From 0f41f196de69850ec4b20b469c7f205e970b459a Mon Sep 17 00:00:00 2001 From: "Wang, Jiyao" Date: Thu, 26 Mar 2020 15:18:37 -0400 Subject: [PATCH] Showed membranes for transmembrane proteins in VAST+ alignment --- CHANGELOG.md | 4 +- README.md | 2 +- icn3d.html | 11 +- package.json | 2 +- src/icn3d/draw/drawing_full.js | 23 +- src/icn3dui/full_ui.js | 19 +- src/icn3dui/parsers/mmcif_mmdb_parser.js | 16 +- .../parsers/mmcif_mmdb_parser_align.js | 94 ++--- src/icn3dui/parsers/mmtf_parser.js | 10 +- src/icn3dui/parsers/pdb_parser.js | 341 ++++++++++++++---- src/icn3dui/selection/commands.js | 107 +++--- 11 files changed, 447 insertions(+), 182 deletions(-) diff --git a/CHANGELOG.md b/CHANGELOG.md index 49436662..500bab3f 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -1,5 +1,7 @@ ## Change Log -[icn3d-2.13.0](https://www.ncbi.nlm.nih.gov/Structure/icn3d/icn3d-2.13.0.zip) was release on March 23, 2020. Added protein symmetry view. +[icn3d-2.13.1](https://www.ncbi.nlm.nih.gov/Structure/icn3d/icn3d-2.13.1.zip) was release on March 26, 2020. Showed membranes for transmembrane proteins in VAST+ alignment. + +[icn3d-2.13.0](https://www.ncbi.nlm.nih.gov/Structure/icn3d/icn3d-2.13.0.zip) was release on March 23, 2020. Added the "Symmetry" feature in the View menu. [icn3d-2.12.1](https://www.ncbi.nlm.nih.gov/Structure/icn3d/icn3d-2.12.1.zip) was release on March 12, 2020. Fixed a bug on hydrogen bonds between residues with the same residue number but different chain names. Removed duplicated names in the menu of "Defined Sets". diff --git a/README.md b/README.md index 506cb5a5..14169663 100644 --- a/README.md +++ b/README.md @@ -4,7 +4,7 @@ ## About iCn3D -"I see in 3D" (iCn3D) Structure Viewer is a WebGL-based 3D viewer using Three.js and jQuery. iCn3D synchronizes the display of 3D structure, 2D interaction, and 1D sequences and annotations. Users' custom display can be saved in a short URL or a PNG image. Complete package of iCn3D including Three.js and jQuery can be downloaded from [https://www.ncbi.nlm.nih.gov/Structure/icn3d/icn3d-2.13.0.zip](https://www.ncbi.nlm.nih.gov/Structure/icn3d/icn3d-2.13.0.zip). The "Download ZIP" link in this page does not include third-party libraries. +"I see in 3D" (iCn3D) Structure Viewer is a WebGL-based 3D viewer using Three.js and jQuery. iCn3D synchronizes the display of 3D structure, 2D interaction, and 1D sequences and annotations. Users' custom display can be saved in a short URL or a PNG image. Complete package of iCn3D including Three.js and jQuery can be downloaded from [https://www.ncbi.nlm.nih.gov/Structure/icn3d/icn3d-2.13.1.zip](https://www.ncbi.nlm.nih.gov/Structure/icn3d/icn3d-2.13.1.zip). The "Download ZIP" link in this page does not include third-party libraries. * View a 3D structure in iCn3D: Open the link https://www.ncbi.nlm.nih.gov/Structure/icn3d/full.html, input a PDB ID, and click "Load". You can also click "File" menu to "Open File" or input other IDs. diff --git a/icn3d.html b/icn3d.html index 1f3e0758..f6456cf7 100644 --- a/icn3d.html +++ b/icn3d.html @@ -597,6 +597,12 @@

iCn3D gallery with live examples ("iCn3D PNG I +
+ +
Protein Symmetry Display (PDB 1KQ2) + +
+

3D Printing (PDB 1TUP) @@ -2096,7 +2102,10 @@

Methods    

Change Log:back to top

-icn3d-2.13.0 was release on March 23, 2020. Added protein symmetry view. +icn3d-2.13.1 was release on March 26, 2020. Showed membranes for transmembrane proteins in VAST+ alignment. +

+ +icn3d-2.13.0 was release on March 23, 2020. Added the "Symmetry" feature in the View menu.

icn3d-2.12.1 was release on March 12, 2020. Fixed a bug on hydrogen bonds between residues with the same residue number but different chain names. Removed duplicated names in the menu of "Defined Sets". diff --git a/package.json b/package.json index 4c51390e..f939e12b 100644 --- a/package.json +++ b/package.json @@ -1,6 +1,6 @@ { "name": "icn3d", - "version": "2.13.0", + "version": "2.13.1", "description": "iCn3D Structure Viewer", "main": "index.html", "scripts": { diff --git a/src/icn3d/draw/drawing_full.js b/src/icn3d/draw/drawing_full.js index b26d5023..19458e86 100644 --- a/src/icn3d/draw/drawing_full.js +++ b/src/icn3d/draw/drawing_full.js @@ -432,17 +432,26 @@ iCn3D.prototype.applySymmetry = function (title) { var me = this; //"use strict" var colorAxis = dataArray[i][2]; var colorPolygon = dataArray[i][3]; var order = dataArray[i][4]; + var chain = dataArray[i][5]; me.createCylinder(start, end, axisRadius, colorAxis, 0); if(symmetryType == 'C' || (symmetryType == 'D' && order == nSide) ) { - // find the center and size of the first protein chain - var selectedChain = Object.keys(this.chains)[0]; - for(var chainid in this.chains) { - var firstSerial = Object.keys(this.chains[chainid])[0]; - if(this.proteins.hasOwnProperty(firstSerial)) { - selectedChain = chainid; - break; + // find the center and size of the selected protein chain + var selectedChain = Object.keys(this.structures)[0] + '_' + chain; + + if(!this.chains.hasOwnProperty(selectedChain)) { + selectedChain = Object.keys(this.structures)[0] + '_' + chain.toLowerCase(); + } + + if(!this.chains.hasOwnProperty(selectedChain)) { + selectedChain = Object.keys(this.chains)[0]; + for(var chainid in this.chains) { + var firstSerial = Object.keys(this.chains[chainid])[0]; + if(this.proteins.hasOwnProperty(firstSerial)) { + selectedChain = chainid; + break; + } } } diff --git a/src/icn3dui/full_ui.js b/src/icn3dui/full_ui.js index 434752c5..67ab39f0 100644 --- a/src/icn3dui/full_ui.js +++ b/src/icn3dui/full_ui.js @@ -13,7 +13,7 @@ if (!$.ui.dialog.prototype._makeDraggableBase) { } var iCn3DUI = function(cfg) { var me = this; //"use strict"; - this.REVISION = '2.13.0'; + this.REVISION = '2.13.1'; me.bFullUi = true; @@ -956,14 +956,27 @@ iCn3DUI.prototype = { renderStructure: function () { var me = this; //"use strict"; if(me.bInitial) { + jQuery.extend(me.icn3d.opts, me.opts); + + if(me.icn3d.bOpm && me.cfg.align !== undefined) { // show membrane + var resid = me.selectedPdbid + '_MEM_1'; + for(var i in me.icn3d.residues[resid]) { + var atom = me.icn3d.atoms[i]; + atom.style = 'stick'; + atom.color = me.icn3d.atomColors[atom.name]; + me.icn3d.atomPrevColors[i] = atom.color; + + me.icn3d.dAtoms[i] = 1; + } + } + if(me.cfg.command !== undefined && me.cfg.command !== '') { me.icn3d.bRender = false; - jQuery.extend(me.icn3d.opts, me.opts); me.icn3d.draw(); } else { - jQuery.extend(me.icn3d.opts, me.opts); + me.icn3d.draw(); } diff --git a/src/icn3dui/parsers/mmcif_mmdb_parser.js b/src/icn3dui/parsers/mmcif_mmdb_parser.js index ab440494..261b9c60 100644 --- a/src/icn3dui/parsers/mmcif_mmdb_parser.js +++ b/src/icn3dui/parsers/mmcif_mmdb_parser.js @@ -206,7 +206,8 @@ iCn3DUI.prototype.loadMmcifData = function(data, mmcifid) { var me = this; //"us //me.loadAtomDataIn(data, data.mmcif, 'mmcifid'); me.deferredOpm = $.Deferred(function() { - me.loadMmcifOpmData(data, mmcifid); + //me.loadMmcifOpmData(data, mmcifid); + me.loadOpmData(data, mmcifid, undefined, 'mmcif'); }); return me.deferredOpm.promise(); @@ -331,13 +332,13 @@ iCn3DUI.prototype.parseMmdbDataPart1 = function (data, type) { var me = this; // iCn3DUI.prototype.parseMmdbData = function (data, type) { var me = this; //"use strict"; if(type === undefined) { - me.deferredOpm = $.Deferred(function() { + //me.deferredOpm = $.Deferred(function() { var id = (data.pdbId !== undefined) ? data.pdbId : data.mmdbId; me.loadMmdbOpmData(data, id, type); - }); + //}); - return me.deferredOpm.promise(); + //return me.deferredOpm.promise(); } else { me.parseMmdbDataPart1(data, type); @@ -597,7 +598,7 @@ iCn3DUI.prototype.getMissingResidues = function (seqArray, type, chainid) { var //type: "mmdbid", "mmcifid", "align" //alignType: "query", "target" for chain to chain 3D alignment -iCn3DUI.prototype.loadAtomDataIn = function (data, id, type, seqalign, alignType, chainCalphaHash2) { var me = this; //"use strict"; +iCn3DUI.prototype.loadAtomDataIn = function (data, id, type, seqalign, alignType) { var me = this; //"use strict"; //me.icn3d.init(); me.icn3d.pmin = new THREE.Vector3( 9999, 9999, 9999); me.icn3d.pmax = new THREE.Vector3(-9999,-9999,-9999); @@ -1254,11 +1255,10 @@ iCn3DUI.prototype.loadAtomDataIn = function (data, id, type, seqalign, alignType } if(type === 'mmcifid') { - me.transformToOpmOri(id, chainCalphaHash2); + me.transformToOpmOri(id); } else if(type === 'mmdbid') { - var bResi_ori = false; // true - me.transformToOpmOri(id, chainCalphaHash2, bResi_ori); + me.transformToOpmOri(id); } // set up sequence alignment diff --git a/src/icn3dui/parsers/mmcif_mmdb_parser_align.js b/src/icn3dui/parsers/mmcif_mmdb_parser_align.js index 3358596f..a776cc8f 100644 --- a/src/icn3dui/parsers/mmcif_mmdb_parser_align.js +++ b/src/icn3dui/parsers/mmcif_mmdb_parser_align.js @@ -124,61 +124,71 @@ iCn3DUI.prototype.downloadAlignment = function (align) { var me = this; //"use s chained.done(function( data ) { // url if (data.atoms !== undefined) { - me.icn3d.init(); + me.deferredOpm = $.Deferred(function() { + //var mmdbidArray = me.inputid.split('_'); + me.mmdbidArray = []; + for(var i = 0, il = data.alignedStructures[0].length; i < il; ++i) { + me.mmdbidArray.push(data.alignedStructures[0][i].pdbId); + } - me.loadAtomDataIn(data, undefined, 'align', seqalign); + me.loadOpmDataForAlign(data, seqalign, me.mmdbidArray); + }); - if(me.cfg.align === undefined && Object.keys(me.icn3d.structures).length == 1) { - $("#" + me.pre + "alternateWrapper").hide(); - } + return me.deferredOpm.promise(); + } + else { + alert('invalid atoms data.'); + return false; + } + }); +}; - // show all - var allAtoms = {}; - for(var i in me.icn3d.atoms) { - allAtoms[i] = 1; - } - me.icn3d.dAtoms = allAtoms; - me.icn3d.hAtoms = allAtoms; +iCn3DUI.prototype.downloadAlignmentPart2 = function (data, seqalign, chainresiCalphaHash2) { var me = this; //"use strict"; + //me.icn3d.init(); + me.loadAtomDataIn(data, undefined, 'align', seqalign); - me.icn3d.setAtomStyleByOptions(me.opts); - // change the default color to "Identity" - me.icn3d.setColorByOptions(me.opts, me.icn3d.atoms); + if(me.cfg.align === undefined && Object.keys(me.icn3d.structures).length == 1) { + $("#" + me.pre + "alternateWrapper").hide(); + } - //var mmdbidArray = me.inputid.split('_'); - me.mmdbidArray = []; - for(var i = 0, il = data.alignedStructures[0].length; i < il; ++i) { - me.mmdbidArray.push(data.alignedStructures[0][i].pdbId); - } + // show all + var allAtoms = {}; + for(var i in me.icn3d.atoms) { + allAtoms[i] = 1; + } + me.icn3d.dAtoms = allAtoms; + me.icn3d.hAtoms = allAtoms; - me.renderStructure(); + me.icn3d.setAtomStyleByOptions(me.opts); + // change the default color to "Identity" + me.icn3d.setColorByOptions(me.opts, me.icn3d.atoms); - if(me.cfg.rotate !== undefined) me.rotStruc(me.cfg.rotate, true); + // memebrane is determined by one structure. But transform both structures + if(chainresiCalphaHash2 !== undefined) me.transformToOpmOriForAlign(me.selectedPdbid, chainresiCalphaHash2, true); - me.html2ddgm = ''; + me.renderStructure(); - //setTimeout(function(){ - // me.set2DDiagramsForAlign(me.mmdbidArray[0].toUpperCase(), me.mmdbidArray[1].toUpperCase()); - //}, 0); + if(me.cfg.rotate !== undefined) me.rotStruc(me.cfg.rotate, true); - // by default, open the seq alignment window - //if(me.cfg.show2d !== undefined && me.cfg.show2d) me.openDialog(me.pre + 'dl_2ddgm', 'Interactions'); - if(me.cfg.showalignseq !== undefined && me.cfg.showalignseq) { - me.openDialog(me.pre + 'dl_alignment', 'Select residues in aligned sequences'); - } + me.html2ddgm = ''; - if(me.cfg.show2d !== undefined && me.cfg.show2d && me.bFullUi) { - me.set2DDiagramsForAlign(me.mmdbidArray[0].toUpperCase(), me.mmdbidArray[1].toUpperCase()); - } + //setTimeout(function(){ + // me.set2DDiagramsForAlign(me.mmdbidArray[0].toUpperCase(), me.mmdbidArray[1].toUpperCase()); + //}, 0); - //if(me.cfg.showseq !== undefined && me.cfg.showseq) me.openDialog(me.pre + 'dl_selectresidues', 'Select residues in sequences'); + // by default, open the seq alignment window + //if(me.cfg.show2d !== undefined && me.cfg.show2d) me.openDialog(me.pre + 'dl_2ddgm', 'Interactions'); + if(me.cfg.showalignseq !== undefined && me.cfg.showalignseq) { + me.openDialog(me.pre + 'dl_alignment', 'Select residues in aligned sequences'); + } - if(me.deferred !== undefined) me.deferred.resolve(); if(me.deferred2 !== undefined) me.deferred2.resolve(); - } - else { - alert('invalid atoms data.'); - return false; - } - }); + if(me.cfg.show2d !== undefined && me.cfg.show2d && me.bFullUi) { + me.set2DDiagramsForAlign(me.mmdbidArray[0].toUpperCase(), me.mmdbidArray[1].toUpperCase()); + } + + //if(me.cfg.showseq !== undefined && me.cfg.showseq) me.openDialog(me.pre + 'dl_selectresidues', 'Select residues in sequences'); + + if(me.deferred !== undefined) me.deferred.resolve(); if(me.deferred2 !== undefined) me.deferred2.resolve(); }; iCn3DUI.prototype.downloadChainAlignment = function (chainalign) { var me = this; //"use strict"; diff --git a/src/icn3dui/parsers/mmtf_parser.js b/src/icn3dui/parsers/mmtf_parser.js index 76460cea..c83b89e6 100644 --- a/src/icn3dui/parsers/mmtf_parser.js +++ b/src/icn3dui/parsers/mmtf_parser.js @@ -14,7 +14,8 @@ iCn3DUI.prototype.downloadMmtf = function (mmtfid) { var me = this; //"use stric var bFull = false; //me.parseMmtfData(mmtfData, bFull); me.deferredOpm = $.Deferred(function() { - me.loadMmtfOpmData(mmtfData, mmtfid, bFull); + //me.loadMmtfOpmData(mmtfData, mmtfid, bFull); + me.loadOpmData(mmtfData, mmtfid, bFull, 'mmtf'); }); return me.deferredOpm.promise(); @@ -29,7 +30,8 @@ iCn3DUI.prototype.downloadMmtf = function (mmtfid) { var me = this; //"use stric var bFull = true; //me.parseMmtfData(mmtfData2, bFull); me.deferredOpm = $.Deferred(function() { - me.loadMmtfOpmData(mmtfData2, mmtfid, bFull); + //me.loadMmtfOpmData(mmtfData2, mmtfid, bFull); + me.loadOpmData(mmtfData2, mmtfid, bFull, 'mmtf'); }); return me.deferredOpm.promise(); @@ -48,7 +50,7 @@ iCn3DUI.prototype.downloadMmtf = function (mmtfid) { var me = this; //"use stric ); }; -iCn3DUI.prototype.parseMmtfData = function (mmtfData, mmtfid, bFull, chainCalphaHash2) { var me = this; //"use strict"; +iCn3DUI.prototype.parseMmtfData = function (mmtfData, mmtfid, bFull) { var me = this; //"use strict"; var cnt = mmtfData.numAtoms; me.icn3d.init(); @@ -435,7 +437,7 @@ iCn3DUI.prototype.parseMmtfData = function (mmtfData, mmtfid, bFull, chainCalpha me.icn3d.oriMaxD = me.icn3d.maxD; me.icn3d.oriCenter = me.icn3d.center.clone(); - me.transformToOpmOri(mmtfid, chainCalphaHash2); + me.transformToOpmOri(mmtfid); if(me.cfg.align === undefined && Object.keys(me.icn3d.structures).length == 1) { $("#" + me.pre + "alternateWrapper").hide(); diff --git a/src/icn3dui/parsers/pdb_parser.js b/src/icn3dui/parsers/pdb_parser.js index c8d8618d..0fe97890 100644 --- a/src/icn3dui/parsers/pdb_parser.js +++ b/src/icn3dui/parsers/pdb_parser.js @@ -26,7 +26,8 @@ iCn3DUI.prototype.downloadPdb = function (pdbid) { var me = this; //"use strict" success: function(data) { //me.loadPdbData(data, pdbid); me.deferredOpm = $.Deferred(function() { - me.loadPdbOpmData(data, pdbid); + //me.loadPdbOpmData(data, pdbid); + me.loadOpmData(data, pdbid, undefined, 'pdb'); }); return me.deferredOpm.promise(); @@ -226,7 +227,48 @@ iCn3DUI.prototype.addMemAtoms = function(dmem, pdbid, dxymax) { var me = this; / } }; -iCn3DUI.prototype.transformToOpmOri = function(pdbid, chainresiCalphaHash2, bResi_ori) { var me = this; //"use strict"; +iCn3DUI.prototype.transformToOpmOri = function(pdbid) { var me = this; //"use strict"; + // apply matrix for each atom + if(me.icn3d.rmsd_supr !== undefined && me.icn3d.rmsd_supr.rot !== undefined) { + var rot = me.icn3d.rmsd_supr.rot; + var centerFrom = me.icn3d.rmsd_supr.trans1; + var centerTo = me.icn3d.rmsd_supr.trans2; + //var rsmd = me.icn3d.rmsd_supr.rsmd; + + var dxymaxsq = 0; + for(var i in me.icn3d.atoms) { + var atom = me.icn3d.atoms[i]; + + atom.coord = me.icn3d.transformMemPro(atom.coord, rot, centerFrom, centerTo); + var xysq = atom.coord.x * atom.coord.x + atom.coord.y * atom.coord.y; + if(Math.abs(atom.coord.z) <= 25 && xysq > dxymaxsq) { + dxymaxsq = xysq; + } + } + + //me.icn3d.center = chainresiCalphaHash2.center; + //me.icn3d.oriCenter = me.icn3d.center.clone(); + + // add membranes + me.addMemAtoms(me.icn3d.halfBilayerSize, pdbid, Math.sqrt(dxymaxsq)); + + // no rotation + me.icn3d.bStopRotate = true; + + me.icn3d.bOpm = true; + + // show transmembrane features + $("#" + me.pre + "togglememli").show(); + $("#" + me.pre + "adjustmemli").show(); + $("#" + me.pre + "selectplaneli").show(); + $("#" + me.pre + "anno_transmemli").show(); + } + else { + me.icn3d.bOpm = false; + } +}; + +iCn3DUI.prototype.transformToOpmOriForAlign = function(pdbid, chainresiCalphaHash2, bResi_ori) { var me = this; //"use strict"; if(chainresiCalphaHash2 !== undefined) { var chainresiCalphaHash1 = me.icn3d.getChainCalpha(me.icn3d.chains, me.icn3d.atoms, bResi_ori); @@ -367,10 +409,10 @@ iCn3DUI.prototype.realign = function() { var me = this; //"use strict"; } }; -iCn3DUI.prototype.loadPdbData = function(data, pdbid, bOpm, chainresiCalphaHash2) { var me = this; //"use strict"; +iCn3DUI.prototype.loadPdbData = function(data, pdbid, bOpm) { var me = this; //"use strict"; me.icn3d.loadPDB(data, pdbid, bOpm); // defined in the core library - me.transformToOpmOri(pdbid, chainresiCalphaHash2); + me.transformToOpmOri(pdbid); if(me.icn3d.biomtMatrices !== undefined && me.icn3d.biomtMatrices.length > 1) { $("#" + me.pre + "assemblyWrapper").show(); @@ -558,12 +600,12 @@ iCn3DUI.prototype.loadPdbDataBase = function(data, calphaonly, bOpm) { var me = }); }; +/* iCn3DUI.prototype.loadPdbOpmData = function(data, pdbid) { var me = this; //"use strict"; var url, dataType; - url = "https://opm-assets.storage.googleapis.com/pdb/" + pdbid.toLowerCase()+ ".pdb"; - - dataType = "text"; + url = "https://www.ncbi.nlm.nih.gov/Structure/mmdb/mmdb_strview.cgi?v=2&program=icn3d&opm&uid=" + pdbid.toLowerCase(); + dataType = "jsonp"; $.ajax({ url: url, @@ -573,8 +615,11 @@ iCn3DUI.prototype.loadPdbOpmData = function(data, pdbid) { var me = this; //"use retryLimit : 1, success: function(opmdata) { me.icn3d.bOpm = true; - var bVector = true; - var chainresiCalphaHash = me.icn3d.loadPDB(opmdata, pdbid, me.icn3d.bOpm, bVector); // defined in the core library + + //var bVector = true; + //var chainresiCalphaHash = me.icn3d.loadPDB(opmdata, pdbid, me.icn3d.bOpm, bVector); // defined in the core library + + me.setOpmData(opmdata); $("#" + me.pre + "selectplane_z1").val(me.icn3d.halfBilayerSize); $("#" + me.pre + "selectplane_z2").val(-me.icn3d.halfBilayerSize); @@ -582,8 +627,8 @@ iCn3DUI.prototype.loadPdbOpmData = function(data, pdbid) { var me = this; //"use $("#" + me.pre + "extra_mem_z").val(me.icn3d.halfBilayerSize); $("#" + me.pre + "intra_mem_z").val(-me.icn3d.halfBilayerSize); - me.icn3d.init(); // remove all previously loaded data - me.loadPdbData(data, pdbid, undefined, chainresiCalphaHash); + //me.icn3d.init(); // remove all previously loaded data + me.loadPdbData(data, pdbid, undefined); if(me.deferredOpm !== undefined) me.deferredOpm.resolve(); }, @@ -601,13 +646,61 @@ iCn3DUI.prototype.loadPdbOpmData = function(data, pdbid) { var me = this; //"use } }); }; +*/ +/* iCn3DUI.prototype.loadMmtfOpmData = function(data, pdbid, bFull) { var me = this; //"use strict"; var url, dataType; - url = "https://opm-assets.storage.googleapis.com/pdb/" + pdbid.toLowerCase()+ ".pdb"; + url = "https://www.ncbi.nlm.nih.gov/Structure/mmdb/mmdb_strview.cgi?v=2&program=icn3d&opm&uid=" + pdbid.toLowerCase(); + dataType = "jsonp"; - dataType = "text"; + $.ajax({ + url: url, + dataType: dataType, + cache: true, + tryCount : 0, + retryLimit : 1, + success: function(opmdata) { + me.icn3d.bOpm = true; + + //var bVector = true; + //var chainresiCalphaHash = me.icn3d.loadPDB(opmdata, pdbid, me.icn3d.bOpm, bVector); // defined in the core library + + me.setOpmData(opmdata); + + $("#" + me.pre + "selectplane_z1").val(me.icn3d.halfBilayerSize); + $("#" + me.pre + "selectplane_z2").val(-me.icn3d.halfBilayerSize); + + $("#" + me.pre + "extra_mem_z").val(me.icn3d.halfBilayerSize); + $("#" + me.pre + "intra_mem_z").val(-me.icn3d.halfBilayerSize); + + //me.icn3d.init(); // remove all previously loaded data + me.parseMmtfData(data, pdbid, bFull); + + if(me.deferredOpm !== undefined) me.deferredOpm.resolve(); + }, + error : function(xhr, textStatus, errorThrown ) { + this.tryCount++; + if (this.tryCount <= this.retryLimit) { + //try again + $.ajax(this); + return; + } + + me.parseMmtfData(data, pdbid, bFull); + if(me.deferredOpm !== undefined) me.deferredOpm.resolve(); + return; + } + }); +}; +*/ + +iCn3DUI.prototype.loadOpmData = function(data, pdbid, bFull, type, pdbid2) { var me = this; //"use strict"; + var url, dataType; + + url = "https://www.ncbi.nlm.nih.gov/Structure/mmdb/mmdb_strview.cgi?v=2&program=icn3d&opm&uid=" + pdbid.toLowerCase(); + dataType = "jsonp"; $.ajax({ url: url, @@ -616,9 +709,101 @@ iCn3DUI.prototype.loadMmtfOpmData = function(data, pdbid, bFull) { var me = this tryCount : 0, retryLimit : 1, success: function(opmdata) { + me.setOpmData(opmdata); // set me.icn3d.bOpm + + $("#" + me.pre + "selectplane_z1").val(me.icn3d.halfBilayerSize); + $("#" + me.pre + "selectplane_z2").val(-me.icn3d.halfBilayerSize); + + $("#" + me.pre + "extra_mem_z").val(me.icn3d.halfBilayerSize); + $("#" + me.pre + "intra_mem_z").val(-me.icn3d.halfBilayerSize); + + if(type === 'mmtf') { + me.parseMmtfData(data, pdbid, bFull); + if(me.deferredOpm !== undefined) me.deferredOpm.resolve(); + } + else if(type === 'mmcif') { + me.loadAtomDataIn(data, data.mmcif, 'mmcifid', undefined, undefined); + me.loadMmcifOpmDataPart2(data, pdbid); + if(me.deferredOpm !== undefined) me.deferredOpm.resolve(); + } + else if(type === 'pdb') { + me.loadPdbData(data, pdbid); + if(me.deferredOpm !== undefined) me.deferredOpm.resolve(); + } + else if(type === 'align') { + if(me.icn3d.bOpm) { + me.downloadAlignmentPart2(pdbid); + if(me.deferredOpm !== undefined) me.deferredOpm.resolve(); + } + else { + if(pdbid2 !== undefined) { + me.loadOpmData(data, pdbid2, bFull, type); + } + else { + me.downloadAlignmentPart2(pdbid); + if(me.deferredOpm !== undefined) me.deferredOpm.resolve(); + } + } + } + + //if(me.deferredOpm !== undefined) me.deferredOpm.resolve(); + }, + error : function(xhr, textStatus, errorThrown ) { + this.tryCount++; + if (this.tryCount <= this.retryLimit) { + //try again + $.ajax(this); + return; + } + + if(type === 'mmtf') { + me.parseMmtfData(data, pdbid, bFull); + if(me.deferredOpm !== undefined) me.deferredOpm.resolve(); + } + else if(type === 'mmcif') { + me.loadAtomDataIn(data, data.mmcif, 'mmcifid', undefined, undefined); + me.loadMmcifOpmDataPart2(data, pdbid); + if(me.deferredOpm !== undefined) me.deferredOpm.resolve(); + } + else if(type === 'pdb') { + me.loadPdbData(data, pdbid); + if(me.deferredOpm !== undefined) me.deferredOpm.resolve(); + } + else if(type === 'align') { + if(pdbid2 !== undefined) { + me.loadOpmData(data, pdbid2, bFull, type); + } + else { + me.downloadAlignmentPart2(pdbid); + if(me.deferredOpm !== undefined) me.deferredOpm.resolve(); + } + } + + //if(me.deferredOpm !== undefined) me.deferredOpm.resolve(); + return; + } + }); +}; + +iCn3DUI.prototype.loadOpmDataForAlign = function(data, seqalign, mmdbidArray) { var me = this; //"use strict"; + var url, dataType; + + url = "https://opm-assets.storage.googleapis.com/pdb/" + mmdbidArray[0].toLowerCase()+ ".pdb"; + + dataType = "text"; + + $.ajax({ + url: url, + dataType: dataType, + cache: true, + //tryCount : 0, + //retryLimit : 1, + success: function(opmdata) { + me.selectedPdbid = mmdbidArray[0]; + me.icn3d.bOpm = true; var bVector = true; - var chainresiCalphaHash = me.icn3d.loadPDB(opmdata, pdbid, me.icn3d.bOpm, bVector); // defined in the core library + var chainresiCalphaHash = me.icn3d.loadPDB(opmdata, mmdbidArray[0], me.icn3d.bOpm, bVector); // defined in the core library $("#" + me.pre + "selectplane_z1").val(me.icn3d.halfBilayerSize); $("#" + me.pre + "selectplane_z2").val(-me.icn3d.halfBilayerSize); @@ -627,20 +812,55 @@ iCn3DUI.prototype.loadMmtfOpmData = function(data, pdbid, bFull) { var me = this $("#" + me.pre + "intra_mem_z").val(-me.icn3d.halfBilayerSize); me.icn3d.init(); // remove all previously loaded data - me.parseMmtfData(data, pdbid, bFull, chainresiCalphaHash); + me.downloadAlignmentPart2(data, seqalign, chainresiCalphaHash); if(me.deferredOpm !== undefined) me.deferredOpm.resolve(); }, error : function(xhr, textStatus, errorThrown ) { +/* this.tryCount++; if (this.tryCount <= this.retryLimit) { //try again $.ajax(this); return; } +*/ + + var url2 = "https://opm-assets.storage.googleapis.com/pdb/" + mmdbidArray[1].toLowerCase()+ ".pdb"; + + $.ajax({ + url: url2, + dataType: dataType, + cache: true, + //tryCount : 0, + //retryLimit : 1, + success: function(opmdata) { + me.selectedPdbid = mmdbidArray[1]; + + me.icn3d.bOpm = true; + var bVector = true; + var chainresiCalphaHash = me.icn3d.loadPDB(opmdata, mmdbidArray[1], me.icn3d.bOpm, bVector); // defined in the core library + + $("#" + me.pre + "selectplane_z1").val(me.icn3d.halfBilayerSize); + $("#" + me.pre + "selectplane_z2").val(-me.icn3d.halfBilayerSize); + + $("#" + me.pre + "extra_mem_z").val(me.icn3d.halfBilayerSize); + $("#" + me.pre + "intra_mem_z").val(-me.icn3d.halfBilayerSize); + + me.icn3d.init(); // remove all previously loaded data + me.downloadAlignmentPart2(data, seqalign, chainresiCalphaHash); + + if(me.deferredOpm !== undefined) me.deferredOpm.resolve(); + }, + error : function(xhr, textStatus, errorThrown ) { + me.icn3d.init(); // remove all previously loaded data + me.downloadAlignmentPart2(data, seqalign); + + if(me.deferredOpm !== undefined) me.deferredOpm.resolve(); + return; + } + }); - me.parseMmtfData(data, pdbid, bFull); - if(me.deferredOpm !== undefined) me.deferredOpm.resolve(); return; } }); @@ -682,12 +902,12 @@ iCn3DUI.prototype.loadMmcifOpmDataPart2 = function(data, pdbid) { var me = this; if(me.deferred !== undefined) me.deferred.resolve(); if(me.deferred2 !== undefined) me.deferred2.resolve(); }; +/* iCn3DUI.prototype.loadMmcifOpmData = function(data, pdbid) { var me = this; //"use strict"; var url, dataType; - url = "https://opm-assets.storage.googleapis.com/pdb/" + pdbid.toLowerCase()+ ".pdb"; - - dataType = "text"; + url = "https://www.ncbi.nlm.nih.gov/Structure/mmdb/mmdb_strview.cgi?v=2&program=icn3d&opm&uid=" + pdbid.toLowerCase(); + dataType = "jsonp"; $.ajax({ url: url, @@ -697,8 +917,11 @@ iCn3DUI.prototype.loadMmcifOpmData = function(data, pdbid) { var me = this; //"u retryLimit : 1, success: function(opmdata) { me.icn3d.bOpm = true; - var bVector = true; - var chainresiCalphaHash = me.icn3d.loadPDB(opmdata, pdbid, me.icn3d.bOpm, bVector); // defined in the core library + + //var bVector = true; + //var chainresiCalphaHash = me.icn3d.loadPDB(opmdata, pdbid, me.icn3d.bOpm, bVector); // defined in the core library + + me.setOpmData(opmdata); $("#" + me.pre + "selectplane_z1").val(me.icn3d.halfBilayerSize); $("#" + me.pre + "selectplane_z2").val(-me.icn3d.halfBilayerSize); @@ -706,10 +929,9 @@ iCn3DUI.prototype.loadMmcifOpmData = function(data, pdbid) { var me = this; //"u $("#" + me.pre + "extra_mem_z").val(me.icn3d.halfBilayerSize); $("#" + me.pre + "intra_mem_z").val(-me.icn3d.halfBilayerSize); - me.icn3d.init(); // remove all previously loaded data - //me.loadPdbData(data, pdbid, undefined, chainresiCalphaHash); + //me.icn3d.init(); // remove all previously loaded data - me.loadAtomDataIn(data, data.mmcif, 'mmcifid', undefined, undefined, chainresiCalphaHash); + me.loadAtomDataIn(data, data.mmcif, 'mmcifid', undefined, undefined); me.loadMmcifOpmDataPart2(data, pdbid); if(me.deferredOpm !== undefined) me.deferredOpm.resolve(); @@ -730,6 +952,7 @@ iCn3DUI.prototype.loadMmcifOpmData = function(data, pdbid) { var me = this; //"u } }); }; +*/ iCn3DUI.prototype.loadMmdbOpmDataPart2 = function(data, pdbid, type) { var me = this; //"use strict"; // set 3d domains @@ -786,53 +1009,37 @@ iCn3DUI.prototype.loadMmdbOpmDataPart2 = function(data, pdbid, type) { var me = }; iCn3DUI.prototype.loadMmdbOpmData = function(data, pdbid, type) { var me = this; //"use strict"; - var url, dataType; - - url = "https://opm-assets.storage.googleapis.com/pdb/" + pdbid.toLowerCase()+ ".pdb"; - - dataType = "text"; - - $.ajax({ - url: url, - dataType: dataType, - cache: true, - tryCount : 0, - retryLimit : 1, - success: function(opmdata) { - me.icn3d.bOpm = true; - var bVector = true; - var chainresiCalphaHash = me.icn3d.loadPDB(opmdata, pdbid, me.icn3d.bOpm, bVector); // defined in the core library - - $("#" + me.pre + "selectplane_z1").val(me.icn3d.halfBilayerSize); - $("#" + me.pre + "selectplane_z2").val(-me.icn3d.halfBilayerSize); - - $("#" + me.pre + "extra_mem_z").val(me.icn3d.halfBilayerSize); - $("#" + me.pre + "intra_mem_z").val(-me.icn3d.halfBilayerSize); + if(data.opm !== undefined && data.opm.rot !== undefined) { + me.icn3d.bOpm = true; - me.icn3d.init(); // remove all previously loaded data - me.parseMmdbDataPart1(data, type); - me.loadAtomDataIn(data, pdbid, 'mmdbid', undefined, type, chainresiCalphaHash); + me.setOpmData(data); - me.loadMmdbOpmDataPart2(data, pdbid, type); + me.parseMmdbDataPart1(data, type); + me.loadAtomDataIn(data, pdbid, 'mmdbid', undefined, type); - if(me.deferredOpm !== undefined) me.deferredOpm.resolve(); - }, - error : function(xhr, textStatus, errorThrown ) { - this.tryCount++; - if (this.tryCount <= this.retryLimit) { - //try again - $.ajax(this); - return; - } + me.loadMmdbOpmDataPart2(data, pdbid, type); + } + else { + me.parseMmdbDataPart1(data, type); + me.loadAtomDataIn(data, pdbid, 'mmdbid', undefined, type); + me.loadMmdbOpmDataPart2(data, pdbid, type); + } +}; - me.parseMmdbDataPart1(data, type); - me.loadAtomDataIn(data, pdbid, 'mmdbid', undefined, type); - me.loadMmdbOpmDataPart2(data, pdbid, type); +iCn3DUI.prototype.setOpmData = function(data) { var me = this; + if(data.opm.rot !== undefined) { + me.icn3d.bOpm = true; - if(me.deferredOpm !== undefined) me.deferredOpm.resolve(); - return; - } - }); + me.icn3d.halfBilayerSize = data.opm.thickness; + me.icn3d.rmsd_supr = {}; + me.icn3d.rmsd_supr.rot = data.opm.rot; + me.icn3d.rmsd_supr.trans1 = new THREE.Vector3(data.opm.trans1[0], data.opm.trans1[1], data.opm.trans1[2]); + me.icn3d.rmsd_supr.trans2 = new THREE.Vector3(data.opm.trans2[0], data.opm.trans2[1], data.opm.trans2[2]); + me.icn3d.rmsd_supr.rsmd = data.opm.rmsd; + } + else { + me.icn3d.bOpm = false; + } }; iCn3DUI.prototype.loadPdbDataRender = function() { diff --git a/src/icn3dui/selection/commands.js b/src/icn3dui/selection/commands.js index af1645ee..e125b72b 100644 --- a/src/icn3dui/selection/commands.js +++ b/src/icn3dui/selection/commands.js @@ -637,65 +637,76 @@ iCn3DUI.prototype.retrieveSymmetry = function (pdbid) { var me = this; //"use st success: function(data) { var symmetryArray = data.rcsb_struct_symmetry; - if(me.icn3d.rmsd_supr !== undefined && me.icn3d.rmsd_supr.rot !== undefined) { - var rot = me.icn3d.rmsd_supr.rot; - var centerFrom = me.icn3d.rmsd_supr.trans1; - var centerTo = me.icn3d.rmsd_supr.trans2; - } - - me.icn3d.symmetryHash = {}; - for(var i = 0, il = symmetryArray.length; i < il; ++i) { - if(symmetryArray[i].symbol == 'C1') continue; - var title = 'no title'; - if(symmetryArray[i].kind == "Pseudo Symmetry") { - title = symmetryArray[i].symbol + ' (pseudo)'; - } - else if(symmetryArray[i].kind == "Global Symmetry") { - title = symmetryArray[i].symbol + ' (global)'; + if(symmetryArray !== undefined) { + if(me.icn3d.rmsd_supr !== undefined && me.icn3d.rmsd_supr.rot !== undefined) { + var rot = me.icn3d.rmsd_supr.rot; + var centerFrom = me.icn3d.rmsd_supr.trans1; + var centerTo = me.icn3d.rmsd_supr.trans2; } - var rotation_axes = symmetryArray[i].rotation_axes; - var axesArray = []; - for(var j = 0, jl = rotation_axes.length; j < jl; ++j) { - var tmpArray = []; - var start = new THREE.Vector3(rotation_axes[j].start[0], rotation_axes[j].start[1], rotation_axes[j].start[2]); - var end = new THREE.Vector3(rotation_axes[j].end[0], rotation_axes[j].end[1], rotation_axes[j].end[2]); - - // apply matrix for each atom - if(me.icn3d.rmsd_supr !== undefined && me.icn3d.rmsd_supr.rot !== undefined) { - start = me.icn3d.transformMemPro(start, rot, centerFrom, centerTo); - end = me.icn3d.transformMemPro(end, rot, centerFrom, centerTo); + me.icn3d.symmetryHash = {}; + for(var i = 0, il = symmetryArray.length; i < il; ++i) { + if(symmetryArray[i].symbol == 'C1') continue; + var title = 'no title'; + if(symmetryArray[i].kind == "Pseudo Symmetry") { + title = symmetryArray[i].symbol + ' (pseudo)'; + } + else if(symmetryArray[i].kind == "Global Symmetry") { + title = symmetryArray[i].symbol + ' (global)'; + } + else if(symmetryArray[i].kind == "Local Symmetry") { + title = symmetryArray[i].symbol + ' (local)'; } - tmpArray.push(start); - tmpArray.push(end); + var rotation_axes = symmetryArray[i].rotation_axes; + var axesArray = []; + for(var j = 0, jl = rotation_axes.length; j < jl; ++j) { + var tmpArray = []; + var start = new THREE.Vector3(rotation_axes[j].start[0], rotation_axes[j].start[1], rotation_axes[j].start[2]); + var end = new THREE.Vector3(rotation_axes[j].end[0], rotation_axes[j].end[1], rotation_axes[j].end[2]); + + // apply matrix for each atom + if(me.icn3d.rmsd_supr !== undefined && me.icn3d.rmsd_supr.rot !== undefined) { + start = me.icn3d.transformMemPro(start, rot, centerFrom, centerTo); + end = me.icn3d.transformMemPro(end, rot, centerFrom, centerTo); + } + + tmpArray.push(start); + tmpArray.push(end); + + // https://www.rcsb.org/pages/help/viewers/jmol_symmetry_view + var colorAxis = me.getAxisColor(symmetryArray[i].symbol, rotation_axes[j].order); + var colorPolygon = me.getPolygonColor(symmetryArray[i].symbol); + tmpArray.push(colorAxis); + tmpArray.push(colorPolygon); + + tmpArray.push(rotation_axes[j].order); - // https://www.rcsb.org/pages/help/viewers/jmol_symmetry_view - var colorAxis = me.getAxisColor(symmetryArray[i].symbol, rotation_axes[j].order); - var colorPolygon = me.getPolygonColor(symmetryArray[i].symbol); - tmpArray.push(colorAxis); - tmpArray.push(colorPolygon); + // selected chain + tmpArray.push(symmetryArray[i].clusters[0].members[0].asym_id); - tmpArray.push(rotation_axes[j].order); + axesArray.push(tmpArray); + } - axesArray.push(tmpArray); + me.icn3d.symmetryHash[title] = axesArray; } - me.icn3d.symmetryHash[title] = axesArray; - } + if(Object.keys(me.icn3d.symmetryHash).length == 0) { + $("#" + me.pre + "dl_symmetry").html("
This structure has no symmetry."); + } + else { + var html = "", index = 0; + for(var title in me.icn3d.symmetryHash) { + var selected = (index == 0) ? 'selected' : ''; + html += ""; + ++index; + } - if(Object.keys(me.icn3d.symmetryHash).length == 0) { - $("#" + me.pre + "dl_symmetry").html("
This structure has no symmetry."); + $("#" + me.pre + "selectSymmetry").html(html); + } } else { - var html = "", index = 0; - for(var title in me.icn3d.symmetryHash) { - var selected = (index == 0) ? 'selected' : ''; - html += ""; - ++index; - } - - $("#" + me.pre + "selectSymmetry").html(html); + $("#" + me.pre + "dl_symmetry").html("
This structure has no symmetry."); } if(me.deferredSymmetry !== undefined) me.deferredSymmetry.resolve(); @@ -707,6 +718,8 @@ iCn3DUI.prototype.retrieveSymmetry = function (pdbid) { var me = this; //"use st $.ajax(this); return; } + $("#" + me.pre + "dl_symmetry").html("
This structure has no symmetry."); + if(me.deferredSymmetry !== undefined) me.deferredSymmetry.resolve(); return; } });