track")){let e=d.split(" | "),t=e[1].substr(8),s=e[2].substr(7),i=e[3].substr(9),n=e[4].substr(5);$("#"+l.pre+"anno_custom")[0]&&($("#"+l.pre+"anno_custom")[0].checked=!0),$("[id^="+l.pre+"custom]").show(),await l.addTrackCls.addExonTracks(t,s,i,n)}else await l.applyCommandCls.applyCommand(l.commands[n])}(n===s||i)&&this.renderFinalStep(n)}pressCommandtext(){let e=this.icn3d,t=e.icn3dui,s=this;$("#"+e.pre+"logtext").keypress((async function(e){let i=s.icn3d;if(i.bAddLogs=!1,13==(e.keyCode?e.keyCode:e.which)){e.preventDefault();let n=$(this).val();i.bRender=!0;let l=n.split("\n"),r=i.logs.length;for(let e=r,n=l.length;e "+i.logs.join("\n> ")+"\n> ").scrollTop($("#"+i.pre+"logtext")[0].scrollHeight)}i.bAddLogs=!0}))}async applyCommandLoad(e){let t=this.icn3d,s=t.icn3dui;t.bAddCommands=!1;let i=e.split("|||")[0].replace(/\s\s/g," ").trim();if(-1!==i.indexOf("load")){let e=i.split(" | "),n=e[0];if(e.length>1){let t=e[e.length-1].indexOf(" ");s.cfg.inpara=e[e.length-1].substr(t+1),"undefined"===s.cfg.inpara&&(s.cfg.inpara="")}let l=n.substr(n.lastIndexOf(" ")+1);if(4==l.length&&(l=l.toUpperCase()),t.bInputPNGWithData||t.structures&&t.structures.hasOwnProperty(l))return;if(t.inputid=l,-1!==i.indexOf("load mmtf"))s.cfg.mmtfid=l,await t.mmtfParserCls.downloadMmtf(l);else if(-1!==i.indexOf("load pdb"))s.cfg.pdbid=l,await t.pdbParserCls.downloadPdb(l);else if(-1!==i.indexOf("load af"))s.cfg.afid=l,await t.pdbParserCls.downloadPdb(l,!0);else if(-1!==i.indexOf("load opm"))s.cfg.opmid=l,await t.opmParserCls.downloadOpm(l);else if(-1!==i.indexOf("load mmcif"))s.cfg.mmcifid=l,await t.mmcifParserCls.downloadMmcif(l);else if(-1!==i.indexOf("load mmdb ")||-1!==i.indexOf("load mmdb1 "))s.cfg.mmdbid=l,s.cfg.bu=1,await t.mmdbParserCls.downloadMmdb(l);else if(-1!==i.indexOf("load mmdb0"))s.cfg.mmdbid=l,s.cfg.bu=0,await t.mmdbParserCls.downloadMmdb(l);else if(-1!==i.indexOf("load mmdbaf1"))s.cfg.mmdbafid=l,s.cfg.bu=1,await t.chainalignParserCls.downloadMmdbAf(l);else if(-1!==i.indexOf("load mmdbaf0"))s.cfg.mmdbafid=l,s.cfg.bu=0,await t.chainalignParserCls.downloadMmdbAf(l);else if(-1!==i.indexOf("load gi"))s.cfg.gi=l,await t.mmdbParserCls.downloadGi(l);else if(-1!==i.indexOf("load refseq"))s.cfg.refseqid=l,await t.mmdbParserCls.downloadRefseq(l);else if(-1!==i.indexOf("load protein"))s.cfg.protein=l,await t.mmdbParserCls.downloadProteinname(l);else if(-1!==i.indexOf("load seq_struct_ids "))t.bSmithwm=!1,t.bLocalSmithwm=!1,await t.mmdbParserCls.downloadBlast_rep_id(l);else if(-1!==i.indexOf("load seq_struct_ids_smithwm "))t.bSmithwm=!0,await t.mmdbParserCls.downloadBlast_rep_id(l);else if(-1!==i.indexOf("load seq_struct_ids_local_smithwm "))t.bLocalSmithwm=!0,await t.mmdbParserCls.downloadBlast_rep_id(l);else if(-1!==i.indexOf("load cid"))s.cfg.cid=l,await t.sdfParserCls.downloadCid(l);else if(-1!==i.indexOf("load alignment"))if(s.cfg.align=l,s.cfg.inpara||-1==s.cfg.inpara.indexOf("atype=2"))await t.alignParserCls.downloadAlignment(s.cfg.align);else{let e=2;await t.chainalignParserCls.downloadMmdbAf(s.cfg.align,void 0,e)}else if(-1!==i.indexOf("load chainalignment")){let e=i.split(" | ");e.length>1&&-1!=e[1].indexOf("resnum")&&(s.cfg.resnum=e[1].substr(e[1].indexOf("resnum")+7)),e.length>2&&-1!=e[2].indexOf("resdef")&&(s.cfg.resdef=e[2].substr(e[1].indexOf("resdef")+7)),e.length>3&&-1!=e[3].indexOf("aligntool")&&(s.cfg.aligntool=e[3].substr(e[1].indexOf("aligntool")+10)),s.cfg.chainalign=l,await t.chainalignParserCls.downloadChainalignment(l,s.cfg.resnum,s.cfg.resdef)}else if(-1!==i.indexOf("load url")){let i=e[1],n=void 0!==i?i.indexOf("type "):-1,r="pdb";-1!==n&&(r=i.substr(n+5)),s.cfg.url=l,await t.pdbParserCls.downloadUrl(l,r)}}t.bAddCommands=!0}async applyCommandMap(e){let t=this.icn3d;t.icn3dui;let s=e.split(" | "),i=s[0].substr(8).split(" ");if(3==i.length&&"sigma"==i[1]){let e=i[2],n=i[0];2==s.length?await t.dsn6ParserCls.dsn6ParserBase(s[1],n,e):await t.dsn6ParserCls.dsn6Parser(t.inputid,n,e)}}async applyCommandEmmap(e){let t=this.icn3d;t.icn3dui;let s=e.substr(10).split(" ");if(2==s.length&&"percentage"==s[0]){let e=s[1],i="em";await t.densityCifParserCls.densityCifParser(t.inputid,i,e,t.emd)}}async applyCommandRealign(e){let t=this.icn3d;t.icn3dui,await t.realignParserCls.realignOnSeqAlign()}async applyCommandRealignByStruct(e){let t=this.icn3d;t.icn3dui,t.drawCls.draw(),await t.realignParserCls.realignOnStructAlign()}async applyCommandAfmap(e,t){let s=this.icn3d;s.icn3dui;let i=e.substr(e.lastIndexOf(" ")+1);await s.contactMapCls.afErrorMap(i,t)}async applyCommandGraphinteraction(e){let t=this.icn3d;t.icn3dui;let s=e.split(" | ");if(s.length>=3){let e,i=s[1].split(" "),n=i[0].split(","),l=i[1].split(","),r=-1!==s[2].indexOf("hbonds"),o=-1!==s[2].indexOf("salt bridge"),a=-1!==s[2].indexOf("interactions"),d=-1!==s[2].indexOf("halogen"),c=-1!==s[2].indexOf("pi-cation"),h=-1!==s[2].indexOf("pi-stacking");s.length>=4&&(e="true"==s[3]),t.applyCommandCls.setStrengthPara(s),await t.viewInterPairsCls.viewInteractionPairs(n,l,e,"graph",r,o,a,d,c,h)}}async applyCommandCartoon2d(e){let t=this.icn3d;t.icn3dui;let s=e.substr(e.lastIndexOf(" ")+1);await t.cartoon2dCls.draw2Dcartoon(s)}async applyCommandAnnotationsAndCddSite(e){let t=this.icn3d;t.icn3dui,"view annotations"==e&&await t.showAnnoCls.showAnnotations()}async applyCommandClinvar(e){let t=this.icn3d;t.icn3dui;let s=e.lastIndexOf(" ");e.substr(s+1),await t.annotationCls.setAnnoTabClinvar()}async applyCommandSnp(e){let t=this.icn3d;t.icn3dui;let s=e.lastIndexOf(" ");e.substr(s+1),await t.annotationCls.setAnnoTabSnp()}async applyCommandPTM(e){let t=this.icn3d;t.icn3dui;let s=e.lastIndexOf(" ");e.substr(s+1),await t.annotationCls.setAnnoTabPTM()}applyCommand3ddomain(e){let t=this.icn3d;t.icn3dui;let s=e.lastIndexOf(" "),i=e.substr(s+1);"3ddomain"!=i&&"all"!=i||t.annotationCls.setAnnoTab3ddomain()}async applyCommandViewinteraction(e){let t=this.icn3d,s=t.icn3dui;if(void 0!==s.cfg.align||void 0!==s.cfg.chainalign){let e=Object.keys(t.structures);await t.ParserUtilsCls.set2DDiagramsForAlign(e[0].toUpperCase(),e[1].toUpperCase())}}async renderFinalStep(e){let t=this.icn3d,s=t.icn3dui;t.bCommandLoad=!1,t.ParserUtilsCls.hideLoading(),e+1===t.commands.length&&(t.bAddCommands=!0),t.bRender=!0;let i=t.commands[e-1]?t.commands[e-1].split("|||"):[];if(2==i.length){let e=JSON.parse(i[1]);t._zoomFactor=e.factor,t.mouseChange.x=e.mouseChange.x,t.mouseChange.y=e.mouseChange.y,t.quaternion._x=e.quaternion._x,t.quaternion._y=e.quaternion._y,t.quaternion._z=e.quaternion._z,t.quaternion._w=e.quaternion._w}if(t.selectionCls.oneStructurePerWindow(),1===e||t.hAtoms&&t.atoms&&Object.keys(t.hAtoms).length===Object.keys(t.atoms).length||void 0!==t.optsHistory[e-1]&&t.optsHistory[e-1].hasOwnProperty("hlatomcount")&&t.optsHistory[e-1].hlatomcount===Object.keys(t.atoms).length)if(t.optsHistory.length>=e){let s=t.optsHistory[e-1].pk;"no"===s?t.pk=0:"atom"===s?t.pk=1:"residue"===s?t.pk=2:"strand"===s&&(t.pk=3),t.hlUpdateCls.updateHlAll(),t.drawCls.draw()}else t.hlUpdateCls.updateHlAll(),t.drawCls.draw();else t.hlUpdateCls.updateHlAll(),t.drawCls.draw();(s.cfg.closepopup||s.cfg.imageonly)&&(setTimeout((function(){t.resizeCanvasCls.closeDialogs()}),100),t.resizeCanvasCls.resizeCanvas(s.htmlCls.WIDTH,s.htmlCls.HEIGHT,!0)),t.bTransparentSurface&&t.bRender&&t.drawCls.render(),s.cfg.imageonly&&t.saveFileCls.saveFile(void 0,"png",void 0,!0)}async replayFirstStep(e){let t=this.icn3d,s=t.icn3dui;t.reinitAfterLoad(),await this.execCommandsBase(e,e,t.STATENUMBER);let i=t.commands[e],n=t.commands[e].indexOf("|");-1!=n&&(i=t.commands[e].substr(0,n));let l=i.length>20?i.substr(0,20)+"...":i,r=t.applyCommandCls.getMenuFromCmd(i);$("#"+t.pre+"replay_cmd").html("Cmd: "+l),$("#"+t.pre+"replay_menu").html("Menu: "+r),s.htmlCls.clickMenuCls.setLogCmd(i,!0),t.bCommandLoad=!1,t.ParserUtilsCls.hideLoading(),t.bRender=!0,t.drawCls.draw()}getHAtoms(e){let t=this.icn3d;t.icn3dui;let s=e.split("|||")[0].trim().split(" | ");if(2==s.length){let e=s[1].split(",");t.hAtoms=t.definedSetsCls.getAtomsFromNameArray(e)}}}class cs{constructor(e){this.icn3d=e}async selectByCommand(e,t,s){let i=this.icn3d,n=i.icn3dui;if(0===e.indexOf("saved atoms")){let s=12,n=e.substr(s);i.definedSetsCls.selectCombinedSets(n,t)}else{let l=e.replace(/ AND /g," and ").replace(/ OR /g," or ").replace(/ or and /g," and ").replace(/ and /g," or and ").replace(/ or not /g," not ").replace(/ not /g," or not "),r=("select"===l.trim().substr(0,6)?l.trim().substr(7):l.trim()).split(" or "),o={};for(let e=0,t=r.length;e1||1==o.length&&"*"!==o[0])&&(h=!1);let C,y,v,_,w=[],S=[];if(w="*"===t?Object.keys(l.structures):t.split(","),"*"===s){let e=Object.keys(l.chains);for(let t=0,s=e.length;t1&&"3"===x[t][0]&&isNaN(x[t][1])&&"-"!==x[t][0]){i=x[t].toUpperCase().substr(1),m=!0}else if(""===x[t]||isNaN(parseInt(x[t]))){if("*"===x[t])h=!0;else if("proteins"!==x[t]&&"nucleotides"!==x[t]&&"chemicals"!==x[t]&&"ions"!==x[t]&&"water"!==x[t]&&"anchors"!==x[t]&&"strands"!==x[t]&&"loops"!==x[t]){s=x[t].toUpperCase(),p=!0}}else v=x[t],_=v,n=!0;for(let a=0,u=S.length;a1?e.substr(0,l-1)===n.atoms[i].name.substr(0,l-1)&&(0===s?t[i]=1:t.hasOwnProperty(i)||delete t[i]):"*"!==e&&e!==n.atoms[i].name||(0===s?t[i]=1:t.hasOwnProperty(i)||delete t[i]),t}}class hs{constructor(e){this.icn3d=e}selectAll(){let e=this.icn3d;e.icn3dui,this.selectAll_base(),e.hlObjectsCls.removeHlObjects(),e.hlUpdateCls.removeHl2D(),e.hlUpdateCls.removeHlMenus(),e.bSelectResidue=!1,e.bSelectAlignResidue=!1,e.hlUpdateCls.removeSeqResidueBkgd(),e.hlUpdateCls.update2DdgmContent(),$("#"+e.pre+"dl_annotations > .icn3d-annotation").show(),e.definedSetsCls.setMode("all"),e.saveFileCls.showTitle()}selectAll_base(){let e=this.icn3d,t=e.icn3dui;e.hAtoms={},e.dAtoms={};for(let s in e.chains)e.hAtoms=t.hashUtilsCls.unionHash(e.hAtoms,e.chains[s]);e.dAtoms=t.hashUtilsCls.cloneHash(e.hAtoms),e.viewSelectionAtoms=t.hashUtilsCls.cloneHash(e.hAtoms),e.ALTERNATE_STRUCTURE=-1}selectAChain(e,t,s,i){let n=this.icn3d,l=n.icn3dui;t=t.replace(/\s/g,"");let r=void 0!==s||s?"select alignChain "+e:"select chain "+e;void 0!==i&&i?(n.hAtoms=l.hashUtilsCls.unionHash(n.hAtoms,n.chains[e]),void 0===n.nameArray&&(n.nameArray=[])):(n.hAtoms={},n.nameArray=[]),n.nameArray.push(e);let o,a=s?n.alnChainsSeq[e]:n.chainsSeq[e];o=void 0===a?0:a.length;let d={};for(let t=0,s=o;t0){if(void 0!==i&&i?void 0===r.nameArray&&(r.nameArray=[]):(r.hAtoms={},r.nameArray=[]),l)for(let t in e)r.hAtoms[t]=1;else for(let t in e)for(let e in r.residues[t])r.hAtoms[e]=1;let o,a;t=t.replace(/\s/g,""),r.nameArray.push(t),l?(o="select "+r.resid2specCls.atoms2spec(r.hAtoms),a=!1):(o="select "+r.resid2specCls.residueids2spec(Object.keys(e)),a=!0);let d=Object.keys(e);this.addCustomSelection(d,t,s,o,a),(void 0===n||n)&&r.hlUpdateCls.updateHlAll(r.nameArray,void 0,i)}}selectMainChains(){let e=this.icn3d,t=e.icn3dui.hashUtilsCls.cloneHash(e.hAtoms);e.hAtoms=e.applyDisplayCls.selectMainChainSubset(t),e.hlUpdateCls.showHighlight()}selectSideChains(){let e=this.icn3d,t=e.icn3dui,s=t.hashUtilsCls.cloneHash(e.hAtoms);e.hAtoms={};for(let i in s)(e.proteins.hasOwnProperty(i)&&"N"!==e.atoms[i].name&&"H"!==e.atoms[i].name&&"C"!==e.atoms[i].name&&"O"!==e.atoms[i].name&&("CA"!==e.atoms[i].name||"C"!==e.atoms[i].elem)&&"HA"!==e.atoms[i].name||e.nucleotides.hasOwnProperty(i)&&-1===t.parasCls.nuclMainArray.indexOf(e.atoms[i].name))&&(e.hAtoms[i]=1);e.hlUpdateCls.showHighlight()}selectMainSideChains(){let e=this.icn3d,t=e.icn3dui,s=e.firstAtomObjCls.getResiduesFromAtoms(e.hAtoms);e.hAtoms={};for(let i in s)e.hAtoms=t.hashUtilsCls.unionHash(e.hAtoms,e.residues[i]),e.dAtoms=t.hashUtilsCls.unionHash(e.dAtoms,e.residues[i]);e.drawCls.draw(),e.hlUpdateCls.showHighlight()}clickShow_selected(){let e=this.icn3d,t=e.icn3dui,s=this;t.myEventCls.onIds(["#"+e.pre+"show_selected","#"+e.pre+"mn2_show_selected"],"click",(function(e){s.icn3d,s.showSelection(),t.htmlCls.clickMenuCls.setLogCmd("show selection",!0)}))}clickHide_selected(){let e=this.icn3d,t=e.icn3dui,s=this;t.myEventCls.onIds("#"+e.pre+"mn2_hide_selected","click",(function(e){s.icn3d,s.hideSelection(),t.htmlCls.clickMenuCls.setLogCmd("hide selection",!0)}))}getGraphDataForDisplayed(){let e=this.icn3d;e.icn3dui;let t=JSON.parse(e.graphStr),s=e.firstAtomObjCls.getResiduesFromAtoms(e.dAtoms),i=[],n=[],l={};for(let e=0,n=t.nodes.length;e0)if(1==s.pk){let n=!0;this.selectResidueList(s.hAtoms,e,t,void 0,void 0,n),this.updateSelectionNameDesc(),i.htmlCls.clickMenuCls.setLogCmd("select "+s.resid2specCls.atoms2spec(s.hAtoms)+" | name "+e,!0)}else this.selectResidueList(s.selectedResidues,e,t),this.updateSelectionNameDesc(),i.htmlCls.clickMenuCls.setLogCmd("select "+s.resid2specCls.residueids2spec(Object.keys(s.selectedResidues))+" | name "+e,!0)}saveSelInCommand(){let e=this.icn3d,t=e.icn3dui;e.selectedResidues=e.firstAtomObjCls.getResiduesFromCalphaAtoms(e.hAtoms),t.htmlCls.clickMenuCls.setLogCmd("select "+e.resid2specCls.residueids2spec(Object.keys(e.selectedResidues)),!0)}saveEachResiInSel(){let e=this.icn3d;e.icn3dui,e.selectionCls.saveSelectionPrep(),e.selectedResidues={},e.selectedResidues=e.firstAtomObjCls.getResiduesFromCalphaAtoms(e.hAtoms);for(let t in e.selectedResidues){let s={};s[t]=1;let i=t+"_"+e.selectedResidues[t];this.selectResidueList(s,i,i)}}removeSelection(){let e=this.icn3d;e.icn3dui,e.bAnnotations||e.hlUpdateCls.removeSeqChainBkgd(),e.bCtrl||e.bShift||(e.hlUpdateCls.removeSeqResidueBkgd(),e.hlUpdateCls.removeSeqChainBkgd()),e.selectedResidues={},e.bSelectResidue=!1,e.hAtoms={},e.hlObjectsCls.removeHlObjects(),e.hlUpdateCls.removeHl2D()}resetAll(){let e=this.icn3d,t=e.icn3dui;e.maxD=e.oriMaxD,e.center=e.oriCenter.clone(),e.opts=t.hashUtilsCls.cloneHash(e.optsOri),e.setOptionCls.setStyle("sidec","nothing"),e.reinitAfterLoad(),e.definedSetsCls.setMode("all"),e.selectionCls.selectAll(),t.htmlCls.clickMenuCls.setLogCmd("reset",!0),e.hlUpdateCls.removeSeqChainBkgd(),e.hlUpdateCls.removeSeqResidueBkgd(),e.hlUpdateCls.removeHl2D(),e.hlUpdateCls.removeHlMenus(),e.loadScriptCls.renderFinalStep(1)}async loadSelection(e){let t=this.icn3d,s=t.icn3dui,i=e.trim().split("\n");for(let e=0,n=i.length;e=t&&l.coord.z<=e)){i[l.structure+"_"+l.chain+"_"+l.resi]=1}}let n="z_planes_"+e+"_"+t,l=n;this.selectResidueList(i,n,l,!1)}}class ps{constructor(e){this.icn3d=e}residueids2spec(e){var t=this.icn3d;t.icn3dui;let s="";if(void 0!==e){let i,n,l,r,o,a,d,c=e.sort((function(e,t){if(""!==e&&!isNaN(e))return parseInt(e)-parseInt(t);{let s=e.lastIndexOf("_"),i=t.lastIndexOf("_");if(e.substr(0,s)t.substr(0,i))return 1;if(e.substr(0,s)==t.substr(0,i)){if(parseInt(e.substr(s+1))parseInt(t.substr(i+1)))return 1;if(parseInt(e.substr(s+1))==parseInt(t.substr(i+1)))return 0}}})),h="",p=0,m=1!=Object.keys(t.structures).length;for(let e=0,u=c.length;e0&&(s+=p===d?m?"$"+o+"."+a+":"+d+" or ":"."+a+":"+d+" or ":m?"$"+o+"."+a+":"+d+"-"+p+" or ":"."+a+":"+d+"-"+p+" or "),d=n;else if(h===i){let e=t.ParserUtilsCls.getResiNCBI(h,p);t.ParserUtilsCls.getResiNCBI(i,n)!=e+1&&(s+=p===d?m?"$"+o+"."+a+":"+d+" or ":"."+a+":"+d+" or ":m?"$"+o+"."+a+":"+d+"-"+p+" or ":"."+a+":"+d+"-"+p+" or ",d=n)}h=i,p=n}}r=h.indexOf("_"),o=h.substr(0,r),a=h.substr(r+1),s+=p===d?m?"$"+o+"."+a+":"+d:"."+a+":"+d:m?"$"+o+"."+a+":"+d+"-"+p:"."+a+":"+d+"-"+p}return s}atoms2spec(e){var t=this.icn3d;t.icn3dui;let s,i="",n=0,l={},r={},o={};for(let a in e)s=t.atoms[a],n>0&&(i+=" or "),i+="$"+s.structure+"."+s.chain+":"+s.resi+"@"+s.name,l[s.structure]=1,r[s.structure+"_"+s.chain]=1,o[s.structure+"_"+s.chain+"_"+s.resi]=1,++n;if(1==Object.keys(o).length){let e="\\$"+s.structure+"\\."+s.chain+":"+s.resi;i=i.replace(new RegExp(e,"g"),"")}else if(1==Object.keys(r).length){let e="\\$"+s.structure+"\\."+s.chain;i=i.replace(new RegExp(e,"g"),"")}else if(1==Object.keys(l).length){let e="\\$"+s.structure;i=i.replace(new RegExp(e,"g"),"")}return i}atoms2residues(e){var t=this.icn3d;t.icn3dui;let s={};for(let t=0,i=e.length;t=parseInt(t)&&e.b<=parseInt(s)&&(i.hAtoms=n.hashUtilsCls.unionHash(i.hAtoms,i.residues[e.structure+"_"+e.chain+"_"+e.resi]))}}else if("percent out"==e){i.bCalcArea=!0,i.opts.surface="solvent accessible surface",i.applyMapCls.applySurfaceOptions(),i.bCalcArea=!1,i.hAtoms={};for(let e in i.resid2area){let l=e.lastIndexOf("_"),r=e.substr(l+1);if(n.parasCls.residueArea.hasOwnProperty(r)){let o=parseInt(i.resid2area[e]/n.parasCls.residueArea[r]*100);if(o>=t&&o<=s){let t=e.substr(0,l);i.hAtoms=n.hashUtilsCls.unionHash(i.hAtoms,i.residues[t])}}}}i.hAtoms=n.hashUtilsCls.intHash(i.hAtoms,l),i.drawCls.draw(),i.hlUpdateCls.updateHlAll()}selectComplement(){let e=this.icn3d,t=e.icn3dui,s={};for(let t in e.atoms)e.hAtoms.hasOwnProperty(t)||(s[t]=1);e.hAtoms=t.hashUtilsCls.cloneHash(s),e.hlUpdateCls.updateHlAll()}switchHighlightLevel(){var e=this.icn3d.icn3dui;if(e.bNode)return;let t=this;document.addEventListener("keydown",(function(s){let i=t.icn3d;38===s.keyCode?(s.preventDefault(),0!=Object.keys(i.pickedAtomList).length&&i.hAtoms.hasOwnProperty(i.firstAtomObjCls.getFirstAtomObj(i.pickedAtomList).serial)||(i.pickedAtomList=e.hashUtilsCls.cloneHash(i.hAtoms)),t.switchHighlightLevelUp(),e.htmlCls.clickMenuCls.setLogCmd("highlight level up",!0)):40===s.keyCode&&(s.preventDefault(),0!=Object.keys(i.pickedAtomList).length&&i.hAtoms.hasOwnProperty(i.firstAtomObjCls.getFirstAtomObj(i.pickedAtomList).serial)||(i.pickedAtomList=e.hashUtilsCls.cloneHash(i.hAtoms)),t.switchHighlightLevelDown(),e.htmlCls.clickMenuCls.setLogCmd("highlight level down",!0))}))}switchHighlightLevelUp(){var e=this.icn3d,t=e.icn3dui;if(!t.bNode){if(e.bShift||e.bCtrl||e.hlObjectsCls.removeHlObjects(),void 0!==e.pickedAtomList&&0!==Object.keys(e.pickedAtomList).length||(e.pickedAtomList=t.hashUtilsCls.cloneHash(e.hAtoms)),0===Object.keys(e.pickedAtomList).length&&(e.pickedAtomList=e.dAtoms),1===e.highlightlevel){e.highlightlevel=2;let s=e.firstAtomObjCls.getFirstAtomObj(e.pickedAtomList);e.bShift||e.bCtrl?e.hAtoms=t.hashUtilsCls.unionHash(e.hAtoms,e.residues[s.structure+"_"+s.chain+"_"+s.resi]):e.hAtoms=t.hashUtilsCls.cloneHash(e.residues[s.structure+"_"+s.chain+"_"+s.resi])}else if(2===e.highlightlevel){e.highlightlevel=3;let s=e.firstAtomObjCls.getFirstAtomObj(e.pickedAtomList);e.bShift||e.bCtrl?e.hAtoms=t.hashUtilsCls.unionHash(e.hAtoms,e.pickingCls.selectStrandHelixFromAtom(s)):e.hAtoms=t.hashUtilsCls.cloneHash(e.pickingCls.selectStrandHelixFromAtom(s))}else if(3===e.highlightlevel){let s;if(void 0!==t.cfg.mmdbid||void 0!==t.cfg.gi){e.highlightlevel=4;let i=e.firstAtomObjCls.getFirstAtomObj(e.pickedAtomList);s=e.pickingCls.select3ddomainFromAtom(i),e.bShift||e.bCtrl?e.hAtoms=t.hashUtilsCls.unionHash(e.hAtoms,s):e.hAtoms=t.hashUtilsCls.cloneHash(s)}if(void 0===t.cfg.mmdbid&&void 0===t.cfg.gi||0==Object.keys(s).length){e.highlightlevel=5;let s=e.firstAtomObjCls.getFirstAtomObj(e.pickedAtomList);e.bShift||e.bCtrl?e.hAtoms=t.hashUtilsCls.unionHash(e.hAtoms,e.chains[s.structure+"_"+s.chain]):e.hAtoms=t.hashUtilsCls.cloneHash(e.chains[s.structure+"_"+s.chain])}}else if(4===e.highlightlevel){e.highlightlevel=5;let s=e.firstAtomObjCls.getFirstAtomObj(e.pickedAtomList);e.bShift||e.bCtrl?e.hAtoms=t.hashUtilsCls.unionHash(e.hAtoms,e.chains[s.structure+"_"+s.chain]):e.hAtoms=t.hashUtilsCls.cloneHash(e.chains[s.structure+"_"+s.chain])}else if(5===e.highlightlevel||6===e.highlightlevel){e.highlightlevel=6;let s=e.firstAtomObjCls.getFirstAtomObj(e.pickedAtomList);e.bShift||e.bCtrl||(e.hAtoms={});let i=e.structures[s.structure];for(let s=0,n=i.length;s3e4)return void(e?console.log("The maximum number of allowed atoms is 30,000. Please try it again with selected chains..."):alert("The maximum number of allowed atoms is 30,000. Please try it again with selected chains..."));let o="";return o+=s.cfg.cid?t.saveFileCls.getAtomPDB(n,!0,void 0,void 0,void 0,void 0,true):t.saveFileCls.getAtomPDB(n,void 0,void 0,void 0,void 0,void 0,true),o+=t.saveFileCls.getAtomPDB(i,!0,void 0,!0),o}async CalcPhi(e,t,s,i,n){let l=this.icn3d;l.icn3dui;let r=await this.CalcPhiPrms(e,t,s,i,n);this.loadPhiData(r,s,i),l.bAjaxPhi=!0,i?l.setOptionCls.setOption("phisurface","phi"):l.setOptionCls.setOption("phimap","phi")}CalcPhiPrms(e,t,s,i,n){let l=this.icn3d,r=l.icn3dui;l.loadPhiFrom="delphi";let o=r.htmlCls.baseUrl+"delphi/delphi.cgi",a=r.cfg.cid?r.cfg.cid:Object.keys(l.structures).toString(),d={};if(n)d={pqr2phi:n,gsize:e,salt:t,pdbid:a};else{let s=this.getPdbStr();d={pdb2phi:s,gsize:e,salt:t,pdbid:a}}return new Promise((function(e,t){$.ajax({url:o,type:"POST",data:d,dataType:"binary",responseType:"arraybuffer",cache:!0,beforeSend:function(){l.ParserUtilsCls.showLoading()},complete:function(){l.ParserUtilsCls.hideLoading()},success:function(t){e(t)},error:function(e,t,s){}})}))}async PhiParser(e,t,s,i){let n,l=this.icn3d,r=l.icn3dui,o=this;n="phiurl"==t||"phiurl2"==t?"arraybuffer":"text";let a=await r.getXMLHttpRqstPromise(e,"GET",n,"potential");"phiurl"==t||"phiurl2"==t?o.loadPhiData(a,s,i):o.loadCubeData(a,s,i),l.bAjaxPhi=!0,i?l.setOptionCls.setOption("phisurface","phi"):l.setOptionCls.setOption("phimap","phi")}loadPhiData(e,t,s){let i=this.icn3d;i.icn3dui;let n={filetype:"phi"},l=e.buffer&&e.buffer instanceof ArrayBuffer?e.buffer:e,r=new Float32Array(l.slice(l.byteLength-24,l.byteLength-8));n.scale=r[0];let o=r[1],a=r[2],d=r[3];n.n=new Int32Array(l.slice(l.byteLength-8,l.byteLength-4)),n.xExtent=n.yExtent=n.zExtent=n.n;let c=1/n.scale*((n.n-1)/2);n.ori=new THREE.Vector3(o-c,a-c,d-c);let h=new Float32Array(l.slice(110,l.byteLength-56));n.bSurface=s,i.mapData.headerPhi=n,i.mapData.dataPhi=h,i.mapData.contourPhi=t;let p=new THREE.Matrix4;p.identity(),p.multiply((new THREE.Matrix4).makeTranslation(n.ori.x,n.ori.y,n.ori.z)),i.mapData.matrixPhi=p}loadCubeData(e,t,s){let i=this.icn3d;i.icn3dui;let n={filetype:"cube"},l=e.split("\n"),r=[];r.push(parseFloat(l[0].substr(0,10))),r.push(parseFloat(l[0].substr(10,6))),r.push(parseFloat(l[0].substr(16,10))),r.push(parseFloat(l[0].substr(26,10))),r.push(parseFloat(l[0].substr(36,10))),n.scale=r[0];let o=r[2],a=r[3],d=r[4];n.n=r[1],n.xExtent=n.yExtent=n.zExtent=n.n;let c=1/n.scale*((n.n-1)/2);n.ori=new THREE.Vector3(o-c,a-c,d-c);let h=[];for(let e=7,t=l.length;e1e4)return void alert("The maximum number of allowed atoms is 10,000. Please try it again with smaller sets...");let o="";o+=e.saveFileCls.getAtomPDB(n);let a,d={pdb:o,pdbid:Object.keys(e.structures).toString()};try{a=await t.getAjaxPostPromise(i,d,!0);let n,l,o,c=a.rcsb_struct_symmetry,h="none";if(void 0!==c){let i;void 0!==e.rmsd_supr&&void 0!==e.rmsd_supr.rot&&(n=e.rmsd_supr.rot,l=e.rmsd_supr.trans1,o=e.rmsd_supr.trans2),void 0===e.symdArray&&(e.symdArray=[]);for(let t=0,n=c.length;tThe selected residues have no detected symmetry with a Z score of "+a.zscore+" from the program SymD ."),t.htmlCls.dialogCls.openDlg("dl_symd","Dynamically Calculated Symmetry Using SymD");else{let n=a.seqalign.replace(/ /g,"").split(","),l=a.nres,o=a.shift,d=a.rmsd,h=Object.keys(r),p={},m={},u=[],g=[],f=0,b=0,C={};for(let e=0,s=n[0].length;et&&(t=C[s].length,e=s);let s=Object.keys(p),i=Object.keys(m);for(let t=0,n=C[e].length;tSymD. The Z score "+a.zscore+" is greater than the threshold Z score 8. The RMSD is "+d+' angstrom. SymD ."),t.htmlCls.dialogCls.openDlg("dl_symd","Dynamically Calculated Symmetry Using SymD");e.symdtitle="none"===h?void 0:h,e.drawCls.draw()}catch(s){return $("#"+e.pre+"dl_symd").html("This structure has no symmetry."),void i.htmlCls.dialogCls.openDlg("dl_symmetry","Symmetry")}let r,o,a,d=t.rcsb_struct_symmetry;if(void 0!==d){void 0!==s.rmsd_supr&&void 0!==s.rmsd_supr.rot&&(r=s.rmsd_supr.rot,o=s.rmsd_supr.trans1,a=s.rmsd_supr.trans2),s.symmetryHash={};for(let e=0,t=d.length;eThis structure has no symmetry.");else{let e="None ",t=0;for(let i in s.symmetryHash){e+=""+i+" ",++t}$("#"+s.pre+"selectSymmetry").html(e)}}else $("#"+s.pre+"dl_symmetry").html("0&&(s=-s),i=0;i=2&&"number"==typeof t[0]&&"number"==typeof t[1]){if(null==s)return null;let e="number"==typeof s?s:s[s.length-1]+1;i=this.bsa_gen_score_matrix(e,t[0],t[1])}else i=t;for(let e=0;eo.length?d:o.length;l=null==l||l<0?c:l;let h,p,m=o.target>d?o.target-d:d-o.target;l=l>m?l:m,"number"==typeof n?(h=0,p=n>0?n:-n):(h=n[0]>0?n[0]:-n[0],p=n[1]>0?n[1]:-n[1]);let u,g=h+p,f=-1073741824,b=[],C=[],y=[],v=0,_=-1,w=-1;if(e)for(let e=0;e<=d;++e)b[e]=C[e]=0;else{b[0]=0,C[0]=-g-g;for(let e=1;e<=d;++e)e>=l?b[e]=C[e]=f:(b[e]=-(g+p*(e-1)),C[e]=-(g+g+p*e))}for(let t=0;tl?t-l:0,u=t+l+10?f:-(g+p*t),n=m>0?f:-(g+g+p*t));for(let t=m;t=o?0:1,a=a>=o?a:o,l=a>=n?l:2,a=a>=n?a:n,l=!e||a>0?l:64,i=a,c=r>a?c:t,r=r>a?r:a,a-=g,a=!e||a>0?a:0,o-=p,l|=o>a?4:0,o=o>a?o:a,C[t]=o,n-=p,l|=n>a?32:0,n=n>a?n:a,s[t]=l}b[u]=i,C[u]=e?0:f,r>v&&(v=r,_=t,w=c)}if(e&&0==v)return null;u=e?v:b[d];let S,A,x,k=[],O=0,R=0;for(e?(A=_,x=w,w!=d-1&&this.push_cigar(k,4,d-1-w)):(A=o.length-1,x=(A+l+1=0&&x>=0&&(S=y[A][x-(A>l?A-l:0)],O=S>>(O<<1)&3,!(0==O&&S>>6));)0==O&&(O=3&S),0==O?(this.push_cigar(k,0,1),--A,--x):1==O?(this.push_cigar(k,2,1),--A):(this.push_cigar(k,1,1),--x);e?(x>=0&&this.push_cigar(k,4,x+1),R=A+1):(A>=0&&this.push_cigar(k,2,A+1),x>=0&&this.push_cigar(k,1,x+1));for(let e=0;e>1;++e)S=k[e],k[e]=k[k.length-1-e],k[k.length-1-e]=S;return[u,R,k]}push_cigar(e,t,s){this.icn3d.icn3dui,0==e.length||t!=(15&e[e.length-1])?e.push(s<<4|t):e[e.length-1]+=s<<4}bsa_cigar2gaps(e,t,s,i){this.icn3d.icn3dui;let n="",l="",r="",o=0,a=s;for(let s=0;s>4;0==r?(n+=t.substr(o,d),l+=e.substr(a,d),o+=d,a+=d):1==r?(n+=t.substr(o,d),l+=Array(d+1).join("-"),o+=d):2==r?(n+=Array(d+1).join("-"),l+=e.substr(a,d),a+=d):4==r&&(o+=d)}let d=l.toUpperCase(),c=n.toUpperCase();for(let e=0;e>4).toString()+"MIDNSHP=XB".charAt(15&e[s]));return t.join("")}}class ys{constructor(e){this.icn3d=e}calculateArea(){var e=this.icn3d,t=e.icn3dui;e.bCalcArea=!0,e.opts.surface="solvent accessible surface",e.applyMapCls.applySurfaceOptions(),$("#"+e.pre+"areavalue").val(e.areavalue),$("#"+e.pre+"areatable").html(e.areahtml),t.htmlCls.dialogCls.openDlg("dl_area","Surface area calculation"),e.bCalcArea=!1}calcBuriedSurface(e,t){var s=this.icn3d,i=s.icn3dui;if(0==e.length)alert("Please select the first set");else{let n=i.hashUtilsCls.cloneHash(s.hAtoms),l=s.definedSetsCls.getAtomsFromNameArray(e),r=s.definedSetsCls.getAtomsFromNameArray(t);s.bCalcArea=!0,s.opts.surface="solvent accessible surface",s.hAtoms=i.hashUtilsCls.cloneHash(l),s.applyMapCls.applySurfaceOptions();let o=s.areavalue,a=i.hashUtilsCls.cloneHash(s.resid2area);s.hAtoms=i.hashUtilsCls.cloneHash(r),s.applyMapCls.applySurfaceOptions();let d=s.areavalue,c=i.hashUtilsCls.cloneHash(s.resid2area);s.hAtoms=i.hashUtilsCls.unionHash(s.hAtoms,l),s.applyMapCls.applySurfaceOptions();let h=s.areavalue,p=i.hashUtilsCls.cloneHash(s.resid2area),m=0,u=0,g=0,f=0;for(let e in a)p.hasOwnProperty(e)&&(f+=parseFloat(p[e]));u=(o-f).toFixed(2);for(let e in c)p.hasOwnProperty(e)&&(g+=parseFloat(p[e]));m=(d-g).toFixed(2),s.bCalcArea=!1,s.hAtoms=i.hashUtilsCls.cloneHash(n);let b=(parseFloat(d)+parseFloat(o)-parseFloat(h)).toFixed(2),C="2 2 2 Buried Surface for Set 1 : "+u+" Å2 Buried Surface for Set 2 : "+m+" Å2 "+t[e]+" (Å)"}r+="";for(let s=0,i=e.length;s"+i+" (Å)'+l[i][s]+" ":r+="0 "}r+=""}r+="
";p+=""+t.toUpperCase()+" ";let m={},u=[],g="",f="",b={};if(i)for(let e in n.dAtoms){let t=n.atoms[e];b[c[t.structure+"_"+t.chain]]=1}let C=Object.keys(e.moleculeInfor),y=Object.keys(e.intrac),v=[];for(let e=0,t=C.length;e0)for(let t in e.intrac){let s=e.intrac[t];for(let e=0,i=s.intrac.length;e0&&(y="#"+n.atoms[e[0]].color.getHexString().toUpperCase())}let S="";n.bInitial&&void 0!==s&&(void 0!==n.alignmolid2color&&n.alignmolid2color[s].hasOwnProperty(l)?(S=n.alignmolid2color[s][l],y="#FF0000"):y="#FFFFFF");let A=d[l],x=" ",k=" ";if(void 0!==c){let e=c.indexOf("_");k=c.substr(e+1),x=k.length>1?k.substr(0,1)+"..":k}else c="Misc";void 0===y&&(y="#FFFFFF");let O=1;if(n.bInitial&&void 0!==n.alnChains[c]){let e=0;for(let t in n.alnChains[c]){let s=n.atoms[t].color.getHexString().toUpperCase();"FF0000"!==s&&"00FF00"!==s||++e}O=1*e/Object.keys(n.chains[c]).length}if(O<.2&&(O=.2),-1===v.indexOf(l)){for(let e=0,t=h.intrac.length;e1){let s=0,i=0;for(let e=0,t=_[l].length;e",p+="Interaction of chain "+c+" with chain "+h+" ",p+="",p+="Interaction of chain "+h+" with chain "+c+" ",p+=" "}return p+=f+g,p+=" ",p+="",n.html2ddgm+=p,$("#"+n.pre+"dl_2ddgm_html").html(n.html2ddgm),p}set2DdgmNote(e){let t="Nodes :◯ Protein▢ Nucleotide♢ Chemical▢ BiopolymerO Protein▢ Nucleotide◇ Chemical▢ BiopolymerLines :Numbers in red :
1)s="inter_"+e+"_"+t;else{let i=e.indexOf("_"),n=t.indexOf("_");s="inter_"+e.substr(i+1)+"_"+t.substr(n+1)}i="select the atoms in chain "+e+" interacting with chain "+t+" in a distance of 4 angstrom";let o="select interaction "+e+","+t;n.selectionCls.addCustomSelection(r,s,i,o,!0)}draw2DProtein(e,t,s,i,n,l,r,o,a,d,c){this.icn3d.icn3dui;let h=20*d,p="";return p+="Chain "+i+": "+l+" ",p+=""+n+" ",""!==r&&(p+=""+r+" "),p+=" ",p}draw2DNucleotide(e,t,s,i,n,l,r,o,a,d,c){this.icn3d.icn3dui;let h=30*d,p=30*d,m="";return m+="Chain "+i+": "+l+" ",m+=""+n+" ",""!==r&&(m+=""+r+" "),m+=" ",m}draw2DChemical(e,t,s,i,n,l,r,o,a,d,c,h){this.icn3d.icn3dui;let p,m,u,g,f,b,C,y,v=30*d;if(h){let s=.5*v/Math.sqrt(3),i=.5*v;p=e-s,m=t-i,u=e+3*s,g=t-i,f=e+s,b=t+i,C=e-3*s,y=t+i}else{let s=.5*v,i=.5*v;p=e-s,m=t,u=e,g=t+i,f=e+s,b=t,C=e,y=t-i}let _=p-e,w=m-t,S=u-e,A=g-t,x=f-e,k=b-t,O=C-e,R=y-t,I="";return I+="Chain "+i+": "+l+" ",I+=""+n+" ",""!==r&&(I+=""+r+" "),I+=" ",I}}class _s{constructor(e){this.icn3d=e}async draw2Dcartoon(e,t){let s=this.icn3d,i=s.icn3dui,n=this;if(i.htmlCls.clickMenuCls.setLogCmd("cartoon 2d "+e,!0),s.cartoon2dType=e,t){let t=n.getCartoonSvg(e,s.graphStr);$("#"+i.svgid_ct).html(t)}else{await this.getNodesLinksForSetCartoon(e),s.graphStr=n.getCartoonData(e,s.node_link);let t=n.getCartoonSvg(e,s.graphStr);$("#"+i.svgid_ct).html(t),n.setEventsForCartoon2d(),i.htmlCls.dialogCls.openDlg("dl_2dctn","2D Cartoon")}}getCartoonSvg(e,t){let s=this.icn3d,i=s.icn3dui,n="",l="",r=JSON.parse(t);s.ctnNodeHash={};for(let t=0,i=r.nodes.length;t":"domain"==e?n+="":"secondary"==e&&(a=s.ctnNodeHash[l].x2,d=i.htmlCls.width2d-s.ctnNodeHash[l].y2,c=s.ctnNodeHash[o].x1,h=i.htmlCls.width2d-s.ctnNodeHash[o].y1,n+="");let p=l+"--"+o;n+="Interaction of "+e+" "+this.getLabelFromId(l,e)+" with "+e+" "+this.getLabelFromId(o,e)+" ",n+=" ",s.nodeid2lineid.hasOwnProperty(l)||(s.nodeid2lineid[l]=[]),s.nodeid2lineid.hasOwnProperty(o)||(s.nodeid2lineid[o]=[]),s.nodeid2lineid[l].push(p),s.nodeid2lineid[o].push(p)}return n+=l,n}setEventsForCartoon2d(){let e=this.icn3d,t=e.icn3dui;$("#"+t.svgid_ct+" .icn3d-ctnode").draggable({start:function(e,t){let s=parseFloat(e.target.getAttribute("cx")),i=parseFloat(e.target.getAttribute("cy"));e.target.setAttribute("cx",s),e.target.setAttribute("cy",i);let n=e.target.getAttribute("ang");if(n)e.target.setAttribute("transform","rotate("+n+","+s+","+i+")");else{let t=parseFloat(e.target.getAttribute("x1")),s=parseFloat(e.target.getAttribute("y1")),i=parseFloat(e.target.getAttribute("x2")),n=parseFloat(e.target.getAttribute("y2"));e.target.setAttribute("x1",t),e.target.setAttribute("y1",s),e.target.setAttribute("x2",i),e.target.setAttribute("y2",n)}},drag:function(s,i){let n=$("#"+t.svgid_ct).offset().left,l=$("#"+t.svgid_ct).offset().top,r=s.target.getAttribute("id"),o=s.target.getAttribute("ang"),a=s.clientX-n,d=s.clientY-l,c=parseFloat(s.target.getAttribute("cx")),h=parseFloat(s.target.getAttribute("cy")),p=(a-c)/e.resizeRatioX,m=(d-h)/e.resizeRatioY,u=parseFloat($("#"+r+"_text").attr("x")),g=parseFloat($("#"+r+"_text").attr("y"));if($("#"+r+"_text").attr("x",u+p),$("#"+r+"_text").attr("y",g+m),s.target.setAttribute("cx",a),s.target.setAttribute("cy",d),o)s.target.setAttribute("transform","rotate("+o+","+a+","+d+")");else{let e=parseFloat(s.target.getAttribute("x1")),t=parseFloat(s.target.getAttribute("y1")),i=parseFloat(s.target.getAttribute("x2")),n=parseFloat(s.target.getAttribute("y2"));if(s.target.setAttribute("x1",e+p),s.target.setAttribute("y1",t+m),s.target.setAttribute("x2",i+p),s.target.setAttribute("y2",n+m),"S"==r.substr(0,1)){let e=parseFloat($("#"+r+"_box").attr("x1")),t=parseFloat($("#"+r+"_box").attr("y1")),s=parseFloat($("#"+r+"_box").attr("x2")),i=parseFloat($("#"+r+"_box").attr("y2"));$("#"+r+"_box").attr("x1",e+p),$("#"+r+"_box").attr("y1",t+m),$("#"+r+"_box").attr("x2",s+p),$("#"+r+"_box").attr("y2",i+m)}}if(e.nodeid2lineid[r])for(let t=0,s=e.nodeid2lineid[r].length;t";return u+=""+e+" "+m+" ","H"==t.substr(0,1)?u+=""+m+" ",u+=" ",u}drawOval(e,t,s,i,n,l,r,o,a,d){let c=this.icn3d.icn3dui,h=this.getLabelFromId(t,e);i=c.htmlCls.width2d-i,r=180-r;let p="chain"==e?"":"";return p+=""+e+" "+h+" ",p+="",p+="",p+=" ",p+=" ",p+=""+h+" ",p+=" ",p}getCartoonData(e,t){let s=this.icn3d;s.icn3dui;let i,n,l=[],r=[];l=t.node;let o=[],a={},d=0;for(let e=0,t=l.length;e0?n.y=s.htmlCls.width2d-n.y:n.y=-n.y,n}async getNodesLinksForSetCartoon(e){let t,s,i,n,l,r=this.icn3d,o=r.icn3dui,a=this,d=[],c=[],h=0,p=o.htmlCls.defaultValue,m="",u="",g="",f=!1,b=!0;if("chain"==e){let e={};for(let t in r.hAtoms){let s=r.atoms[t];if("DUM"==s.chain)continue;let i=s.structure+"_"+s.chain;(r.proteins.hasOwnProperty(t)||r.nucleotides.hasOwnProperty(t))&&(e.hasOwnProperty(i)||(e[i]={}),e[i][s.serial]=s)}let t=r.contactCls.getExtent(r.atoms),s=9999,i=9999,n=-9999,a=-9999,h=-9999,p=[];for(let d in e){r.hAtom={},r.hAtoms=o.hashUtilsCls.cloneHash(r.chains[d]);let e=r.axesCls.setPc1Axes(),c=e[0],m=e[1].distanceTo(e[0]),u=e[2].distanceTo(e[0]),g=180*new THREE.Vector2(e[1].x-e[0].x,e[1].y-e[0].y).angle()/Math.PI;g>180&&(g-=180);let f=Object.keys(r.hAtoms)[0],b=r.atoms[f];l=d,c=this.projectTo2d(c);let C=c.x,y=c.y;Cn&&(n=C),ya&&(a=y);let v=.5;m=v*o.htmlCls.width2d*m/(t[1][0]-t[0][0]),u=v*o.htmlCls.width2d*u/(t[1][1]-t[0][1]),m>h&&(h=m),u>h&&(h=u),p.push({id:d,r:l,x:C,y:y,rx:m,ry:u,ang:g,c:b.color.getHexString()})}let m=h+2,u=n-s,g=a-i;for(let e=0,t=p.length;e1&&(e+="__"+S.structure),a.push(e)),g==S.chain&&f&&S.ssend){let o=this.projectTo2d(t.coord.clone()),d=o.x,g=o.y,x=this.projectTo2d(S.coord.clone()),k=x.x,O=x.y;s=.5*(d+k),i=.5*(g+O),d=.5*(s+d),g=.5*(i+g),k=.5*(s+k),O=.5*(i+O),d_&&(_=d),gw&&(w=g),k_&&(_=k),Ow&&(w=O),f=!1,b=!0,n+="-"+S.resi,l+="-"+S.resi,n+="__"+S.chain,Object.keys(r.structures).length>1&&(n+="__"+S.structure);for(let t=0,s=a.length;t0&&m==S.chain&&c.push('{"source": "'+u+'", "target": "'+n+'", "v": '+p+', "c": "'+t.color.getHexString().toUpperCase()+'"}'),A.push({id:n,r:l,ss:C,x:s,y:i,x1:d,y1:g,x2:k,y2:O,c:S.color.getHexString()}),m=S.chain,u=n,++h}}}let x=S+2,k=_-y,O=w-v;for(let e=0,t=A.length;e1&&(v+="__"+i.substr(0,i.indexOf("_")));let _=g[b],w=f[b];t.hAtoms={};for(let e=0,n=_.length;e180&&(O-=180);let R=Object.keys(t.hAtoms)[0],I=t.atoms[R];A=this.projectTo2d(A);let T=A.x,E=A.y;Tc&&(c=T),Eh&&(h=E);let P=.5;x=P*s.htmlCls.width2d*x/(o[1][0]-o[0][0]),k=P*s.htmlCls.width2d*k/(o[1][1]-o[0][1]),x>p&&(p=x),k>p&&(p=k),void 0!==C&&n.push('{"source": "'+C+'", "target": "'+v+'", "v": '+l+', "c": "'+y.color.getHexString().toUpperCase()+'"}'),m.push({id:v,from:_+"",to:w+"",x:T,y:E,rx:x,ry:k,ang:O,c:I.color.getHexString()}),C=v,y=I}}let g=p+2,f=c-a,b=h-d;for(let e=0,t=m.length;e=2?d+"_"+e[1]:Object.keys(i.chains)[0];for(let e=0,t=o.length;e0&&(void 0===i||i)&&n.drawCls.draw()}}windowResize(){let e=this.icn3d.icn3dui,t=this;e.cfg.resize&&!e.utilsCls.isMobile()&&$(window).resize((function(){let s=t.icn3d;e.utilsCls.setViewerWidthHeight(s.icn3dui);let i=e.htmlCls.WIDTH,n=e.htmlCls.HEIGHT;void 0===s||s.bFullscreen||t.resizeCanvas(i,n)}))}openFullscreen(e){this.icn3d.icn3dui.bNode||document.fullscreenElement||document.mozFullScreenElement||document.webkitFullscreenElement||document.msFullscreenElement||(e.requestFullscreen?e.requestFullscreen():e.mozRequestFullScreen?e.mozRequestFullScreen():e.webkitRequestFullscreen?e.webkitRequestFullscreen():e.msRequestFullscreen&&e.msRequestFullscreen())}rotStruc(e,t){var s=this.icn3d;s.icn3dui;let i=this;if(s.bStopRotate)return!1;if(s.transformCls.rotateCount>s.transformCls.rotateCountMax)return s.transformCls.resetOrientation(),!1;if(++s.transformCls.rotateCount,t)if("left"===e)s.ROT_DIR="left";else if("right"===e)s.ROT_DIR="right";else if("up"===e)s.ROT_DIR="up";else{if("down"!==e)return!1;s.ROT_DIR="down"}if("left"===e&&"left"===s.ROT_DIR)s.transformCls.rotateLeft(1);else if("right"===e&&"right"===s.ROT_DIR)s.transformCls.rotateRight(1);else if("up"===e&&"up"===s.ROT_DIR)s.transformCls.rotateUp(1);else{if("down"!==e||"down"!==s.ROT_DIR)return!1;s.transformCls.rotateDown(1)}setTimeout((function(){i.rotStruc(e)}),100)}async back(){var e=this.icn3d;e.icn3dui,e.backForward=!0,e.STATENUMBER--,e.bAddCommands=!1,e.bAddLogs=!1,e.bNotLoadStructure=!0,e.STATENUMBER<1?e.STATENUMBER=1:await e.loadScriptCls.execCommands(0,e.STATENUMBER-1,e.STATENUMBER,!0),e.setStyleCls.adjustIcon(),e.bAddCommands=!0,e.bAddLogs=!0}async forward(){var e=this.icn3d;e.icn3dui,e.backForward=!0,e.STATENUMBER++,e.bAddCommands=!1,e.bAddLogs=!1,e.bNotLoadStructure=!0,e.STATENUMBER>e.commands.length?e.STATENUMBER=e.commands.length:await e.loadScriptCls.execCommands(0,e.STATENUMBER-1,e.STATENUMBER,!0),e.setStyleCls.adjustIcon(),e.bAddCommands=!0,e.bAddLogs=!0}async replayon(){var e=this.icn3d;e.icn3dui,e.CURRENTNUMBER=0,e.bReplay=1,$("#"+e.pre+"replay").show(),e.commands.length>0&&await e.loadScriptCls.replayFirstStep(e.CURRENTNUMBER)}async replayoff(){var e=this.icn3d;e.icn3dui,e.bReplay=0,$("#"+e.pre+"replay").hide(),++e.CURRENTNUMBER,await e.loadScriptCls.execCommands(e.CURRENTNUMBER,e.STATENUMBER-1,e.STATENUMBER)}closeDialogs(){var e=this.icn3d,t=e.icn3dui;let s=["dl_2ddgm","dl_2dctn","dl_alignment","dl_sequence2","dl_definedsets","dl_setsmenu","dl_command","dl_setoperations","dl_vast","dl_foldseek","dl_mmtfid","dl_pdbid","dl_afid","dl_opmid","dl_pdbfile","dl_pdbfile_app","dl_rescolorfile","dl_customcolor","dl_align","dl_alignaf","dl_chainalign","dl_chainalign2","dl_chainalign3","dl_mutation","dl_mol2file","dl_sdffile","dl_xyzfile","dl_afmapfile","dl_urlfile","dl_mmciffile","dl_mmcifid","dl_mmdbid","dl_mmdbafid","dl_blast_rep_id","dl_yournote","dl_proteinname","dl_refseqid","dl_cid","dl_pngimage","dl_state","dl_fixedversion","dl_selection","dl_dsn6","dl_dsn6url","dl_clr","dl_symmetry","dl_symd","dl_contact","dl_hbonds","dl_realign","dl_realignbystruct","dl_allinteracton","dl_interactionsorted","dl_linegraph","dl_linegraphcolor","dl_scatterplot","dl_scatterploitcolor","dl_contactmap","dl_alignerrormap","dl_elecmap2fofc","dl_elecmapfofc","dl_emmap","dl_aroundsphere","dl_adjustmem","dl_selectplane","dl_addlabel","dl_addlabelselection","dl_labelColor","dl_distance","dl_stabilizer","dl_disttwosets","dl_distmanysets","dl_stabilizer_rm","dl_thickness","dl_thickness2","dl_addtrack","dl_addtrack_tabs","dl_saveselection","dl_copyurl","dl_selectannotations","dl_annotations_tabs","dl_anno_view_tabs","dl_annotations","dl_graph","dl_svgcolor","dl_area","dl_colorbyarea","dl_rmsd","dl_buriedarea","dl_propbypercentout","dl_propbybfactor","dl_legend","dl_disttable"];for(let i in s){let n=s[i];t.cfg.notebook?$("#"+e.pre+n).hide():$("#"+e.pre+n).hasClass("ui-dialog-content")&&$("#"+e.pre+n).dialog("isOpen")&&$("#"+e.pre+n).dialog("close").remove()}t.cfg.notebook||this.resizeCanvas(t.htmlCls.WIDTH,t.htmlCls.HEIGHT,!0)}}class Ss{constructor(e){this.icn3d=e}resetOrientation(){let e=this.icn3d;e.icn3dui;let t=!1;if(e.commands.length>0){let s=e.commands[0].split("|||");if(2==s.length){let i=JSON.parse(s[1]);e._zoomFactor=i.factor,e.mouseChange.x=i.mouseChange.x,e.mouseChange.y=i.mouseChange.y,e.quaternion._x=i.quaternion._x,e.quaternion._y=i.quaternion._y,e.quaternion._z=i.quaternion._z,e.quaternion._w=i.quaternion._w,t=!0}}t||(e._zoomFactor=1,e.mouseChange=new THREE.Vector2(0,0),e.quaternion=new THREE.Quaternion(0,0,0,1)),e.maxD=e.oriMaxD,e.center=e.oriCenter.clone(),"show"==e.ori_chemicalbinding?e.bSkipChemicalbinding=!1:"hide"==e.ori_chemicalbinding&&(e.bSkipChemicalbinding=!0)}rotateLeft(e){let t=this.icn3d,s=t.icn3dui,i=new THREE.Vector3(0,1,0),n=-e/180*Math.PI;t.bControlGl&&!s.bNode?i.applyQuaternion(window.cam.quaternion).normalize():i.applyQuaternion(t.cam.quaternion).normalize();let l=new THREE.Quaternion;l.setFromAxisAngle(i,-n);let r={};r.quaternion=l,r.update=!0,t.bControlGl&&!s.bNode?window.controls.update(r):t.controls.update(r),t.bRender&&t.drawCls.render()}rotateRight(e){let t=this.icn3d,s=t.icn3dui,i=new THREE.Vector3(0,1,0),n=e/180*Math.PI;t.bControlGl&&!s.bNode?i.applyQuaternion(window.cam.quaternion).normalize():i.applyQuaternion(t.cam.quaternion).normalize();let l=new THREE.Quaternion;l.setFromAxisAngle(i,-n);let r={};r.quaternion=l,r.update=!0,t.bControlGl&&!s.bNode?window.controls.update(r):t.controls.update(r),t.bRender&&t.drawCls.render()}rotateUp(e){this.icn3d.icn3dui,this.rotate_base(-e)}rotateDown(e){this.icn3d.icn3dui,this.rotate_base(e)}rotate_base(e){let t=this.icn3d,s=t.icn3dui,i=new THREE.Vector3(1,0,0),n=e/180*Math.PI;t.bControlGl&&!s.bNode?i.applyQuaternion(window.cam.quaternion).normalize():i.applyQuaternion(t.cam.quaternion).normalize();let l=new THREE.Quaternion;l.setFromAxisAngle(i,-n);let r={};r.quaternion=l,r.update=!0,t.bControlGl&&!s.bNode?window.controls.update(r):t.controls.update(r),t.bRender&&t.drawCls.render()}setRotation(e,t){let s=this.icn3d,i=s.icn3dui;s.bControlGl&&!i.bNode&&window.cam?e.applyQuaternion(window.cam.quaternion).normalize():s.cam&&e.applyQuaternion(s.cam.quaternion).normalize();let n=new THREE.Quaternion;n.setFromAxisAngle(e,-t);let l={};l.quaternion=n,l.update=!0,s.bControlGl&&!i.bNode&&window.controls?window.controls.update(l):s.controls&&s.controls.update(l),s.bRender&&s.drawCls.render()}translateLeft(e){this.icn3d.icn3dui,this.translate_base(-e,0)}translateRight(e){this.icn3d.icn3dui,this.translate_base(e,0)}translateUp(e){this.icn3d.icn3dui,this.translate_base(0,-e)}translateDown(e){this.icn3d.icn3dui,this.translate_base(0,e)}translate_base(e,t){let s=this.icn3d,i=s.icn3dui,n=new THREE.Vector2(0,0);n.x+=e/100,n.y+=t/100;let l={};l.mouseChange=n,l.update=!0,s.bControlGl&&!i.bNode?window.controls.update(l):s.controls.update(l),s.bRender&&s.drawCls.render()}zoominSelection(e){let t=this.icn3d,s=t.icn3dui,i={};if(i._zoomFactor=1/t._zoomFactor,i.update=!0,t.bControlGl&&!s.bNode?window.controls&&window.controls.update(i):t.controls&&t.controls.update(i),void 0===e&&(e=s.hashUtilsCls.hash2Atoms(t.hAtoms,t.atoms)),Object.keys(e).length>1){let s=t.applyCenterCls.centerAtoms(e);t.maxD=s.maxD,t.maxD<5&&(t.maxD=5),t.center=s.center,t.applyCenterCls.setCenter(t.center),t.cameraCls.setCamera()}}getTransformationStr(e){this.icn3d.icn3dui;let t={factor:1,mouseChange:{x:0,y:0},quaternion:{_x:0,_y:0,_z:0,_w:1}};return t.factor=parseFloat(e.factor).toPrecision(4),t.mouseChange.x=parseFloat(e.mouseChange.x).toPrecision(4),t.mouseChange.y=parseFloat(e.mouseChange.y).toPrecision(4),t.quaternion._x=parseFloat(e.quaternion._x).toPrecision(4),t.quaternion._y=parseFloat(e.quaternion._y).toPrecision(4),t.quaternion._z=parseFloat(e.quaternion._z).toPrecision(4),t.quaternion._w=parseFloat(e.quaternion._w).toPrecision(4),"1.0000"==t.factor&&(t.factor=1),"0.0000"==t.mouseChange.x&&(t.mouseChange.x=0),"0.0000"==t.mouseChange.y&&(t.mouseChange.y=0),"0.0000"==t.quaternion._x&&(t.quaternion._x=0),"0.0000"==t.quaternion._y&&(t.quaternion._y=0),"0.0000"==t.quaternion._z&&(t.quaternion._z=0),"1.0000"==t.quaternion._w&&(t.quaternion._w=1),JSON.stringify(t)}}class As{constructor(e){this.icn3d=e}saveFile(e,t,s,i){let n,l=this.icn3d,r=l.icn3dui,o=this;if("command"===t){let e=l.loadCmd?l.loadCmd+"\n":"";for(let t=0,s=l.commands.length;t4e3||0!==s.indexOf("http")||l.bInputfile&&!l.bInputUrlfile?$("#"+l.pre+"viewer").html("'+""+document.getElementById(e).innerHTML+" "}savePng(e,t,s){let i=this.icn3d,n=i.icn3dui;if(n.bNode)return"";let l=$("#"+e).width(),r=$("#"+e).height();s&&(r=l);let o=document.getElementById(e),a=o.getBBox(),d=o.cloneNode(!0);i.lineGraphCls.copyStylesInline(d,o);let c=document.createElement("CANVAS");c.width=l,c.height=r;let h=c.getContext("2d");h.clearRect(0,0,a.width,a.height);let p=this.getSvgXml(e,l,r,s),m=window.URL||window.webkitURL||window,u=new Blob([p],{type:"image/svg+xml;charset=utf-8"}),g=new Image;g.src=m.createObjectURL(u),g.onload=function(){if(h.drawImage(g,0,0),m.revokeObjectURL(this.src),n.utilsCls.isIE()){let e=c.msToBlob();e&&(saveAs(e,t),c.remove())}else c.toBlob((function(e){e&&(saveAs(e,t),c.remove())}))}}exportCustomAtoms(e){var t=this.icn3d;t.icn3dui;let s="",i=void 0!==t.defNames2Residues?Object.keys(t.defNames2Residues).sort():[];for(let n=0,l=i.length;n0)if(s){let s={};for(let e=0,l=t.length;eparseInt(p)+1&&(s.ss=" ",f.push(s)),"helix"==t.ss?(s.ss="H",f.push(s)):"sheet"==t.ss&&(s.ss="S",f.push(s)),t.ssend){let e=a.hashUtilsCls.cloneHash(s);e.ss=" ",f.push(e)}p=t.resi}let b,C,y=0,v=!1,_=!1;for(let e=0,t=f.length;e1,A=1,x="",k="",O=0,R="",I={};for(let l in e){let e=o.atoms[l];if(s&&e.het)continue;if(e.structure!=x){r&&S||(d+=w,w="",A>1&&(d+="\nENDMDL\n"),S&&(d+="MODEL "+A+"\n"));let t=n?"Mutated chain_residue "+Object.keys(n)+"; ":"";i||r&&S||(d+=this.getPDBHeader(A-1,g,t,e.structure)),++A}e.chain!=k&&e.structure==x&&k&&(d+="TER\n");let p=e.chain+"_"+e.resi;if(n&&n.hasOwnProperty(p)){I.hasOwnProperty(p)||(d+=n[p],I[p]=1);continue}let m="";m+=e.het?"HETATM":"ATOM ",m+=l.toString().padStart(5," "),m+=" ";let u=e.name.trim();isNaN(u.substr(0,1))||(u=u.substr(1)+u.substr(0,1)),4==u.length?m+=u:(m+=" ",u=u.replace(/\*/g,"'"),"O1P"==u?u="OP1":"O2P"==u?u="OP2":"C5M"==u&&(u="C7 "),m+=u.padEnd(3," ")),m+=" ";let f=e.resn;if(m+=f.length<=3?f.padStart(3," "):f.substr(0,3),r&&A>2&&(o.proteins.hasOwnProperty(e.serial)||o.nucleotides.hasOwnProperty(e.serial)))e.structure==x&&e.chain==k||(R=O<36?"abcdefghijklmnopqrstuvwxyz0123456789"[O]:"?",++O),m+=" "+R;else if(e.chain.length>=2){m+=e.chain.replace(/_/gi,"").substr(0,2)}else 1==e.chain.length?m+=" "+e.chain.substr(0,1):0==e.chain.length&&(m+=" A");let b=e.resi;!isNaN(b)&&e.chain.length>3&&!isNaN(e.chain.substr(3))&&(b=b-1+parseInt(e.chain.substr(3)));let C=parseInt(b);m+=C.toString().length<=4?C.toString().padStart(4," "):C.toString().substr(0,4);let y=e.resi.toString().substr(e.resi.toString().length-1,1);if(isNaN(y)?m+=y:m+=" ",m+=" ".padStart(3," "),m+=e.coord.x.toFixed(3).toString().padStart(8," "),m+=e.coord.y.toFixed(3).toString().padStart(8," "),m+=e.coord.z.toFixed(3).toString().padStart(8," "),t&&e.het){let t=1.5,s=0;"C"==e.elem?t=1.908:"N"==e.elem?t=1.824:"O"==e.elem?t=1.6612:"H"==e.elem?t=1.25:"S"==e.elem?t=2:"P"==e.elem?t=2.1:a.parasCls.vdwRadii.hasOwnProperty(e.elem)&&(t=a.parasCls.vdwRadii[e.elem]),void 0!==a.cfg.cid&&void 0!==e.crg?s=e.crg:c.hasOwnProperty(l)?s=1.38:h.hasOwnProperty(l)?s=-.595:a.parasCls.ionCharges.hasOwnProperty(e.elem)&&(s=a.parasCls.ionCharges[e.elem]),m+=s.toFixed(4).toString().padStart(8," "),m+=t.toFixed(4).toString().padStart(7," ")}else m+="1.00".padStart(6," "),m+=e.b?parseFloat(e.b).toFixed(2).toString().padStart(6," "):" ".padStart(6," "),m+=" ".padStart(10," "),m+=e.elem.padStart(2," "),m+=" ".padStart(2," ");if(e.het&&e.bonds.length>0){w+="CONECT"+l.toString().padStart(5," ");let t={};for(let s=0,i=e.bonds.length;s50?n.molTitle.substr(0,47)+"...":n.molTitle;-1!=e.indexOf('"')&&(e=""),s&&(e=s+e),l+="TITLE "+e+"\n"}return t&&t[r]&&(l+=t[r]),l}showTitle(){var e=this.icn3d,t=e.icn3dui;let s=e.molTitle?e.molTitle:"",i="black"==e.opts.background?t.htmlCls.GREYD:"black";if(void 0===e.inputid)s.length>40&&(s=s.substr(0,40)+"..."),$("#"+e.pre+"title").html(s);else if(void 0!==t.cfg.cid){let t=this.getLinkToStructureSummary();$("#"+e.pre+"title").html("PubChem CID "+e.inputid.toUpperCase()+" : "+s)}else if(void 0!==t.cfg.align)s="VAST+ alignment of "+Object.keys(e.structures),$("#"+e.pre+"title").html(s);else if(void 0!==t.cfg.chainalign){s="Dynamic Structure Alignment of Chains: "+t.cfg.chainalign.split(","),$("#"+e.pre+"title").html(s)}else{let n=Object.keys(t.utilsCls.getStructures(e.dAtoms));if(n.length>1){s="Multiple structures: ";for(let e=0,t=n.length;e'+n[e]+"",e5?"https://alphafold.ebi.ac.uk/entry/"+n[0]:"https://www.ncbi.nlm.nih.gov/structure/?term="+n[0];this.setStructureTitle(e,s,i)}}}setStructureTitle(e,t,s){var i=this.icn3d,n=i.icn3dui;t.length>40&&(t=t.substr(0,40)+"...");let l,r,o=i.inputid;if(-1!=o.indexOf("http"))r="Data from",e=o,l=o;else{let e=n.utilsCls.getHlStructures(),s=!1,a=!1;for(let t in e)t.length>5?a=!0:s=!0;let d=Object.keys(e);if(o=d.join(","),l=n.cfg.refseqid||n.cfg.protein?i.inputid:o.toUpperCase(),s&&a?r="AlphaFold/PDB ID":s?r="PDB ID":a&&(r="AlphaFold ID"),d.length>1&&(r+="s"),i.molTitleHash){t="";for(let e=0,s=d.length;e20&&(e=e.substr(0,17)+"..."),l="Query: "+e+"; target: "+s,$("#"+i.pre+"title").html(l+", "+t)}else $("#"+i.pre+"title").html(r+" "+l+" : "+t);else $("#"+i.pre+"title").html(t)}getLinkToStructureSummary(e){var t=this.icn3d,s=t.icn3dui;let i="https://www.ncbi.nlm.nih.gov/structure/?term=";if(i=void 0!==s.cfg.cid?"https://www.ncbi.nlm.nih.gov/pccompound/?term=":void 0!==s.cfg.refseqid?"https://www.ncbi.nlm.nih.gov/protein/":void 0!==s.cfg.afid?"https://alphafold.ebi.ac.uk/search/text/":Object.keys(t.structures).length>1?"https://www.ncbi.nlm.nih.gov/structure/?term=":s.htmlCls.baseUrl+"pdb/",void 0===t.inputid)i="https://www.ncbi.nlm.nih.gov/pccompound/?term="+t.molTitle;else{let n=t.inputid.split("_");1===n.length?(i+=t.inputid,e&&s.htmlCls.clickMenuCls.setLogCmd("link to "+t.inputid+": "+i,!1)):2===n.length&&(s.cfg.afid?i+=n[0]+" "+n[1]:i+=n[0]+" OR "+n[1],e&&s.htmlCls.clickMenuCls.setLogCmd("link to structures "+n[0]+" and "+n[1]+": "+i,!1))}return i}setEntrezLinks(e){var t=this.icn3d,s=t.icn3dui;let i,n=Object.keys(t.structures);if(1===n.length){i="https://www.ncbi.nlm.nih.gov/"+e+"/?term="+n[0],s.htmlCls.clickMenuCls.setLogCmd("Entrez "+e+" about PDB "+n[0]+": "+i,!1);let l=t.structures&&Object.keys(t.structures).length>0?"_blank":"_self";window.open(i,l)}else if(2===n.length){i="https://www.ncbi.nlm.nih.gov/"+e+"/?term="+n[0]+" OR "+n[1],s.htmlCls.clickMenuCls.setLogCmd("Entrez "+e+" about PDB "+n[0]+" OR "+n[1]+": "+i,!1);let l=t.structures&&Object.keys(t.structures).length>0?"_blank":"_self";window.open(i,l)}}}class xs{constructor(e){this.icn3d=e}async shareLink(e,t){let s=this.icn3d,i=s.icn3dui,n=this.shareLinkUrl(),l=n.length>4e3||0!==n.indexOf("http"),r=Object.keys(s.structures).join("_");if(r==s.defaultPdbId&&(s.filename?r=s.filename:s.inputid&&(r=s.inputid)),e){if(t||s.bInputfile||l)return void s.saveFileCls.saveFile(r+"_icn3d_loadable.png","png")}else{if(s.bInputfile&&!s.bInputUrlfile)return void alert("Share Link does NOT work when the data are from custom files. Please save 'iCn3D PNG Image' in the File menu and open it in iCn3D.");if(l)return void alert("The url is more than 4000 characters and may not work. Please save 'iCn3D PNG Image' or 'State File' and open them in iCn3D.");i.htmlCls.clickMenuCls.setLogCmd("share link: "+n,!1)}let o="Problem in getting shortened URL";if(!i.cfg.notebook){let t=await this.getShareLinkPrms(n,e);if(void 0!==t.shortLink&&(o=t.shortLink,e)){let e=o.split("/"),t=e[e.length-1];s.saveFileCls.saveFile(r+"-"+t+".png","png");let i='\n\n",s.saveFileCls.saveFile(r+"-"+t+".html","html",i)}e&&void 0===t.shortLink&&s.saveFileCls.saveFile(r+"_icn3d_loadable.png","png");let i=o.split("page.link/");2==i.length&&(o="https://structure.ncbi.nlm.nih.gov/icn3d/share.html?"+i[1]),$("#"+s.pre+"short_url").val(o),$("#"+s.pre+"short_url_title").val(o+"&t="+s.yournote)}let a=this.shareLinkUrl(void 0,!0),d="view = icn3dpy.view(q='"+(i.cfg.url?"url="+i.cfg.url:i.cfg.idname+"="+i.cfg.idvalue)+"',command='"+a+"')\nview";(i.cfg.url||i.cfg.idname)&&$("#"+s.pre+"jn_commands").val(d),$("#"+s.pre+"ori_url").val(n),e||i.htmlCls.dialogCls.openDlg("dl_copyurl","Copy a Share Link URL or Jupyter Notebook Commands")}getShareLinkPrms(e,t){let s=this.icn3d,i=s.icn3dui;return new Promise((function(n,l){$.ajax({url:"https://firebasedynamiclinks.googleapis.com/v1/shortLinks?key=AIzaSyBxl9CgM0dY5lagHL4UOhEpLWE1fuwdnvc",type:"POST",data:{longDynamicLink:"https://icn3d.page.link/?link="+encodeURIComponent(e)},dataType:"json",success:function(e){n(e)},error:function(n,l,r){let o="Problem in getting shortened URL";$("#"+s.pre+"ori_url").val(e),$("#"+s.pre+"short_url").val(o),$("#"+s.pre+"short_url_title").val(o+"&t="+s.yournote),t||i.htmlCls.dialogCls.openDlg("dl_copyurl","Copy a Share Link URL")}})}))}shareLinkUrl(e,t){let s=this.icn3d,i=s.icn3dui,n=i.htmlCls.baseUrl+"icn3d/?",l="";if(i.cfg.bSidebyside&&(n=i.htmlCls.baseUrl+"icn3d/full2.html?"),s.bInputUrlfile){n=window.location.href.split("?")[0]+"?"+s.inputurl+"&"}let r,o={};for(let e in s.cfg){let t=s.cfg[e];"inpara"!==e&&"command"!==e&&"usepdbnum"!==e&&"date"!==e&&"v"!==e&&void 0!==t&&("width"===e&&"100%"===t||"height"===e&&"100%"===t||"resize"===e&&!0===t||"showmenu"===e&&!0===t||"showtitle"===e&&!0===t||"showcommand"===e&&!0===t||"mobilemenu"===e&&!1===t||"showanno"===e&&!1===t||"showseq"===e&&!1===t||"showalignseq"===e&&!1===t||"show2d"===e&&!1===t||"showsets"===e&&!1===t||"rotate"===e&&"right"===t||"command"!==e&&("options"===e?Object.keys(t).length>0&&(o[e]=JSON.stringify(t)):!0===t?o[e]=1:!1===t?o[e]=0:""!==t&&(o[e]=t)))}s.bAfMem?o.afmem="on":(i.cfg.afid||1==Object.keys(s.structures).length&&Object.keys(s.structures)[0].length>5)&&(o.afmem="off");let a=-1;void 0!==i.cfg.inpara&&(a=i.cfg.inpara.indexOf("&command=")),r=-1!==a?i.cfg.inpara.substr(0,a):i.cfg.inpara;let d=!1;if(!s.bInputUrlfile){let e=r&&r.substr(1)?r.substr(1).split("&"):[];for(let t=0,s=e.length;tc){u=s.commands[c].split("|||")[0].split("&command=")[0].trim(),-1!==u.indexOf(g)&&++f}let b,C=c+1,y="";for(let e=s.commands.length;C0&&f%2==0&&u!==g&&(y+=g+"; "),y+=u+"|||"+s.transformCls.getTransformationStr(p),m+=u+"|||"+s.transformCls.getTransformationStr(p)+"\n"),n+=y,l=y,m=m.replace(/!/g,Object.keys(s.structures)[0]+"_"),(s.bEsmfold||s.bInputfile&&!s.bInputUrlfile||s.bInputUrlfile&&s.bAppend||n.length>4e3)&&(n=m),void 0!==s.structures&&1==Object.keys(s.structures).length&&void 0!==s.inputid&&(b=Object.keys(s.structures)[0],n=n.replace(new RegExp(b+"_","g"),"!"),l=l.replace(new RegExp(b+"_","g"),"!")),void 0!==i.cfg.blast_rep_id&&(n=n.replace(new RegExp("blast_rep_id=!","g"),"blast_rep_id="+b+"_")),t?l:n}getPngText(){let e,t=this.icn3d;t.icn3dui;let s="";if(t.bInputfile)e=this.shareLinkUrl(true),"http"==e.substr(0,4)?s+="\nShare Link: "+e:(s+="\nStart of type file======\n",s+=t.InputfileType+"\n",s+="End of type file======\n",s+="Start of data file======\n",s+=t.saveFileCls.getAtomPDB(t.atoms),s+="End of data file======\n",s+="Start of state file======\n",s+=e+"\n",s+="End of state file======\n");else{e=this.shareLinkUrl(),e.length>4e3||0!==e.indexOf("http")?(e=this.shareLinkUrl(true),s+="\nStart of state file======\n",s+=e+"\n",s+="End of state file======\n"):s+="\nShare Link: "+e}return s=s.replace(/!/g,Object.keys(t.structures)[0]+"_"),s}}class ks{constructor(e){this.icn3d=e}setThichknessFor3Dprint(){let e=this.icn3d,t=e.icn3dui;e.lineRadius=1,e.coilWidth=1.2,e.cylinderRadius=.8,e.crosslinkRadius=.8,e.traceRadius=1,e.dotSphereScale=.6,e.sphereRadius=1.5,e.ribbonthickness=1,e.helixSheetWidth=2,e.nucleicAcidWidth=1.4,t.htmlCls.setHtmlCls.setCookieForThickness()}prepareFor3Dprint(){let e=this.icn3d,t=e.icn3dui;if(e.bShowHighlight=!1,e.hlObjectsCls.removeHlObjects(),e.bDashedLines=!1,e.bSetThickness||void 0!==t.cfg.cid||this.setThichknessFor3Dprint(),void 0!==e.lines.hbond)for(let t=0,s=e.lines.hbond.length;tt.substr(0,s))return 1;if(e.substr(0,s)==t.substr(0,s)){if(parseInt(e.substr(s+1))parseInt(t.substr(i+1)))return 1;if(parseInt(e.substr(s+1))==parseInt(t.substr(i+1)))return 0}}})),n="Structure Chain Residue Number "+i[e].substr(0,t)+" "+i[e].substr(t+1,s-t-1)+" "+i[e].substr(s+1)+" "}let l=Object.keys(t.utilsCls.getHlStructures()).join(",");e.saveFileCls.saveFile(l+"_residues.txt","html",n)}addStabilizer(){let e=this.icn3d,t=e.icn3dui,s=3.5;if(Object.keys(e.dAtoms).length>0){let i,n={},l=12.25,r=3.2*3.2;for(let t in e.dAtoms){let s=e.atoms[t];!e.nucleotides.hasOwnProperty(s.serial)||"N1"!==s.name&&"N2"!==s.name&&"N3"!==s.name&&"N4"!==s.name&&"N6"!==s.name&&"O2"!==s.name&&"O6"!==s.name||(i=s.structure+"_"+s.chain+"_"+s.resi+"_"+s.name,n[i]=s)}let o=Object.keys(n),a=o.length;void 0===e.pairArray&&(e.pairArray=[]);for(let t=0;ts)continue;let h=Math.abs(n[a].coord.y-n[d].coord.y);if(h>s)continue;let p=Math.abs(n[a].coord.z-n[d].coord.z);if(p>s)continue;let m=c*c+h*h+p*p;m>l||ms+1||rs+2||rs+4||r0&&o.length>0)if(a){let t=parseInt((r.length+.5)/2);e.pairArray.push(o[0]),e.pairArray.push(r[t])}else{let t=10,s=parseInt(r.length/(t+1));for(let i=0,n=o.length;i1&&t.bAssembly&&(t.threshbox=180/Math.pow(t.biomtMatrices.length,.33),t.applyMapCls.removeSurfaces(),t.applyMapCls.applySurfaceOptions(),t.applyMapCls.removeMaps(),t.applyMapCls.applyMapOptions(),t.applyMapCls.removeEmmaps(),t.applyMapCls.applyEmmapOptions());let i=this.saveStlFile(),n=Object.keys(s.utilsCls.getHlStructures()).join(",");if(t.saveFileCls.saveFile(n+e+".stl","binary",i),void 0!==t.biomtMatrices&&t.biomtMatrices.length>1&&t.bAssembly&&Object.keys(t.dAtoms).length*t.biomtMatrices.length>t.maxAtoms3DMultiFile){alert(t.biomtMatrices.length+" files will be generated for this assembly. Please merge these files using some software and 3D print the merged file.");let s=new THREE.Matrix4;s.identity();let l=1;for(let r=0;r1&&t.bAssembly&&(t.threshbox=180/Math.pow(t.biomtMatrices.length,.33),t.applyMapCls.removeSurfaces(),t.applyMapCls.applySurfaceOptions(),t.applyMapCls.removeMaps(),t.applyMapCls.applyMapOptions(),t.applyMapCls.removeEmmaps(),t.applyMapCls.applyEmmapOptions());let i=this.saveVrmlFile(),n=Object.keys(s.utilsCls.getHlStructures()).join(",");if(t.saveFileCls.saveFile(n+e+".wrl","text",i),void 0!==t.biomtMatrices&&t.biomtMatrices.length>1&&t.bAssembly&&Object.keys(t.dAtoms).length*t.biomtMatrices.length>t.maxAtoms3DMultiFile){alert(t.biomtMatrices.length+" files will be generated for this assembly. Please merge these files using some software and 3D print the merged file.");let s=new THREE.Matrix4;s.identity();let n=1;for(let l=0;l7e4)return alert("Please display a subset of the structure to export 3D files. Then merge the files for 3D printing..."),[""];t.threeDPrintCls.prepareFor3Dprint();let i=0;i+=this.getFaceCnt(t.mdl),i+=this.getFaceCnt(t.mdl_ghost);let n=[],l=new Uint8Array(84),r="STL file for the structure(s) ",o=Object.keys(t.structures);for(let e=0,t=o.length;e80&&(r=r.substr(0,80));for(let e=0;e<80;++e)e1&&t.bAssembly&&Object.keys(t.dAtoms).length*t.biomtMatrices.length<=t.maxAtoms3DMultiFile?this.updateArray(l,s.convertTypeCls.passInt32([i*t.biomtMatrices.length]),80):this.updateArray(l,s.convertTypeCls.passInt32([i]),80),n.push(new Blob([l],{type:"application/octet-stream"})),n=this.processStlMeshGroup(t.mdl,n,e),n=this.processStlMeshGroup(t.mdl_ghost,n,e),void 0!==t.biomtMatrices&&t.biomtMatrices.length>1&&t.bAssembly&&Object.keys(t.dAtoms).length*t.biomtMatrices.length<=t.maxAtoms3DMultiFile){let e=new THREE.Matrix4;e.identity();for(let s=0;s5e4)return alert("Please display a subset of the structure to export 3D files. Then merge the files for 3D printing..."),[""];t.threeDPrintCls.prepareFor3Dprint();let s=[];s.push("#VRML V2.0 utf8\n");let i=0,n=this.processVrmlMeshGroup(t.mdl,s,i,e);if(s=n.vrmlStrArray,i=n.vertexCnt,n=this.processVrmlMeshGroup(t.mdl_ghost,s,i,e),s=n.vrmlStrArray,i=n.vertexCnt,void 0!==t.biomtMatrices&&t.biomtMatrices.length>1&&t.bAssembly&&Object.keys(t.dAtoms).length*t.biomtMatrices.length<=t.maxAtoms3DMultiFile){let e=new THREE.Matrix4;e.identity();for(let l=0;l0?h.z=-1:h.z=1,s.cam===s.perspectiveCamera?(s.cam_z>0?h.z=-1:h.z=1,h.unproject(s.cam),s.raycaster.set(s.cam.position,h.sub(s.cam.position).normalize())):s.cam===s.orthographicCamera&&(s.cam_z>0?h.z=1:h.z=-1,h.unproject(s.cam),s.raycaster.set(h,new THREE.Vector3(0,0,-1).transformDirection(s.cam.matrixWorld)));let p=this.isIntersect(s.objects,s.mdl,t,d,c);p||(p=this.isIntersect(s.objects_ghost,s.mdl_ghost,t,d,c))}isIntersect(e,t,s,i,n){let l=this.icn3d;l.icn3dui;let r=l.raycaster.intersectObjects(e),o=!1,a=t.position;if(r.length>0){r[0].point.sub(a);let e=l.rayThreshold,t=this.getAtomsFromPosition(r[0].point,e);for(;!t&&e<10;)e+=.5,t=this.getAtomsFromPosition(r[0].point,e);t?(o=!0,l.pickpair?s&&(l.pAtomNum%2==0?l.pAtom=t:l.pAtom2=t,++l.pAtomNum):l.pAtom=t,s?l.pickingCls.showPicking(t):l.pickingCls.showPicking(t,i,n)):console.log("No atoms were found in 10 andstrom range")}return o}getAtomsFromPosition(e,t){let s,i=this.icn3d,n=i.icn3dui;for(s in null==t&&(t=1),i.dAtoms){let l=i.atoms[s];if(i.ions.hasOwnProperty(s)&&"sphere"===i.opts.ions){let s=n.parasCls.vdwRadii[l.elem.toUpperCase()];if(Math.abs(l.coord.x-e.x)-s>t)continue;if(Math.abs(l.coord.y-e.y)-s>t)continue;if(Math.abs(l.coord.z-e.z)-s>t)continue}else{if(l.coord.xe.x+t)continue;if(l.coord.ye.y+t)continue;if(l.coord.ze.z+t)continue}return l}return null}}class Is{constructor(e){this.icn3d=e}setControl(){let e=this.icn3d,t=e.icn3dui;if(t.bNode)return;let s=this;e.WIDTH=e.container.width(),e.HEIGHT=e.container.height(),e.applyCenterCls.setWidthHeight(e.WIDTH,e.HEIGHT),e._zoomFactor=1,e.mouseChange=new THREE.Vector2(0,0),e.quaternion=new THREE.Quaternion(0,0,0,1),e.container.bind("contextmenu",(function(e){e.preventDefault()})),e.typetext=!1,$(document).bind("keyup",(function(t){16===t.keyCode&&(e.bShift=!1),17!==t.keyCode&&224!==t.keyCode&&91!==t.keyCode||(e.bCtrl=!1)})),$("input[type=text], textarea").focus((function(){e.typetext=!0})),$("input[type=text], textarea").blur((function(){e.typetext=!1})),$(document).bind("keydown",(async function(s){if((s.shiftKey||16===s.keyCode)&&(e.bShift=!0),(s.ctrlKey||17===s.keyCode||224===s.keyCode||91===s.keyCode)&&(e.bCtrl=!0),!e.bControlGl&&!e.controls||e.bControlGl&&!window.controls)return;e.bStopRotate=!0;let i=e.bShift?90:5;if(!e.typetext)if(90===s.keyCode){let s={};e.bControlGl&&!t.bNode?window.cam===e.perspectiveCamera?s._zoomFactor=.9:window.cam===e.orthographicCamera&&(e._zoomFactor<.1?e._zoomFactor=.1:e._zoomFactor>1&&(e._zoomFactor=1),s._zoomFactor=.8*e._zoomFactor,s._zoomFactor<.1&&(s._zoomFactor=.1)):e.cam===e.perspectiveCamera?s._zoomFactor=.9:e.cam===e.orthographicCamera&&(e._zoomFactor<.1?e._zoomFactor=.1:e._zoomFactor>1&&(e._zoomFactor=1),s._zoomFactor=.8*e._zoomFactor,s._zoomFactor<.1&&(s._zoomFactor=.1)),s.update=!0,e.bControlGl&&!t.bNode?window.controls.update(s):e.controls.update(s),e.bRender&&e.drawCls.render()}else if(88===s.keyCode){let s={};e.bControlGl&&!t.bNode?window.cam===e.perspectiveCamera?s._zoomFactor=1.03:window.cam===e.orthographicCamera&&(e._zoomFactor>10?e._zoomFactor=10:e._zoomFactor<1&&(e._zoomFactor=1),s._zoomFactor=1.01*e._zoomFactor,s._zoomFactor>10&&(s._zoomFactor=10)):e.cam===e.perspectiveCamera?s._zoomFactor=1.03:e.cam===e.orthographicCamera&&(e._zoomFactor>10?e._zoomFactor=10:e._zoomFactor<1&&(e._zoomFactor=1),s._zoomFactor=1.01*e._zoomFactor,s._zoomFactor>10&&(s._zoomFactor=10)),s.update=!0,e.bControlGl&&!t.bNode?window.controls.update(s):e.controls.update(s),e.bRender&&e.drawCls.render()}else if(76===s.keyCode){let t=new THREE.Vector3(0,1,0),s=-i/180*Math.PI;e.transformCls.setRotation(t,s)}else if(74===s.keyCode){let t=new THREE.Vector3(0,1,0),s=i/180*Math.PI;e.transformCls.setRotation(t,s)}else if(73===s.keyCode){let t=new THREE.Vector3(1,0,0),s=-i/180*Math.PI;e.transformCls.setRotation(t,s)}else if(77===s.keyCode){let t=new THREE.Vector3(1,0,0),s=i/180*Math.PI;e.transformCls.setRotation(t,s)}else 65===s.keyCode&&Object.keys(e.structures).length>1&&await e.alternateCls.alternateWrapper()})),e.container.bind("mouseup",(function(t){e.isDragging=!1})),e.container.bind("touchend",(function(t){e.isDragging=!1})),e.container.bind("mousedown",(function(s){if(e.isDragging=!0,e.scene){if(e.bStopRotate=!0,e.pk&&(s.altKey||s.ctrlKey||s.shiftKey||18===s.keyCode||16===s.keyCode||17===s.keyCode||224===s.keyCode||91===s.keyCode)){e.highlightlevel=e.pk;let t=!0;e.rayCls.rayCaster(s,t)}e.bControlGl&&!t.bNode?(window.controls.handleResize(),window.controls.update()):(e.controls.handleResize(),e.controls.update()),e.bRender&&e.drawCls.render()}})),e.container.bind("touchstart",(function(s){if(s.preventDefault(),e.isDragging=!0,!e.scene)return;e.bStopRotate=!0,$("#"+e.pre+"popup").hide();e.rayCls.rayCaster(s,!0),e.bControlGl&&!t.bNode?(window.controls.handleResize(),window.controls.update()):(e.controls.handleResize(),e.controls.update()),e.bRender&&e.drawCls.render()})),e.container.bind("mousemove touchmove",(function(e){s.mouseMove(e)})),e.container.bind("mousewheel",(function(s){s.preventDefault(),e.scene&&(e.bStopRotate=!0,e.bControlGl&&!t.bNode?(window.controls.handleResize(),window.controls.update()):(e.controls.handleResize(),e.controls.update()),e.bRender&&e.drawCls.render())})),e.container.bind("DOMMouseScroll",(function(s){s.preventDefault(),e.scene&&(e.bStopRotate=!0,e.bControlGl&&!t.bNode?(window.controls.handleResize(),window.controls.update()):(e.controls.handleResize(),e.controls.update()),e.bRender&&e.drawCls.render())}))}mouseMove(e){let t=this.icn3d,s=t.icn3dui;if(s.bNode)return;if(e.preventDefault(),!t.scene)return;$("#"+t.pre+"popup").hide();if(t.rayCls.rayCaster(e,!1),t.bControlGl&&!s.bNode){window.controls.handleResize(),window.controls.update();for(let e in window.icn3duiHash){let t=window.icn3duiHash[e].icn3d;t.bRender&&t.drawCls.render()}}else t.controls.handleResize(),t.controls.update(),t.bRender&&t.drawCls.render()}}class Ts{constructor(e){this.icn3d=e}showPicking(e,t,s){let i=this.icn3d,n=i.icn3dui;if(void 0!==n.cfg.cid&&0!=i.pk&&(i.pk=1),i.highlightlevel=i.pk,this.showPickingBase(e,t,s),0!=i.pk)if(void 0!==t&&void 0!==s){null!=n.cfg.showmenu&&1==n.cfg.showmenu&&(s+=n.htmlCls.MENU_HEIGHT);let l,r=1==i.pk?e.resn+e.resi+"@"+e.name:e.resn+e.resi,o=e.structure+"_"+e.chain;if(void 0!==i.structures&&Object.keys(i.structures).length>1?(r=o+" "+r,l=i.chainid2refpdbname&&i.chainid2refpdbname[o]?240:160,$("#"+i.pre+"popup").css("width",l+"px")):(l=i.chainid2refpdbname&&i.chainid2refpdbname[o]?160:80,$("#"+i.pre+"popup").css("width",l+"px")),i.chainid2refpdbname&&i.chainid2refpdbname[o]){let t=i.resid2refnum[o+"_"+e.resi];t&&(r+=", Ig: "+t)}$("#"+i.pre+"popup").html(r),$("#"+i.pre+"popup").css("top",s).css("left",t+20).show()}else{i.hlUpdateCls.updateHlAll();let t={};t.factor=i._zoomFactor,t.mouseChange=i.mouseChange,t.quaternion={},t.quaternion._x=parseFloat(i.quaternion._x).toPrecision(5),t.quaternion._y=parseFloat(i.quaternion._y).toPrecision(5),t.quaternion._z=parseFloat(i.quaternion._z).toPrecision(5),t.quaternion._w=parseFloat(i.quaternion._w).toPrecision(5),n.htmlCls.clickMenuCls.setLogCmd("pickatom "+e.serial,!0),i.selectionCls.saveSelInCommand(),i.bSphereCalc=!1,i.bHbondCalc=!1}}showPickingBase(e,t,s){this.icn3d.icn3dui,void 0===t&&void 0===s&&this.showPickingHilight(e)}getPickedAtomList(e,t){let s=this.icn3d;s.icn3dui;let i={};if(1===e)i[t.serial]=1;else if(2===e){let e=t.structure+"_"+t.chain+"_"+t.resi;i=s.residues[e]}else if(3===e)i=this.selectStrandHelixFromAtom(t);else if(4===e)i=this.select3ddomainFromAtom(t);else if(5===e){let e=t.structure+"_"+t.chain;i=s.chains[e]}return i}showPickingHilight(e){let t=this.icn3d,s=t.icn3dui;t.bShift||t.bCtrl||t.hlObjectsCls.removeHlObjects(),t.pickedAtomList=this.getPickedAtomList(t.pk,e),0===t.pk?t.bShowHighlight=!1:t.bShowHighlight=!0;let i=Object.keys(t.hAtoms).length==Object.keys(t.atoms).length?{}:s.hashUtilsCls.intHash(t.hAtoms,t.pickedAtomList),n=Object.keys(i).length;if(t.bShift||t.bCtrl)if(t.bShift){if(void 0===t.prevPickedAtomList)t.hAtoms=s.hashUtilsCls.unionHash(t.hAtoms,t.pickedAtomList);else{let e=t.firstAtomObjCls.getFirstAtomObj(t.prevPickedAtomList),i=t.firstAtomObjCls.getFirstAtomObj(t.pickedAtomList);if(e.structure+"_"+e.chain!=i.structure+"_"+i.chain)t.hAtoms=s.hashUtilsCls.unionHash(t.hAtoms,t.pickedAtomList);else{let e;e=s.hashUtilsCls.unionHash(e,t.prevPickedAtomList),e=s.hashUtilsCls.unionHash(e,t.pickedAtomList);let i=t.firstAtomObjCls.getFirstAtomObj(e),n=t.firstAtomObjCls.getLastAtomObj(e);for(let e=i.serial;e<=n.serial;++e)t.hAtoms[e]=1}}t.prevPickedAtomList=s.hashUtilsCls.cloneHash(t.pickedAtomList)}else t.bCtrl&&(t.hAtoms=n>0?s.hashUtilsCls.exclHash(t.hAtoms,t.pickedAtomList):s.hashUtilsCls.unionHash(t.hAtoms,t.pickedAtomList));else t.hAtoms=s.hashUtilsCls.cloneHash(t.pickedAtomList);t.hlObjectsCls.removeHlObjects(),t.hlObjectsCls.addHlObjects()}select3ddomainFromAtom(e){let t,s=this.icn3d,i=s.icn3dui,n=e.structure+"_"+e.chain,l=n+"_"+e.resi;for(let e in s.tddomains){let i=e.indexOf("_3d_domain");if(e.substr(0,i)==n&&-1!==Object.keys(s.tddomains[e]).indexOf(l)){t=e;break}}let r={};for(let e in s.tddomains[t])r=i.hashUtilsCls.unionHash(r,s.residues[e]);return r}selectStrandHelixFromAtom(e){let t=this.icn3d,s=t.icn3dui,i=e,n=e,l={},r=i.resi;if(!i.ssbegin&&!isNaN(i.resi)){for(let e=i.resi-1;e>0;--e){let s=i.structure+"_"+i.chain+"_"+e;if(!t.residues.hasOwnProperty(s))break;let n=t.firstAtomObjCls.getFirstCalphaAtomObj(t.residues[s]);if(r=n.resi,"coil"!==i.ss&&n.ss===i.ss&&n.ssbegin||"coil"===i.ss&&n.ss!==i.ss){"coil"===i.ss&&n.ss!==i.ss&&(r=parseInt(n.resi)+1);break}}for(let e=r;e<=i.resi;++e){let n=i.structure+"_"+i.chain+"_"+e;l=s.hashUtilsCls.unionHash(l,s.hashUtilsCls.hash2Atoms(t.residues[n],t.atoms))}}let o=n.resi,a=t.firstAtomObjCls.getLastAtomObj(t.chains[n.structure+"_"+n.chain]).resi;for(let e=parseInt(n.resi)+1;e<=parseInt(a);++e){let s=n.structure+"_"+n.chain+"_"+e;if(!t.residues.hasOwnProperty(s))break;let i=t.firstAtomObjCls.getFirstCalphaAtomObj(t.residues[s]);if(o=i.resi,"coil"!==n.ss&&i.ss===n.ss&&i.ssend||"coil"===n.ss&&i.ss!==n.ss){"coil"!==n.ss||i.ss===n.ss||isNaN(i.resi)||(o=i.resi-1);break}}for(let e=parseInt(n.resi)+1;e<=parseInt(o);++e){let i=n.structure+"_"+n.chain+"_"+e;l=s.hashUtilsCls.unionHash(l,s.hashUtilsCls.hash2Atoms(t.residues[i],t.atoms))}return l}}class Es{constructor(e){this.icn3d=e,this.xrSessionIsGranted=!1}createButton(e,t){let s=this.icn3d,i=s.icn3dui;t&&console.error('THREE.VRButton: The "options" parameter has been removed. Please set the reference space type via renderer.xr.setReferenceSpaceType() instead.');const n=document.createElement("button");function l(){n.style.display="",n.style.cursor="auto",n.style.left="calc(33% - 75px)",n.style.width="150px",n.onmouseenter=null,n.onmouseleave=null,n.onclick=null}let r=this;if("xr"in navigator)return n.id=i.pre+"VRButton",n.style.display="none",(o=n).style.position="absolute",o.style.bottom="20px",o.style.padding="12px 6px",o.style.border="1px solid #fff",o.style.borderRadius="4px",o.style.background="#000",o.style.color="#f8b84e",o.style.font="bold 13px sans-serif",o.style.textAlign="center",o.style.opacity="0.8",o.style.outline="none",o.style.zIndex="999",navigator.xr.isSessionSupported("immersive-vr").then((function(t){t?function(){let t=null;async function i(s){s.addEventListener("end",l),await e.xr.setSession(s),n.textContent="EXIT VR",t=s}function l(){s.transformCls.resetOrientation(),s.bVr=!1,s.drawCls.draw(),t.removeEventListener("end",l),n.textContent="ENTER VR",t=null}n.style.display="",n.style.cursor="pointer",n.style.left="calc(33% - 50px)",n.style.width="100px",n.textContent="ENTER VR",n.onmouseenter=function(){n.style.opacity="1.0"},n.onmouseleave=function(){n.style.opacity="0.8"},n.onclick=function(){if(s.bImpo=!1,s.bVr=!0,s.drawCls.draw(s.bVr),null===t){const e={optionalFeatures:["local-floor","bounded-floor","hand-tracking","layers"]};navigator.xr.requestSession("immersive-vr",e).then(i)}else t.end()}}():(l(),n.style.display="none"),t&&r.xrSessionIsGranted&&n.click()})).catch((function(e){l(),console.warn("Exception when trying to call xr.isSessionSupported",e),n.style.display="none"})),n;return document.createElement("span");var o}registerSessionGrantedListener(){"xr"in navigator&&navigator.xr.addEventListener("sessiongranted",(()=>{this.xrSessionIsGranted=!0}))}}class Ps{constructor(e){this.icn3d=e,this.xrSessionIsGranted=!1}createButton(e,t={}){let s=this.icn3d,i=s.icn3dui;const n=document.createElement("button");function l(){n.style.display="",n.style.cursor="auto",n.style.left="calc(66% - 50px)",n.style.width="150px",n.onmouseenter=null,n.onmouseleave=null,n.onclick=null}function r(e){e.style.position="absolute",e.style.bottom="20px",e.style.padding="12px 6px",e.style.border="1px solid #fff",e.style.borderRadius="4px",e.style.background="#000",e.style.color="#f8b84e",e.style.font="bold 13px sans-serif",e.style.textAlign="center",e.style.opacity="0.8",e.style.outline="none",e.style.zIndex="999"}if(i.utilsCls.isAndroid()&&i.utilsCls.isChrome()){if("xr"in navigator)return n.id=i.pre+"ARButton",n.style.display="none",r(n),navigator.xr.isSessionSupported("immersive-ar").then((function(i){i?function(){if(void 0===t.domOverlay){const e=document.createElement("div");e.style.display="none",document.body.appendChild(e);const s=document.createElementNS("http://www.w3.org/2000/svg","svg");s.setAttribute("width",38),s.setAttribute("height",38),s.style.position="absolute",s.style.right="20px",s.style.top="20px",s.addEventListener("click",(function(){i.end()})),e.appendChild(s);const n=document.createElementNS("http://www.w3.org/2000/svg","path");n.setAttribute("d","M 12,12 L 28,28 M 28,12 12,28"),n.setAttribute("stroke","#fff"),n.setAttribute("stroke-width",2),s.appendChild(n),void 0===t.optionalFeatures&&(t.optionalFeatures=[]),t.optionalFeatures.push("dom-overlay"),t.domOverlay={root:e}}let i=null;async function l(s){s.addEventListener("end",r),e.xr.setReferenceSpaceType("local"),await e.xr.setSession(s),n.textContent="STOP AR",t.domOverlay.root.style.display="",i=s}function r(){s.transformCls.resetOrientation(),s.bAr=!1,s.drawCls.draw(),i.removeEventListener("end",r),n.textContent="START AR",t.domOverlay.root.style.display="none",i=null}n.style.display="",n.style.cursor="pointer",n.style.left="calc(66% - 50px)",n.style.width="100px",n.textContent="START AR",n.onmouseenter=function(){n.style.opacity="1.0"},n.onmouseleave=function(){n.style.opacity="0.8"},n.onclick=function(){s.bImpo=!1,s.opts.background="transparent",s.bAr=!0,s.drawCls.draw(s.bAr),null===i?navigator.xr.requestSession("immersive-ar",t).then(l):i.end()}}():(l(),n.style.display="none")})).catch((function(e){l(),console.warn("Exception when trying to call xr.isSessionSupported",e),n.style.display="none"})),n;return document.createElement("span")}return n.id=i.pre+"ARButton",n.style.display="none",r(n),l(),n.style.display="none",n}}class Ms{constructor(e){let t,s,i,n=e;if(this.icn3dui=e,this.id=this.icn3dui.pre+"canvas",this.pre=this.icn3dui.pre,this.container=$("#"+this.id),this.oriContainer=$("#"+this.id),this.bControlGl=!1,this.maxatomcnt=1e5,this.overdraw=0,this.bDrawn=!1,this.bOpm=!1,this.crossstrucinter=0,this.bSecondaryStructure=!1,this.bHighlight=1,this.renderOrderPicking=-1,this.bInitial=!0,this.bDoublecolor=!1,this.originSize=1,this.ALTERNATE_STRUCTURE=-1,this.bUsePdbNum=!0,!this.icn3dui.bNode){let e=document.createElement("canvas");t=!(!window.WebGLRenderingContext||!e.getContext("webgl")&&!e.getContext("experimental-webgl")),e.remove(),e=document.createElement("canvas"),s=!(!window.WebGLRenderingContext||!e.getContext("webgl2")),e.remove(),i="xr"in navigator,t?(s&&i?(this.renderer=new THREE.WebGLRenderer({canvas:this.oriContainer.get(0),antialias:!0,preserveDrawingBuffer:!0,sortObjects:!1,alpha:!0}),this.renderer.xr.enabled=!0):this.renderer=new THREE.WebGL1Renderer({canvas:this.oriContainer.get(0),antialias:!0,preserveDrawingBuffer:!0,sortObjects:!1,alpha:!0}),this.overdraw=0):alert("Currently your web browser has a problem on WebGL. If you are using Chrome, open a new tab for the same URL and WebGL may work again.")}this.frac=new THREE.Color(.1,.1,.1),this.shininess=40,this.emissive=1118481,this.light1=.8,this.light2=.4,this.light3=.2,this.lineRadius=.1,this.coilWidth=.3,this.cylinderRadius=.4,this.crosslinkRadius=.4,this.traceRadius=.4,this.dotSphereScale=.3,this.sphereRadius=1.5,this.cylinderHelixRadius=1.6,this.ribbonthickness=.2,this.helixSheetWidth=1.3,this.nucleicAcidWidth=.8,this.scaleFactor=1,this.labelScale=1,this.resizeRatioX=1,this.resizeRatioY=1,this.bImpo=!0,this.bInstanced=!0,this.chainMissingResidueArray={},this._zoomFactor=1,this.transparentRenderOrder=!1,this.AFUniprotVersion="v4",this.defaultPdbId="stru",this.icn3dui.bNode||(s&&i?(this.bExtFragDepth=!0,this.bImpo=!0,this.bInstanced=!0):(this.bExtFragDepth=this.renderer.extensions.get("EXT_frag_depth"),this.bExtFragDepth?console.log("EXT_frag_depth is supported. All spheres and cylinders are drawn using shaders."):(this.bImpo=!1,console.log("EXT_frag_depth is NOT supported. All spheres and cylinders are drawn using geometry.")),this.bInstanced=this.renderer.extensions.get("ANGLE_instanced_arrays"),this.bInstanced?console.log("ANGLE_instanced_arrays is supported. Assembly is drawn with one copy of the asymmetric unit using hardware instancing."):console.log("ANGLE_instanced_arrays is NOT supported. Assembly is drawn by making copies of the asymmetric unit."))),this.posArray=new Array,this.colorArray=new Array,this.pos2Array=new Array,this.color2Array=new Array,this.radiusArray=new Array,this.posArraySphere=new Array,this.colorArraySphere=new Array,this.radiusArraySphere=new Array,this.axis=!1,this.pk=1,this.highlightlevel=1,this.pickpair=!1,this.pAtomNum=0,this.pAtom=void 0,this.pAtom2=void 0,this.bCtrl=!1,this.bShift=!1,this.bStopRotate=!1,this.bCalphaOnly=!1,this.bConsiderNeighbors=!1,this.bShowCrossResidueBond=!0,this.bExtrude=!0,this.effects={none:this.renderer},this.maxD=500,this.oriMaxD=this.maxD,this.cam_z=2*this.maxD,this.commands=[],this.optsHistory=[],this.logs=[],this.bRender=!0,this.hColor=new THREE.Color(16777011),this.sphereGeometry=new THREE.SphereGeometry(1,32,32),this.boxGeometry=new THREE.BoxGeometry(1,1,1),this.cylinderGeometry=new THREE.CylinderGeometry(1,1,1,32,1),this.cylinderGeometryOutline=new THREE.CylinderGeometry(1,1,1,32,1,!0),this.axisDIV=15,this.strandDIV=6,this.tubeDIV=8,this.nucleicAcidStrandDIV=6,this.linewidth=1,this.hlLineRadius=.1,this.threshbox=180,this.maxAtoms3DMultiFile=4e4,this.tsHbond=3.8,this.tsIonic=6,this.tsContact=4,this.tsHalogen=3.8,this.tsPication=6,this.tsPistacking=5.5,this.LABELSIZE=30,this.rayThreshold=.5,this.colorBlackbkgd="#ffff00",this.colorWhitebkgd="#000000",this.optsOri={},this.optsOri.camera="perspective",this.optsOri.background="black",this.optsOri.color="chain",this.optsOri.proteins="ribbon",this.optsOri.sidec="nothing",this.optsOri.nucleotides="nucleotide cartoon",this.optsOri.ntbase="nothing",this.optsOri.surface="nothing",this.optsOri.opacity="1.0",this.optsOri.wireframe="no",this.optsOri.map="nothing",this.optsOri.mapwireframe="yes",this.optsOri.emmap="nothing",this.optsOri.emmapwireframe="yes",this.optsOri.phimap="nothing",this.optsOri.phimapwireframe="yes",this.optsOri.phisurface="nothing",this.optsOri.phisurftype="nothing",this.optsOri.phisurfop="1.0",this.optsOri.phisurfwf="yes",this.optsOri.chemicals="stick",this.optsOri.water="nothing",this.optsOri.ions="sphere",this.optsOri.hbonds="no",this.optsOri.saltbridge="no",this.optsOri.contact="no",this.optsOri.halogen="no",this.optsOri["pi-cation"]="no",this.optsOri["pi-stacking"]="no",this.optsOri.ssbonds="yes",this.optsOri.clbonds="yes",this.optsOri.rotationcenter="molecule center",this.optsOri.axis="no",this.optsOri.fog="no",this.optsOri.slab="no",this.optsOri.pk="residue",this.optsOri.chemicalbinding="hide",this.opts=n.hashUtilsCls.cloneHash(this.optsOri),this.sheetcolor="green",this.bShowHighlight=!0,this.mapData={},this.bFullUi=!0,this.divid=this.icn3dui.cfg.divid,this.inputid="",this.setOperation="or",this.ROT_DIR="right",this.currSelectedSets=[],this.selectedResidues={},this.ncbi2resid={},this.resid2ncbi={},this.shapeCmdHash={},this.bHideSelection=!0,this.bSelectResidue=!1,this.bSelectAlignResidue=!1,this.bAnnoShown=!1,this.bSetChainsAdvancedMenu=!1,this.b2DShown=!1,this.bCrashed=!1,this.bAddCommands=!0,this.bAddLogs=!0,this.bNotLoadStructure=!1,this.InputfileData="",this.bVr=!1,this.bAr=!1,this.startColor="blue",this.midColor="white",this.endColor="red",this.startValue=0,this.midValue=50,this.endValue=100,this.crosslinkRadius=.4,this.sceneCls=new Ie(this),this.cameraCls=new Te(this),this.fogCls=new Ee(this),this.boxCls=new Pe(this),this.brickCls=new Me(this),this.curveStripArrowCls=new De(this),this.curveCls=new He(this),this.cylinderCls=new Fe(this),this.lineCls=new Le(this),this.reprSubCls=new Ne(this),this.sphereCls=new qe(this),this.stickCls=new Ue(this),this.strandCls=new $e(this),this.stripCls=new je(this),this.tubeCls=new Be(this),this.cartoonNuclCls=new ze(this),this.surfaceCls=new Qe(this),this.labelCls=new Ve(this),this.axesCls=new We(this),this.glycanCls=new Ye(this),this.applyCenterCls=new Ze(this),this.applyClbondsCls=new et(this),this.applyMissingResCls=new tt(this),this.applyDisplayCls=new st(this),this.applyMapCls=new rt(this),this.applyOtherCls=new it(this),this.applySsbondsCls=new nt(this),this.applySymdCls=new lt(this),this.hlObjectsCls=new Ht(this),this.residueLabelsCls=new ot(this),this.alternateCls=new ct(this),this.drawCls=new ht(this),this.firstAtomObjCls=new ms(this),this.impostorCls=new at(this),this.instancingCls=new dt(this),this.contactCls=new pt(this),this.hBondCls=new mt(this),this.piHalogenCls=new ut(this),this.saltbridgeCls=new gt(this),this.loadPDBCls=new ls(this),this.vastplusCls=new rs(this),this.transformCls=new Ss(this),this.setStyleCls=new ft(this),this.setColorCls=new bt(this),this.threeDPrintCls=new ks(this),this.export3DCls=new Os(this),this.annoCddSiteCls=new vt(this),this.annoContactCls=new _t(this),this.annoPTMCls=new wt(this),this.annoCrossLinkCls=new St(this),this.annoDomainCls=new At(this),this.annoSnpClinVarCls=new xt(this),this.annoSsbondCls=new kt(this),this.annoTransMemCls=new Ot(this),this.domain3dCls=new Rt(this),this.addTrackCls=new It(this),this.annotationCls=new Tt(this),this.showAnnoCls=new Et(this),this.showSeqCls=new Pt(this),this.hlSeqCls=new Mt(this),this.hlUpdateCls=new Dt(this),this.lineGraphCls=new Ft(this),this.getGraphCls=new Nt(this),this.showInterCls=new qt(this),this.viewInterPairsCls=new Ut(this),this.drawGraphCls=new $t(this),this.contactMapCls=new jt(this),this.alignParserCls=new Bt(this),this.chainalignParserCls=new zt(this),this.dsn6ParserCls=new Gt(this),this.mmcifParserCls=new Vt(this),this.mmdbParserCls=new Wt(this),this.mmtfParserCls=new Yt(this),this.mol2ParserCls=new Xt(this),this.opmParserCls=new Kt(this),this.pdbParserCls=new Jt(this),this.sdfParserCls=new Qt(this),this.xyzParserCls=new Zt(this),this.realignParserCls=new es(this),this.densityCifParserCls=new ts(this),this.ParserUtilsCls=new ss(this),this.loadAtomDataCls=new is(this),this.setSeqAlignCls=new ns(this),this.applyCommandCls=new os(this),this.definedSetsCls=new as(this),this.legendTableCls=new yt(this),this.loadScriptCls=new ds(this),this.selByCommCls=new cs(this),this.selectionCls=new hs(this),this.resid2specCls=new ps(this),this.delphiCls=new us(this),this.dsspCls=new gs(this),this.refnumCls=new Lt(this),this.scapCls=new fs(this),this.symdCls=new bs(this),this.alignSWCls=new Cs(this),this.analysisCls=new ys(this),this.resizeCanvasCls=new ws(this),this.saveFileCls=new As(this),this.setOptionCls=new Ct(this),this.shareLinkCls=new xs(this),this.diagram2dCls=new vs(this),this.cartoon2dCls=new _s(this),this.rayCls=new Rs(this),this.controlCls=new Is(this),this.pickingCls=new Ts(this),this.VRButtonCls=new Es(this),this.ARButtonCls=new Ps(this),this.matShader=this.setColorCls.setOutlineColor("yellow")}}Ms.prototype.init=function(e){this.init_base(),this.molTitle="",this.ssbondpnts={},this.clbondpnts={},this.biomtMatrices=[],this.bAssembly=!0,this.bDrawn=!1,this.bSecondaryStructure=!1,this.bHighlight=1,this.axes=[]},Ms.prototype.init_base=function(e){this.resetConfig(),this.structures={},this.chains={},this.tddomains={},this.residues={},this.secondaries={},this.alnChains={},this.chainsSeq={},this.chainsColor={},this.chainsGene={},this.chainsAn={},this.chainsAnTitle={},this.chainsMapping={},this.resid2refnum={},this.residIgLoop={},this.refnum2residArray={},this.bShowRefnum=!1,this.alnChainsSeq={},this.alnChainsAnno={},this.alnChainsAnTtl={},this.pickedAtomList={},this.prevHighlightObjects=[],this.prevHighlightObjects_ghost=[],this.prevSurfaces=[],this.prevMaps=[],this.prevEmmaps=[],this.prevPhimaps=[],this.prevOtherMesh=[],this.defNames2Residues={},this.defNames2Atoms={},this.defNames2Descr={},this.defNames2Command={},this.residueId2Name={},this.atoms={},this.dAtoms={},this.hAtoms={},this.proteins={},this.sidec={},this.ntbase={},this.nucleotides={},this.nucleotidesO3={},this.chemicals={},this.ions={},this.water={},this.calphas={},this.hbondpnts=[],this.saltbridgepnts=[],this.contactpnts=[],this.stabilizerpnts=[],this.halogenpnts=[],this.picationpnts=[],this.pistackingpnts=[],this.distPnts=[],this.doublebonds={},this.triplebonds={},this.aromaticbonds={},this.atomPrevColors={},this.style2atoms={},this.labels={},this.lines={},this.resids2inter={},this.resids2interAll={},this.transformCls.rotateCount=0,this.transformCls.rotateCountMax=20,e&&(this.commands=[]),this.axes=[],this.bGlycansCartoon=0,this.bMembrane=1,this.bCmdWindow=0,this.chainMissingResidueArray={},this.nTotalGap=0},Ms.prototype.reinitAfterLoad=function(){let e=this,t=e.icn3dui;e.resetConfig(),e.setStyleCls.setAtomStyleByOptions(),e.setColorCls.setColorByOptions(e.opts,e.atoms),e.dAtoms=t.hashUtilsCls.cloneHash(e.atoms),e.hAtoms=t.hashUtilsCls.cloneHash(e.atoms),e.prevHighlightObjects=[],e.prevHighlightObjects_ghost=[],e.prevSurfaces=[],e.prevMaps=[],e.prevEmmaps=[],e.prevPhimaps=[],e.prevOtherMesh=[],e.labels={},e.lines={},e.shapeCmdHash={},e.bAssembly=!0},Ms.prototype.resetConfig=function(){let e=this,t=e.icn3dui;if(this.opts=t.hashUtilsCls.cloneHash(this.optsOri),void 0===t.cfg.align&&void 0===t.cfg.chainalign||(this.opts.color="identity",this.opts.proteins="c alpha trace",this.opts.nucleotides="o3 trace"),void 0!==t.cfg.cid&&(this.opts.color="atom",this.opts.pk="atom",this.opts.chemicals="ball and stick"),(void 0!==t.cfg.afid||e.bEsmfold)&&(this.opts.color="confidence"),void 0!==t.cfg.blast_rep_id&&(this.opts.color="conservation"),void 0!==t.cfg.mmdbafid){let s=t.cfg.mmdbafid.split(",");if(s.length>1)e.opts.color="structure";else if(1==s.length){let t=s[0];isNaN(t)&&t.length>5?this.opts.color="confidence":e.opts.color="chain"}}void 0!==t.cfg.options&&$.extend(this.opts,t.cfg.options)};class Ds{constructor(e){this.cfg=e,this.pre=this.cfg.divid+"_",this.REVISION="3.28.4",this.bNode=Object.keys(window).length<2,void 0===this.cfg.command&&(this.cfg.command=""),void 0===this.cfg.width&&(this.cfg.width="100%"),void 0===this.cfg.height&&(this.cfg.height="100%"),void 0===this.cfg.resize&&(this.cfg.resize=!0),void 0===this.cfg.showmenu&&(this.cfg.showmenu=!0),void 0===this.cfg.showtitle&&(this.cfg.showtitle=!0),void 0===this.cfg.showcommand&&(this.cfg.showcommand=!0),void 0===this.cfg.mobilemenu&&(this.cfg.mobilemenu=!1),void 0===this.cfg.imageonly&&(this.cfg.imageonly=!1),void 0===this.cfg.closepopup&&(this.cfg.closepopup=!1),void 0===this.cfg.showanno&&(this.cfg.showanno=!1),void 0===this.cfg.showseq&&(this.cfg.showseq=!1),void 0===this.cfg.showalignseq&&(this.cfg.showalignseq=!1),void 0===this.cfg.show2d&&(this.cfg.show2d=!1),void 0===this.cfg.showsets&&(this.cfg.showsets=!1),void 0===this.cfg.rotate&&(this.cfg.rotate="right"),void 0===this.cfg.hidelicense&&(this.cfg.hidelicense=!1),this.hashUtilsCls=new t(this),this.utilsCls=new s(this),this.parasCls=new i(this),this.myEventCls=new n(this),this.rmsdSuprCls=new l(this),this.subdivideCls=new r(this),this.convertTypeCls=new o(this),this.htmlCls=new g(this)}allCustomEvents(){}}Ds.prototype.show3DStructure=async function(e){let t=this;t.cfg.menuicon?(t.htmlCls.wifiStr=' ',t.htmlCls.licenseStr=' '):(t.htmlCls.wifiStr="",t.htmlCls.licenseStr=""),t.setIcn3d();let s=t.icn3d;t.utilsCls.isSessionStorageSupported()&&s.setStyleCls.getCommandsBeforeCrash();let i=t.htmlCls.WIDTH,n=t.htmlCls.HEIGHT;t.oriWidth=i,t.oriHeight=n,t.htmlCls.eventsCls.allEventFunctions(),this.allCustomEvents();let l=0;if((null==t.cfg.showmenu||t.cfg.showmenu)&&(l+=t.htmlCls.MENU_HEIGHT),(null==t.cfg.showcommand||t.cfg.showcommand)&&(l+=t.htmlCls.CMD_HEIGHT),null!=t.cfg.showmenu&&0==t.cfg.showmenu?t.htmlCls.setMenuCls.hideMenu():t.htmlCls.setMenuCls.showMenu(),null!=t.cfg.showtitle&&0==t.cfg.showtitle?$("#"+s.pre+"title").hide():$("#"+s.pre+"title").show(),$("#"+s.pre+"viewer").width(i).height(parseInt(n)+l),$("#"+s.pre+"canvas").width(i).height(parseInt(n)),$("#"+s.pre+"canvas").resizable({resize:function(e,i){t.htmlCls.WIDTH=i.size.width,t.htmlCls.HEIGHT=i.size.height,void 0===s||t.icn3d.bFullscreen||s.resizeCanvasCls.resizeCanvas(t.htmlCls.WIDTH,t.htmlCls.HEIGHT,!0)}}),void 0!==t.cfg.usepdbnum?t.icn3d.bUsePdbNum=t.cfg.usepdbnum:void 0!==t.cfg.date?t.icn3d.bUsePdbNum=parseInt(t.cfg.date)>=20201222:"1tup"==t.cfg.mmdbid&&1==t.cfg.showanno&&1==t.cfg.show2d&&1==t.cfg.showsets||"118496"==t.cfg.mmdbid&&0==t.cfg.showanno&&-1!=t.cfg.inpara.indexOf("bu=1")||"163605,1,91105,1,1,1"==t.cfg.align&&-1!=t.cfg.inpara.indexOf("atype=1")?t.icn3d.bUsePdbNum=!1:t.icn3d.bUsePdbNum=!0,t.cfg.replay?(s.bReplay=1,$("#"+s.pre+"replay").show()):(s.bReplay=0,$("#"+s.pre+"replay").hide()),t.utilsCls.isMobile()&&(s.threshbox=60),t.cfg.controlGl&&(s.bControlGl=!0,s.container=s.bControlGl&&!t.bNode?$(document):$("#"+s.id)),s.setStyleCls.handleContextLost(),s.applyCenterCls.setWidthHeight(i,n),s.ori_chemicalbinding=s.opts.chemicalbinding,void 0!==t.cfg.bCalphaOnly&&(s.bCalphaOnly=t.cfg.bCalphaOnly),s.opts=t.hashUtilsCls.cloneHash(s.opts),s.STATENUMBER=s.commands.length,t.utilsCls.isSessionStorageSupported()&&s.bCrashed){s.bCrashed=!1;let e=s.commandsBeforeCrash.split("|||")[0],i=e.substr(e.lastIndexOf(" ")+1);if(i===t.cfg.mmtfid||i===t.cfg.pdbid||i===t.cfg.opmid||i===t.cfg.mmdbid||i===t.cfg.gi||i===t.cfg.blast_rep_id||i===t.cfg.cid||i===t.cfg.mmcifid||i===t.cfg.align||i===t.cfg.chainalign||i===t.cfg.mmdbafid)return void await s.loadScriptCls.loadScript(s.commandsBeforeCrash,!0)}if(s.molTitle="",s.loadCmd,t.htmlCls.clickMenuCls.getHiddenMenusFromCache(),t.htmlCls.clickMenuCls.applyShownMenus(),e){if(s.init(),s.bInputfile=!0,s.InputfileType="pdb",s.InputfileData=s.InputfileData?s.InputfileData+"\nENDMDL\n"+e:e,await s.pdbParserCls.loadPdbData(e),void 0!==t.cfg.resdef&&void 0!==t.cfg.chains){let e=Object.keys(s.structures),i=t.cfg.chains.split(" | "),n=[];if(e.length==i.length){for(let t=0,s=e.length;t0&&(l+=","),l+=n[e].substr(0,n[e].indexOf("_"));s.chainidArray=[e].concat(n),s.chainidArray=s.chainalignParserCls.addPostfixForChainids(s.chainidArray),t.htmlCls.clickMenuCls.setLogCmd("resdef "+t.cfg.resdef,!0),s.loadCmd="vast_search_chainid "+s.chainidArray,t.htmlCls.clickMenuCls.setLogCmd(s.loadCmd,!0),s.bMmdbafid=!0;let r=!0;await s.chainalignParserCls.downloadMmdbAf(l,r)}}else if(void 0!==t.cfg.url){s.bInputUrlfile=!0;let e=t.cfg.url.split("|"),i=e[0],n=e[1];s.molTitle="",s.inputid=n,s.inputurl="type="+i+"&url="+encodeURIComponent(n),s.loadCmd="load url "+n+" | type "+i,t.htmlCls.clickMenuCls.setLogCmd(s.loadCmd,!0),await s.pdbParserCls.downloadUrl(n,i,t.cfg.command)}else if(void 0!==t.cfg.mmtfid)s.inputid=t.cfg.mmtfid,s.loadCmd="load mmtf "+t.cfg.mmtfid,t.htmlCls.clickMenuCls.setLogCmd(s.loadCmd,!0),await s.mmtfParserCls.downloadMmtf(t.cfg.mmtfid);else if(void 0!==t.cfg.pdbid)s.inputid=t.cfg.pdbid,s.loadCmd="load pdb "+t.cfg.pdbid,t.htmlCls.clickMenuCls.setLogCmd(s.loadCmd,!0),await s.pdbParserCls.downloadPdb(t.cfg.pdbid);else if(void 0!==t.cfg.afid){s.inputid=t.cfg.afid,s.loadCmd="load af "+t.cfg.afid,t.htmlCls.clickMenuCls.setLogCmd(s.loadCmd,!0);let e=!0;await s.pdbParserCls.downloadPdb(t.cfg.afid,e)}else if(void 0!==t.cfg.opmid)s.inputid=t.cfg.opmid,s.loadCmd="load opm "+t.cfg.opmid,t.htmlCls.clickMenuCls.setLogCmd(s.loadCmd,!0),await s.opmParserCls.downloadOpm(t.cfg.opmid);else if(void 0!==t.cfg.mmdbid)s.inputid=t.cfg.mmdbid,s.loadCmd="load mmdb "+t.cfg.mmdbid+" | parameters "+t.cfg.inpara,t.htmlCls.clickMenuCls.setLogCmd(s.loadCmd,!0),await s.mmdbParserCls.downloadMmdb(t.cfg.mmdbid);else if(void 0!==t.cfg.gi)s.loadCmd="load gi "+t.cfg.gi,t.htmlCls.clickMenuCls.setLogCmd(s.loadCmd,!0),await s.mmdbParserCls.downloadGi(t.cfg.gi);else if(void 0!==t.cfg.refseqid)s.inputid=t.cfg.refseqid,s.loadCmd="load refseq "+t.cfg.refseqid,t.htmlCls.clickMenuCls.setLogCmd(s.loadCmd,!0),await s.mmdbParserCls.downloadRefseq(t.cfg.refseqid);else if(void 0!==t.cfg.protein)s.inputid=t.cfg.protein,s.loadCmd="load protein "+t.cfg.protein,t.htmlCls.clickMenuCls.setLogCmd(s.loadCmd,!0),await s.mmdbParserCls.downloadProteinname(t.cfg.protein);else if(void 0!==t.cfg.blast_rep_id)if(s.inputid=t.cfg.query_id+","+t.cfg.blast_rep_id,t.cfg.oriQuery_id=t.cfg.query_id,t.cfg.oriBlast_rep_id=t.cfg.blast_rep_id,"Query"!==t.cfg.query_id.substr(0,5)&&void 0===t.cfg.rid)"icn3d"==t.cfg.from&&"1TSR_A"==t.cfg.blast_rep_id&&"NP_001108451.1"==t.cfg.query_id&&(t.cfg.command="view annotations; set annotation cdd; set annotation site; set view detailed view; select chain 1TSR_A; show selection"),"smithwm"==t.cfg.alg?(s.loadCmd="load seq_struct_ids_smithwm "+t.cfg.query_id+","+t.cfg.blast_rep_id,s.bSmithwm=!0):"local_smithwm"==t.cfg.alg?(s.loadCmd="load seq_struct_ids_local_smithwm "+t.cfg.query_id+","+t.cfg.blast_rep_id,s.bLocalSmithwm=!0):(s.loadCmd="load seq_struct_ids "+t.cfg.query_id+","+t.cfg.blast_rep_id,s.bSmithwm=!1,s.bLocalSmithwm=!1),t.htmlCls.clickMenuCls.setLogCmd(s.loadCmd,!0),await s.mmdbParserCls.downloadBlast_rep_id(t.cfg.query_id+","+t.cfg.blast_rep_id);else if(void 0!==t.cfg.rid){let e="https://blast.ncbi.nlm.nih.gov/Blast.cgi?RESULTS_FILE=on&FORMAT_TYPE=JSON2_S&FORMAT_OBJECT=Alignment&CMD=Get&RID="+t.cfg.rid,i=await t.getAjaxPromise(e,"json",!1,"The RID "+t.cfg.rid+" may have expired...");for(let e=0,n=i.BlastOutput2.length;e
",s="All atoms Selection ";e.utilsCls.setViewerWidthHeight(e),e.utilsCls.isMobile()||e.cfg.mobilemenu?e.htmlCls.setMenuCls.setTopMenusHtmlMobile(e.cfg.divid,t,s):e.htmlCls.setMenuCls.setTopMenusHtml(e.cfg.divid,t,s),e.icn3d=new Ms(e),e.icn3d.controlCls.setControl(),e.setDialogAjax()},Ds.prototype.getMmtfPromise=function(e){return new Promise((function(t,s){MMTF.fetch(e,(async function(e){t(e)}),(function(e){s("error")}))}))},Ds.prototype.getMmtfReducedPromise=function(e){return new Promise((function(t,s){MMTF.fetchReduced(e,(async function(e){t(e)}),(function(e){s("error")}))}))},Ds.prototype.getXMLHttpRqstPromise=function(e,t,s,i){let n=this;return new Promise((function(l,r){let o=new XMLHttpRequest;o.open(t,e,!0),o.responseType=s,o.onreadystatechange=function(){if(4==this.readyState)if(200==this.status){let e=o.response;l(e)}else"2fofc"==i||"fofc"==i?alert("Density server at EBI has no corresponding electron density map for this structure."):"em"==i?alert("Density server at EBI has no corresponding EM density map for this structure."):"rcsbEdmaps"==i?alert("RCSB server has no corresponding eletron density map for this structure."):alert("The "+i+" file is unavailable..."),r("error");else n.icn3d.ParserUtilsCls.showLoading()},o.send()}))},Ds.prototype.getAjaxPromise=function(e,t,s,i,n,l,r){let o=this;return new Promise((function(r,a){$.ajax({url:e,dataType:t,cache:!0,beforeSend:function(){s&&o.icn3d.ParserUtilsCls.showLoading()},complete:function(){l&&o.icn3d.ParserUtilsCls.hideLoading()},success:function(e){r(e)},error:function(){i&&alert(i),n&&console.log(n),a("error")}})}))},Ds.prototype.getAjaxPostPromise=async function(e,t,s,i,n,l,r,o){let a=this;return r=r||"json",new Promise((function(o,d){$.ajax({url:e,type:"POST",data:t,dataType:r,cache:!0,beforeSend:function(){s&&a.icn3d.ParserUtilsCls.showLoading()},complete:function(){l&&a.icn3d.ParserUtilsCls.hideLoading()},success:function(e){o(e)},error:function(){i&&alert(i),n&&console.log(n),d("error")}})}))},Ds.prototype.setDialogAjax=function(){this.bNode||$.ui.dialog.prototype._makeDraggableBase||($.ui.dialog.prototype._makeDraggableBase=$.ui.dialog.prototype._makeDraggable,$.ui.dialog.prototype._makeDraggable=function(){this._makeDraggableBase(),this.uiDialog.draggable("option","containment",!1)}),$.ajaxTransport("+binary",(function(e,t,s){if(window.FormData&&(e.dataType&&"binary"==e.dataType||e.data&&(window.ArrayBuffer&&e.data instanceof ArrayBuffer||window.Blob&&e.data instanceof Blob)))return{send:function(t,s){let i=new XMLHttpRequest,n=e.url,l=e.type,r=e.async||!0,o=e.responseType||"blob",a=e.data||null;i.addEventListener("load",(function(){let t={};t[e.dataType]=i.response,s(i.status,i.statusText,t,i.getAllResponseHeaders())})),i.open(l,n,r);for(let e in t)i.setRequestHeader(e,t[e]);i.responseType=o,i.send(a)},abort:function(){s.abort()}}}))};return e.ARButton=Ps,e.AddTrack=It,e.AlignParser=Bt,e.AlignSW=Cs,e.AlignSeq=m,e.Alternate=ct,e.Analysis=ys,e.AnnoCddSite=vt,e.AnnoContact=_t,e.AnnoCrossLink=St,e.AnnoDomain=At,e.AnnoSnpClinVar=xt,e.AnnoSsbond=kt,e.AnnoTransMem=Ot,e.Annotation=Tt,e.ApplyCenter=Ze,e.ApplyClbonds=et,e.ApplyCommand=os,e.ApplyDisplay=st,e.ApplyMap=rt,e.ApplyOther=it,e.ApplySsbonds=nt,e.ApplySymd=lt,e.Axes=We,e.Box=Pe,e.Brick=Me,e.Camera=Te,e.CartoonNucl=ze,e.ChainalignParser=zt,e.ClickMenu=a,e.Contact=pt,e.Control=Is,e.ConvertTypeCls=o,e.Curve=He,e.CurveStripArrow=De,e.Cylinder=Fe,e.DefinedSets=as,e.Delphi=us,e.DensityCifParser=ts,e.Diagram2d=vs,e.Dialog=c,e.Domain3d=Rt,e.Draw=ht,e.DrawGraph=$t,e.Dsn6Parser=Gt,e.Dssp=gs,e.ElectronMap=Je,e.Events=p,e.Export3D=Os,e.FirstAtomObj=ms,e.Fog=Ee,e.GetGraph=Nt,e.Glycan=Ye,e.HBond=mt,e.HashUtilsCls=t,e.HlObjects=Ht,e.HlSeq=Mt,e.HlUpdate=Dt,e.Html=g,e.Impostor=at,e.Instancing=dt,e.Label=Ve,e.Line=Le,e.LineGraph=Ft,e.LoadAtomData=is,e.LoadPDB=ls,e.LoadScript=ds,e.MarchingCube=Xe,e.MmcifParser=Vt,e.MmdbParser=Wt,e.MmtfParser=Yt,e.Mol2Parser=Xt,e.MyEventCls=n,e.OpmParser=Kt,e.ParasCls=i,e.ParserUtils=ss,e.PdbParser=Jt,e.PiHalogen=ut,e.Picking=Ts,e.ProteinSurface=Ke,e.Ray=Rs,e.RealignParser=es,e.Refnum=Lt,e.ReprSub=Ne,e.Resid2spec=ps,e.ResidueLabels=ot,e.ResizeCanvas=ws,e.RmsdSuprCls=l,e.Saltbridge=gt,e.SaveFile=As,e.Scap=fs,e.Scene=Ie,e.SdfParser=Qt,e.SelectByCommand=cs,e.Selection=hs,e.SetColor=bt,e.SetDialog=h,e.SetHtml=u,e.SetMenu=d,e.SetOption=Ct,e.SetSeqAlign=ns,e.SetStyle=ft,e.ShareLink=xs,e.ShowAnno=Et,e.ShowInter=qt,e.ShowSeq=Pt,e.Sphere=qe,e.Stick=Ue,e.Strand=$e,e.Strip=je,e.SubdivideCls=r,e.Surface=Qe,e.Symd=bs,e.ThreeDPrint=ks,e.Transform=Ss,e.Tube=Be,e.UtilsCls=s,e.VRButton=Es,e.Vastplus=rs,e.ViewInterPairs=Ut,e.XyzParser=Zt,e.iCn3D=Ms,e.iCn3DUI=Ds,e.printMsg=class{constructor(){console.log("This is a message from the icn3d package")}},Object.defineProperty(e,"__esModule",{value:!0}),e}({});
diff --git a/build/icn3d.module.js b/build/icn3d.module.js
index 8a65e61a..f97f50fc 100644
--- a/build/icn3d.module.js
+++ b/build/icn3d.module.js
@@ -6860,7 +6860,7 @@ class ClickMenu {
});
me.myEventCls.onIds("#" + me.pre + "mn1_dsn6", "click", function(e) { me.icn3d; //e.preventDefault();
- me.htmlCls.dialogCls.openDlg('dl_dsn6', 'Please input the DSN6 file to display electron density map');
+ me.htmlCls.dialogCls.openDlg('dl_dsn6', 'Please input the map file to display electron density map');
});
@@ -6887,7 +6887,7 @@ class ClickMenu {
me.myEventCls.onIds("#" + me.pre + "mn1_dsn6url", "click", function(e) { me.icn3d; //e.preventDefault();
- me.htmlCls.dialogCls.openDlg('dl_dsn6url', 'Please input the DSN6 file to display electron density map');
+ me.htmlCls.dialogCls.openDlg('dl_dsn6url', 'Please input the map file to display electron density map');
});
me.myEventCls.onIds("#" + me.pre + "mn1_exportState", "click", function(e) { let ic = me.icn3d; //e.preventDefault();
@@ -9448,7 +9448,7 @@ class SetMenu {
html += this.getMenuSep();
- html += this.getMenuText('mn1_dsn6wrap', 'Electron Density(DSN6)', undefined, undefined, 2);
+ html += this.getMenuText('mn1_dsn6wrap', 'Electron Density', undefined, undefined, 2);
html += "Option 2 , search with PDB ID and chain name:Option 3 , search with a PDB file:Foldseek web server.AlphaFold Uniprot ID: "+e.htmlCls.inputTextStr+"id='"+e.pre+"afid' value='"+o+"' size=10>Orientations of Proteins in Membranes(OPM) PDB ID: "+e.htmlCls.inputTextStr+"id='"+e.pre+"opmid' value='6JXR' size=8> ",s+=e.htmlCls.buttonStr+"reload_opm'>Load",s+="",s+=e.htmlCls.divStr+"dl_pdbfile' class='"+n+"'>",s+=this.addNotebookTitle("dl_pdbfile","Please input a PDB file"),s+='Note: Several PDB files could be concatenated into a single PDB file. Use the line "ENDMDL" to separate PDB files.The custom JSON file on residue colors has the following format for proteins("ALA" and "ARG") and nucleotides("G" and "A"):
The custom file for the structure has two columns separated by space or tab: ',s+='residue number, and score in the range of 0-100. If you click "Apply Custom Color" button, ',s+='the scores 0, 50 and 100 correspond to the three colors specified below. If you click "Apply Custom Tube", ',s+='the selected residues will be displayed in a style similar to "B-factor Tube".
Score to Color: 0: ",s+=e.htmlCls.optionStr+"'red'>Red",s+=e.htmlCls.optionStr+"'green'>Green",s+=e.htmlCls.optionStr+"'blue' selected>Blue",s+=" ",s+="50 : ",s+=e.htmlCls.optionStr+"'white' selected>White",s+=e.htmlCls.optionStr+"'black'>Black",s+=" ",s+="100 : ",s+=e.htmlCls.optionStr+"'red' selected>Red",s+=e.htmlCls.optionStr+"'green'>Green",s+=e.htmlCls.optionStr+"'blue'>Blue",s+=" You can define your own reference numbers in a custom file using Excel, and then export it as a CSV file. An example file is shown below with cells separated by commas.
',s+="
refnum,11,12,,21,22,,10C,11C,20C ",s+="1TUP_C,,,,,,,200,201,230",s+='The first row defines the reference residue numbers, which could be any strings. The 1st cell could be anything. The rest cells are reference residue numbers (e.g., 11, 21, 10C, etc.) or empty cells. Each chain has a separate row. The first cell of the second row is the chain ID "1TUP_A". The rest cells are the corresponding real residue numbers for reference residue numbers in the first row. For example, the reference numbers for residues 100, 101, and 132 in the chain 1TUP_A are 11, 12, and 22, respectively. The fourth row shows another set of reference numners for the chain "1TUP_C". It could be a chain from a different structure.
',s+='To select all residues corresponding to the reference numbers, you can simplay replace ":" with "%" in the
Specification . For example, "%12" selects the residue 101 in 1TUP_A and the residue 111 in 1TUP_B. ".A%12" has the chain "A" filter and selects the residue 101 in 1TUP_A.
',s+="
VAST+ based on VAST : "+e.htmlCls.buttonStr+"reload_align_ori'>All Matching Molecules Superposed"+e.htmlCls.space3+e.htmlCls.buttonStr+"reload_align_refined'>Invariant Substructure SuperposedVAST+ based on TM-align : "+e.htmlCls.buttonStr+"reload_align_tmalign'>All Matching Molecules SuperposedAlphaFold Uniprot IDs: ",s+="All chains will be aligned to the first chain in the comma-separated chain IDs. Each chain ID has the form of PDBID_chain (e.g., 1HHO_A, case sensitive) or UniprotID (e.g., P69905 for AlphaFold structures).Chain IDs : "+e.htmlCls.inputTextStr+"id='"+e.pre+"chainalignids' value='P69905,P01942,1HHO_A' size=50>Align with TM-align "+e.htmlCls.buttonStr+"reload_chainalign_asym' style='margin-left:30px'>Align with VAST
",s+=e.htmlCls.divStr+"dl_chainalign2' class='"+n+"'>",s+=this.addNotebookTitle("dl_chainalign2","Align chains"),s+="",s+="All chains will be aligned to the first chain in the comma-separated chain IDs. Each chain ID has the form of PDBID_chain (e.g., 1HHO_A, case sensitive) or UniprotID (e.g., P69905 for AlphaFold structures).Chain IDs : "+e.htmlCls.inputTextStr+"id='"+e.pre+"chainalignids2' value='P69905,P01942,1HHO_A' size=50>Align by Sequence Alignment
",s+=e.htmlCls.divStr+"dl_chainalign3' class='"+n+"'>",s+=this.addNotebookTitle("dl_chainalign3","Align chains"),s+="",s+=this.getHtmlAlignResidueByResidue("chainalignids3","predefinedres","reload_chainalign_asym3"),s+="
",s+=e.htmlCls.divStr+"dl_realignresbyres' class='"+n+"'>",s+=this.addNotebookTitle("dl_realignresbyres","Realign residue by residue"),s+="",s+="
Option 1 : "+e.htmlCls.buttonStr+"realignSelection'>
Realign Current Selection Residue by Residue ",s+="
Option 2 :
",s+="
"+this.getHtmlAlignResidueByResidue("chainalignids4","predefinedres2","reload_chainalign_asym4")+"
",s+="
",s+='Please specify the mutations with a comma separated mutation list. Each mutation can be specified as "[
uppercase PDB ID or AlphaFold UniProt ID]_[Chain Name]_[Residue Number]_[One Letter Mutant Residue]". E.g., the mutation of N501Y in the E chain of PDB 6M0J can be specified as "6M0J_E_501_Y". For AlphaFold structures, the "Chain ID" is "A".
If you load a custom structure without PDB or UniProt ID, you can open "Seq. & Annotations" window and find the chain ID such as "stru_A". The part before the underscore is the structure ID, which can be used to specify the mutation such as "stru_A_...". Remember to choose "Show Mutation in: Current Page".
',s+="
Mutations:
"+e.htmlCls.inputTextStr+"id='"+e.pre+"mutationids' value='6M0J_E_484_K,6M0J_E_501_Y,6M0J_E_417_N' size=50>
",s+="
ID Type : ",s+='
PDB ID',s+='
AlphaFold UniProt ID
',s+="
Show Mutation in : ",s+='
Current Page',s+='
New Page
',s+=e.htmlCls.buttonStr+"reload_mutation_3d' title='Show the mutations in 3D using the scap program'>3D with scap",s+=e.htmlCls.buttonStr+"reload_mutation_inter' style='margin-left:20px' title='Show the mutations in 3D and the change of interactions'>Interactions",s+=e.htmlCls.buttonStr+"reload_mutation_pdb' style='margin-left:20px' title='Show the mutations in 3D and export the PDB of the mutant within 10 angstrom'>PDB",s+="
",s+=e.htmlCls.optionStr+"'pdb' selected>PDB",s+=e.htmlCls.optionStr+"'mmcif'>mmCIF",s+=e.htmlCls.optionStr+"'mol2'>Mol2",s+=e.htmlCls.optionStr+"'sdf'>SDF",s+=e.htmlCls.optionStr+"'xyz'>XYZ",s+=e.htmlCls.optionStr+"'icn3dpng'>iCn3D PNG",s+=e.htmlCls.optionStr+"'pae'>AlphaFold PAE",s+=" Note : The "biological unit " is the biochemically active form of a biomolecule ,
',s+=e.htmlCls.divStr+"asu_bu' style='display:none;'>",s+='which can range from a monomer (single protein molecule) to an oligomer of 100+ protein molecules.asymmetric unit " is the raw 3D structure data resolved by X-ray crystallography, NMR, or Cryo-electron microscopy. The asymmetric unit is equivalent to the biological unit in approximately 60% of structure records. In the remaining 40% of the records, the asymmetric unit represents a portion of the biological unit that can be reconstructed using crystallographic symmetry, or it represents multiple copies of the biological unit.',s+="",s+=e.htmlCls.divStr+"dl_mmdbafid' class='"+n+"' style='max-width:600px'>",s+=this.addNotebookTitle("dl_mmdbafid","Please input a list of PDB/AlphaFold IDs"),s+="List of PDB, MMDB, or AlphaFold UniProt structures: "+e.htmlCls.inputTextStr+"id='"+e.pre+"mmdbafid' placeholder='e.g., 1HHO,4N7N,P69905,P01942' size=30>
"+e.htmlCls.buttonStr+"reload_mmdbaf' style='width:150px'>Load Biological Unit"+e.htmlCls.buttonStr+"reload_mmdbaf_asym' style='margin-left:30px; width:250px'>Load Asymmetric Unit (All Chains)or
"+e.htmlCls.buttonStr+"reload_mmdbaf_append' style='width:150px'>Append Biological Unit"+e.htmlCls.buttonStr+"reload_mmdbaf_asym_append' style='margin-left:30px; width:250px'>Append Asymmetric Unit (All Chains)Note : The "biological unit " is the biochemically active form of a biomolecule ,
',s+=e.htmlCls.divStr+"asu_bu2' style='display:none;'>",s+='which can range from a monomer (single protein molecule) to an oligomer of 100+ protein molecules.asymmetric unit " is the raw 3D structure data resolved by X-ray crystallography, NMR, or Cryo-electron microscopy. The asymmetric unit is equivalent to the biological unit in approximately 60% of structure records. In the remaining 40% of the records, the asymmetric unit represents a portion of the biological unit that can be reconstructed using crystallographic symmetry, or it represents multiple copies of the biological unit.',s+="",s+=e.htmlCls.divStr+"dl_blast_rep_id' style='max-width:600px;' class='"+n+"'>",s+=this.addNotebookTitle("dl_blast_rep_id","Align sequence to structure"),s+="Enter a Sequence ID (or FASTA sequence) and the aligned protein accession, which can be found using the BLAST search with the Sequence ID or FASTA sequence as input. If the protein accession is not a PDB chain, the corresponding AlphaFold UniProt structure is used.Sequence ID (NCBI protein accession of a sequence): "+e.htmlCls.inputTextStr+"id='"+e.pre+"query_id' value='NP_001108451.1' size=8>NCBI protein accession (or a chain of a PDB): "+e.htmlCls.inputTextStr+"id='"+e.pre+"blast_rep_id' value='1TSR_A' size=8>ESM Metagenomic Atlas . The sequence should be less than 400 characters. For any sequence longer than 400, please see the discussion here .Note : Always load a PDB file before loading DSN6 files. 2fofc contour at: ";let a=["0","0.5","1","1.5","2","3","4","5","6","7","8","9","10"];s+=e.htmlCls.setHtmlCls.getOptionHtml(a,3),s+=" σ fofc contour at: ",s+=e.htmlCls.setHtmlCls.getOptionHtml(a,5),s+=" σ Note : Always load a PDB file before loading DSN6 files. 2fofc contour at: ",s+=e.htmlCls.setHtmlCls.getOptionHtml(a,3),s+=" σ fofc contour at: ",s+=e.htmlCls.setHtmlCls.getOptionHtml(a,5),s+=" σ ",s+=" "+e.htmlCls.space3,s+=e.htmlCls.buttonStr+"applysymmetry'>Apply"+e.htmlCls.space3,s+=e.htmlCls.buttonStr+"clearsymmetry'>Clear",s+="",s+=e.htmlCls.divStr+"dl_symd' style='max-width:400px' class='"+n+"'>Distance: ",s+=e.htmlCls.setHtmlCls.getOptionHtml(["4","5","6","7","8","9","10"],4),s+=" ",s+="Contact Type: ",s+=e.htmlCls.optionStr+"'calpha' >between C-alpha Atoms",s+=e.htmlCls.optionStr+"'cbeta' selected>between C-beta Atoms",s+=e.htmlCls.optionStr+"'heavyatoms' >between Heavy Atoms",s+=" "+e.htmlCls.buttonStr+"applycontactmap'>Display ",s+=""+e.htmlCls.inputCheckStr+"id='"+e.pre+"analysis_hbond' checked>Hydrogen Bonds "+e.htmlCls.space3+" ",s+="",s+=e.htmlCls.divNowrapStr+" ";let d=["3.2","3.3","3.4","3.5","3.6","3.7","3.8","3.9","4.0","4.1","4.2"];s+=e.htmlCls.setHtmlCls.getOptionHtml(d,6),s+=" Å"+e.htmlCls.space3+" ",s+=""+e.htmlCls.inputCheckStr+"id='"+e.pre+"analysis_saltbridge' checked>Salt Bridge/Ionic "+e.htmlCls.space3+" ",s+="",s+=e.htmlCls.divNowrapStr+" ";let c=["3","4","5","6","7","8"];s+=e.htmlCls.setHtmlCls.getOptionHtml(c,3),s+=" Å"+e.htmlCls.space3+" ",s+=""+e.htmlCls.inputCheckStr+"id='"+e.pre+"analysis_contact' checked>Contacts/Interactions "+e.htmlCls.space3+" ",s+="",s+=e.htmlCls.divNowrapStr+" ",s+=e.htmlCls.setHtmlCls.getOptionHtml(c,1),s+=" Å"+e.htmlCls.space3+" ",s+=" ",s+="",s+=""+e.htmlCls.inputCheckStr+"id='"+e.pre+"analysis_halogen' checked>Halogen Bonds "+e.htmlCls.space3+" ",s+="",s+=e.htmlCls.divNowrapStr+" ",s+=e.htmlCls.setHtmlCls.getOptionHtml(d,6),s+=" Å"+e.htmlCls.space3+" ",s+=""+e.htmlCls.inputCheckStr+"id='"+e.pre+"analysis_pication' checked>π-Cation "+e.htmlCls.space3+" ",s+="",s+=e.htmlCls.divNowrapStr+" ",s+=e.htmlCls.setHtmlCls.getOptionHtml(c,3),s+=" Å"+e.htmlCls.space3+" ",s+=""+e.htmlCls.inputCheckStr+"id='"+e.pre+"analysis_pistacking' checked>π-Stacking "+e.htmlCls.space3+" ",s+="",s+=e.htmlCls.divNowrapStr+" ",s+=e.htmlCls.setHtmlCls.getOptionHtml(["3","4","5"],99),s+=e.htmlCls.optionStr+"'5.5' selected>5.5",s+=e.htmlCls.setHtmlCls.getOptionHtml(["6","7","8"],99),s+=" Å"+e.htmlCls.space3+" ",s+="
",s+=e.htmlCls.divNowrapStr+"2. Select the first set:",s+="",s+="
",s+=" ",s+=e.htmlCls.divNowrapStr+"3. Select the second set:",s+="",s+="
",s+="
",s+="4. "+e.htmlCls.buttonStr+"applyhbonds'>3D Display Interactions
"+e.htmlCls.buttonStr+"hbondWindow'>Highlight Interactions in TableSort Interactions on : "+e.htmlCls.buttonStr+"sortSet1'> Set 1"+e.htmlCls.buttonStr+"sortSet2' style='margin-left:12px'>Set 2
"+e.htmlCls.buttonStr+"hbondLineGraph'>2D Interaction Network "+e.htmlCls.buttonStr+"hbondLineGraph2' style='margin-left:12px'>2D Network with Reference Numbers to show two lines of residue nodes
"+e.htmlCls.buttonStr+"hbondScatterplot'>2D Interaction Map "+e.htmlCls.buttonStr+"hbondScatterplot2' style='margin-left:12px'>2D Map with Reference Numbers to show map
Helix or Sheet'+r+e.pre+'dist_ss" size="4" value="100"> ',s+="Coil or Nucleotide"+r+e.pre+'dist_coil" size="4" value="50"> ',s+="Disulfide Bonds"+r+e.pre+'dist_ssbond" size="4" value="50"> Hydrogen Bonds"+r+e.pre+'dist_hbond" size="4" value="50"> ',s+="Salt Bridge/Ionic"+r+e.pre+'dist_ionic" size="4" value="50"> ',s+="Contacts"+r+e.pre+'dist_inter" size="4" value="25"> Halogen Bonds"+r+e.pre+'dist_halogen" size="4" value="50"> ',s+="π-Cation"+r+e.pre+'dist_pication" size="4" value="50"> ',s+="π-Stacking"+r+e.pre+'dist_pistacking" size="4" value="50">
(Note: you can also adjust thresholds at #1 to add/remove interactions.)
"+e.htmlCls.buttonStr+"areaWindow'>Buried Surface Area
5. "+e.htmlCls.buttonStr+"hbondReset'>Reset and select new sets
",s+="",s+=e.htmlCls.divStr+"dl_realign' class='"+n+"'>",s+=this.addNotebookTitle("dl_realign","Realign by sequence"),s+=e.htmlCls.divNowrapStr+"1. Select sets below ",s+="
2. "+e.htmlCls.buttonStr+"applyRealign'>Realign by Sequence
1 . Select sets below or use your current selection.
",s+="
2 . "+e.htmlCls.buttonStr+"applyRealignByStruct_tmalign'>Realign with TM-align"+e.htmlCls.buttonStr+"applyRealignByStruct' style='margin-left:30px'>Realign with VAST
",s+="
3. "+e.htmlCls.buttonStr+"applyRealignByStruct_vastplus'>VAST+ Alignment based on TM-align
",s+="
",s+="2. "+e.htmlCls.buttonStr+"applyColorSpectrumAcrossSets'>Spectrum Color for Sets
",s+="
",s+="2. "+e.htmlCls.buttonStr+"applyColorSpectrumBySets'>Spectrum Color for Residues in Sets
",s+="
",s+="2. "+e.htmlCls.buttonStr+"applyColorRainbowAcrossSets'>Rainbow Color for Sets
",s+="
",s+="2. "+e.htmlCls.buttonStr+"applyColorRainbowBySets'>Rainbow Color for Residues in Sets
',s+=e.htmlCls.space2+"Hold Ctrl key to select multiple nodes/lines.",s+=e.htmlCls.divStr+"dl_linegraphcolor' style='display:block;'>",s+=e.htmlCls.setHtmlCls.setColorHints(),s+="Scale : ";let h=["0.1","0.2","0.4","0.6","0.8","1","2","4","6","8","10"];s+=e.htmlCls.setHtmlCls.getOptionHtml(h,5),s+="
',s+="",s+=e.htmlCls.divStr+"dl_scatterplot' style='background-color:white' class='"+n+"'>",s+=this.addNotebookTitle("dl_scatterplot","2D Interaction Map"),s+=e.htmlCls.divNowrapStr+"Hold Ctrl key to select multiple nodes."+e.htmlCls.space3,s+='
',s+=e.htmlCls.divStr+"dl_scatterplotcolor' style='display:none;'>",s+=e.htmlCls.setHtmlCls.setColorHints(),s+="",e.scatterplotid=e.pre+"scatterplot",s+=e.htmlCls.divNowrapStr+l+e.scatterplotid+'_svg">SVG'+e.htmlCls.space2,s+=l+e.scatterplotid+'_png">PNG'+e.htmlCls.space2,s+=l+e.scatterplotid+'_json">JSON'+e.htmlCls.space4,s+="Scale : ",s+=e.htmlCls.setHtmlCls.getOptionHtml(h,5),s+="
',s+="",s+=e.htmlCls.divStr+"dl_contactmap' style='background-color:white' class='"+n+"'>",s+=this.addNotebookTitle("dl_contactmap","Contact Map"),s+=e.htmlCls.divNowrapStr+"Hold Ctrl key to select multiple nodes."+e.htmlCls.space3+"",e.contactmapid=e.pre+"contactmap",s+=e.htmlCls.divNowrapStr+l+e.contactmapid+'_svg">SVG'+e.htmlCls.space2,s+=l+e.contactmapid+'_png">PNG'+e.htmlCls.space2,s+=l+e.contactmapid+'_json">JSON'+e.htmlCls.space4,s+="Scale : ";let p=["0.01","0.02","0.04","0.06","0.08","0.1","0.2","0.4","0.6","0.8","1"];s+=e.htmlCls.setHtmlCls.getOptionHtml(p,10),s+="
',s+="",s+=e.htmlCls.divStr+"dl_alignerrormap' style='background-color:white' class='"+n+"'>",s+=this.addNotebookTitle("dl_alignerrormap","PAE Map"),s+=e.htmlCls.divNowrapStr+"Hold Ctrl key to select multiple nodes."+e.htmlCls.space3+"",e.alignerrormapid=e.pre+"alignerrormap",s+=e.htmlCls.divNowrapStr+l+e.alignerrormapid+'_svg">SVG'+e.htmlCls.space2,s+=l+e.alignerrormapid+'_png">PNG (slow)'+e.htmlCls.space2,s+=l+e.alignerrormapid+'_json">JSON'+e.htmlCls.space4,s+='Scale : ',s+=e.htmlCls.setHtmlCls.getOptionHtml(p,2),s+="
",s+="
0 5 10 15 20 25 30 Expected position error (Angstroms)
',s+="",s+=e.htmlCls.divStr+"dl_elecmap2fofc' class='"+n+"'>",s+=this.addNotebookTitle("dl_elecmap2fofc","Electron Density 2F0-Fc Map"),s+="Contour at: ",s+=e.htmlCls.setHtmlCls.getOptionHtml(a,3),s+=" σ "+e.htmlCls.buttonStr+"applymap2fofc'>Display "+e.htmlCls.buttonStr+"elecmapNo2'>Remove Map ",s+="",s+=e.htmlCls.divStr+"dl_elecmapfofc' class='"+n+"'>",s+=this.addNotebookTitle("dl_elecmapfofc","Electron Density F0-Fc Map"),s+="Contour at: ",s+=e.htmlCls.setHtmlCls.getOptionHtml(a,5),s+=" σ "+e.htmlCls.buttonStr+"applymapfofc'>Display "+e.htmlCls.buttonStr+"elecmapNo3'>Remove Map ",s+="",s+=e.htmlCls.divStr+"dl_emmap' class='"+n+"'>",s+=this.addNotebookTitle("dl_emmap","EM Density Map"),s+="Contour at: ",s+=e.htmlCls.setHtmlCls.getOptionHtml(["0","10","20","30","40","50","60","70","80","90","100"],3),s+=" % of maximum EM values "+e.htmlCls.buttonStr+"applyemmap'>Display "+e.htmlCls.buttonStr+"emmapNo2'>Remove EM Map ",s+="",s+=e.htmlCls.divStr+"dl_aroundsphere' class='"+n+"'>",s+=this.addNotebookTitle("dl_aroundsphere","Select a sphere around a set of residues"),s+=e.htmlCls.divNowrapStr+"1. Select the first set:",s+="",s+="
",s+="
"+e.htmlCls.buttonStr+"sphereExport'>Save interacting/contacting residue pairs in a file
",s+="",s+=e.htmlCls.divStr+"dl_adjustmem' class='"+n+"'>",s+=this.addNotebookTitle("dl_adjustmem","Adjust membranes"),s+="Note : The membranes are parallel to the X-Y plane. The center of the membranes is at Z = 0. Note : The membranes are parallel to the X-Y plane. The center of the membranes is at Z = 0. ",s+=e.htmlCls.divNowrapStr+"First set:",s+="",s+="
",s+=" ",s+=e.htmlCls.divNowrapStr+"Second set:",s+="",s+="
",s+="
",s+=e.htmlCls.spanNowrapStr+"2. Color: "+e.htmlCls.inputTextStr+"id='"+e.pre+"distancecolor2' value='"+"#ffff00' size=4>",s+=e.htmlCls.divNowrapStr+"First set:",s+="",s+="
",s+=" ",s+=e.htmlCls.divNowrapStr+"Second set:",s+="",s+="
",s+="
",s+=e.htmlCls.divNowrapStr+"2. Line style: ",s+=e.htmlCls.setHtmlCls.getOptionHtml(["Solid","Dashed"],0),s+=" ",s+=e.htmlCls.setHtmlCls.getOptionHtml(["1.0","0.9","0.8","0.7","0.6","0.5","0.4","0.3","0.2","0.1"],7),s+=" ",s+="
",s+=e.htmlCls.setHtmlCls.getOptionHtml(["Sphere","Cube"],0),s+=" ",s+=e.htmlCls.setHtmlCls.getOptionHtml(["1.0","0.9","0.8","0.7","0.6","0.5","0.4","0.3","0.2","0.1"],7),s+=" ",s+=e.htmlCls.divNowrapStr+"First sets:",s+="",s+="
",s+=" ",s+=e.htmlCls.divNowrapStr+"Second sets:",s+="",s+="
",s+="
",s+=e.htmlCls.spanNowrapStr+"2. "+e.htmlCls.buttonStr+"applydisttable'>Distances in Table",s+="",s+=e.htmlCls.divStr+"dl_stabilizer_rm' class='"+n+"'>",s+=this.addNotebookTitle("dl_stabilizer_rm","Remove a stabilizer"),e.utilsCls.isMobile()?s+=e.htmlCls.spanNowrapStr+"1. Touch TWO atomsNote : The following parameters will be saved in cache. You just need to set them once. Note: The full protein sequences with gaps in MSA are listed one by one. The sequence of the structure is listed at the top. Each sequence has a title line starting with \">\".
Precalculated Multiple Sequence Alignment (MSA) :Position of the first residue in Sequences & Annotations window : "+e.htmlCls.inputTextStr+"id='"+e.pre+"fasta_startpos' value='1' size=2> ",s+=e.htmlCls.optionStr+"'identity' selected>Identity",s+=e.htmlCls.optionStr+"'conservation'>Conservation",s+=" Note: Show exons for all isoforms of the protein in the same gene as specified below.
NCBI Gene IDPosition of the first residue in Sequences & Annotations window : "+e.htmlCls.inputTextStr+"id='"+e.pre+"fasta_startpos2' value='1' size=2> Save Clear URLs Used in Browsers iCn3D GitHub )Commands Used in Jupyter Noteboook Show All Chains Zoom : mouse wheel; "+e.htmlCls.space3+" Move : left button; "+e.htmlCls.space3+" Select Multiple Nodes : Ctrl Key and drag an Area"+e.htmlCls.space3,s+='
',s+=e.htmlCls.divStr+"dl_svgcolor' style='display:none;'>",s+=e.htmlCls.divNowrapStr+'Click "View > H-Bonds & Interactions" to adjust parameters and relaunch the graph ',s+=e.htmlCls.divNowrapStr+'Green : H-Bonds; ',s+='Cyan : Salt Bridge/Ionic; ',s+='Grey : contacts; ',s+='Orange : disulfide bonds',s+=e.htmlCls.divNowrapStr+'Magenta : Halogen Bonds; ',s+='Red : π-Cation; ',s+='Blue : π-Stacking',s+="",s+=e.htmlCls.divNowrapStr+l+e.svgid+'_svg">SVG'+e.htmlCls.space2,s+=l+e.svgid+'_png">PNG'+e.htmlCls.space2,s+=l+e.svgid+'_json">JSON',s+=e.htmlCls.space3+"Force on Nodes : ",s+=e.htmlCls.optionStr+"'0'>No",s+=e.htmlCls.optionStr+"'1'>X-axis",s+=e.htmlCls.optionStr+"'2'>Y-axis",s+=e.htmlCls.optionStr+"'3'>Circle",s+=e.htmlCls.optionStr+"'4' selected>Random",s+="
",s+=e.htmlCls.space3+"Label Size : ",r="icn3d-node-text",s+=e.htmlCls.optionStr+"'"+r+"0'>No",s+=e.htmlCls.optionStr+"'"+r+"4'>4px",s+=e.htmlCls.optionStr+"'"+r+"8' selected>8px",s+=e.htmlCls.optionStr+"'"+r+"12'>12px",s+=e.htmlCls.optionStr+"'"+r+"16'>16px",s+=e.htmlCls.optionStr+"'"+r+"24'>24px",s+=e.htmlCls.optionStr+"'"+r+"32'>32px",s+=" ",s+=e.htmlCls.space3+"Internal Edges : ",s+=e.htmlCls.optionStr+"'1' selected>Hide",s+=e.htmlCls.optionStr+"'0'>Show",s+="
",s+="",s+='EDTSurf algorithm : Toal : "+e.htmlCls.inputTextStr+"id='"+e.pre+"areavalue' value='' size='10'> Å2
",s+="",s+=e.htmlCls.divStr+"dl_colorbyarea' class='"+n+"'>",s+=this.addNotebookTitle("dl_colorbyarea","Color by surface area"),s+="Color each residue based on the percentage of solvent accessilbe surface area. The color ranges from blue, to white, to red for a percentage of 0, 35(variable), and 100, respectively.
Middle Percentage(White) : "+e.htmlCls.inputTextStr+"id='"+e.pre+"midpercent' value='35' size='10'>% Color Select residue based on the percentage of solvent accessilbe surface area. The values are in the range of 0-100.
Min Percentage : "+e.htmlCls.inputTextStr+"id='"+e.pre+"minpercentout' value='0' size='10'>% Max Percentage : "+e.htmlCls.inputTextStr+"id='"+e.pre+"maxpercentout' value='100' size='10'>% Apply Select residue based on B-factor/pLDDT. The values are in the range of 0-100.
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t=this.icn3dui,s=t.icn3d,i=e?"pdbfile_app":"pdbfile";s.bInitial=!0,t.cfg.notebook||dialog.dialog("close"),t.cfg.notebook?s.resizeCanvasCls.closeDialogs():$(".ui-dialog-content").dialog("close");let n=$("#"+t.pre+i)[0].files;n[0]?(t.htmlCls.setHtmlCls.fileSupport(),s.molTitle="",s.dataStrAll="",this.readFile(e,n,0,""),e&&(s.bSetChainsAdvancedMenu&&s.definedSetsCls.showSets(),s.bAnnoShown&&await s.showAnnoCls.showAnnotations())):alert("Please select a file before clicking 'Load'")}saveHtml(e){let t=this.icn3dui.icn3d,s="";s+='0?"_blank":"_self";window.open(i+"?"+l+"="+r+"&command=scap interaction "+o,a)}})),e.myEventCls.onIds("#"+e.pre+"reload_mmcif","click",(function(t){let n=e.icn3d;t.preventDefault(),e.cfg.notebook||dialog.dialog("close"),s.setLogCmd("load mmcif "+$("#"+e.pre+"mmcifid").val(),!1);let l=n.structures&&Object.keys(n.structures).length>0?"_blank":"_self";window.open(i+"?mmcifid="+$("#"+e.pre+"mmcifid").val(),l)})),e.myEventCls.onIds("#"+e.pre+"mmcifid","keyup",(function(t){let n=e.icn3d;if(13===t.keyCode){t.preventDefault(),e.cfg.notebook||dialog.dialog("close"),s.setLogCmd("load mmcif "+$("#"+e.pre+"mmcifid").val(),!1);let l=n.structures&&Object.keys(n.structures).length>0?"_blank":"_self";window.open(i+"?mmcifid="+$("#"+e.pre+"mmcifid").val(),l)}})),e.myEventCls.onIds("#"+e.pre+"reload_mmdb","click",(function(t){let n=e.icn3d;t.preventDefault(),s.setLogCmd("load mmdb1 "+$("#"+e.pre+"mmdbid").val(),!1);let l=n.structures&&Object.keys(n.structures).length>0?"_blank":"_self";window.open(i+"?mmdbid="+$("#"+e.pre+"mmdbid").val()+"&bu=1",l)})),e.myEventCls.onIds("#"+e.pre+"reload_mmdb_asym","click",(function(t){let n=e.icn3d;t.preventDefault(),s.setLogCmd("load mmdb0 "+$("#"+e.pre+"mmdbid").val(),!1);let l=n.structures&&Object.keys(n.structures).length>0?"_blank":"_self";window.open(i+"?mmdbid="+$("#"+e.pre+"mmdbid").val()+"&bu=0",l)})),e.myEventCls.onIds("#"+e.pre+"reload_mmdbaf","click",(function(t){e.icn3d,t.preventDefault();let n=$("#"+e.pre+"mmdbafid").val();s.launchMmdb(n,1,i)})),e.myEventCls.onIds("#"+e.pre+"reload_mmdbaf_asym","click",(function(t){e.icn3d,t.preventDefault();let n=$("#"+e.pre+"mmdbafid").val();s.launchMmdb(n,0,i)})),e.myEventCls.onIds("#"+e.pre+"reload_mmdbaf_append","click",(function(t){e.icn3d,t.preventDefault();let n=$("#"+e.pre+"mmdbafid").val();s.launchMmdb(n,1,i,!0)})),e.myEventCls.onIds("#"+e.pre+"reload_mmdbaf_asym_append","click",(function(t){e.icn3d,t.preventDefault();let n=$("#"+e.pre+"mmdbafid").val();s.launchMmdb(n,0,i,!0)})),e.myEventCls.onIds("#"+e.pre+"mmdbid","keyup",(function(t){let n=e.icn3d;if(13===t.keyCode){t.preventDefault(),s.setLogCmd("load mmdb1 "+$("#"+e.pre+"mmdbid").val(),!1);let l=n.structures&&Object.keys(n.structures).length>0?"_blank":"_self";window.open(i+"?mmdbid="+$("#"+e.pre+"mmdbid").val()+"&bu=1",l)}})),e.myEventCls.onIds("#"+e.pre+"mmdbafid","keyup",(function(t){if(e.icn3d,13===t.keyCode){t.preventDefault();let n=$("#"+e.pre+"mmdbafid").val();s.launchMmdb(n,1,i)}})),e.myEventCls.onIds("#"+e.pre+"reload_blast_rep_id","click",(function(t){let n=e.icn3d;t.preventDefault(),e.cfg.notebook||dialog.dialog("close");let l=$("#"+e.pre+"query_id").val(),r=encodeURIComponent($("#"+e.pre+"query_fasta").val()),o=$("#"+e.pre+"blast_rep_id").val();s.setLogCmd("load seq_struct_ids "+l+","+o,!1),l=""!==l&&void 0!==l?l:r;let a=n.structures&&Object.keys(n.structures).length>0?"_blank":"_self";window.open(i+"?from=icn3d&alg=blast&blast_rep_id="+o+"&query_id="+l+"&command=view annotations; set annotation cdd; set annotation site; set view detailed view; select chain "+o+"; show selection",a)})),e.myEventCls.onIds("#"+e.pre+"run_esmfold","click",(async function(t){let i=e.icn3d;t.preventDefault(),e.cfg.notebook||dialog.dialog("close"),$("#"+e.pre+"dl_mmdbafid").hasClass("ui-dialog-content")&&$("#"+e.pre+"dl_mmdbafid").dialog("close");let n=$("#"+e.pre+"esmfold_fasta").val(),l="stru--";if(-1!=n.indexOf(">")){let e=n.indexOf("\n");if(i.esmTitle=n.substr(1,e-1).trim(),-1!=i.esmTitle.indexOf("|")){let e=i.esmTitle.split("|");l=e.length>2?e[1]:i.esmTitle}else l=-1!=i.esmTitle.indexOf(" ")?i.esmTitle.substr(0,i.esmTitle.indexOf(" ")):i.esmTitle;l.length<6&&(l=l.padEnd(6,"-")),n=n.substr(e+1)}if(n=n.replace(/\s/g,""),n.length>400)return void alert("Your sequence is larger than 400 characters. 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"+i,!0)})),$(document).on("click",".icn3d-hideicon",(function(t){let s=e.icn3d;t.stopImmediatePropagation();let i=$(this).attr("pid");if(!e.cfg.notebook)if(void 0===s.dialogHashHideDone&&(s.dialogHashHideDone={}),void 0===s.dialogHashPosToRight&&(s.dialogHashPosToRight={}),s.dialogHashHideDone.hasOwnProperty(i)){let e=s.dialogHashHideDone[i].width,t=s.dialogHashHideDone[i].height,n=s.dialogHashHideDone[i].position;$("#"+i).dialog("option","width",e),$("#"+i).dialog("option","height",t),$("#"+i).dialog("option","position",n),delete s.dialogHashHideDone[i]}else{s.dialogHashHideDone[i]={width:$("#"+i).dialog("option","width"),height:$("#"+i).dialog("option","height"),position:$("#"+i).dialog("option","position")};let e,t=160,n=80;$("#"+i).dialog("option","width",t),$("#"+i).dialog("option","height",n),s.dialogHashPosToRight.hasOwnProperty(i)?e=s.dialogHashPosToRight[i]:(e=Object.keys(s.dialogHashPosToRight).length*(t+10),s.dialogHashPosToRight[i]=e);let l={my:"right bottom",at:"right-"+e+" bottom+60",of:"#"+s.divid,collision:"none"};$("#"+i).dialog("option","position",l)}})),$(document).on("click","."+e.pre+"selres",(function(t){let i=e.icn3d;t.stopImmediatePropagation(),i.bSelOneRes=!1;let n=$("."+e.pre+"seloneres");for(let e=0,t=n.length;e0&&(r+=" or "),r+=i.selectionCls.selectOneResid(t)}i.hlUpdateCls.updateHlAll(),s.setLogCmd(r,!0)})),$(document).on("click","."+e.pre+"seloneres",(function(t){let s=e.icn3d;t.stopImmediatePropagation(),s.bSelOneRes||(s.hAtoms={},s.selectedResidues={},s.bSelOneRes=!0);let i=$(this).attr("resid"),n=$(this).attr("id");$("#"+n).length&&$("#"+n)[0].checked?s.selectionCls.selectOneResid(i):$("#"+n).length&&!$("#"+n)[0].checked&&s.selectionCls.selectOneResid(i,!0),s.hlUpdateCls.updateHlAll()})),$(document).on("click","."+e.pre+"selset",(async function(t){let i=e.icn3d;t.stopImmediatePropagation(),i.bSelOneRes=!1;let n=$("."+e.pre+"seloneres");for(let e=0,t=n.length;e0))return{sequencesHtml:a,maxSeqCnt:d};c[s]=1}let h,p=void 0===t||t;p&&(o.hAtoms={});let m,u,g=0,f=0;for(let t=0,l=e.length;t0?m:l,p&&(o.hAtoms=r.hashUtilsCls.unionHash(o.hAtoms,o.alnChains[l]));let b=[],C="",y=void 0!==o.alnChainsSeq[l]?o.alnChainsSeq[l].length:0;y>d&&(d=y);let v,_,w=u.indexOf("_"),S=u.substr(0,w),A=u.substr(w+1);for(let e=0,t=y;e=0;--e)if("-"!=o.alnChainsSeq[l][e].resn){_=o.alnChainsSeq[l][e].resi;break}C+=""+v+" ",h=!(void 0===e||!c.hasOwnProperty(u));for(let e=0,t=y;e"}""!==a?-1!=o.alnChainsSeq[l][e].resi?C+=""+o.alnChainsSeq[l][e].resn+" ":C+=""+o.alnChainsSeq[l][e].resn+" ":C+=""+o.alnChainsSeq[l][e].resn+" "}C+=""+_+" ";let x=e.length,k=void 0!==o.alnChainsAnno[l]?o.alnChainsAnno[l].length:0;for(let t=0,s=k;t";for(let e=0,i=o.alnChainsAnno[l][t].length;e ':' ';else if("E"==i)if(void 0!==o.alnChainsSeq[s][e]){let i=s+"_"+o.alnChainsSeq[s][e].resi;if(o.residues.hasOwnProperty(i)){o.firstAtomObjCls.getFirstCalphaAtomObj(o.residues[i]).ssend?b[t]+=' ':b[t]+=' '}else b[t]+=' '}else b[t]+=' ';else b[t]+="c"==i?' ':"o"==i?' ':""+i+" "}b[t]+="'+O+'
'+C+" "+t+" "+t+" "}getMenuUrl(e,t,s,i,n){let l=this.icn3dui;return l.icn3d,l.htmlCls.allMenus[e]=s,n&&(l.htmlCls.allMenusSel[e]=n),i&&(l.htmlCls.simpleMenus[e]=1),""+s+" "+t+" "+t+" "}getRadio(e,t,s,i,n,l){let r=this.icn3dui;r.icn3d,r.htmlCls.allMenus[t]=s,l&&(r.htmlCls.allMenusSel[t]=l),n&&(r.htmlCls.simpleMenus[t]=1);let o=i?" checked":"";return""+r.htmlCls.inputRadioStr+"name='"+r.pre+e+"' class='"+r.pre+e+"' v='"+s+"'"+o+">"+s+" "+o.htmlCls.inputRadioStr+"name='"+o.pre+e+"'"+a+">"+o.htmlCls.space3+" "+s+" ",n+="Select: "+t.htmlCls.inputTextStr+"id='"+t.pre+"command"+s+"' placeholder='$[structures].[chains]:[residues]@[atoms]' size='60'> Name: "+t.htmlCls.inputTextStr+"id='"+t.pre+"command_name"+s+"' placeholder='my_selection' size='60'> "+t.htmlCls.space3+t.htmlCls.buttonStr+"command_apply"+s+"'>Save Selection to Defined Sets
",n+='Specification Tips:
Specification: In the selection "$1HHO,4N7N.A,B,C:5-10,LV,3AlaVal,chemicals@CA,C,C*":',n+='"$1HHO,4N7N" uses "$" to indicate structure selection. ".A,B,C" uses "." to indicate chain selection. ":5-10,LV,3LeuVal,chemicals" uses the colon ":" to indicate residue selection. Residue selection could be residue number(5-10), one-letter IUPAC residue name abbreviations(LV), three-letter residue names(AlaVal, "3" indicates each residue name has three letters), or predefined names: "proteins", "nucleotides", "chemicals", "ions", and "water". IUPAC abbreviations can be written either as a contiguous string(e.g., ":LV"), in order to find all instances of that sequence in the structure, or they can be separated by commas(e.g., ":L,V") to select all residues of a given type in the structure(in the latter case, select all Leucine and Valine in the structure). "@CA,C,C*" uses "@" to indicate atom name selection. "C*" selects any atom names starting with "C". Partial definition is allowed, e.g., ":1-10" selects all residue IDs 1-10 in all chains. Different selections can be unioned(with "or ", default), intersected(with "and "), or negated(with "not "). For example, ":1-10 or :K" selects all residues 1-10 and all Lys residues. ":1-10 and :K" selects all Lys residues in the range of residue number 1-10. ":1-10 or not :K" selects all residues 1-10, which are not Lys residues. The wild card character "X" or "x" can be used to represent any character.',n+=" Set Operation: ",n+='Users can select multiple sets in the menu "Select > Defined Sets". Different sets can be unioned(with "or ", default), intersected(with "and "), or negated(with "not "). For example, if the "Defined Sets" menu has four sets ":1-10", ":11-20", ":5-15", and ":7-8", the command "saved atoms :1-10 or :11-20 and :5-15 not :7-8" unions all residues 1-10 and 11-20 to get the residues 1-20, then intersects with the residues 5-15 to get the residues 5-15, then exclude the residues 7-8 to get the final residues 5-6 and 9-15. Full commands in url or command window: ",n+="Select without saving the set: select $1HHO,4N7N.A,B,C:5-10,LV,chemicals@CA,C,C* Select and save: select $1HHO,4N7N.A,B,C:5-10,LV,chemicals@CA,C,C* | name my_name
",n+="",n}getOptionHtml(e,t){let s=this.icn3dui;s.icn3d;let i="";for(let n=0,l=e.length;n"+l+"":s.htmlCls.optionStr+"'"+l+"'>"+l+""}return i}setColorHints(){let e=this.icn3dui;e.icn3d;let t="";return t+=e.htmlCls.divNowrapStr+'Green : H-Bonds; ',t+='Cyan : Salt Bridge/Ionic; ',t+='Grey : contacts',t+=e.htmlCls.divNowrapStr+'Magenta : Halogen Bonds; ',t+='Red : π-Cation; ',t+='Blue : π-Stacking',t}setThicknessHtml(e){let t=this.icn3dui,s=t.icn3d,i="",n="3dprint"==e?"1":"0.1",l="3dprint"==e?"1.2":"0.3",r="3dprint"==e?"0.8":"0.4",o="3dprint"==e?"0.8":"0.4",a="3dprint"==e?"1":"0.4",d="3dprint"==e?"0.6":"0.3",c="3dprint"==e?"1":"0.2",h="3dprint"==e?"2":"1.3",p="3dprint"==e?"1.4":"0.8",m=40,u=.8,g=.4,f=.2,b=0,C=1,y=0;if("style"==e){if(""!=this.getCookie("shininess")&&(m=parseFloat(this.getCookie("shininess"))),""!=this.getCookie("light1")&&(u=parseFloat(this.getCookie("light1")),g=parseFloat(this.getCookie("light2")),f=parseFloat(this.getCookie("light3"))),""!=this.getCookie("lineRadius")){n=parseFloat(this.getCookie("lineRadius")),l=parseFloat(this.getCookie("coilWidth")),r=parseFloat(this.getCookie("cylinderRadius"));let e=this.getCookie("crosslinkRadius");o=isNaN(e)?s.crosslinkRadius:parseFloat(e),a=parseFloat(this.getCookie("traceRadius")),d=parseFloat(this.getCookie("dotSphereScale")),c=parseFloat(this.getCookie("ribbonthickness")),h=parseFloat(this.getCookie("helixSheetWidth")),p=parseFloat(this.getCookie("nucleicAcidWidth"))}""!=this.getCookie("glycan")&&(b=parseFloat(this.getCookie("glycan"))),""!=this.getCookie("membrane")&&(C=parseFloat(this.getCookie("membrane"))),""!=this.getCookie("cmdwindow")&&(y=parseFloat(this.getCookie("cmdwindow"))),i+="Note : The following parameters will be saved in cache. You just need to set them once. 1. Shininess : "+t.htmlCls.inputTextStr+"id='"+t.pre+"shininess' value='"+m+"' size=4>"+t.htmlCls.space3+"(for the shininess of the 3D objects, default 40)2. Three directional lights : Key Light : "+t.htmlCls.inputTextStr+"id='"+t.pre+"light1' value='"+u+"' size=4>"+t.htmlCls.space3+"(for the light strength of the key light, default 0.8)Fill Light : "+t.htmlCls.inputTextStr+"id='"+t.pre+"light2' value='"+g+"' size=4>"+t.htmlCls.space3+"(for the light strength of the fill light, default 0.4)Back Light : "+t.htmlCls.inputTextStr+"id='"+t.pre+"light3' value='"+f+"' size=4>"+t.htmlCls.space3+"(for the light strength of the back light, default 0.2)3. Thickness : Line Radius : "+t.htmlCls.inputTextStr+"id='"+t.pre+"linerad_"+e+"' value='"+n+"' size=4>"+t.htmlCls.space3+"(for stabilizers, hydrogen bonds, distance lines, default 0.1)Coil Radius : "+t.htmlCls.inputTextStr+"id='"+t.pre+"coilrad_"+e+"' value='"+l+"' size=4>"+t.htmlCls.space3+"(for coils, default 0.3)Stick Radius : "+t.htmlCls.inputTextStr+"id='"+t.pre+"stickrad_"+e+"' value='"+r+"' size=4>"+t.htmlCls.space3+"(for sticks, default 0.4)Cross-Linkage Radius : "+t.htmlCls.inputTextStr+"id='"+t.pre+"crosslinkrad_"+e+"' value='"+o+"' size=4>"+t.htmlCls.space3+"(for cross-linkages, default 0.4)Trace Radius : "+t.htmlCls.inputTextStr+"id='"+t.pre+"tracerad_"+e+"' value='"+a+"' size=4>"+t.htmlCls.space3+"(for C alpha trace, O3' trace, default 0.4)Ribbon Thickness : "+t.htmlCls.inputTextStr+"id='"+t.pre+"ribbonthick_"+e+"' value='"+c+"' size=4>"+t.htmlCls.space3+"(for helix and sheet ribbons, nucleotide ribbons, default 0.2)Protein Ribbon Width : "+t.htmlCls.inputTextStr+"id='"+t.pre+"prtribbonwidth_"+e+"' value='"+h+"' size=4>"+t.htmlCls.space3+"(for helix and sheet ribbons, default 1.3)Nucleotide Ribbon Width : "+t.htmlCls.inputTextStr+"id='"+t.pre+"nucleotideribbonwidth_"+e+"' value='"+p+"' size=4>"+t.htmlCls.space3+"(for nucleotide ribbons, default 0.8)Ball Scale : "+t.htmlCls.inputTextStr+"id='"+t.pre+"ballscale_"+e+"' value='"+d+"' size=4>"+t.htmlCls.space3+"(for styles 'Ball and Stick' and 'Dot', default 0.3)4. Show Glycan Cartoon : "+t.htmlCls.inputTextStr+"id='"+t.pre+"glycan' value='"+b+"' size=4>"+t.htmlCls.space3+"(0: hide, 1: show, default 0)5. Show Membrane : "+t.htmlCls.inputTextStr+"id='"+t.pre+"membrane' value='"+C+"' size=4>"+t.htmlCls.space3+"(0: hide, 1: show, default 1)6. Enlarge Command Window : "+t.htmlCls.inputTextStr+"id='"+t.pre+"cmdwindow' value='"+y+"' size=4>"+t.htmlCls.space3+"(0: Regular, 1: Large, default 0)":(n+='
',n+="Selection: Name: "+s.htmlCls.inputTextStr+"id='"+s.pre+"seq_command_name"+e+"' value='seq_"+l+"' size='5'> "+s.htmlCls.space2+"Save Clear
Residue labeling: standard residue with coordinates: UPPER case letter; nonstandard residue with coordinates: the first UPPER case letter plus a period except that water residue uses the letter 'O'; residue missing coordinates: lower case letter."+(s.utilsCls.isMac()&&!s.utilsCls.isMobile()?"Turn on scroll bar: System preferences -> General -> show scroll bars -> check Always":"")+"
',n+="Selection: Name: "+s.htmlCls.inputTextStr+"id='"+s.pre+"alignseq_command_name' value='alseq_"+l+"' size='10'> "+s.htmlCls.space2+"Save Clear
Residue labeling: aligned residue with coordinates: UPPER case letter; non-aligned residue with coordinates: lower case letter which can be highlighted; residue missing coordinates: lower case letter which can NOT be highlighted."+(s.utilsCls.isMac()&&!s.utilsCls.isMobile()?"Turn on scroll bar: System preferences -> General -> show scroll bars -> check Always":"")+"Select Aligned Sequences: touch to select, touch again to deselect, multiple selection is allowed without Ctrl key, click "Save Selection" to save the current selection.Select on 1D sequences: drag to select, drag again to deselect, multiple selection is allowed without Ctrl key, click "Save Selection" to save the current selection.Select on 2D interaction diagram: click on the nodes or lines. The nodes are chains and can be united with the Ctrl key. The lines are interactions and can NOT be united. Each click on the lines selects half of the lines, i.e., select the interacting residues in one of the two chains.Select on 3D structures: "+(e.utilsCls.isMobile()?"use finger to pick":'hold "Alt" and use mouse to pick')+', click the second time to deselect, hold "Ctrl" to union selection, hold "Shift" to select a range, press the up/down arrow to switch among atom/residue/strand/chain/structure, click "Save Selection" to save the current selection.Save the current selection (either on 3D structure, 2D interactions, or 1D sequence): open the menu "Select -> Save Selection", specify the name and description for the selection, and click "Save".Grid Size: ";s+=this.getOptionHtml(["65","97","129"],0),s+=" ",s+="Salt Concentration: ";return s+=this.getOptionHtml(["0","0.15"],1),s+=" M ";return"delphi"==e?s.cfg.cid?i+="
Note : Partial charges(MMFF94) are from PubChem Compound SDF files.
":(i+="
Note : Only the selected residues are used for
DelPhi potential calculation by solving linear Poisson-Boltzmann equation.",i+='
',i+=s.htmlCls.divStr+t+"' style='display:none;'>",i+="
The hydrogens and partial charges of proteins and nucleotides are added using
DelPhiPKa with the Amber charge and size files. The hydrogens of ligands are added using
Open Babel . The partial charges of ligands are calculated using
Antechamber with the Gasteiger charge method. All partial charges are calculated at pH 7.
",i+='Lipids are treated as ligands. Please use "HETATM" instead of "ATOM " for each lipid atom in your PDB file. Each phosphate in lipids is assigned with a charge of -1. You can download PQR and modify it, or prepare your PQR file using other tools. Then load the PQR file at the menu "Analysis > Load PQR/Potential".
',i+="
Note : Always load a PDB file before loading a PQR or DelPhi potential file.",i+='
DelPhi Web Server and be exported as a Cube file. ',"url"==e&&(i+="The PQR or potential file can be accessed in a URL if it is located in the same host as iCn3D."),i+="Potential contour at: ";let d;a+=this.getOptionHtml(["0.5","1","2","3","4","5","6","7","8","9","10"],2),a+=" kT/e(25.6mV at 298K) "+s.htmlCls.buttonStr+n+"mapNo'>Remove Map ",a+=s.htmlCls.divStr+n+"tab1_"+i+"'>",a+=this.addGsizeSalt(i)+"PQR File : "+s.htmlCls.inputFileStr+"id='"+s.pre+i+"file'> Phi File : "+s.htmlCls.inputFileStr+"id='"+s.pre+n+"file'> Cube File : "+s.htmlCls.inputFileStr+"id='"+s.pre+l+"file'> "+s.htmlCls.buttonStr+n+"mapNo'>Remove Map ",a+=s.htmlCls.divStr+n+"tab1_"+i+"2'>",a+=this.addGsizeSalt(i)+"PQR URL in the same host: "+s.htmlCls.inputTextStr+"id='"+s.pre+i+"file'> Phi URL in the same host: "+s.htmlCls.inputTextStr+"id='"+s.pre+n+"file'> Cube URL in the same host: "+s.htmlCls.inputTextStr+"id='"+s.pre+l+"file'> Surface with max potential at: ";a+=this.getOptionHtml(["0.5","1","2","3","4","5","6","7","8","9","10"],2),a+=" kT/e(25.6mV at 298K) Surface : ",a+="Van der Waals ",a+="Molecular Surface ",a+="Solvent Accessible ",a+=" ",a+="Opacity : ";return a+=this.getOptionHtml(["1.0","0.9","0.8","0.7","0.6","0.5","0.4","0.3","0.2","0.1"],0),a+=" Wireframe : ",a+="Yes ",a+="No ",a+=" "+s.htmlCls.buttonStr+n+"mapNo2'>Remove Surface ",a+=s.htmlCls.divStr+n+"tab2_"+i+"'>",a+=this.addGsizeSalt(i+"2")+"PQR File : "+s.htmlCls.inputFileStr+"id='"+s.pre+i+"file2'> Phi File : "+s.htmlCls.inputFileStr+"id='"+s.pre+n+"file2'> Cube File : "+s.htmlCls.inputFileStr+"id='"+s.pre+l+"file2'> "+s.htmlCls.buttonStr+n+"mapNo2'>Remove Surface ",a+=s.htmlCls.divStr+n+"tab2_"+i+"2'>",a+=this.addGsizeSalt(i+"2")+"PQR URL in the same host: "+s.htmlCls.inputTextStr+"id='"+s.pre+i+"file2'> Phi URL in the same host: "+s.htmlCls.inputTextStr+"id='"+s.pre+n+"file2'> Cube URL in the same host: "+s.htmlCls.inputTextStr+"id='"+s.pre+l+"file2'> Save File > iCn3D PNG Image"...');else if(-1!=l){let t=e.substr(l+n.length);s.htmlCls.clickMenuCls.setLogCmd("load iCn3D PNG image "+$("#"+s.pre+"pngimage").val(),!1),window.open(t,"_self")}else if(-1!=o){let n="Start of data file======\n",l=e.indexOf(n);i.bInputfile=-1!=l,i.bInputPNGWithData=i.bInputfile;let a,d=t?t.replace(/;/g,"\n"):"";if(i.bInputfile){let t=e.indexOf("End of data file======\n"),s=e.substr(l+n.length,t-l-n.length);i.InputfileData=i.InputfileData?i.InputfileData+"\nENDMDL\n"+s:s;let c="Start of type file======\n",h=e.indexOf(c),p=e.indexOf("End of type file======\n"),m=e.substr(h+c.length,p-h-c.length-1);i.InputfileType=m;let u=e.indexOf("End of state file======\n");a=e.substr(o+r.length,u-o-r.length),a=decodeURIComponent(a+"\n"+d),"pdb"===m?(await i.pdbParserCls.loadPdbData(s),i.commands=[],i.optsHistory=[]):("mol2"===m?await i.mol2ParserCls.loadMol2Data(s):"sdf"===m?await i.sdfParserCls.loadSdfData(s):"xyz"===m?await i.xyzParserCls.loadXyzData(s):"mmcif"===m&&await i.mmcifParserCls.loadMmcifData(s),i.commands=[],i.optsHistory=[])}else{let t=e.indexOf("End of state file======\n");a=e.substr(o+r.length,t-o-r.length),a=decodeURIComponent(a+"\n"+d),i.commands=[],i.optsHistory=[]}await i.loadScriptCls.loadScript(a,!0),s.htmlCls.clickMenuCls.setLogCmd("load iCn3D PNG image "+$("#"+s.pre+"pngimage").val(),!1)}}fileSupport(){window.File&&window.FileReader&&window.FileList&&window.Blob||alert("The File APIs are not fully supported in this browser.")}getLinkColor(){let e="";return e+=", linkmap: {\n",e+='3: {"type": "peptidebond", "c":""},\n',e+='4: {"type": "ssbond", "c":"FFA500"},\n',e+='5: {"type": "ionic", "c":"0FF"},\n',e+='6: {"type": "ionicInside", "c":"FFF"},\n',e+='11: {"type": "contact", "c":"888"},\n',e+='12: {"type": "contactInside", "c":"FFF"},\n',e+='13: {"type": "hbond", "c":"0F0"},\n',e+='14: {"type": "hbondInside", "c":"FFF"},\n',e+='15: {"type": "clbond", "c":"006400"},\n',e+='17: {"type": "halogen", "c":"F0F"},\n',e+='18: {"type": "halogenInside", "c":"FFF"},\n',e+='19: {"type": "pication", "c":"F00"},\n',e+='20: {"type": "picationInside", "c":"FFF"},\n',e+='21: {"type": "pistacking", "c":"00F"},\n',e+='22: {"type": "pistackingInside", "c":"FFF"}\n',e+="}}\n",', linkmap: {\n3: {"type": "peptidebond", "c":""},\n4: {"type": "ssbond", "c":"FFA500"},\n5: {"type": "ionic", "c":"0FF"},\n6: {"type": "ionicInside", "c":"FFF"},\n11: {"type": "contact", "c":"888"},\n12: {"type": "contactInside", "c":"FFF"},\n13: {"type": "hbond", "c":"0F0"},\n14: {"type": "hbondInside", "c":"FFF"},\n15: {"type": "clbond", "c":"006400"},\n17: {"type": "halogen", "c":"F0F"},\n18: {"type": "halogenInside", "c":"FFF"},\n19: {"type": "pication", "c":"F00"},\n20: {"type": "picationInside", "c":"FFF"},\n21: {"type": "pistacking", "c":"00F"},\n22: {"type": "pistackingInside", "c":"FFF"}\n}}\n'}setCookieForThickness(){let e=this.icn3dui,t=e.icn3d;if(!e.bNode){let e=3650;this.setCookie("lineRadius",t.lineRadius,e),this.setCookie("coilWidth",t.coilWidth,e),this.setCookie("cylinderRadius",t.cylinderRadius,e),this.setCookie("crosslinkRadius",t.crosslinkRadius,e),this.setCookie("traceRadius",t.traceRadius,e),this.setCookie("dotSphereScale",t.dotSphereScale,e),this.setCookie("ribbonthickness",t.ribbonthickness,e),this.setCookie("helixSheetWidth",t.helixSheetWidth,e),this.setCookie("nucleicAcidWidth",t.nucleicAcidWidth,e)}}setLineThickness(e,t){let s=this.icn3dui,i=s.icn3d;if(i.bSetThickness=!0,"style"==e&&(t&&($("#"+s.pre+"shininess").val("40"),$("#"+s.pre+"light1").val("0.8"),$("#"+s.pre+"light2").val("0.4"),$("#"+s.pre+"light3").val("0.2"),$("#"+s.pre+"glycan").val("0"),$("#"+s.pre+"membrane").val("1"),$("#"+s.pre+"cmdwindow").val("0")),i.shininess=parseFloat($("#"+s.pre+"shininess").val()),i.light1=parseFloat($("#"+s.pre+"light1").val()),i.light2=parseFloat($("#"+s.pre+"light2").val()),i.light3=parseFloat($("#"+s.pre+"light3").val()),i.bGlycansCartoon=parseInt($("#"+s.pre+"glycan").val()),i.bMembrane=parseInt($("#"+s.pre+"membrane").val()),i.bCmdWindow=parseInt($("#"+s.pre+"cmdwindow").val())),t&&($("#"+s.pre+"linerad_"+e).val(.1),$("#"+s.pre+"coilrad_"+e).val(.3),$("#"+s.pre+"stickrad_"+e).val(.4),$("#"+s.pre+"crosslinkrad_"+e).val(.4),$("#"+s.pre+"tracerad_"+e).val(.4),$("#"+s.pre+"ballscale_"+e).val(.3),$("#"+s.pre+"ribbonthick_"+e).val(.2),$("#"+s.pre+"prtribbonwidth_"+e).val(1.3),$("#"+s.pre+"nucleotideribbonwidth_"+e).val(.8)),i.lineRadius=parseFloat($("#"+s.pre+"linerad_"+e).val()),i.coilWidth=parseFloat($("#"+s.pre+"coilrad_"+e).val()),i.cylinderRadius=parseFloat($("#"+s.pre+"stickrad_"+e).val()),i.crosslinkRadius=parseFloat($("#"+s.pre+"crosslinkrad_"+e).val()),i.traceRadius=parseFloat($("#"+s.pre+"tracerad_"+e).val()),i.dotSphereScale=parseFloat($("#"+s.pre+"ballscale_"+e).val()),i.ribbonthickness=parseFloat($("#"+s.pre+"ribbonthick_"+e).val()),i.helixSheetWidth=parseFloat($("#"+s.pre+"prtribbonwidth_"+e).val()),i.nucleicAcidWidth=parseFloat($("#"+s.pre+"nucleotideribbonwidth_"+e).val()),!s.bNode){let e=3650;this.setCookie("shininess",i.shininess,e),this.setCookie("light1",i.light1,e),this.setCookie("light2",i.light2,e),this.setCookie("light3",i.light3,e),this.setCookie("glycan",i.bGlycansCartoon,e),this.setCookie("membrane",i.bMembrane,e),this.setCookie("cmdwindow",i.bCmdWindow,e)}if(this.setCookieForThickness(),e=t){let e="reset thickness";s.htmlCls.clickMenuCls.setLogCmd(e,!0),i.bSetThickness=!1,i.threeDPrintCls.resetAfter3Dprint()}else s.htmlCls.clickMenuCls.setLogCmd("set thickness | linerad "+i.lineRadius+" | coilrad "+i.coilWidth+" | stickrad "+i.cylinderRadius+" | crosslinkrad "+i.crosslinkRadius+" | tracerad "+i.traceRadius+" | ribbonthick "+i.ribbonthickness+" | proteinwidth "+i.helixSheetWidth+" | nucleotidewidth "+i.nucleicAcidWidth+" | ballscale "+i.dotSphereScale,!0),s.htmlCls.clickMenuCls.setLogCmd("set glycan "+i.bGlycansCartoon,!0),s.htmlCls.clickMenuCls.setLogCmd("set membrane "+i.bMembrane,!0),s.htmlCls.clickMenuCls.setLogCmd("set cmdwindow "+i.bCmdWindow,!0);i.drawCls.draw()}setCookie(e,t,s){let i=new Date;i.setTime(i.getTime()+24*s*60*60*1e3);let n="expires="+i.toUTCString();document.cookie=e+"="+t+";"+n+";path=/"}updateSurfPara(e){let t=this.icn3dui,s=t.icn3d;s.phisurftype=$("#"+t.pre+e+"surftype").val(),s.phisurfop=$("#"+t.pre+e+"surfop").val(),s.phisurfwf=$("#"+t.pre+e+"surfwf").val()}exportPdb(){let e=this.icn3dui,t=e.icn3d,s="",i=e.hashUtilsCls.intHash(t.dAtoms,t.hAtoms);if(s+=t.saveFileCls.getAtomPDB(i),!e.bNode){let i=Object.keys(e.utilsCls.getHlStructures()).join(",");t.saveFileCls.saveFile(i+"_icn3d.pdb","text",[s])}return s}exportSecondary(){let e=this.icn3dui,t=e.icn3d,s="",i=e.hashUtilsCls.intHash(t.dAtoms,t.hAtoms);if(s+=t.saveFileCls.getSecondary(i),!e.bNode){let i=Object.keys(e.utilsCls.getHlStructures()).join(",");t.saveFileCls.saveFile(i+"_icn3d_ss.txt","text",[s])}return s}}class g{constructor(e){let t=e;this.icn3dui=e,this.cfg=this.icn3dui.cfg,this.opts={},this.opts.background="black",this.allMenus={},this.allMenusSel={},this.simpleMenus={},this.shownMenus={},this.WIDTH=400,this.HEIGHT=400,this.RESIDUE_WIDTH=10,t.utilsCls.isMobile()||this.cfg.mobilemenu?this.MENU_HEIGHT=0:this.MENU_HEIGHT=40,this.LOG_HEIGHT=65,this.MENU_WIDTH=750,this.LESSWIDTH=20,this.LESSWIDTH_RESIZE=20,this.LESSHEIGHT=20,this.width2d=200,this.CMD_HEIGHT=.8*this.LOG_HEIGHT,this.EXTRAHEIGHT=this.MENU_HEIGHT+this.CMD_HEIGHT,null!=this.cfg.showmenu&&0==this.cfg.showmenu&&(this.EXTRAHEIGHT-=this.MENU_HEIGHT),null!=this.cfg.showcommand&&0==this.cfg.showcommand&&(this.EXTRAHEIGHT-=this.CMD_HEIGHT),this.GREY8="#AAAAAA",this.GREYB="#CCCCCC",this.GREYC="#DDDDDD",this.GREYD="#EEEEEE",this.ORANGE="#FFA500",this.themecolor="blue",this.defaultValue=1,this.ssValue=3,this.coilValue=3,this.contactValue=11,this.contactInsideValue=12,this.hbondValue=13,this.hbondInsideValue=14,this.ssbondValue=4,this.ionicValue=5,this.ionicInsideValue=6,this.clbondValue=15,this.halogenValue=17,this.halogenInsideValue=18,this.picationValue=19,this.picationInsideValue=20,this.pistackingValue=21,this.pistackingInsideValue=22,this.contactColor="888",this.contactInsideColor="FFF",this.hbondColor="0F0",this.hbondInsideColor="FFF",this.ssbondColor="FFA500",this.ionicColor="0FF",this.ionicInsideColor="FFF",this.clbondColor="006400",this.halogenColor="F0F",this.halogenInsideColor="FFF",this.picationColor="F00",this.picationInsideColor="FFF",this.pistackingColor="00F",this.pistackingInsideColor="FFF",this.hideedges=1,this.force=4,this.simulation=void 0,this.baseUrl=window&&window.location&&"structure.ncbi.nlm.nih.gov"==window.location.hostname?"https://structure.ncbi.nlm.nih.gov/Structure/":"https://www.ncbi.nlm.nih.gov/Structure/",this.divStr="",this.spanNowrapStr="
",this.inputTextStr="=0&&void 0===r[t]&&console.warn('THREE.GLTFLoader: Unknown extension "'+t+'".')}}a.setExtensions(l),a.setPlugins(r),a.parse(s,i)}parseAsync(e,t){const s=this;return new Promise((function(i,n){s.parse(e,t,i,n)}))}}function b(){let e={};return{get:function(t){return e[t]},add:function(t,s){e[t]=s},remove:function(t){delete e[t]},removeAll:function(){e={}}}}const C={KHR_BINARY_GLTF:"KHR_binary_glTF",KHR_DRACO_MESH_COMPRESSION:"KHR_draco_mesh_compression",KHR_LIGHTS_PUNCTUAL:"KHR_lights_punctual",KHR_MATERIALS_CLEARCOAT:"KHR_materials_clearcoat",KHR_MATERIALS_IOR:"KHR_materials_ior",KHR_MATERIALS_PBR_SPECULAR_GLOSSINESS:"KHR_materials_pbrSpecularGlossiness",KHR_MATERIALS_SHEEN:"KHR_materials_sheen",KHR_MATERIALS_SPECULAR:"KHR_materials_specular",KHR_MATERIALS_TRANSMISSION:"KHR_materials_transmission",KHR_MATERIALS_UNLIT:"KHR_materials_unlit",KHR_MATERIALS_VOLUME:"KHR_materials_volume",KHR_TEXTURE_BASISU:"KHR_texture_basisu",KHR_TEXTURE_TRANSFORM:"KHR_texture_transform",KHR_MESH_QUANTIZATION:"KHR_mesh_quantization",EXT_TEXTURE_WEBP:"EXT_texture_webp",EXT_MESHOPT_COMPRESSION:"EXT_meshopt_compression"};class y{constructor(e){this.parser=e,this.name=C.KHR_LIGHTS_PUNCTUAL,this.cache={refs:{},uses:{}}}_markDefs(){const e=this.parser,t=this.parser.json.nodes||[];for(let s=0,i=t.length;s=0)throw new Error("THREE.GLTFLoader: setKTX2Loader must be called before loading KTX2 textures");return null}return t.loadTextureImage(e,n.source,l)}}class R{constructor(e){this.parser=e,this.name=C.EXT_TEXTURE_WEBP,this.isSupported=null}loadTexture(e){const t=this.name,s=this.parser,i=s.json,n=i.textures[e];if(!n.extensions||!n.extensions[t])return null;const l=n.extensions[t],r=i.images[l.source];let o=s.textureLoader;if(r.uri){const e=s.options.manager.getHandler(r.uri);null!==e&&(o=e)}return this.detectSupport().then((function(n){if(n)return s.loadTextureImage(e,l.source,o);if(i.extensionsRequired&&i.extensionsRequired.indexOf(t)>=0)throw new Error("THREE.GLTFLoader: WebP required by asset but unsupported.");return s.loadTexture(e)}))}detectSupport(){return this.isSupported||(this.isSupported=new Promise((function(e){const t=new Image;t.src="data:image/webp;base64,UklGRiIAAABXRUJQVlA4IBYAAAAwAQCdASoBAAEADsD+JaQAA3AAAAAA",t.onload=t.onerror=function(){e(1===t.height)}}))),this.isSupported}}class I{constructor(e){this.name=C.EXT_MESHOPT_COMPRESSION,this.parser=e}loadBufferView(e){const t=this.parser.json,s=t.bufferViews[e];if(s.extensions&&s.extensions[this.name]){const e=s.extensions[this.name],i=this.parser.getDependency("buffer",e.buffer),n=this.parser.options.meshoptDecoder;if(!n||!n.supported){if(t.extensionsRequired&&t.extensionsRequired.indexOf(this.name)>=0)throw new Error("THREE.GLTFLoader: setMeshoptDecoder must be called before loading compressed files");return null}return Promise.all([i,n.ready]).then((function(t){const s=e.byteOffset||0,i=e.byteLength||0,l=e.count,r=e.byteStride,o=new ArrayBuffer(l*r),a=new Uint8Array(t[0],s,i);return n.decodeGltfBuffer(new Uint8Array(o),l,r,a,e.mode,e.filter),o}))}return null}}const T="glTF",E=1313821514,P=5130562;class M{constructor(e){this.name=C.KHR_BINARY_GLTF,this.content=null,this.body=null;const t=new DataView(e,0,12);if(this.header={magic:THREE.LoaderUtils.decodeText(new Uint8Array(e.slice(0,4))),version:t.getUint32(4,!0),length:t.getUint32(8,!0)},this.header.magic!==T)throw new Error("THREE.GLTFLoader: Unsupported glTF-Binary header.");if(this.header.version<2)throw new Error("THREE.GLTFLoader: Legacy binary file detected.");const s=this.header.length-12,i=new DataView(e,12);let n=0;for(;n",t).replace("#include ",s).replace("#include ",i).replace("#include ",n).replace("#include ",l)},Object.defineProperties(this,{specular:{get:function(){return r.specular.value},set:function(e){r.specular.value=e}},specularMap:{get:function(){return r.specularMap.value},set:function(e){r.specularMap.value=e,e?this.defines.USE_SPECULARMAP="":delete this.defines.USE_SPECULARMAP}},glossiness:{get:function(){return r.glossiness.value},set:function(e){r.glossiness.value=e}},glossinessMap:{get:function(){return r.glossinessMap.value},set:function(e){r.glossinessMap.value=e,e?(this.defines.USE_GLOSSINESSMAP="",this.defines.USE_UV=""):(delete this.defines.USE_GLOSSINESSMAP,delete this.defines.USE_UV)}}}),delete this.metalness,delete this.roughness,delete this.metalnessMap,delete this.roughnessMap,this.setValues(e)}copy(e){return super.copy(e),this.specularMap=e.specularMap,this.specular.copy(e.specular),this.glossinessMap=e.glossinessMap,this.glossiness=e.glossiness,delete this.metalness,delete this.roughness,delete this.metalnessMap,delete this.roughnessMap,this}}class L{constructor(){this.name=C.KHR_MATERIALS_PBR_SPECULAR_GLOSSINESS,this.specularGlossinessParams=["color","map","lightMap","lightMapIntensity","aoMap","aoMapIntensity","emissive","emissiveIntensity","emissiveMap","bumpMap","bumpScale","normalMap","normalMapType","displacementMap","displacementScale","displacementBias","specularMap","specular","glossinessMap","glossiness","alphaMap","envMap","envMapIntensity"]}getMaterialType(){return F}extendParams(e,t,s){const i=t.extensions[this.name];e.color=new Color(1,1,1),e.opacity=1;const n=[];if(Array.isArray(i.diffuseFactor)){const t=i.diffuseFactor;e.color.fromArray(t),e.opacity=t[3]}if(void 0!==i.diffuseTexture&&n.push(s.assignTexture(e,"map",i.diffuseTexture,sRGBEncoding)),e.emissive=new Color(0,0,0),e.glossiness=void 0!==i.glossinessFactor?i.glossinessFactor:1,e.specular=new Color(1,1,1),Array.isArray(i.specularFactor)&&e.specular.fromArray(i.specularFactor),void 0!==i.specularGlossinessTexture){const t=i.specularGlossinessTexture;n.push(s.assignTexture(e,"glossinessMap",t)),n.push(s.assignTexture(e,"specularMap",t,sRGBEncoding))}return Promise.all(n)}createMaterial(e){const t=new F(e);return t.fog=!0,t.color=e.color,t.map=void 0===e.map?null:e.map,t.lightMap=null,t.lightMapIntensity=1,t.aoMap=void 0===e.aoMap?null:e.aoMap,t.aoMapIntensity=1,t.emissive=e.emissive,t.emissiveIntensity=1,t.emissiveMap=void 0===e.emissiveMap?null:e.emissiveMap,t.bumpMap=void 0===e.bumpMap?null:e.bumpMap,t.bumpScale=1,t.normalMap=void 0===e.normalMap?null:e.normalMap,t.normalMapType=TangentSpaceNormalMap,e.normalScale&&(t.normalScale=e.normalScale),t.displacementMap=null,t.displacementScale=1,t.displacementBias=0,t.specularMap=void 0===e.specularMap?null:e.specularMap,t.specular=e.specular,t.glossinessMap=void 0===e.glossinessMap?null:e.glossinessMap,t.glossiness=e.glossiness,t.alphaMap=null,t.envMap=void 0===e.envMap?null:e.envMap,t.envMapIntensity=1,t}}class N{constructor(){this.name=C.KHR_MESH_QUANTIZATION}}class q extends THREE.Interpolant{constructor(e,t,s,i){super(e,t,s,i)}copySampleValue_(e){const t=this.resultBuffer,s=this.sampleValues,i=this.valueSize,n=e*i*3+i;for(let e=0;e!==i;e++)t[e]=s[n+e];return t}}q.prototype.beforeStart_=q.prototype.copySampleValue_,q.prototype.afterEnd_=q.prototype.copySampleValue_,q.prototype.interpolate_=function(e,t,s,i){const n=this.resultBuffer,l=this.sampleValues,r=this.valueSize,o=2*r,a=3*r,d=i-t,c=(s-t)/d,h=c*c,p=h*c,m=e*a,u=m-a,g=-2*p+3*h,f=p-h,b=1-g,C=f-h+c;for(let e=0;e!==r;e++){const t=l[u+e+r],s=l[u+e+o]*d,i=l[m+e+r],a=l[m+e]*d;n[e]=b*t+C*s+g*i+f*a}return n};const U=new THREE.Quaternion;class j extends q{interpolate_(e,t,s,i){const n=super.interpolate_(e,t,s,i);return U.fromArray(n).normalize().toArray(n),n}}const B=0,z=1,G=2,V=3,W=4,Y=5,X=6,K={5120:Int8Array,5121:Uint8Array,5122:Int16Array,5123:Uint16Array,5125:Uint32Array,5126:Float32Array},J={9728:THREE.NearestFilter,9729:THREE.LinearFilter,9984:THREE.NearestMipmapNearestFilter,9985:THREE.LinearMipmapNearestFilter,9986:THREE.NearestMipmapLinearFilter,9987:THREE.LinearMipmapLinearFilter},Q={33071:THREE.ClampToEdgeWrapping,33648:THREE.MirroredRepeatWrapping,10497:THREE.RepeatWrapping},Z={SCALAR:1,VEC2:2,VEC3:3,VEC4:4,MAT2:4,MAT3:9,MAT4:16},ee={POSITION:"position",NORMAL:"normal",TANGENT:"tangent",TEXCOORD_0:"uv",TEXCOORD_1:"uv2",COLOR_0:"color",WEIGHTS_0:"skinWeight",JOINTS_0:"skinIndex"},te={scale:"scale",translation:"position",rotation:"quaternion",weights:"morphTargetInfluences"},se={CUBICSPLINE:void 0,LINEAR:THREE.InterpolateLinear,STEP:THREE.InterpolateDiscrete},ie="OPAQUE",ne="MASK",le="BLEND";function re(e,t,s){for(const i in s.extensions)void 0===e[i]&&(t.userData.gltfExtensions=t.userData.gltfExtensions||{},t.userData.gltfExtensions[i]=s.extensions[i])}function oe(e,t){void 0!==t.extras&&("object"==typeof t.extras?Object.assign(e.userData,t.extras):console.warn("THREE.GLTFLoader: Ignoring primitive type .extras, "+t.extras))}function ae(e,t){if(e.updateMorphTargets(),void 0!==t.weights)for(let s=0,i=t.weights.length;s{const s=this.associations.get(e);null!=s&&this.associations.set(t,s);for(const[s,i]of e.children.entries())n(i,t.children[s])};return n(s,i),i.name+="_instance_"+e.uses[t]++,i}_invokeOne(e){const t=Object.values(this.plugins);t.push(this);for(let s=0;s=2&&m.setY(t,c[e*l+1]),l>=3&&m.setZ(t,c[e*l+2]),l>=4&&m.setW(t,c[e*l+3]),l>=5)throw new Error("THREE.GLTFLoader: Unsupported itemSize in sparse BufferAttribute.")}}return m}))}loadTexture(e){const t=this.json,s=this.options,i=t.textures[e].source,n=t.images[i];let l=this.textureLoader;if(n.uri){const e=s.manager.getHandler(n.uri);null!==e&&(l=e)}return this.loadTextureImage(e,i,l)}loadTextureImage(e,t,s){const i=this,n=this.json,l=n.textures[e],r=n.images[t],o=(r.uri||r.bufferView)+":"+l.sampler;if(this.textureCache[o])return this.textureCache[o];const a=this.loadImageSource(t,s).then((function(t){t.flipY=!1,l.name&&(t.name=l.name);const s=(n.samplers||{})[l.sampler]||{};return t.magFilter=J[s.magFilter]||LinearFilter,t.minFilter=J[s.minFilter]||LinearMipmapLinearFilter,t.wrapS=Q[s.wrapS]||RepeatWrapping,t.wrapT=Q[s.wrapT]||RepeatWrapping,i.associations.set(t,{textures:e}),t})).catch((function(){return null}));return this.textureCache[o]=a,a}loadImageSource(e,t){const s=this,i=this.json,n=this.options;if(void 0!==this.sourceCache[e])return this.sourceCache[e].then((e=>e.clone()));const l=i.images[e],r=self.URL||self.webkitURL;let o=l.uri||"",a=!1;if(void 0!==l.bufferView)o=s.getDependency("bufferView",l.bufferView).then((function(e){a=!0;const t=new Blob([e],{type:l.mimeType});return o=r.createObjectURL(t),o}));else if(void 0===l.uri)throw new Error("THREE.GLTFLoader: Image "+e+" is missing URI and bufferView");const d=Promise.resolve(o).then((function(e){return new Promise((function(s,i){let l=s;!0===t.isImageBitmapLoader&&(l=function(e){const t=new Texture(e);t.needsUpdate=!0,s(t)}),t.load(THREE.LoaderUtils.resolveURL(e,n.path),l,void 0,i)}))})).then((function(e){var t;return!0===a&&r.revokeObjectURL(o),e.userData.mimeType=l.mimeType||((t=l.uri).search(/\.jpe?g($|\?)/i)>0||0===t.search(/^data\:image\/jpeg/)?"image/jpeg":t.search(/\.webp($|\?)/i)>0||0===t.search(/^data\:image\/webp/)?"image/webp":"image/png"),e})).catch((function(e){throw console.error("THREE.GLTFLoader: Couldn't load texture",o),e}));return this.sourceCache[e]=d,d}assignTexture(e,t,s,i){const n=this;return this.getDependency("texture",s.index).then((function(l){if(void 0===s.texCoord||0==s.texCoord||"aoMap"===t&&1==s.texCoord||console.warn("THREE.GLTFLoader: Custom UV set "+s.texCoord+" for texture "+t+" not yet supported."),n.extensions[C.KHR_TEXTURE_TRANSFORM]){const e=void 0!==s.extensions?s.extensions[C.KHR_TEXTURE_TRANSFORM]:void 0;if(e){const t=n.associations.get(l);l=n.extensions[C.KHR_TEXTURE_TRANSFORM].extendTexture(l,e),n.associations.set(l,t)}}return void 0!==i&&(l.encoding=i),e[t]=l,l}))}assignFinalMaterial(e){const t=e.geometry;let s=e.material;const i=void 0===t.attributes.tangent,n=void 0!==t.attributes.color,l=void 0===t.attributes.normal;if(e.isPoints){const e="PointsMaterial:"+s.uuid;let t=this.cache.get(e);t||(t=new PointsMaterial,Material.prototype.copy.call(t,s),t.color.copy(s.color),t.map=s.map,t.sizeAttenuation=!1,this.cache.add(e,t)),s=t}else if(e.isLine){const e="LineBasicMaterial:"+s.uuid;let t=this.cache.get(e);t||(t=new LineBasicMaterial,Material.prototype.copy.call(t,s),t.color.copy(s.color),this.cache.add(e,t)),s=t}if(i||n||l){let e="ClonedMaterial:"+s.uuid+":";s.isGLTFSpecularGlossinessMaterial&&(e+="specular-glossiness:"),i&&(e+="derivative-tangents:"),n&&(e+="vertex-colors:"),l&&(e+="flat-shading:");let t=this.cache.get(e);t||(t=s.clone(),n&&(t.vertexColors=!0),l&&(t.flatShading=!0),i&&(t.normalScale&&(t.normalScale.y*=-1),t.clearcoatNormalScale&&(t.clearcoatNormalScale.y*=-1)),this.cache.add(e,t),this.associations.set(t,this.associations.get(s))),s=t}s.aoMap&&void 0===t.attributes.uv2&&void 0!==t.attributes.uv&&t.setAttribute("uv2",t.attributes.uv),e.material=s}getMaterialType(){return MeshStandardMaterial}loadMaterial(e){const t=this,s=this.json,i=this.extensions,n=s.materials[e];let l;const r={},o=n.extensions||{},a=[];if(o[C.KHR_MATERIALS_PBR_SPECULAR_GLOSSINESS]){const e=i[C.KHR_MATERIALS_PBR_SPECULAR_GLOSSINESS];l=e.getMaterialType(),a.push(e.extendParams(r,n,t))}else if(o[C.KHR_MATERIALS_UNLIT]){const e=i[C.KHR_MATERIALS_UNLIT];l=e.getMaterialType(),a.push(e.extendParams(r,n,t))}else{const s=n.pbrMetallicRoughness||{};if(r.color=new Color(1,1,1),r.opacity=1,Array.isArray(s.baseColorFactor)){const e=s.baseColorFactor;r.color.fromArray(e),r.opacity=e[3]}void 0!==s.baseColorTexture&&a.push(t.assignTexture(r,"map",s.baseColorTexture,sRGBEncoding)),r.metalness=void 0!==s.metallicFactor?s.metallicFactor:1,r.roughness=void 0!==s.roughnessFactor?s.roughnessFactor:1,void 0!==s.metallicRoughnessTexture&&(a.push(t.assignTexture(r,"metalnessMap",s.metallicRoughnessTexture)),a.push(t.assignTexture(r,"roughnessMap",s.metallicRoughnessTexture))),l=this._invokeOne((function(t){return t.getMaterialType&&t.getMaterialType(e)})),a.push(Promise.all(this._invokeAll((function(t){return t.extendMaterialParams&&t.extendMaterialParams(e,r)}))))}!0===n.doubleSided&&(r.side=DoubleSide);const d=n.alphaMode||ie;if(d===le?(r.transparent=!0,r.depthWrite=!1):(r.transparent=!1,d===ne&&(r.alphaTest=void 0!==n.alphaCutoff?n.alphaCutoff:.5)),void 0!==n.normalTexture&&l!==MeshBasicMaterial&&(a.push(t.assignTexture(r,"normalMap",n.normalTexture)),r.normalScale=new Vector2(1,1),void 0!==n.normalTexture.scale)){const e=n.normalTexture.scale;r.normalScale.set(e,e)}return void 0!==n.occlusionTexture&&l!==MeshBasicMaterial&&(a.push(t.assignTexture(r,"aoMap",n.occlusionTexture)),void 0!==n.occlusionTexture.strength&&(r.aoMapIntensity=n.occlusionTexture.strength)),void 0!==n.emissiveFactor&&l!==MeshBasicMaterial&&(r.emissive=(new Color).fromArray(n.emissiveFactor)),void 0!==n.emissiveTexture&&l!==MeshBasicMaterial&&a.push(t.assignTexture(r,"emissiveMap",n.emissiveTexture,sRGBEncoding)),Promise.all(a).then((function(){let s;return s=l===F?i[C.KHR_MATERIALS_PBR_SPECULAR_GLOSSINESS].createMaterial(r):new l(r),n.name&&(s.name=n.name),oe(s,n),t.associations.set(s,{materials:e}),n.extensions&&re(i,s,n),s}))}createUniqueName(e){const t=PropertyBinding.sanitizeNodeName(e||"");let s=t;for(let e=1;this.nodeNamesUsed[s];++e)s=t+"_"+e;return this.nodeNamesUsed[s]=!0,s}loadGeometries(e){const t=this,s=this.extensions,i=this.primitiveCache;function n(e){return s[C.KHR_DRACO_MESH_COMPRESSION].decodePrimitive(e,t).then((function(s){return ue(s,e,t)}))}const l=[];for(let s=0,r=e.length;s0&&ae(h,n),h.name=t.createUniqueName(n.name||"mesh_"+e),oe(h,n),c.extensions&&re(i,h,c),t.assignFinalMaterial(h),a.push(h)}for(let s=0,i=a.length;s1?new Group:1===t.length?t[0]:new Object3D,r!==t[0])for(let e=0,s=t.length;e{const t=new Map;for(const[e,s]of n.associations)(e instanceof Material||e instanceof Texture)&&t.set(e,s);return e.traverse((e=>{const s=n.associations.get(e);null!=s&&t.set(e,s)})),t})(l),l}))}}function me(e,t,s,i){const n=s.nodes[e];return i.getDependency("node",e).then((function(e){if(void 0===n.skin)return e;let t;return i.getDependency("skin",n.skin).then((function(e){t=e;const s=[];for(let e=0,n=t.joints.length;e{const s=n[e];return s&&(l={profileId:e,profilePath:`${t}/${s.path}`,deprecated:!!s.deprecated}),!!l})),!l){if(!s)throw new Error("No matching profile name found");const e=n[s];if(!e)throw new Error(`No matching profile name found and default profile "${s}" missing.`);l={profileId:s,profilePath:`${t}/${e.path}`,deprecated:!!e.deprecated}}const r=await be(l.profilePath);let o;if(i){let t;if(t="any"===e.handedness?r.layouts[Object.keys(r.layouts)[0]]:r.layouts[e.handedness],!t)throw new Error(`No matching handedness, ${e.handedness}, in profile ${l.profileId}`);t.assetPath&&(o=l.profilePath.replace("profile.json",t.assetPath))}return{profile:r,assetPath:o}}const ye={xAxis:0,yAxis:0,button:0,state:fe.ComponentState.DEFAULT};class ve{constructor(e){this.componentProperty=e.componentProperty,this.states=e.states,this.valueNodeName=e.valueNodeName,this.valueNodeProperty=e.valueNodeProperty,this.valueNodeProperty===fe.VisualResponseProperty.TRANSFORM&&(this.minNodeName=e.minNodeName,this.maxNodeName=e.maxNodeName),this.value=0,this.updateFromComponent(ye)}updateFromComponent({xAxis:e,yAxis:t,button:s,state:i}){const{normalizedXAxis:n,normalizedYAxis:l}=function(e=0,t=0){let s=e,i=t;if(Math.sqrt(e*e+t*t)>1){const n=Math.atan2(t,e);s=Math.cos(n),i=Math.sin(n)}return{normalizedXAxis:.5*s+.5,normalizedYAxis:.5*i+.5}}(e,t);switch(this.componentProperty){case fe.ComponentProperty.X_AXIS:this.value=this.states.includes(i)?n:.5;break;case fe.ComponentProperty.Y_AXIS:this.value=this.states.includes(i)?l:.5;break;case fe.ComponentProperty.BUTTON:this.value=this.states.includes(i)?s:0;break;case fe.ComponentProperty.STATE:this.valueNodeProperty===fe.VisualResponseProperty.VISIBILITY?this.value=this.states.includes(i):this.value=this.states.includes(i)?1:0;break;default:throw new Error(`Unexpected visualResponse componentProperty ${this.componentProperty}`)}}}class _e{constructor(e,t){if(!(e&&t&&t.visualResponses&&t.gamepadIndices&&0!==Object.keys(t.gamepadIndices).length))throw new Error("Invalid arguments supplied");this.id=e,this.type=t.type,this.rootNodeName=t.rootNodeName,this.touchPointNodeName=t.touchPointNodeName,this.visualResponses={},Object.keys(t.visualResponses).forEach((e=>{const s=new ve(t.visualResponses[e]);this.visualResponses[e]=s})),this.gamepadIndices=Object.assign({},t.gamepadIndices),this.values={state:fe.ComponentState.DEFAULT,button:void 0!==this.gamepadIndices.button?0:void 0,xAxis:void 0!==this.gamepadIndices.xAxis?0:void 0,yAxis:void 0!==this.gamepadIndices.yAxis?0:void 0}}get data(){return{id:this.id,...this.values}}updateFromGamepad(e){if(this.values.state=fe.ComponentState.DEFAULT,void 0!==this.gamepadIndices.button&&e.buttons.length>this.gamepadIndices.button){const t=e.buttons[this.gamepadIndices.button];this.values.button=t.value,this.values.button=this.values.button<0?0:this.values.button,this.values.button=this.values.button>1?1:this.values.button,t.pressed||1===this.values.button?this.values.state=fe.ComponentState.PRESSED:(t.touched||this.values.button>fe.ButtonTouchThreshold)&&(this.values.state=fe.ComponentState.TOUCHED)}void 0!==this.gamepadIndices.xAxis&&e.axes.length>this.gamepadIndices.xAxis&&(this.values.xAxis=e.axes[this.gamepadIndices.xAxis],this.values.xAxis=this.values.xAxis<-1?-1:this.values.xAxis,this.values.xAxis=this.values.xAxis>1?1:this.values.xAxis,this.values.state===fe.ComponentState.DEFAULT&&Math.abs(this.values.xAxis)>fe.AxisTouchThreshold&&(this.values.state=fe.ComponentState.TOUCHED)),void 0!==this.gamepadIndices.yAxis&&e.axes.length>this.gamepadIndices.yAxis&&(this.values.yAxis=e.axes[this.gamepadIndices.yAxis],this.values.yAxis=this.values.yAxis<-1?-1:this.values.yAxis,this.values.yAxis=this.values.yAxis>1?1:this.values.yAxis,this.values.state===fe.ComponentState.DEFAULT&&Math.abs(this.values.yAxis)>fe.AxisTouchThreshold&&(this.values.state=fe.ComponentState.TOUCHED)),Object.values(this.visualResponses).forEach((e=>{e.updateFromComponent(this.values)}))}}class we{constructor(e,t,s){if(!e)throw new Error("No xrInputSource supplied");if(!t)throw new Error("No profile supplied");this.xrInputSource=e,this.assetUrl=s,this.id=t.profileId,this.layoutDescription=t.layouts[e.handedness],this.components={},Object.keys(this.layoutDescription.components).forEach((e=>{const t=this.layoutDescription.components[e];this.components[e]=new _e(e,t)})),this.updateFromGamepad()}get gripSpace(){return this.xrInputSource.gripSpace}get targetRaySpace(){return this.xrInputSource.targetRaySpace}get data(){const e=[];return Object.values(this.components).forEach((t=>{e.push(t.data)})),e}updateFromGamepad(){Object.values(this.components).forEach((e=>{e.updateFromGamepad(this.xrInputSource.gamepad)}))}}class Se extends THREE.Object3D{constructor(){super(),this.motionController=null,this.envMap=null}setEnvironmentMap(e){return this.envMap==e||(this.envMap=e,this.traverse((e=>{e.isMesh&&(e.material.envMap=this.envMap,e.material.needsUpdate=!0)}))),this}updateMatrixWorld(e){super.updateMatrixWorld(e),this.motionController&&(this.motionController.updateFromGamepad(),Object.values(this.motionController.components).forEach((e=>{Object.values(e.visualResponses).forEach((e=>{const{valueNode:t,minNode:s,maxNode:i,value:n,valueNodeProperty:l}=e;t&&(l===fe.VisualResponseProperty.VISIBILITY?t.visible=n:l===fe.VisualResponseProperty.TRANSFORM&&(t.quaternion.slerpQuaternions(s.quaternion,i.quaternion,n),t.position.lerpVectors(s.position,i.position,n)))}))})))}}function Ae(e,t){!function(e,t){Object.values(e.components).forEach((e=>{const{type:s,touchPointNodeName:i,visualResponses:n}=e;if(s===fe.ComponentType.TOUCHPAD)if(e.touchPointNode=t.getObjectByName(i),e.touchPointNode){const t=new SphereGeometry(.001),s=new MeshBasicMaterial({color:255}),i=new Mesh(t,s);e.touchPointNode.add(i)}else console.warn(`Could not find touch dot, ${e.touchPointNodeName}, in touchpad component ${e.id}`);Object.values(n).forEach((e=>{const{valueNodeName:s,minNodeName:i,maxNodeName:n,valueNodeProperty:l}=e;if(l===fe.VisualResponseProperty.TRANSFORM){if(e.minNode=t.getObjectByName(i),e.maxNode=t.getObjectByName(n),!e.minNode)return void console.warn(`Could not find ${i} in the model`);if(!e.maxNode)return void console.warn(`Could not find ${n} in the model`)}e.valueNode=t.getObjectByName(s),e.valueNode||console.warn(`Could not find ${s} in the model`)}))}))}(e.motionController,t),e.envMap&&t.traverse((t=>{t.isMesh&&(t.material.envMap=e.envMap,t.material.needsUpdate=!0)})),e.add(t)}class xe{constructor(e=null){this.gltfLoader=e,this.path="https://cdn.jsdelivr.net/npm/@webxr-input-profiles/assets@1.0/dist/profiles",this._assetCache={},this.gltfLoader||(this.gltfLoader=new f)}createControllerModel(e){const t=new Se;let s=null;return e.addEventListener("connected",(e=>{const i=e.data;"tracked-pointer"===i.targetRayMode&&i.gamepad&&Ce(i,this.path,"generic-trigger").then((({profile:e,assetPath:n})=>{t.motionController=new we(i,e,n);const l=this._assetCache[t.motionController.assetUrl];if(l)s=l.scene.clone(),Ae(t,s);else{if(!this.gltfLoader)throw new Error("GLTFLoader not set.");this.gltfLoader.setPath(""),this.gltfLoader.load(t.motionController.assetUrl,(e=>{this._assetCache[t.motionController.assetUrl]=e,s=e.scene.clone(),Ae(t,s)}),null,(()=>{throw new Error(`Asset ${t.motionController.assetUrl} missing or malformed.`)}))}})).catch((e=>{console.warn(e)}))})),e.addEventListener("disconnected",(()=>{t.motionController=null,t.remove(s),s=null})),t}}class ke extends THREE.EventDispatcher{constructor(e){if(super(),void 0===e)return void console.error("ControllerGestures must be passed a renderer");const t=new THREE.Clock;this.controller1=e.xr.getController(0),this.controller1.userData.gestures={index:0},this.controller1.userData.selectPressed=!1,this.controller1.addEventListener("selectstart",i),this.controller1.addEventListener("selectend",n),this.controller2=e.xr.getController(1),this.controller2.userData.gestures={index:1},this.controller2.userData.selectPressed=!1,this.controller2.addEventListener("selectstart",i),this.controller2.addEventListener("selectend",n),this.doubleClickLimit=.2,this.pressMinimum=.4,this.right=new THREE.Vector3(1,0,0),this.up=new THREE.Vector3(0,1,0),this.type="unknown",this.prevTap="none",this.clock=t;const s=this;function i(){const e=this.userData.gestures;e.startPosition=void 0,e.startTime=t.getElapsedTime(),-1==s.type.indexOf("tap")&&(e.taps=0),s.type="unknown",this.userData.selectPressed=!0}function n(){const e=this.userData.gestures;e.endTime=t.getElapsedTime();e.endTime-e.startTime.05&&(e.startPosition=this.controller1.position.clone())),this.controller2.userData.selectPressed&&void 0===t.startPosition&&(i=s-t.startTime,i>.05&&(t.startPosition=this.controller2.position.clone())),!this.controller1.userData.selectPressed&&"tap"===this.type&&(i=this.clock.getElapsedTime()-e.endTime,i>this.doubleClickLimit)){switch(e.taps){case 1:self.prevTap="tap";break;case 2:this.dispatchEvent({type:"doubletap",position:this.controller1.position,matrixWorld:this.controller1.matrixWorld}),self.prevTap="doubletap"}this.type="unknown",e.taps=0}if("unknown"===this.type&&this.touch)"doubletap"==self.prevTap?(this.type="pinch",this.startDistance=this.controller1.position.distanceTo(this.controller2.position),this.dispatchEvent({type:"pinch",delta:new THREE.Vector3(0,0,0),scale:1,initialise:!0})):(this.type="pan",this.startPosition=this.controller1.position.clone(),this.dispatchEvent({type:"pan",delta:new THREE.Vector3(0,0,0),initialise:!0}));else if(("pinch"===this.type||"pan"===this.type)&&"doubletap"==self.prevTap&&this.controller2.position){const e=this.controller1.position.distanceTo(this.controller2.position)/this.startDistance,t=this.controller1.position.clone().sub(this.startPosition);this.dispatchEvent({type:"pinch",delta:t,scale:e})}}}class Oe{constructor(e,t){this.config=void 0===t?{panelSize:{width:1,height:1},width:512,height:512,opacity:.7,body:{fontFamily:"Arial",fontSize:30,padding:2,backgroundColor:"#000",fontColor:"#fff",borderRadius:6}}:t,void 0===this.config.width&&(this.config.width=512),void 0===this.config.height&&(this.config.height=512),void 0===this.config.body&&(this.config.body={fontFamily:"Arial",size:30,padding:2,backgroundColor:"#000",fontColor:"#fff",borderRadius:6});const s=this.config.body;void 0===s.borderRadius&&(s.borderRadius=6),void 0===s.fontFamily&&(s.fontFamily="Arial"),void 0===s.padding&&(s.padding=2),void 0===s.fontSize&&(s.fontSize=30),void 0===s.backgroundColor&&(s.backgroundColor="#000"),void 0===s.fontColor&&(s.fontColor="#fff"),Object.entries(this.config).forEach((([e,t])=>{if(!("object"!=typeof t||"panelSize"===e||t instanceof THREE.WebGLRenderer||t instanceof THREE.Scene)){const e=void 0!==t.position?t.position:{x:0,y:0};void 0!==e.left&&void 0===e.x&&(e.x=e.left),void 0!==e.top&&void 0===e.y&&(e.y=e.top);const s=void 0!==t.width?t.width:this.config.width,i=void 0!==t.height?t.height:this.config.height;void 0!==e.right&&void 0===e.x&&(e.x=this.config.width-e.right-s),void 0!==e.bottom&&void 0===e.y&&(e.y=this.config.height-e.bottom-i),void 0===e.x&&(e.x=0),void 0===e.y&&(e.y=0),t.position=e,void 0===t.type&&(t.type="text")}}));const i=this.createOffscreenCanvas(this.config.width,this.config.height);this.context=i.getContext("2d"),this.context.save();const n=void 0!==this.config.opacity?this.config.opacity:.7,l=new THREE.MeshBasicMaterial({transparent:!0,opacity:n});this.panelSize=void 0!==this.config.panelSize?this.config.panelSize:{width:1,height:1};const r=new THREE.PlaneGeometry(this.panelSize.width,this.panelSize.height);this.mesh=new THREE.Mesh(r,l),this.texture=new THREE.CanvasTexture(i),this.mesh.material.map=this.texture,this.scene=this.config.scene;if(Object.values(this.config).filter((e=>"input-text"===e.type)).length>0){this.keyboard=new Re(this.panelSize.width,this.config.renderer);this.keyboard.mesh.position.set(0,-.3,.2),this.mesh.add(this.keyboard.mesh)}if(void 0===e)this.content={body:""},this.config.body.type="text";else{this.content=e;Object.values(t).filter((e=>"button"===e.type||"scroll"===e.overflow||"input-text"===e.type)).length>0&&(void 0===t||void 0===t.renderer?console.warn("CanvasUI: button, scroll or input-text in the config but no renderer"):(this.renderer=t.renderer,this.initControllers()))}this.selectedElements=[void 0,void 0],this.selectPressed=[!1,!1],this.scrollData=[void 0,void 0],this.intersects=[void 0,void 0],this.needsUpdate=!0,this.update()}getIntersectY(e){const t=this.config.height||512,s=this.intersects[e];return void 0===s||void 0===s.uv?0:(1-s.uv.y)*t}initControllers(){this.vec3=new THREE.Vector3,this.mat4=new THREE.Matrix4,this.raycaster=new THREE.Raycaster;const e=this;function t(t){const s=t.target===e.controller?0:1,i=e.selectedElements[s];if(void 0!==i)if("button"==i.type)e.select(s);else if("input-text"==i.type&&e.keyboard)if(e.keyboard.visible)e.keyboard.linkedUI=void 0,e.keyboard.linkedText=void 0,e.keyboard.linkedElement=void 0,e.keyboard.visible=!1;else{let t;e.keyboard.linkedUI=e,Object.entries(e.config).forEach((([e,s])=>{s==i&&(t=e)}));const s=(.5-(i.position.y+i.height+e.config.body.padding)/e.config.height)*e.panelSize.height,n=Math.max(e.panelSize.width,e.panelSize.height)/2;e.keyboard.position.set(0,-n/1.5-s,.1),e.keyboard.linkedText=e.content[t],e.keyboard.linkedName=t,e.keyboard.linkedElement=i,e.keyboard.visible=!0}}function s(t){const s=t.target===e.controller?0:1;if(e.selectPressed[s]=!0,void 0!==e.selectedElements[s]&&"scroll"==e.selectedElements[s].overflow){const t=e.selectedElements[s];e.scrollData[s]={scrollY:t.scrollY,rayY:e.getIntersectY(s)}}}function i(t){const s=t.target===e.controller?0:1;e.selectPressed[s]=!1,void 0!==e.selectedElements[s]&&"scroll"==e.selectedElements[s].overflow&&(e.scrollData[s]=void 0)}if(this.controller=this.renderer.xr.getController(0),this.controller.addEventListener("select",t),this.controller.addEventListener("selectstart",s),this.controller.addEventListener("selectend",i),this.controller1=this.renderer.xr.getController(1),this.controller1.addEventListener("select",t),this.controller1.addEventListener("selectstart",s),this.controller1.addEventListener("selectend",i),this.scene){const e=.015,t=new THREE.IcosahedronBufferGeometry(e),s=new THREE.MeshBasicMaterial({color:170}),i=new THREE.Mesh(t,s);i.visible=!1,this.scene.add(i);const n=new THREE.Mesh(t,s);n.visible=!1,this.scene.add(n),this.intersectMesh=[i,n]}}setClip(e){const t=this.context;if(t.restore(),t.save(),void 0!==e.clipPath){const s=new Path2D(e.clipPath);t.clip(s)}else{const s=void 0!==e.position?e.position:{x:0,y:0},i=e.borderRadius||0,n=e.width||this.config.width,l=e.height||this.config.height;if(t.beginPath(),0!==i){const e=Math.PI/2;t.moveTo(s.x+i,s.y),t.arc(s.x+i,s.y+i,i,e,2*e,!0),t.lineTo(s.x,s.y+l-i),t.arc(s.x+i,s.y+l-i,i,0,e,!0),t.lineTo(s.x+n-i,s.y+l),t.arc(s.x+n-i,s.y+l-i,i,3*e,4*e,!0),t.lineTo(s.x+n,s.y+i),t.arc(s.x+n-i,s.y+i,i,2*e,3*e,!0),t.closePath(),t.clip()}else t.rect(s.x,s.y,n,l),t.clip()}}setPosition(e,t,s){void 0!==this.mesh&&this.mesh.position.set(e,t,s)}setRotation(e,t,s){void 0!==this.mesh&&this.mesh.rotation.set(e,t,s)}updateElement(e,t){let s=this.content[e];void 0!==s?("object"==typeof s?s.content=t:s=t,this.content[e]=s,this.needsUpdate=!0):console.warn(`CanvasGUI.updateElement: No ${e} found`)}get panel(){return this.mesh}getElementAtLocation(e,t){const s=this,i=Object.entries(this.config).filter((([i,n])=>{if(!("object"!=typeof n||"panelSize"===i||"body"===i||n instanceof THREE.WebGLRenderer||n instanceof THREE.Scene)){const i=n.position,l=void 0!==n.width?n.width:s.config.width,r=void 0!==n.height?n.height:s.config.height;return e>=i.x&&e=i.y&&t0?(this.hover(t,s[0].uv),this.intersects[t]=s[0],this.scroll(t)):(this.hover(t),this.intersects[t]=void 0,this.scroll(t))}update(){if(void 0===this.mesh)return;if(this.controller&&this.handleController(this.controller,0),this.controller1&&this.handleController(this.controller1,1),this.keyboard&&this.keyboard.visible&&this.keyboard.update(),!this.needsUpdate)return;let e=this.context;e.clearRect(0,0,this.config.width,this.config.height);const t=this.config.body.backgroundColor?this.config.body.backgroundColor:"#000";!this.config.body.fontFamily||this.config.body.fontFamily;const s=this.config.body.fontColor?this.config.body.fontColor:"#fff";!this.config.body.fontSize||this.config.body.fontSize,this.setClip(this.config.body),e.fillStyle=t,e.fillRect(0,0,this.config.width,this.config.height);const i=this;Object.entries(this.content).forEach((([t,n])=>{const l=void 0!==i.config[t]?i.config[t]:i.config.body;if("none"!==(void 0!==l.display?l.display:"block")){const r=void 0!==l.position?l.position:{x:0,y:0},o=void 0!==l.width?l.width:i.config.width,a=void 0!==l.height?l.height:i.config.height;"button"!=l.type||n.toLowerCase().startsWith("")||(void 0===l.borderRadius&&(l.borderRadius=6),void 0===l.textAlign&&(l.textAlign="center")),i.setClip(l);const d=n.toLowerCase().startsWith(""),c=void 0!==i.selectedElements[0]&&this.selectedElements[0]===l||void 0!==i.selectedElements[1]&&this.selectedElements[1]===l;if(void 0!==l.backgroundColor&&(c&&"button"==l.type&&void 0!==l.hover?e.fillStyle=l.hover:e.fillStyle=l.backgroundColor,e.fillRect(r.x,r.y,o,a)),"text"==l.type||"button"==l.type||"input-text"==l.type){let h=!1;if(c?(d||"button"!=l.type?e.fillStyle=void 0!==l.hover?l.hover:void 0!==l.fontColor?l.fontColor:s:e.fillStyle=void 0!==l.fontColor?l.fontColor:s,h=void 0===l.hover):e.fillStyle=void 0!==l.fontColor?l.fontColor:s,d){const t=n.toUpperCase().substring(6,n.length-7);e.save(),e.translate(r.x,r.y);const s=new Path2D(t);e.fill(s),e.restore()}else i.wrapText(t,n);h&&(e.beginPath(),e.strokeStyle="#fff",e.lineWidth=2,e.rect(r.x,r.y,o,a),e.stroke())}else if("img"==l.type)if(void 0===l.img)this.loadImage(n).then((e=>{console.log(`w: ${e.width} | h: ${e.height}`),l.img=e,i.needsUpdate=!0,i.update()})).catch((e=>console.error(e)));else{const t=o/(l.img.width/l.img.height);e.drawImage(l.img,r.x,r.y,o,t)}}})),this.needsUpdate=!1,this.texture.needsUpdate=!0}loadImage(e){return new Promise(((t,s)=>{const i=new THREE.Image;i.addEventListener("load",(()=>t(i))),i.addEventListener("error",(e=>s(e))),i.src=e}))}createOffscreenCanvas(e,t){const s=document.createElement("canvas");return s.width=e,s.height=t,s}fillRoundedRect(e,t,s,i,n){const l=this.context;l.beginPath(),l.moveTo(e+n,t),l.lineTo(e+s-n,t),l.quadraticCurveTo(e+s,t,e+s,t+n),l.lineTo(e+s,t+i-n),l.quadraticCurveTo(e+s,t+i,e+s-n,t+i),l.lineTo(e+n,t+i),l.quadraticCurveTo(e,t+i,e,t+i-n),l.lineTo(e,t+n),l.quadraticCurveTo(e,t,e+n,t),l.closePath(),l.fill()}lookAt(e){void 0!==this.mesh&&(e instanceof Vector3?this.mesh.lookAt(e):console.error("CanvasUI lookAt called parameter not a THREE.Vector3"))}get visible(){return void 0!==this.mesh&&this.mesh.visible}set visible(e){this.mesh&&(this.mesh.visible=e)}get position(){if(void 0!==this.mesh)return this.mesh.position}set position(e){void 0!==this.mesh&&(e instanceof Vector3?this.mesh.position.copy(e):console.error("CanvasUI trying to set the mesh position using a parameter that is not a THREE.Vector3"))}get quaternion(){if(void 0!==this.mesh)return this.mesh.quaternion}set quaternion(e){void 0!==this.mesh&&(e instanceof QUaternion?this.mesh.quaternion.copy(e):console.error("CanvasUI trying to set the mesh quaternion using a parameter that is not a THREE.Quaternion"))}wrapText(e,t){const s=t.split(" ");let i="";const n=[],l=void 0!==this.config[e]?this.config[e]:this.config.body,r=void 0!==l.width?l.width:this.config.width,o=void 0!==l.height?l.height:this.config.height,a=void 0!==l.position?l.position:{x:0,y:0},d=void 0!==l.padding?l.padding:void 0!==this.config.body.padding?this.config.body.padding:10,c=void 0!==l.paddingTop?l.paddingTop:d,h=void 0!==l.paddingLeft?l.paddingLeft:d,p=void 0!==l.paddingBottom?l.paddingBottom:d,m=void 0!==l.paddingRight?l.paddingRight:d,u={x:a.x+h,y:a.y+c,width:r-h-m,height:o-c-p},g=void 0!==l.textAlign?l.textAlign:void 0!==this.config.body.textAlign?this.config.body.textAlign:"left",f=void 0!==l.fontSize?l.fontSize:void 0!==this.config.body.fontSize?this.config.body.fontSize:30,b=void 0!==l.fontFamily?l.fontFamily:void 0!==this.config.body.fontFamily?this.config.body.fontFamily:"Arial",C=f+(void 0!==l.leading?l.leading:void 0!==this.config.body.leading?this.config.body.leading:8),y=this.context;y.textAlign=g,y.font=`${f}px '${b}'`,s.forEach((function(e){let t=s.length>1?`${i}${e} `:e,l=y.measureText(t);if(l.width>u.width&&e.length>1)if(0==i.length&&l.width>u.width){for(;l.width>u.width;){let s=0;do{s++,t=e.substr(0,s),l=y.measureText(t)}while(l.widthu.height&&"scroll"===l.overflow){void 0===l.scrollY&&(l.scrollY=0);const e=void 0!==l.fontColor?l.fontColor:this.config.body.fontColor;y.fillStyle="#aaa",this.fillRoundedRect(a.x+r-12,a.y,12,o,6),y.fillStyle="#666";const t=u.height/v,s=t*o,i=-l.scrollY*t;this.fillRoundedRect(a.x+r-12,a.y+i,12,s,6),y.fillStyle=e,_=l.scrollY,l.minScrollY=u.height-v}let w,S=_+u.y+f/2;switch(g){case"center":w=u.x+u.width/2;break;case"right":w=u.x+u.width;break;default:w=u.x}n.forEach((e=>{S+C>0&&y.fillText(e,w,S),S+=C}))}}class Re{constructor(e,t,s="EN"){const i=this.getConfig(s);i.panelSize={width:e,height:.5*e},i.height=256,i.body={backgroundColor:"#555"},i.renderer=t;const n=this.getContent(s);this.keyboard=new Oe(n,i),this.keyboard.mesh.visible=!1,this.shift=!1}get mesh(){return this.keyboard.mesh}getConfig(e){const t={};let s=10;const i=39.2,n=49,l="#333",r="#000";let o=s,a=s;for(let e=0;e<10;e++){const d={type:"button",position:{x:a,y:o},width:i,height:n,padding:s,paddingTop:20,backgroundColor:r,borderRadius:6,hover:l,onSelect:this.onSelect.bind(this,e)};t[`btn${e}`]=d,a+=49.2}o+=59,a=s;for(let e=0;e<10;e++){const d={type:"button",position:{x:a,y:o},width:i,height:n,padding:s,paddingTop:20,backgroundColor:r,borderRadius:6,hover:l,onSelect:this.onSelect.bind(this,e+10)};t[`btn${e+10}`]=d,a+=49.2}o+=59,a=s;for(let e=0;e<9;e++){const d=0==e||8==e?1.5*i+5:i,c={type:"button",position:{x:a,y:o},width:d,height:n,padding:s,paddingTop:20,backgroundColor:r,borderRadius:6,hover:l,onSelect:this.onSelect.bind(this,e+20)};t[`btn${e+20}`]=c,a+=d+s}o+=59,a=s;for(let e=0;e<5;e++){const d=0==e||4==e?88.4:2==e?186.8:i,c={type:"button",position:{x:a,y:o},width:d,height:n,padding:s,paddingTop:20,backgroundColor:r,borderRadius:6,hover:l,onSelect:this.onSelect.bind(this,e+30)};0==e&&(c.fontSize=20),t[`btn${e+30}`]=c,a+=d+s}return t}getContent(e,t=0){let s,i={};switch(this.language=e,this.keyboardIndex=t,t){case 0:s=["q","w","e","r","t","y","u","i","o","p","a","s","d","f","g","h","j","k","l","@","⇧","z","x","c","v","b","n","m","⇦","","?123",","," ",".","↲"];for(let e=0;e","_","`","~",":",";","⇦","","abc",","," ",".","↲"];for(let e=0;e=0;e--){let s=t.scene.children[e];t.scene.remove(s)}else t.scene=new THREE.Scene;if(void 0!==t.scene_ghost)for(let e=t.scene_ghost.children.length-1;e>=0;e--){let s=t.scene_ghost.children[e];t.scene_ghost.remove(s)}else t.scene_ghost=new THREE.Scene;if(""!=s.htmlCls.setHtmlCls.getCookie("shininess")){let e=parseFloat(s.htmlCls.setHtmlCls.getCookie("shininess"));t.shininess!=e&&s.htmlCls.clickMenuCls.setLogCmd("set shininess "+e,!0),t.shininess=e}if(!s.bNode&&""!=s.htmlCls.setHtmlCls.getCookie("light1")){let e=parseFloat(s.htmlCls.setHtmlCls.getCookie("light1")),i=parseFloat(s.htmlCls.setHtmlCls.getCookie("light2")),n=parseFloat(s.htmlCls.setHtmlCls.getCookie("light3"));t.light1==e&&t.light2==i&&t.light3==n||s.htmlCls.clickMenuCls.setLogCmd("set light | light1 "+e+" | light2 "+i+" | light3 "+n,!0),t.light1=e,t.light2=i,t.light3=n}t.directionalLight=new THREE.DirectionalLight(16777215,t.light1),t.directionalLight2=new THREE.DirectionalLight(16777215,t.light2),t.directionalLight3=new THREE.DirectionalLight(16777215,t.light3),t.cam_z>0?(t.directionalLight.position.set(-1,1,1),t.directionalLight2.position.set(1,1,1),t.directionalLight3.position.set(1,1,-1),t.lightPos=new THREE.Vector3(-1,1,1),t.lightPos2=new THREE.Vector3(1,1,1),t.lightPos3=new THREE.Vector3(1,1,-1)):(t.directionalLight.position.set(-1,1,-1),t.directionalLight2.position.set(1,1,-1),t.directionalLight3.position.set(1,1,1),t.lightPos=new THREE.Vector3(-1,1,-1),t.lightPos2=new THREE.Vector3(1,1,-1),t.lightPos3=new THREE.Vector3(1,1,1));let i=new THREE.AmbientLight(4210752);if(t.scene.add(t.directionalLight),t.scene.add(i),void 0!==t.mdl)for(let e=t.mdl.children.length-1;e>=0;e--){let s=t.mdl.children[e];s.geometry&&s.geometry.dispose(),s.material&&s.material.dispose(),t.mdl.remove(s)}if(void 0!==t.mdlImpostor){for(let e=t.mdlImpostor.children.length-1;e>=0;e--){let s=t.mdlImpostor.children[e];s.geometry&&s.geometry.dispose(),s.material&&s.material.dispose(),t.mdlImpostor.remove(s)}t.mdlImpostor.children.length=0}s.bNode||t.renderer.renderLists.dispose(),t.mdl=new THREE.Object3D,t.mdlImpostor=new THREE.Object3D,t.scene.add(t.mdl),t.scene.add(t.mdlImpostor),t.mdl_ghost=new THREE.Object3D,t.scene_ghost.add(t.mdl_ghost),t.objects=[],t.objects_ghost=[],t.raycaster=new THREE.Raycaster,t.projector=new THREE.Projector,t.mouse=new THREE.Vector2;let n=s.parasCls.backgroundColors[t.opts.background.toLowerCase()];s.bNode||("transparent"===t.opts.background.toLowerCase()?t.renderer.setClearColor(n,0):t.renderer.setClearColor(n,1)),t.perspectiveCamera=new THREE.PerspectiveCamera(20,t.container.whratio,.1,1e4),t.perspectiveCamera.position.set(0,0,t.cam_z),t.perspectiveCamera.lookAt(new THREE.Vector3(0,0,0)),t.orthographicCamera=new THREE.OrthographicCamera,t.orthographicCamera.position.set(0,0,t.cam_z),t.orthographicCamera.lookAt(new THREE.Vector3(0,0,0)),t.cams={perspective:t.perspectiveCamera,orthographic:t.orthographicCamera}}setVrAr(){let e=this.icn3d;e.icn3dui;let t=this;e.bSetVrAr=!0,e.bVr?(e.canvasUI=this.createUI(),e.raycasterVR=new THREE.Raycaster,e.workingMatrix=new THREE.Matrix4,e.workingVector=new THREE.Vector3,e.origin=new THREE.Vector3,e.dolly=new THREE.Object3D,e.dolly.position.z=5,e.dolly.add(e.cam),e.scene.add(e.dolly),e.dollyId=e.dolly.id,e.dummyCam=new THREE.Object3D,e.cam.add(e.dummyCam),e.clock=new THREE.Clock,e.controllers=this.getControllers(),e.controllers.forEach((s=>{s.addEventListener("connected",(function(e){try{const s={},i="https://cdn.jsdelivr.net/npm/@webxr-input-profiles/assets@1.0/dist/profiles",n="generic-trigger";Ce(e.data,i,n).then((({profile:i,assetPath:n})=>{s.name=i.profileId,s.targetRayMode=e.data.targetRayMode,Object.entries(i.layouts).forEach((([e,t])=>{const i={};Object.values(t.components).forEach((e=>{i[e.rootNodeName]=e.gamepadIndices})),s[e]=i})),t.updateControllers(s)}))}catch(e){}})),s.addEventListener("disconnected",(function(){this.remove(this.children[0]),e.controllers.forEach((e=>{}))}))}))):e.bAr&&(e.gestures=new ke(e.renderer),e.scene.add(e.gestures.controller1),e.scene.add(e.gestures.controller2),e.gestures.addEventListener("doubletap",(e=>{t.positionCenter()})),e.gestures.addEventListener("pinch",(s=>{if(void 0!==s.initialise)t.startPosition=e.mdl.position.clone(),t.startScale=e.mdl.scale.clone();else{let i=1;const n=t.startScale.clone().multiplyScalar(s.scale*i);e.mdl.scale.copy(n)}})))}positionCenter(){let e=this.icn3d;e.icn3dui;const t=e.gestures.controller1;e.mdl.position.set(-.06,0,-.6).applyMatrix4(t.matrixWorld),e.mdl.scale.copy(new THREE.Vector3(.005,.005,.005))}setVrArButtons(){let e=this.icn3d,t=e.icn3dui;e.bSetVrArButtons=!0,t.bNode||($("#"+t.pre+"VRButton").remove(),$("#"+t.pre+"viewer").get(0).appendChild(e.VRButtonCls.createButton(e.renderer)),$("#"+t.pre+"ARButton").remove(),$("#"+t.pre+"viewer").get(0).appendChild(e.ARButtonCls.createButton(e.renderer)))}updateControllers(e){this.icn3d.icn3dui,this.addEventForController(e,"right"),this.addEventForController(e,"left")}addEventForController(e,t){let s=this.icn3d;s.icn3dui;const i="right"==t?s.renderer.xr.getController(0):s.renderer.xr.getController(1),n="right"==t?e.right:e.left;if(i&&void 0!==n){let e=!1,t=!1;Object.keys(n).forEach((i=>{-1!=i.indexOf("trigger")&&(e=!0),-1!=i.indexOf("squeeze")&&(t=!0),-1==i.indexOf("thumbstick")&&-1==i.indexOf("touchpad")||(s.xAxisIndex=n[i].xAxis,s.yAxisIndex=n[i].yAxis)})),e&&(i.addEventListener("selectstart",(function(){this.userData.selectPressed=!0})),i.addEventListener("selectend",(function(){this.userData.selectPressed=!1,this.userData.selected=void 0}))),t&&(i.addEventListener("squeezestart",(function(){this.userData.squeezePressed=!0,s.cam.add(s.canvasUI.mesh)})),i.addEventListener("squeezeend",(function(){this.userData.squeezePressed=!1,s.cam.remove(s.canvasUI.mesh)})))}}createUI(){let e=this.icn3d,t=e.icn3dui,s=94,i=50,n=94,l=34,r=12,o="#1c94c4",a="#ccc",d="#fbcb09",c=20;const h={panelSize:{width:2,height:1.6},height:400,select:{type:"button",paddingTop:c,position:{top:6,left:6},width:s,height:i,fontColor:"#000",fontSize:14,backgroundColor:a},residue:{type:"button",paddingTop:c,position:{top:62,left:6},width:s,height:i,fontColor:o,fontSize:r,backgroundColor:a,hover:d,onSelect:function(){e.pk=2,e.pAtomNum||(e.pAtomNum=0),e.cam.remove(e.canvasUI.mesh)}},secondarySelect:{type:"button",paddingTop:12,position:{top:118,left:6},width:s,height:i,fontColor:o,fontSize:r,backgroundColor:a,hover:d,onSelect:function(){e.pk=3,e.pAtomNum||(e.pAtomNum=0),e.cam.remove(e.canvasUI.mesh)}},chainSelect:{type:"button",paddingTop:c,position:{top:174,left:6},width:s,height:i,fontColor:o,fontSize:r,backgroundColor:a,hover:d,onSelect:function(){e.pk=5,e.pAtomNum||(e.pAtomNum=0),e.cam.remove(e.canvasUI.mesh)}},atom:{type:"button",paddingTop:c,position:{top:230,left:6},width:s,height:i,fontColor:o,fontSize:r,backgroundColor:a,hover:d,onSelect:function(){e.pk=1,e.pAtomNum||(e.pAtomNum=0),e.cam.remove(e.canvasUI.mesh)}},reset:{type:"button",paddingTop:c,position:{top:286,left:6},width:s,height:i,fontColor:o,fontSize:r,backgroundColor:a,hover:d,onSelect:function(){e.viewInterPairsCls.resetInteractionPairs(),e.selectionCls.resetAll(),e.cam.remove(e.canvasUI.mesh)}},togglehl:{type:"button",paddingTop:12,position:{top:342,left:6},width:s,height:i,fontColor:o,fontSize:r,backgroundColor:a,hover:d,onSelect:function(){e.hlUpdateCls.toggleHighlight(),e.cam.remove(e.canvasUI.mesh)}},style:{type:"button",paddingTop:c,position:{top:6,left:106},width:s,height:i,fontColor:"#000",fontSize:14,backgroundColor:a},ribbon:{type:"button",paddingTop:c,position:{top:62,left:106},width:s,height:i,fontColor:o,fontSize:r,backgroundColor:a,hover:d,onSelect:function(){e.setOptionCls.setStyle("proteins","ribbon"),e.setOptionCls.setStyle("nucleotides","nucleotide cartoon"),e.cam.remove(e.canvasUI.mesh)}},schematic:{type:"button",paddingTop:c,position:{top:118,left:106},width:s,height:i,fontColor:o,fontSize:r,backgroundColor:a,hover:d,onSelect:function(){e.setOptionCls.setStyle("proteins","schematic"),e.setOptionCls.setStyle("nucleotides","schematic"),e.cam.remove(e.canvasUI.mesh)}},stick:{type:"button",paddingTop:c,position:{top:174,left:106},width:s,height:i,fontColor:o,fontSize:r,backgroundColor:a,hover:d,onSelect:function(){e.setOptionCls.setStyle("proteins","stick"),e.setOptionCls.setStyle("nucleotides","stick"),e.cam.remove(e.canvasUI.mesh)}},sphere:{type:"button",paddingTop:c,position:{top:230,left:106},width:s,height:i,fontColor:o,fontSize:r,backgroundColor:a,hover:d,onSelect:function(){e.setOptionCls.setStyle("proteins","sphere"),e.setOptionCls.setStyle("nucleotides","sphere"),e.cam.remove(e.canvasUI.mesh)}},surface:{type:"button",paddingTop:c,position:{top:286,left:106},width:s,height:i,fontColor:o,fontSize:r,backgroundColor:a,hover:d,onSelect:function(){e.opts.surface="molecular surface",e.applyMapCls.applySurfaceOptions(),e.cam.remove(e.canvasUI.mesh)}},surfaceTrn:{type:"button",paddingTop:12,position:{top:342,left:106},width:s,height:i,fontColor:o,fontSize:r,backgroundColor:a,hover:d,onSelect:function(){e.opts.surface="molecular surface",e.opts.opacity="0.2",e.applyMapCls.applySurfaceOptions(),e.cam.remove(e.canvasUI.mesh)}},color:{type:"button",paddingTop:c,position:{top:6,left:206},width:s,height:i,fontColor:"#000",fontSize:14,backgroundColor:a},rainbow:{type:"button",paddingTop:c,position:{top:62,left:206},width:s,height:i,fontColor:o,fontSize:r,backgroundColor:a,hover:d,onSelect:function(){e.setOptionCls.setOption("color","rainbow for chains"),e.cam.remove(e.canvasUI.mesh)}},atomColor:{type:"button",paddingTop:c,position:{top:118,left:206},width:s,height:i,fontColor:o,fontSize:r,backgroundColor:a,hover:d,onSelect:function(){e.setOptionCls.setOption("color","atom"),e.cam.remove(e.canvasUI.mesh)}},chainColor:{type:"button",paddingTop:c,position:{top:174,left:206},width:s,height:i,fontColor:o,fontSize:r,backgroundColor:a,hover:d,onSelect:function(){e.setOptionCls.setOption("color","chain"),e.cam.remove(e.canvasUI.mesh)}},secondaryColor:{type:"button",paddingTop:12,position:{top:230,left:206},width:s,height:i,fontColor:o,fontSize:r,backgroundColor:a,hover:d,onSelect:function(){e.setOptionCls.setOption("color","secondary structure green"),e.cam.remove(e.canvasUI.mesh)}},charge:{type:"button",paddingTop:c,position:{top:342,left:206},width:s,height:i,fontColor:o,fontSize:r,backgroundColor:a,hover:d,onSelect:function(){e.setOptionCls.setOption("color","charge"),e.cam.remove(e.canvasUI.mesh)}},AlphaFold:{type:"button",paddingTop:c,position:{top:286,left:206},width:s,height:i,fontColor:o,fontSize:r,backgroundColor:a,hover:d,onSelect:function(){e.setOptionCls.setOption("color","confidence"),e.cam.remove(e.canvasUI.mesh)}},unicolor:{type:"button",paddingTop:c,position:{top:6,left:306},width:s,height:i,fontColor:"#000",fontSize:14,backgroundColor:a},red:{type:"button",position:{top:i,left:300},width:n,height:l,fontColor:"red",hover:d,onSelect:function(){e.setOptionCls.setOption("color","red"),e.cam.remove(e.canvasUI.mesh)}},green:{type:"button",position:{top:78,left:300},width:n,height:l,fontColor:"green",hover:d,onSelect:function(){e.setOptionCls.setOption("color","green"),e.cam.remove(e.canvasUI.mesh)}},blue:{type:"button",position:{top:106,left:300},width:n,height:l,fontColor:"blue",hover:d,onSelect:function(){e.setOptionCls.setOption("color","blue"),e.cam.remove(e.canvasUI.mesh)}},blueviolet:{type:"button",position:{top:134,left:300},width:n,height:l,fontColor:"#8A2BE2",hover:d,onSelect:function(){e.setOptionCls.setOption("color","8A2BE2"),e.cam.remove(e.canvasUI.mesh)}},magenta:{type:"button",position:{top:162,left:300},width:n,height:l,fontColor:"magenta",hover:d,onSelect:function(){e.setOptionCls.setOption("color","magenta"),e.cam.remove(e.canvasUI.mesh)}},yellow:{type:"button",position:{top:190,left:300},width:n,height:l,fontColor:"yellow",hover:d,onSelect:function(){e.setOptionCls.setOption("color","yellow"),e.cam.remove(e.canvasUI.mesh)}},orange:{type:"button",position:{top:218,left:300},width:n,height:l,fontColor:"orange",hover:d,onSelect:function(){e.setOptionCls.setOption("color","FFA500"),e.cam.remove(e.canvasUI.mesh)}},cyan:{type:"button",position:{top:246,left:300},width:n,height:l,fontColor:"cyan",hover:d,onSelect:function(){e.setOptionCls.setOption("color","cyan"),e.cam.remove(e.canvasUI.mesh)}},gray:{type:"button",position:{top:274,left:300},width:n,height:l,fontColor:"gray",hover:d,onSelect:function(){e.setOptionCls.setOption("color","888888"),e.cam.remove(e.canvasUI.mesh)}},white:{type:"button",position:{top:302,left:300},width:n,height:l,fontColor:"white",hover:d,onSelect:function(){e.setOptionCls.setOption("color","white"),e.cam.remove(e.canvasUI.mesh)}},analysis:{type:"button",paddingTop:c,position:{top:6,left:406},width:s,height:i,fontColor:"#000",fontSize:14,backgroundColor:a},distance:{type:"button",paddingTop:c,position:{top:62,left:406},width:s,height:i,fontColor:o,fontSize:r,backgroundColor:a,hover:d,onSelect:function(){try{e.bMeasureDistance=!0;let s=e.pickingCls.getPickedAtomList(e.pk,e.pAtom),i=e.pickingCls.getPickedAtomList(e.pk,e.pAtom2),n=e.applyCenterCls.centerAtoms(t.hashUtilsCls.hash2Atoms(s,e.atoms)).center,l=e.applyCenterCls.centerAtoms(t.hashUtilsCls.hash2Atoms(i,e.atoms)).center,r=0,o=0,a="#FFFF00",d=(n.x+l.x)/2,c=(n.y+l.y)/2,h=(n.z+l.z)/2,p=!0;e.analysisCls.addLine(n.x,n.y,n.z,l.x,l.y,l.z,a,p,"distance");let m=(parseInt(10*n.distanceTo(l))/10).toString()+" A";e.analysisCls.addLabel(m,d,c,h,r,a,o,"distance"),e.drawCls.draw(),e.cam.remove(e.canvasUI.mesh)}catch(e){}}},interaction:{type:"button",paddingTop:c,position:{top:118,left:406},width:s,height:i,fontColor:o,fontSize:r,backgroundColor:a,hover:d,onSelect:function(){try{e.viewInterPairsCls.viewInteractionPairs(["selected"],["non-selected"],!1,"3d",1,1,1,1,1,1),e.cam.remove(e.canvasUI.mesh)}catch(e){}}},delphi:{type:"button",paddingTop:c,position:{top:174,left:406},width:s,height:i,fontColor:o,fontSize:r,backgroundColor:a,hover:d,onSelect:async function(){e.phisurftype=22,e.phisurfop=1,e.phisurfwf="no",await e.delphiCls.CalcPhi(65,.15,2,!0),e.cam.remove(e.canvasUI.mesh)}},removeLabel:{type:"button",paddingTop:c,position:{top:230,left:406},width:s,height:i,fontColor:o,fontSize:r,backgroundColor:a,hover:d,onSelect:function(){for(let t in e.labels)e.labels[t]=[];e.drawCls.draw(),e.cam.remove(e.canvasUI.mesh)}},renderer:e.renderer},p=new Oe({select:"Select",residue:"Residue",secondarySelect:"Secondary Structure",chainSelect:"Chain",atom:"Atom",reset:"Reset",togglehl:"Toggle Highlight",style:"Style",ribbon:"Ribbon",schematic:"Schematic",stick:"Stick",sphere:"Sphere",surface:"Surface",surfaceTrn:"Transparent Surface",color:"Color",rainbow:"Rainbow",atomColor:"Atom",chainColor:"Chain",secondaryColor:"Secondary Structure",AlphaFold:"AlphaFold",charge:"Charge",unicolor:"UniColor",red:"M 100 15 L 15 15 L 15 100 L 100 100 Z",green:"M 100 15 L 15 15 L 15 100 L 100 100 Z",blue:"M 100 15 L 15 15 L 15 100 L 100 100 Z",blueviolet:"M 100 15 L 15 15 L 15 100 L 100 100 Z",magenta:"M 100 15 L 15 15 L 15 100 L 100 100 Z",yellow:"M 100 15 L 15 15 L 15 100 L 100 100 Z",orange:"M 100 15 L 15 15 L 15 100 L 100 100 Z",cyan:"M 100 15 L 15 15 L 15 100 L 100 100 Z",gray:"M 100 15 L 15 15 L 15 100 L 100 100 Z",white:"M 100 15 L 15 15 L 15 100 L 100 100 Z",analysis:"Analysis",distance:"Distance",interaction:"Interaction",delphi:"DelPhi Potential",removeLabel:"Remove Label"},h);return p.mesh.position.set(0,0,-3),p}createUILog(){let e=this.icn3d;e.icn3dui;const t={panelSize:{width:2,height:2},height:512,info:{type:"text",overflow:"scroll",position:{top:6,left:6},width:506,height:506,backgroundColor:"#aaa",fontColor:"#000"},renderer:e.renderer},s=new Oe({info:"Debug info"},t);return s.mesh.position.set(0,-1,-2),s}getControllers(){let e=this.icn3d;e.icn3dui;const t=new xe,s=(new THREE.BufferGeometry).setFromPoints([new THREE.Vector3(0,0,0),new THREE.Vector3(0,0,-1)]),i=new THREE.Line(s);i.name="line",i.scale.z=50;const n=[];for(let s=0;s<=1;s++){const l=e.renderer.xr.getController(s);if(!l)continue;e.dolly.add(l),l.add(i.clone()),l.userData.selectPressed=!1,e.cam.add(l),n.push(l);const r=e.renderer.xr.getControllerGrip(s);r.add(t.createControllerModel(r)),e.scene.add(r)}return n}}class Te{constructor(e){this.icn3d=e}setCamera(){let e=this.icn3d,t=e.icn3dui;if(e.bControlGl&&!t.bNode){window.cam=e.cams[e.opts.camera.toLowerCase()];let s=e.maxD;if(window.cam===e.perspectiveCamera){let i=void 0!==e.biomtMatrices&&e.biomtMatrices.length*e.cnt>e.maxatomcnt;i?window.camMaxDFactor=1:void 0!==window.camMaxDFactorFog?window.camMaxDFactor=window.camMaxDFactorFog:window.camMaxDFactor=3,window.cam_z>0?window.cam.position.z=s*window.camMaxDFactor:window.cam.position.z=-s*window.camMaxDFactor,"yes"===e.opts.slab?i?window.cam.near=.1:void 0!==window.camMaxDFactorFog?window.cam.near=s*window.camMaxDFactorFog-10:window.cam.near=s*window.camMaxDFactor:window.cam.near=.1,window.cam.far=1e4,e.bControlGl&&!t.bNode?window.controls=new THREE.TrackballControls(window.cam,void 0,e):t.bNode?e.controls=new THREE.TrackballControls(e.cam,document,e):e.controls=new THREE.TrackballControls(e.cam,document.getElementById(e.id),e)}else window.cam===e.orthographicCamera&&(void 0!==e.biomtMatrices&&e.biomtMatrices.length*e.cnt>10*e.maxatomcnt?window.cam.right=e.maxD/2*1.5:window.cam.right=e.maxD/2*2.5,window.cam.left=-window.cam.right,window.cam.top=window.cam.right/e.container.whratio,window.cam.bottom=-window.cam.right/e.container.whratio,"yes"===e.opts.slab?window.cam.near=2*e.maxD:window.cam.near=0,window.cam.far=1e4,e.bControlGl&&!t.bNode?window.controls=new THREE.OrthographicTrackballControls(window.cam,void 0,e):t.bNode?e.controls=new THREE.OrthographicTrackballControls(e.cam,document,e):e.controls=new THREE.OrthographicTrackballControls(e.cam,document.getElementById(e.id),e));window.cam.updateProjectionMatrix()}e.cam=e.cams[e.opts.camera.toLowerCase()];let s=e.maxD;if(e.cam===e.perspectiveCamera){let i=void 0!==e.biomtMatrices&&e.biomtMatrices.length*e.cnt>e.maxatomcnt;i?e.camMaxDFactor=1:void 0!==e.camMaxDFactorFog?e.camMaxDFactor=e.camMaxDFactorFog:e.camMaxDFactor=3,e.cam_z>0?e.cam.position.z=s*e.camMaxDFactor:e.cam.position.z=-s*e.camMaxDFactor,"yes"===e.opts.slab?i?e.cam.near=.1:void 0!==e.camMaxDFactorFog?e.cam.near=s*e.camMaxDFactorFog-10:e.cam.near=s*e.camMaxDFactor:e.cam.near=.1,e.cam.far=1e4,e.bControlGl&&!t.bNode?window.controls=new THREE.TrackballControls(e.cam,void 0,e):t.bNode?e.controls=new THREE.TrackballControls(e.cam,document,e):e.controls=new THREE.TrackballControls(e.cam,document.getElementById(e.id),e)}else e.cam===e.orthographicCamera&&(void 0!==e.biomtMatrices&&e.biomtMatrices.length*e.cnt>10*e.maxatomcnt?e.cam.right=e.maxD/2*1.5:e.cam.right=e.maxD/2*2.5,e.cam.left=-e.cam.right,e.cam.top=e.cam.right/e.container.whratio,e.cam.bottom=-e.cam.right/e.container.whratio,"yes"===e.opts.slab?e.cam.near=2*e.maxD:e.cam.near=0,e.cam.far=1e4,e.bControlGl&&!t.bNode?window.controls=new THREE.OrthographicTrackballControls(e.cam,void 0,e):t.bNode?e.controls=new THREE.OrthographicTrackballControls(e.cam,document,e):e.controls=new THREE.OrthographicTrackballControls(e.cam,document.getElementById(e.id),e));e.cam.updateProjectionMatrix()}}class Ee{constructor(e){this.icn3d=e}setFog(e){let t=this.icn3d,s=t.icn3dui.parasCls.backgroundColors[t.opts.background.toLowerCase()];if(e){let e=t.applyCenterCls.centerAtoms(t.hAtoms);t.maxD=e.maxD,t.maxD<25&&(t.maxD=25)}let i=void 0!==t.biomtMatrices&&t.biomtMatrices.length*t.cnt>t.maxatomcnt;if("yes"===t.opts.fog)if("perspective"===t.opts.camera)if(i)t.scene.fog=void 0,t.bSetFog=!1;else{let e=t._zoomFactor>1?1*t._zoomFactor:t._zoomFactor;t.scene.fog=new THREE.Fog(s,2.5*t.maxD*e,4*t.maxD*e),t.bSetFog=!0,t.camMaxDFactorFog=3}else"orthographic"===t.opts.camera&&(t.scene.fog=void 0,t.bSetFog=!1);else t.scene.fog=void 0,t.bSetFog=!1}}class Pe{constructor(e){this.icn3d=e}createBox(e,t,s,i,n,l){let r=this.icn3d,o=r.icn3dui;if(o.bNode)return;void 0===t&&(t=.8),void 0===s&&(s=!1),void 0===i&&(i=.8),l?void 0===n&&(n=r.hColor):void 0===n&&(n=e.color);let a=s?t:(o.parasCls.vdwRadii[e.elem.toUpperCase()]||t)*(i||1);this.createBox_base(e.coord,a,n,l)}createBox_base(e,t,s,i,n,l,r){let o,a=this.icn3d;a.icn3dui.bNode||(void 0===r&&(r=l?.5:1),new THREE.BoxGeometry(1,1,1),o=new THREE.Mesh(a.boxGeometry,new THREE.MeshPhongMaterial({transparent:!0,opacity:r,specular:a.frac,shininess:a.shininess,emissive:a.emissive,color:s})),o.scale.x=o.scale.y=o.scale.z=t,o.position.copy(e),a.mdl.add(o),i?a.prevHighlightObjects.push(o):n?a.prevOtherMesh.push(o):a.objects.push(o))}createBoxRepresentation_P_CA(e,t,s){let i=this.icn3d;if(i.icn3dui.bNode)return;let n=this;i.reprSubCls.createRepresentationSub(e,(function(e){"CA"!==e.name&&"O3'"!==e.name&&"O3*"!==e.name||n.createBox(e,void 0,void 0,t,void 0,s)}))}}class Me{constructor(e){this.icn3d=e}createBrick(e,t,s,i){let n=this.icn3d;if(n.icn3dui.bNode)return;let l=new THREE.CylinderGeometry(1,1,1,4,1),r=new THREE.Mesh(l,new THREE.MeshPhongMaterial({specular:n.frac,shininess:n.shininess,emissive:n.emissive,color:i}));r.position.copy(e).add(t).multiplyScalar(.5),r.matrixAutoUpdate=!1,r.lookAt(t.clone().sub(e)),r.updateMatrix(),r.matrix.multiply((new THREE.Matrix4).makeScale(s,s,e.distanceTo(t))).multiply((new THREE.Matrix4).makeRotationX(.5*Math.PI)),n.mdl.add(r)}}class De{constructor(e){this.icn3d=e}createCurveSubArrow(e,t,s,i,n,l,r,o,a,d,c,h,p,m,u){if(this.icn3d.icn3dui.bNode)return;let g=[],f=[];g.push(e),f.push(o),this.prepareStrand(g,f,t,s,i,void 0,n,l,r,a,d,!1,c,h,p,m,u),g=[],f=[]}createStripArrow(e,t,s,i,n,l,r,o,a,d,c,h,p,m,u,g){if(this.icn3d.icn3dui.bNode)return;let f=[],b=[];f.push(e),f.push(t),b.push(o),b.push(a),this.prepareStrand(f,b,void 0,s,i,n,l,void 0,r,d,c,!0,h,p,m,u,g),f=[],b=[]}prepareStrand(e,t,s,i,n,l,r,o,a,d,c,h,p,m,u,g,f){let b=this.icn3d,C=b.icn3dui;if(1===d.length)return;let y=i,v=!u,_=[];_.push(i[i.length-2]),_.push(i[i.length-1]),n=n||b.axisDIV;let w,S,A,x,k=2/(a-1),O={};for(let e=0,s=t.length;e1)if(void 0!==d){let i,n,l=[];for(let r=0,o=p.length;r0&&i.tubeCls.createTube(a,"CA",i.coilWidth,s),Object.keys(d).length>0&&i.strandCls.createStrand(d,void 0,void 0,!0,0,i.helixSheetWidth,!1,2*i.ribbonthickness,s)):(Object.keys(a).length>0&&i.tubeCls.createTube(a,"CA",i.coilWidth),Object.keys(d).length>0&&i.strandCls.createStrand(d,void 0,void 0,!0,0,i.helixSheetWidth,!1,2*i.ribbonthickness))}createCylinderCurve(e,t,s,i,n){let l=this.icn3d;if(l.icn3dui.bNode)return;let r,o,a,d,c,h,p=null;for(a in e)if(d=e[a],!d.het&&(c=d.structure+"_"+d.chain,h=d.structure+"_"+r,-1!=t.indexOf(d.name))){if(null!==p&&r===d.chain&&l.ParserUtilsCls.getResiNCBI(h,o)+1===l.ParserUtilsCls.getResiNCBI(c,d.resi)&&Math.abs(p.coord.x-d.coord.x)<8&&Math.abs(p.coord.y-d.coord.y)<8&&Math.abs(p.coord.z-d.coord.z)<8){let e=p.coord.clone().add(d.coord).multiplyScalar(.5);if(n)1===n&&(this.createCylinder(p.coord,e,s,p.color,n),this.createCylinder(e,d.coord,s,d.color,n),l.sphereCls.createSphere(d,s,!0,1,n));else if(i){let t=l.lineCls.createSingleLine(p.coord,e,p.color,!1);l.mdl.add(t),l.objects.push(t),t=l.lineCls.createSingleLine(e,d.coord,d.color,!1),l.mdl.add(t),l.objects.push(t)}else this.createCylinder(p.coord,e,s,p.color),this.createCylinder(e,d.coord,s,d.color),l.sphereCls.createSphere(d,s,!0,1,n)}p=d,r=d.chain,o=d.resi,l.sphereCls.createSphere(d,s,!0,1,n),2===n&&l.boxCls.createBox(d,void 0,void 0,void 0,void 0,n)}if(null!==p&&r===d.chain&&l.ParserUtilsCls.getResiNCBI(h,o)+1===l.ParserUtilsCls.getResiNCBI(c,d.resi)&&Math.abs(p.coord.x-d.coord.x)<8&&Math.abs(p.coord.y-d.coord.y)<8&&Math.abs(p.coord.z-d.coord.z)<8){let e=p.coord.add(d.coord).multiplyScalar(.5);if(n)1===n&&(this.createCylinder(p.coord,e,s,p.color,n),this.createCylinder(e,d.coord,s,d.color,n),l.sphereCls.createSphere(d,s,!0,1,n));else if(i){let t=l.lineCls.createSingleLine(p.coord,e,p.color,!1);l.mdl.add(t),l.objects.push(t),t=l.lineCls.createSingleLine(e,d.coord,d.color,!1),l.mdl.add(t),l.objects.push(t)}else this.createCylinder(p.coord,e,s,p.color),this.createCylinder(e,d.coord,s,d.color)}}}class Le{constructor(e){this.icn3d=e}createLineRepresentation(e,t){let s=this.icn3d;if(s.icn3dui.bNode)return;let i=new THREE.BufferGeometry,n=[],l=[],r=0,o=0;s.reprSubCls.createRepresentationSub(e,void 0,(function(e,t){if(e.color===t.color)n[r++]=e.coord.x,n[r++]=e.coord.y,n[r++]=e.coord.z,n[r++]=t.coord.x,n[r++]=t.coord.y,n[r++]=t.coord.z,l[o++]=e.color.r,l[o++]=e.color.g,l[o++]=e.color.b,l[o++]=t.color.r,l[o++]=t.color.g,l[o++]=t.color.b;else{let s=e.coord.clone().add(t.coord).multiplyScalar(.5);n[r++]=e.coord.x,n[r++]=e.coord.y,n[r++]=e.coord.z,n[r++]=s.x,n[r++]=s.y,n[r++]=s.z,n[r++]=t.coord.x,n[r++]=t.coord.y,n[r++]=t.coord.z,n[r++]=s.x,n[r++]=s.y,n[r++]=s.z,l[o++]=e.color.r,l[o++]=e.color.g,l[o++]=e.color.b,l[o++]=e.color.r,l[o++]=e.color.g,l[o++]=e.color.b,l[o++]=t.color.r,l[o++]=t.color.g,l[o++]=t.color.b,l[o++]=t.color.r,l[o++]=t.color.g,l[o++]=t.color.b}}));if(i.setAttribute("position",new THREE.BufferAttribute(new Float32Array(n),3)),i.setAttribute("color",new THREE.BufferAttribute(new Float32Array(l),3)),2!==t){let e;1===t||(e=new THREE.LineSegments(i,new THREE.LineBasicMaterial({linewidth:s.linewidth,vertexColors:!0})),s.mdl.add(e)),1===t?s.prevHighlightObjects.push(e):s.objects.push(e)}else 2===t&&s.boxCls.createBoxRepresentation_P_CA(e,.8,t)}createConnCalphSidechain(e,t){let s=this.icn3d;if(s.icn3dui.bNode)return;let i={};for(let s in e){let n=e[s];if(!n.het&&n.style2===t){i[n.structure+"_"+n.chain+"_"+n.resi]=1}}let n=[],l=[];for(let e in i){let t=s.firstAtomObjCls.getFirstAtomObjByName(s.residues[e],"CA");if(void 0!==t)for(let e=0,i=t.bonds.length;e=t.bonds.length&&e.bonds.length>1)s=e.serial,l=e.bonds[0],d=e.bonds[1];else{if(!(t.bonds.length>=e.bonds.length&&t.bonds.length>1))return void console.log("Double bond was not drawn due to the undefined cross plane");s=t.serial,l=t.bonds[0],d=t.bonds[1]}let i=r.atoms[s].coord.clone();i.sub(r.atoms[l].coord);let n=r.atoms[s].coord.clone();n.sub(r.atoms[d].coord),i.cross(n),0==parseInt(1e4*i.length())&&(i=new THREE.Vector3(.2,.3,.5)),c=t.coord.clone(),c.sub(e.coord),c.cross(i).normalize().multiplyScalar(.2*o),0==parseInt(1e4*c.length())&&(i=new THREE.Vector3(.5,.3,.2),c.cross(i).normalize().multiplyScalar(.2*o))}e.color===t.color?r.dAtoms.hasOwnProperty(e.serial)&&r.dAtoms.hasOwnProperty(t.serial)&&(r.cylinderCls.createCylinder(e.coord.clone().add(c),t.coord.clone().add(c),a,e.color,n),r.cylinderCls.createCylinder(e.coord.clone().sub(c),t.coord.clone().sub(c),a,e.color,n)):r.bImpo?r.dAtoms.hasOwnProperty(e.serial)&&r.dAtoms.hasOwnProperty(t.serial)&&(r.cylinderCls.createCylinder(e.coord.clone().add(c),t.coord.clone().add(c),a,e.color,n,t.color),r.cylinderCls.createCylinder(e.coord.clone().sub(c),t.coord.clone().sub(c),a,e.color,n,t.color)):r.dAtoms.hasOwnProperty(e.serial)&&r.dAtoms.hasOwnProperty(t.serial)&&(r.cylinderCls.createCylinder(e.coord.clone().add(c),i.clone().add(c),a,e.color,n),r.cylinderCls.createCylinder(t.coord.clone().add(c),i.clone().add(c),a,t.color,n),r.cylinderCls.createCylinder(e.coord.clone().sub(c),i.clone().sub(c),a,e.color,n),r.cylinderCls.createCylinder(t.coord.clone().sub(c),i.clone().sub(c),a,t.color,n))}else if(r.aromaticbonds.hasOwnProperty(l)){let s,l,d;if(e.bonds.length>t.bonds.length&&e.bonds.length>1)s=e.serial,l=e.bonds[0],d=e.bonds[1];else{if(!(t.bonds.length>1))return;s=t.serial,l=t.bonds[0],d=t.bonds[1]}let c=r.atoms[s].coord.clone();c.sub(r.atoms[l].coord);let h=r.atoms[s].coord.clone();h.sub(r.atoms[d].coord),c.cross(h);let p=t.coord.clone();p.sub(e.coord),p.cross(c).normalize().multiplyScalar(.2*o);let m=0;for(let s=0,i=e.bondOrder.length;so+1?(s=k.clone(),i=d.atoms[G[G.length-1-o-1]].coord.clone(),i.sub(s)):s=new THREE.Vector3(Math.random(),Math.random(),Math.random()))):d.bCalphaOnly&&"CA"===b.name&&(G.length>o+1?(s=k.clone(),i=d.atoms[G[G.length-1-o-1]].coord.clone(),i.sub(s)):s=new THREE.Vector3(Math.random(),Math.random(),Math.random())),s.normalize(),s.multiplyScalar(f),null!==I&&s.dot(I)<0&&s.negate(),I=s;for(let e=0,s=2/(t-1);e6||c&&Math.abs(S.y-c.y)>6||c&&Math.abs(S.z-c.z)>6;if((u!==b.chain||b.ssbegin||b.ssend||B===j-1||p)&&m[0].length>0){let c="CA",u=[],g=[];if(isNaN(d.atoms[M].resi))u=[];else{let e=d.atoms[M].structure+"_"+d.atoms[M].chain+"_"+(parseInt(d.atoms[M].resi)-1).toString(),t=d.firstAtomObjCls.getAtomCoordFromResi(e,c);u=void 0!==t?[t]:[]}if(!isNaN(d.atoms[M].resi)){let e=d.atoms[M].structure+"_"+d.atoms[M].chain+"_"+(parseInt(d.atoms[M].resi)+1).toString(),t=d.firstAtomObjCls.getAtomCoordFromResi(e,c);void 0!==t&&g.push(t);let s=d.atoms[M].structure+"_"+d.atoms[M].chain+"_"+(parseInt(d.atoms[M].resi)+2).toString(),i=d.firstAtomObjCls.getAtomCoordFromResi(s,c);void 0!==i&&g.push(i)}if(!p){1===a||2===a?w.push(d.hColor):w.push(R),f=b.ssend&&"sheet"===b.ss?0:"coil"===T&&b.ssbegin||E&&b.ssbegin||"coil"===b.ss?n:l;let s,i,o=4;"O"===b.name?(s=A.clone(),s.sub(S)):d.bCalphaOnly&&"CA"===b.name&&(G.length>o?(s=S.clone(),i=d.atoms[G[G.length-1-o]].coord.clone(),i.sub(s)):s=new THREE.Vector3(Math.random(),Math.random(),Math.random())),s.normalize(),s.multiplyScalar(f),null!==I&&s.dot(I)<0&&s.negate(),I=s;for(let e=0,s=2/(t-1);e0){let e="CA",n=[],l=[];if(isNaN(d.atoms[M].resi))n=[];else{let t=d.atoms[M].structure+"_"+d.atoms[M].chain+"_"+(parseInt(d.atoms[M].resi)-1).toString();d.firstAtomObjCls.getAtomCoordFromResi(t,e)}for(let e=0;!i&&e0;--e){let t=a.structure+"_"+a.chain+"_"+e;if(!c.residues.hasOwnProperty(t))break;let s=c.firstAtomObjCls.getFirstCalphaAtomObj(c.residues[t]);if(s.ss===a.ss&&s.ssbegin){g=s.resi;break}}for(let e=g;e0&&(o!==c.chain||Math.abs(c.coord.x-h.coord.x)>6||Math.abs(c.coord.y-h.coord.y)>6||Math.abs(c.coord.z-h.coord.z)>6||r.ParserUtilsCls.getResiNCBI(c.structure+"_"+o,a)+13||Math.abs(c.coord.y-h.coord.y)>3||Math.abs(c.coord.z-h.coord.z)>3))){if(2!==i){if(!isNaN(d.resi)&&!isNaN(h.resi)){let e=d.structure+"_"+d.chain+"_"+(parseInt(d.resi)-1).toString(),i=r.firstAtomObjCls.getAtomCoordFromResi(e,t);g=void 0!==i?[i]:[];let l=h.structure+"_"+h.chain+"_"+(parseInt(h.resi)+1).toString(),o=h.structure+"_"+h.chain+"_"+(parseInt(h.resi)+2).toString(),a=h.structure+"_"+h.chain+"_"+(parseInt(h.resi)+3).toString();if(r.residues.hasOwnProperty(l)){let e=r.firstAtomObjCls.getAtomFromResi(l,t);void 0!==e&&e.ssbegin&&(l=h.structure+"_"+h.chain+"_"+(parseInt(h.resi)+2).toString(),o=h.structure+"_"+h.chain+"_"+(parseInt(h.resi)+3).toString(),p.push(e.coord),n?u.push(this.getCustomtubesize(l)):u.push(this.getRadius(s,e)),m.push(e.color))}if(1==p.length&&r.residues.hasOwnProperty(l)){let e=r.firstAtomObjCls.getAtomFromResi(l,t);if(e){p.push(e.coord),m.push(e.color);let t=this.getRadius(s,c);u.push(t),l=o,o=a}}let b=r.firstAtomObjCls.getAtomCoordFromResi(l,t);void 0!==b&&f.push(b);let C=r.firstAtomObjCls.getAtomCoordFromResi(o,t);void 0!==C&&f.push(C)}C.push({pnts:p,colors:m,radii:u,prevone:g,nexttwo:f})}p=[],m=[],u=[],g=[],f=[],d=c,b=0}if(0==p.length&&!isNaN(c.resi)){let e=c.structure+"_"+c.chain+"_"+(parseInt(c.resi)-1).toString();r.residues.hasOwnProperty(e)&&(h=r.firstAtomObjCls.getAtomFromResi(e,t),void 0!==h&&h.ssend&&(p.push(h.coord),n?u.push(this.getCustomtubesize(e)):u.push(this.getRadius(s,h)),m.push(h.color)))}let e;p.push(c.coord),e=n?this.getCustomtubesize(c.structure+"_"+c.chain+"_"+c.resi):this.getRadius(s,c),u.push(e),m.push(c.color),1===b&&(m[m.length-2]=c.color),o=c.chain,a=c.resi;let l=1.2;2!==i||c.ssbegin||r.boxCls.createBox(c,void 0,void 0,l,void 0,i),++b,h=c}if(2!==i){if(g=[],void 0!==d&&!isNaN(d.resi)){let e=d.structure+"_"+d.chain+"_"+(parseInt(d.resi)-1).toString(),s=r.firstAtomObjCls.getAtomCoordFromResi(e,t);g=void 0!==s?[s]:[]}if(f=[],void 0!==c&&!isNaN(c.resi)){let e=c.structure+"_"+c.chain+"_"+(parseInt(c.resi)+1).toString(),i=c.structure+"_"+c.chain+"_"+(parseInt(c.resi)+2).toString(),n=c.structure+"_"+c.chain+"_"+(parseInt(c.resi)+3).toString();if(1==p.length&&r.residues.hasOwnProperty(e)){let l=r.firstAtomObjCls.getAtomFromResi(e,t);if(l){p.push(l.coord),m.push(l.color);let t=this.getRadius(s,c);u.push(t),e=i,i=n}}let l=r.firstAtomObjCls.getAtomCoordFromResi(e,t);void 0!==l&&f.push(l);let o=r.firstAtomObjCls.getAtomCoordFromResi(i,t);void 0!==o&&f.push(o)}C.push({pnts:p,colors:m,radii:u,prevone:g,nexttwo:f})}for(let e=0,t=C.length;e1?a.parasCls.thr(t[t.length-2]):a.parasCls.thr(t[e]),f[y++]=d.r,f[y++]=d.g,f[y++]=d.b}}let x,k=0;for(let e=0,t=w.length-1;er&&(l=r,e=1);for(let t=0;t0&&t.b<=100?.01*t.b:t.b>100?1:s.coilWidth),i}}class ze{constructor(e){this.icn3d=e}drawCartoonNucleicAcid(e,t,s,i){this.drawStrandNucleicAcid(e,2,t,!0,void 0,s,i)}drawStrandNucleicAcid(e,t,s,i,n,l,r){let o,a,d,c=this.icn3d;if(c.icn3dui.bNode)return;2===r&&(t=void 0,l=void 0),n=n||c.nucleicAcidWidth,s=s||c.axisDIV,t=t||c.nucleicAcidStrandDIV;let h=[];for(d=0;dy?y=C:C=y);let v=.8*b/y;if(g.width=C,g.height=y,f.clearRect(0,0,C,y),h)if(f.fillStyle="rgba("+n.r+","+n.g+","+n.b+","+n.a+")",f.strokeStyle="rgba("+l.r+","+l.g+","+l.b+","+l.a+")",f.lineWidth=r,p){let e=.4*C;this.circle(f,0,0,C,y,e)}else{let e=0;this.roundRect(f,0,0,C,y,e)}f.font="Bold "+a+"px "+o,f.textAlign="center",f.textBaseline="middle",f.fillStyle="rgba("+u.r+", "+u.g+", "+u.b+", 1.0)",f.strokeStyle="rgba("+u.r+", "+u.g+", "+u.b+", 1.0)",f.fillText(e,.5*C,.5*y);let _=new THREE.Texture(g);_.needsUpdate=!0;let w=new THREE.SpriteMaterial({map:_,depthTest:!1,depthWrite:!1});w.map.minFilter=THREE.LinearFilter;let S=new THREE.Sprite(w);return p?S.scale.set(.3*d,.3*d,1):S.scale.set(v*d,d,1),S.renderOrder=1,S}roundRect(e,t,s,i,n,l){e.beginPath(),e.moveTo(t+l,s),e.lineTo(t+i-l,s),e.quadraticCurveTo(t+i,s,t+i,s+l),e.lineTo(t+i,s+n-l),e.quadraticCurveTo(t+i,s+n,t+i-l,s+n),e.lineTo(t+l,s+n),e.quadraticCurveTo(t,s+n,t,s+n-l),e.lineTo(t,s+l),e.quadraticCurveTo(t,s,t+l,s),e.closePath(),e.fill(),e.stroke()}circle(e,t,s,i,n,l){e.beginPath(),e.arc(t+i/2,.9*(s+n/2),l,0,2*Math.PI,!0),e.closePath(),e.fill(),e.stroke()}}class Ve{constructor(e){this.icn3d=e,this.textSpriteCls=new Ge(e)}createLabelRepresentation(e){let t=this.icn3d;t.icn3dui;let s=t.oriMaxD/100;s<.4&&(s=.4);let i=3*s*t.labelScale;for(let s in e){let n=void 0!==e[s]?e[s]:[],l="black"!=t.opts.background?t.colorWhitebkgd:t.colorBlackbkgd;for(let e=0,r=n.length;e.99999)h.set(0,0,0,1);else if(e.y<-.99999)h.set(1,0,0,0);else{let t=new THREE.Vector3;t.set(e.z,0,-e.x).normalize();let s=Math.acos(e.y);h.setFromAxisAngle(t,s)}return c.applyQuaternion(h),c.scale.set(l,n,l),c.position.copy(t),c}setPc1Axes(){let e=this.icn3d,t=e.icn3dui;if(t.bNode)return;let s=t.hashUtilsCls.intHash(e.hAtoms,e.dAtoms),i=[],n=Object.keys(s).length<100;for(let t in s){let s=e.atoms[t],l=s.structure+"_"+s.chain+"_"+s.resi;(n||""!=l)&&i.push(s.coord.clone())}let l=t.rmsdSuprCls.getEigenForSelection(i,i.length),r=new THREE.Vector3(l.h1[0],l.h1[1],l.h1[2]);if(0==l.k&&e.bRender)return void alert("Can't determine the first principal component. Please select a subset and try it again.");let o=e.applyCenterCls.centerAtoms(s),a=o.maxD,d=o.center,c=d.clone().add(r.normalize().multiplyScalar(.4*a)),h=new THREE.Vector3(l.h2[0],l.h2[1],l.h2[2]),p=d.clone().add(h.normalize().multiplyScalar(.3*a)),m=new THREE.Vector3(l.h3[0],l.h3[1],l.h3[2]),u=d.clone().add(m.normalize().multiplyScalar(.3*a));this.buildAxes(void 0,d,c,p,u,!0);let g=[d,c,p,u];return e.axes.push(g),e.drawCls.draw(),g}}class Ye{constructor(e){this.icn3d=e}showGlycans(){let e=this.icn3d,t=e.icn3dui;if(t.bNode)return;let s={},i=e.dAtoms;for(let n in i){let i=e.atoms[n];i.het&&-1!=t.parasCls.glycanHash.hasOwnProperty(i.resn)&&(void 0===s[i.resn]&&(s[i.resn]={}),"Misc"!=i.chain&&(s[i.resn][i.structure+"_"+i.chain+"_"+i.resi]=1))}let n=Object.keys(s);for(let i=0,l=n.length;i>2))+i+((2&t)>>1))*c+n+(1&t)]&this.ISDONE)<=3&&(t.push(t[i]),i=t.length-1,t.push(t[n]),n=t.length-1,t.push(t[l]),l=t.length-1),s.push(i),s.push(n),s.push(l)}}},Xe.prototype.laplacianSmooth=function(e,t,s){let i,n,l,r,o,a=new Array(t.length);for(i=0,n=t.length;ithis.origextent[1][0])&&(!(tthis.origextent[1][1])&&!(sthis.origextent[1][2]))},Ke.prototype.getFacesAndVertices=function(){let e,t,s=this.verts;for(e=0,t=s.length;eh&&(h=this.pmaxy-this.pminy),this.pmaxz-this.pminz>h&&(h=this.pmaxz-this.pminz),this.scaleFactor=(c-1)/h,this.scaleFactor=this.defaultScaleFactor,this.defaultScaleFactor*h>this.threshbox&&(c=Math.floor(this.threshbox),this.scaleFactor=(this.threshbox-1)/h),this.bCalcArea&&(this.scaleFactor=this.defaultScaleFactor),this.pLength=Math.ceil(this.scaleFactor*(this.pmaxx-this.pminx))+1,this.pWidth=Math.ceil(this.scaleFactor*(this.pmaxy-this.pminy))+1,this.pHeight=Math.ceil(this.scaleFactor*(this.pmaxz-this.pminz))+1,this.boundingatom(t),this.cutRadius=this.probeRadius*this.scaleFactor,this.vpBits=new Uint8Array(this.pLength*this.pWidth*this.pHeight),this.vpDistance=new Float64Array(this.pLength*this.pWidth*this.pHeight),this.vpAtomID=new Int32Array(this.pLength*this.pWidth*this.pHeight),this.vpColor=[],this.vpPot=[]},Ke.prototype.boundingatom=function(e){let t,s,i,n,l=[];for(let r in this.vdwRadii){if(!this.vdwRadii.hasOwnProperty(r))continue;let o=this.vdwRadii[r];l[r]=e?(o+this.probeRadius)*this.scaleFactor+.5:o*this.scaleFactor+.5,i=l[r]*l[r],this.widxz[r]=Math.floor(l[r])+1,this.depty[r]=new Int32Array(this.widxz[r]*this.widxz[r]),n=0;for(let e=0;ei?this.depty[r][n]=-1:(s=Math.sqrt(i-t),this.depty[r][n]=Math.floor(s)),n++}},Ke.prototype.fillvoxels=function(e,t){let s,i,n,l;for(s=0,l=this.vpBits.length;sc&&(a=c),C>h&&(C=h),v>p&&(v=p);let _,w=g[o*m+d*u+y],S=g[a*m+d*u+y],A=g[o*m+C*u+y],x=g[o*m+d*u+v],k=g[a*m+C*u+y],O=g[o*m+C*u+v],R=g[a*m+d*u+v],I=g[a*m+C*u+v],T=r.x-o,E=r.y-d,P=r.z-y,M=((w*(1-T)+S*T)*(1-E)+(A*(1-T)+k*T)*E)*(1-P)+((x*(1-T)+R*T)*(1-E)+(O*(1-T)+I*T)*E)*P,D=s*f+i*b+n;this.vpPot[D]=M,M>this.isovalue&&(M=this.isovalue),M<-this.isovalue&&(M=-this.isovalue),M>0?(M/=1*this.isovalue,_=new THREE.Color(1-M,1-M,1)):(M/=-1*this.isovalue,_=new THREE.Color(1,1-M,1-M)),this.vpColor[D]=_}}for(s=0,l=this.vpBits.length;s=this.pLength||g>=this.pWidth||f>=this.pHeight)continue;let h=u*S+g*this.pHeight+f;if(this.vpBits[h]&this.INOUT){let p=t[this.vpAtomID[h]];p.serial!=e.serial&&(l=s+a-Math.floor(.5+this.scaleFactor*(p.x+this.ptranx)),r=i+d-Math.floor(.5+this.scaleFactor*(p.y+this.ptrany)),o=n+c-Math.floor(.5+this.scaleFactor*(p.z+this.ptranz)),a*a+d*d+c*c=this.pLength||p>=this.pWidth||m>=this.pHeight)continue;let u=h*S+p*this.pHeight+m;if(this.vpBits[u]&this.ISDONE){let h=t[this.vpAtomID[u]];h.serial!=e.serial&&(l=s+a-Math.floor(.5+this.scaleFactor*(h.x+this.ptranx)),r=i+d-Math.floor(.5+this.scaleFactor*(h.y+this.ptrany)),o=n+c-Math.floor(.5+this.scaleFactor*(h.z+this.ptranz)),a*a+d*d+c*c-1&&r-1&&a-1&&o=h)||(this.vpBits[n]|=this.ISBOUND))},Ke.prototype.fastoneshell=function(e,t){let s,i,n,l,r,o,a,d,c,h,p,m,u=[];if(0===e.length)return u;let g={ix:-1,iy:-1,iz:-1},f=this.pWidth*this.pHeight;for(a=0,c=e.length;a-1&&g.iy-1&&g.iz-1&&(m=g.ix*f+this.pHeight*g.iy+g.iz,this.vpBits[m]&this.INOUT&&!(this.vpBits[m]&this.ISDONE)?(t.set(g.ix,g.iy,n+this.nb[d][2],p),l=g.ix-p.ix,r=g.iy-p.iy,o=g.iz-p.iz,h=l*l+r*r+o*o,this.vpDistance[m]=h,this.vpBits[m]|=this.ISDONE,this.vpBits[m]|=this.ISBOUND,u.push({ix:g.ix,iy:g.iy,iz:g.iz})):this.vpBits[m]&this.INOUT&&this.vpBits[m]&this.ISDONE&&(l=g.ix-p.ix,r=g.iy-p.iy,o=g.iz-p.iz,h=l*l+r*r+o*o,h-1&&g.iy-1&&g.iz-1&&(m=g.ix*f+this.pHeight*g.iy+g.iz,this.vpBits[m]&this.INOUT&&!(this.vpBits[m]&this.ISDONE)?(t.set(g.ix,g.iy,n+this.nb[d][2],p),l=g.ix-p.ix,r=g.iy-p.iy,o=g.iz-p.iz,h=l*l+r*r+o*o,this.vpDistance[m]=h,this.vpBits[m]|=this.ISDONE,this.vpBits[m]|=this.ISBOUND,u.push({ix:g.ix,iy:g.iy,iz:g.iz})):this.vpBits[m]&this.INOUT&&this.vpBits[m]&this.ISDONE&&(l=g.ix-p.ix,r=g.iy-p.iy,o=g.iz-p.iz,h=l*l+r*r+o*o,h-1&&g.iy-1&&g.iz
![](https://pubchem.ncbi.nlm.nih.gov/image/imgsrv.fcgi?sid="+d+")
":""+e+"",$("#"+n.pre+"dl_annotations").append("