From d1229bd3d06419ae8436dc499ae6d1f46d4f3032 Mon Sep 17 00:00:00 2001 From: my-name Date: Thu, 25 Apr 2024 18:56:41 +0200 Subject: [PATCH] Debugging ACEYOW YETBUV --- cell2mol/classes.py | 16 +- cell2mol/test/ACEYOW/ACEYOW.cif | 195 +++ cell2mol/test/ACEYOW/ACEYOW.info | 133 ++ cell2mol/test/ACEYOW/Cell_ACEYOW.cell | Bin 0 -> 1229809 bytes cell2mol/test/ACEYOW/Ref_Cell_ACEYOW.cell | Bin 0 -> 51190 bytes cell2mol/test/ACEYOW/cell2mol.out | 1470 +++++++++++++++++++++ cell2mol/test/ACEYOW/cif2cell.err | 0 cell2mol/test/ACEYOW/error_0.out | 2 + cell2mol/test/YETBUV/Ref_Cell_YETBUV.cell | Bin 0 -> 211475 bytes cell2mol/test/YETBUV/YETBUV.cif | 224 ++++ cell2mol/test/YETBUV/YETBUV.info | 1077 +++++++++++++++ cell2mol/test/YETBUV/YETBUV.xyz | 978 ++++++++++++++ cell2mol/test/YETBUV/YETBUV_ref.xyz | 64 + cell2mol/test/YETBUV/cell2mol.out | 457 +++++++ cell2mol/test/YETBUV/cif2cell.err | 0 15 files changed, 4610 insertions(+), 6 deletions(-) create mode 100644 cell2mol/test/ACEYOW/ACEYOW.cif create mode 100644 cell2mol/test/ACEYOW/ACEYOW.info create mode 100644 cell2mol/test/ACEYOW/Cell_ACEYOW.cell create mode 100644 cell2mol/test/ACEYOW/Ref_Cell_ACEYOW.cell create mode 100644 cell2mol/test/ACEYOW/cell2mol.out create mode 100644 cell2mol/test/ACEYOW/cif2cell.err create mode 100644 cell2mol/test/ACEYOW/error_0.out create mode 100644 cell2mol/test/YETBUV/Ref_Cell_YETBUV.cell create mode 100644 cell2mol/test/YETBUV/YETBUV.cif create mode 100644 cell2mol/test/YETBUV/YETBUV.info create mode 100644 cell2mol/test/YETBUV/YETBUV.xyz create mode 100644 cell2mol/test/YETBUV/YETBUV_ref.xyz create mode 100644 cell2mol/test/YETBUV/cell2mol.out create mode 100644 cell2mol/test/YETBUV/cif2cell.err diff --git a/cell2mol/classes.py b/cell2mol/classes.py index 2ac91437..11bb3052 100644 --- a/cell2mol/classes.py +++ b/cell2mol/classes.py @@ -1291,7 +1291,7 @@ def get_reference_molecules(self, ref_labels: list, ref_fracs: list, cov_factor: return self.refmoleclist ####################################################### - def get_moleclist(self, blocklist=None, debug: int=0): + def get_moleclist(self, debug: int=0): if debug > 0: print(f"Entered CELL.MOLECLIST with debug={debug}") if not hasattr(self,"labels") or not hasattr(self,"coord"): if debug > 0: print(f"CELL.MOLECLIST. Labels or coordinates not found. Returning None") @@ -1302,10 +1302,13 @@ def get_moleclist(self, blocklist=None, debug: int=0): if debug > 0: print(f"CELL.MOLECLIST passed initial checks") cov_factor = 1.3 - if blocklist is None: blocklist = split_species(self.labels, self.coord, cov_factor=cov_factor, debug=debug) - if blocklist is None: return None - if debug > 0: print(f"CELL.MOLECLIST: found {len(blocklist)} blocks") - if debug > 0: print(f"CELL.MOLECLIST: {blocklist=}") + blocklist = split_species(self.labels, self.coord, cov_factor=cov_factor, debug=debug) + + if blocklist is None: + return None + else : + if debug > 0: print(f"CELL.MOLECLIST: found {len(blocklist)} blocks") + if debug > 0: print(f"CELL.MOLECLIST: {blocklist=}") self.moleclist = [] for b in blocklist: @@ -1370,7 +1373,8 @@ def reconstruct(self, cov_factor: float=None, metal_factor: float=None, debug: i if metal_factor is None: metal_factor = self.refmoleclist[0].metal_factor ## Get the fragments, which is the moleclist of a fragmented cell - fragments = self.get_moleclist(debug=debug).copy() + fragments = self.get_moleclist(debug=debug) + if fragments is None: self.error_get_fragments = True return # Stopping. self.error_get_fragments must be False to reconstruct the cell diff --git a/cell2mol/test/ACEYOW/ACEYOW.cif b/cell2mol/test/ACEYOW/ACEYOW.cif new file mode 100644 index 00000000..9d31a4ab --- /dev/null +++ b/cell2mol/test/ACEYOW/ACEYOW.cif @@ -0,0 +1,195 @@ + +####################################################################### +# +# Cambridge Crystallographic Data Centre +# CCDC +# +####################################################################### +# +# If this CIF has been generated from an entry in the Cambridge +# Structural Database, then it will include bibliographic, chemical, +# crystal, experimental, refinement or atomic coordinate data resulting +# from the CCDC's data processing and validation procedures. +# +####################################################################### + +data_CSD_CIF_ACEYOW +_audit_creation_date 2002-02-27 +_audit_creation_method CSD-ConQuest-V1 +_database_code_CSD ACEYOW +_database_code_depnum_ccdc_archive 'CCDC 175987' +_chemical_formula_sum 'C12 H18 F12 Fe1 N6 Sb2' +_chemical_formula_moiety +; +C12 H18 Fe1 N6 2+,2(F6 Sb1 1-) +; +_journal_coeditor_code "IUCr YA6066" +_journal_coden_Cambridge 1370 +_journal_volume 57 +_journal_year 2001 +_journal_page_first m545 +_journal_name_full 'Acta Crystallogr.,Sect.E:Struct.Rep.Online ' +loop_ +_publ_author_name +"W.W.Brennessel" +"N.R.Brooks" +"M.P.Mehn" +"L.Que Junior" +"V.G.Young Junior" +_chemical_name_systematic +; +hexakis(Acetonitrile)-iron(ii) hexafluoroantimonate +; +_cell_volume 1933.086 +_exptl_crystal_colour 'colorless' +_exptl_crystal_density_diffrn 1.994 +_exptl_special_details +; +isostructural with the Ni complex + +; +_exptl_crystal_description 'hexagonal prism' +_exptl_crystal_preparation 'diethyl ether/acetonitrile' +_diffrn_ambient_temperature 173 +#These two values have been output from a single CSD field. +_refine_ls_R_factor_gt 0.024 +_refine_ls_wR_factor_gt 0.024 +_symmetry_cell_setting rhombohedral +_symmetry_space_group_name_H-M 'R -3' +_symmetry_Int_Tables_number 148 +loop_ +_symmetry_equiv_pos_site_id +_symmetry_equiv_pos_as_xyz +1 x,y,z +2 -y,x-y,z +3 -x+y,-x,z +4 2/3+x,1/3+y,1/3+z +5 2/3-y,1/3+x-y,1/3+z +6 2/3-x+y,1/3-x,1/3+z +7 1/3+x,2/3+y,2/3+z +8 1/3-y,2/3+x-y,2/3+z +9 1/3-x+y,2/3-x,2/3+z +10 -x,-y,-z +11 y,-x+y,-z +12 x-y,x,-z +13 -2/3-x,-1/3-y,-1/3-z +14 -2/3+y,-1/3-x+y,-1/3-z +15 -2/3+x-y,-1/3+x,-1/3-z +16 -1/3-x,-2/3-y,-2/3-z +17 -1/3+y,-2/3-x+y,-2/3-z +18 -1/3+x-y,-2/3+x,-2/3-z +_cell_length_a 11.3398(6) +_cell_length_b 11.3398(6) +_cell_length_c 17.3584(11) +_cell_angle_alpha 90 +_cell_angle_beta 90 +_cell_angle_gamma 120 +_cell_formula_units_Z 3 +loop_ +_atom_type_symbol +_atom_type_radius_bond +C 0.68 +H 0.23 +F 0.64 +Fe 1.34 +N 0.68 +Sb 1.46 +loop_ +_atom_site_label +_atom_site_type_symbol +_atom_site_fract_x +_atom_site_fract_y +_atom_site_fract_z +Fe1 Fe 0.66670 0.33330 0.33330 +N1 N 0.6659(2) 0.4906(2) 0.40253(12) +C1 C 0.6658(2) 0.5774(2) 0.43437(14) +C2 C 0.6651(3) 0.6881(3) 0.4763(2) +H1 H 0.67230 0.67600 0.53160 +H2 H 0.58000 0.68780 0.46570 +H3 H 0.74250 0.77510 0.45970 +Sb1 Sb 0.66670 0.33330 0.661838(14) +F1 F 0.6682(3) 0.1981(3) 0.7195(2) +F2 F 0.5350(3) 0.1968(3) 0.60083(19) +N1A N 0.5094(2) 0.1753(2) 0.40253(12) +C1A C 0.4226(2) 0.0884(2) 0.43437(14) +C2A C 0.3119(3) -0.0230(3) 0.4763(2) +H1A H 0.32400 -0.00370 0.53160 +H2A H 0.31220 -0.10780 0.46570 +H3A H 0.22490 -0.03260 0.45970 +N1B N 0.8247(2) 0.3341(2) 0.40253(12) +C1B C 0.9116(2) 0.3342(2) 0.43437(14) +C2B C 1.0230(3) 0.3349(3) 0.4763(2) +H1B H 1.00370 0.32770 0.53160 +H2B H 1.10780 0.42000 0.46570 +H3B H 1.03260 0.25750 0.45970 +N1L N 0.667433(200) 0.176067(200) 0.264137(120) +C1L C 0.667533(200) 0.089267(200) 0.232297(140) +C2L C 0.668233(300) -0.021433(300) 0.190367(200) +H1L H 0.66103 -0.00933 0.13507 +H2L H 0.75333 -0.02113 0.20097 +H3L H 0.59083 -0.10843 0.20697 +N1M N 0.823933(200) 0.491367(200) 0.264137(120) +C1M C 0.910733(200) 0.578267(200) 0.232297(140) +C2M C 1.021433(300) 0.689667(300) 0.190367(200) +H1M H 1.00933 0.67037 0.13507 +H2M H 1.02113 0.77447 0.20097 +H3M H 1.10843 0.69927 0.20697 +N1N N 0.508633(200) 0.332567(200) 0.264137(120) +C1N C 0.421733(200) 0.332467(200) 0.232297(140) +C2N C 0.310333(300) 0.331767(300) 0.190367(200) +H1N H 0.32963 0.33897 0.13507 +H2N H 0.22553 0.24667 0.20097 +H3N H 0.30073 0.40917 0.20697 +F1A F 0.8019(3) 0.4701(3) 0.7195(2) +F1B F 0.5299(3) 0.3318(3) 0.7195(2) +F2A F 0.8032(3) 0.3382(3) 0.60083(19) +F2B F 0.6618(3) 0.4650(3) 0.60083(19) +loop_ +_geom_bond_atom_site_label_1 +_geom_bond_atom_site_label_2 +_geom_bond_distance +_geom_bond_site_symmetry_1 +_geom_bond_site_symmetry_2 +Fe1 N1 2.155 1_555 1_555 +N1 C1 1.129 1_555 1_555 +C1 C2 1.455 1_555 1_555 +C2 H1 0.979 1_555 1_555 +H2 C2 0.981 1_555 1_555 +H3 C2 0.980 1_555 1_555 +Sb1 F1 1.838 1_555 1_555 +F2 Sb1 1.854 1_555 1_555 +N1A Fe1 2.154 1_555 1_555 +C1A N1A 1.129 1_555 1_555 +C2A C1A 1.455 1_555 1_555 +H1A C2A 0.979 1_555 1_555 +H2A C2A 0.981 1_555 1_555 +H3A C2A 0.980 1_555 1_555 +N1B Fe1 2.154 1_555 1_555 +C1B N1B 1.129 1_555 1_555 +C2B C1B 1.455 1_555 1_555 +H1B C2B 0.979 1_555 1_555 +H2B C2B 0.981 1_555 1_555 +H3B C2B 0.980 1_555 1_555 +N1L Fe1 2.153 1_555 1_555 +C1L N1L 1.129 1_555 1_555 +C2L C1L 1.455 1_555 1_555 +H1L C2L 0.979 1_555 1_555 +H2L C2L 0.981 1_555 1_555 +H3L C2L 0.980 1_555 1_555 +N1M Fe1 2.153 1_555 1_555 +C1M N1M 1.129 1_555 1_555 +C2M C1M 1.455 1_555 1_555 +H1M C2M 0.979 1_555 1_555 +H2M C2M 0.981 1_555 1_555 +H3M C2M 0.980 1_555 1_555 +N1N Fe1 2.154 1_555 1_555 +C1N N1N 1.129 1_555 1_555 +C2N C1N 1.455 1_555 1_555 +H1N C2N 0.979 1_555 1_555 +H2N C2N 0.981 1_555 1_555 +H3N C2N 0.980 1_555 1_555 +F1A Sb1 1.839 1_555 1_555 +F1B Sb1 1.839 1_555 1_555 +F2A Sb1 1.853 1_555 1_555 +F2B Sb1 1.854 1_555 1_555 +#END diff --git a/cell2mol/test/ACEYOW/ACEYOW.info b/cell2mol/test/ACEYOW/ACEYOW.info new file mode 100644 index 00000000..83f9eca2 --- /dev/null +++ b/cell2mol/test/ACEYOW/ACEYOW.info @@ -0,0 +1,133 @@ +CIF2CELL 2.0.0 +2024-04-23 15:31 +Output for None (hexakis(Acetonitrile)-iron(ii) hexafluoroantimonate) +CIF file exported from Cambridge Structural Database. +Database reference code: ACEYOW. + BIBLIOGRAPHIC INFORMATION +W.W.Brennessel et al., Acta Crystallogr.,Sect.E:Struct.Rep.Online 57, m545- (2001) + INPUT CELL INFORMATION +Symmetry information: +Trigonal crystal system. +Space group number : 148 +Hall symbol : -R 3 +Hermann-Mauguin symbol : R-3 + +Lattice parameters: + a b c + 11.3398000 11.3398000 17.3584000 + alpha beta gamma + 90.0000000 90.0000000 120.0000000 +Representative sites : +Atom x y z +Fe 0.6667000 0.3333000 0.3333000 +N 0.6659000 0.4906000 0.4025300 +C 0.6658000 0.5774000 0.4343700 +C 0.6651000 0.6881000 0.4763000 +H 0.6723000 0.6760000 0.5316000 +H 0.5800000 0.6878000 0.4657000 +H 0.7425000 0.7751000 0.4597000 +Sb 0.6667000 0.3333000 0.6618380 +F 0.6682000 0.1981000 0.7195000 +F 0.5350000 0.1968000 0.6008300 +N 0.5094000 0.1753000 0.4025300 +C 0.4226000 0.0884000 0.4343700 +C 0.3119000 -0.0230000 0.4763000 +H 0.3240000 -0.0037000 0.5316000 +H 0.3122000 -0.1078000 0.4657000 +H 0.2249000 -0.0326000 0.4597000 +N 0.8247000 0.3341000 0.4025300 +C 0.9116000 0.3342000 0.4343700 +C 1.0230000 0.3349000 0.4763000 +H 1.0037000 0.3277000 0.5316000 +H 1.1078000 0.4200000 0.4657000 +H 1.0326000 0.2575000 0.4597000 +N 0.6674330 0.1760670 0.2641370 +C 0.6675330 0.0892670 0.2322970 +C 0.6682330 -0.0214330 0.1903670 +H 0.6610300 -0.0093300 0.1350700 +H 0.7533300 -0.0211300 0.2009700 +H 0.5908300 -0.1084300 0.2069700 +N 0.8239330 0.4913670 0.2641370 +C 0.9107330 0.5782670 0.2322970 +C 1.0214330 0.6896670 0.1903670 +H 1.0093300 0.6703700 0.1350700 +H 1.0211300 0.7744700 0.2009700 +H 1.1084300 0.6992700 0.2069700 +N 0.5086330 0.3325670 0.2641370 +C 0.4217330 0.3324670 0.2322970 +C 0.3103330 0.3317670 0.1903670 +H 0.3296300 0.3389700 0.1350700 +H 0.2255300 0.2466700 0.2009700 +H 0.3007300 0.4091700 0.2069700 +F 0.8019000 0.4701000 0.7195000 +F 0.5299000 0.3318000 0.7195000 +F 0.8032000 0.3382000 0.6008300 +F 0.6618000 0.4650000 0.6008300 + + OUTPUT CELL INFORMATION +Symmetry information: +Trigonal crystal system. +Space group number : 148 +Hall symbol : -R 3 +Hermann-Mauguin symbol : R-3 + +Bravais lattice vectors : + 6.5470366 0.0000000 5.7861333 + -3.2735183 5.6699000 5.7861333 + -3.2735183 -5.6699000 5.7861333 +All sites, (cartesian coordinates): +Atom x y z +Fe 0.0000000 0.0000000 0.0000000 +N -3.2810474 -3.8821805 6.9872768 +N 3.2810474 3.8821805 10.3711232 +N -5.0025907 0.9003801 10.3711232 +N -1.7215433 4.7825606 6.9872768 +N 1.7215433 -4.7825606 10.3711232 +N 5.0025907 -0.9003801 6.9872768 +C -3.2820294 -2.8973189 7.5399682 +C 3.2820294 2.8973189 9.8184318 +C -4.1501665 1.3936614 9.8184318 +C -0.8681371 4.2909803 7.5399682 +C 0.8681371 -4.2909803 9.8184318 +C 4.1501665 -1.3936614 7.5399682 +C -3.2889038 -1.6380341 8.2678059 +C 3.2889038 1.6380341 9.0905941 +C -3.0630311 2.0292572 9.0905941 +C 0.2258728 3.6672913 8.2678059 +C -0.2258728 -3.6672913 9.0905941 +C 3.0630311 -2.0292572 8.2678059 +H -3.2181958 -1.8160690 9.2277254 +H 3.2181958 1.8160690 8.1306746 +H -3.1818598 1.8790049 8.1306746 +H 0.0363361 3.6950738 9.2277254 +H -0.0363361 -3.6950738 8.1306746 +H 3.1818598 -1.8790049 9.2277254 +H -4.1246330 -1.1589276 8.0838069 +H 4.1246330 1.1589276 9.2745931 +H -3.0659772 2.9925732 9.2745931 +H 1.0586558 4.1515008 8.0838069 +H -1.0586558 -4.1515008 9.2745931 +H 3.0659772 -2.9925732 8.0838069 +H -2.5287929 -1.0903218 7.9796565 +H 2.5287929 1.0903218 9.3787435 +H -2.2086428 1.6448380 9.3787435 +H 0.3201501 2.7351598 7.9796565 +H -0.3201501 -2.7351598 9.3787435 +H 2.2086428 -1.6448380 7.9796565 +Sb 0.0000000 0.0000000 5.7023154 +Sb 0.0000000 0.0000000 11.6560846 +F 0.0150582 -1.5422128 6.7032355 +F -0.0150582 1.5422128 10.6551645 +F -1.3280664 -0.7841472 10.6551645 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z1BwS^dw|^X8U>>snu?||UgIsuGSSk@62qt%*Y^;6IzX1S^4Ougzd@g@O-stKBv@j& zQQ!jZ7TinC>F^7V$se*OfBKR9O%HB6a1tz>7D{QkeAvn5c9KJxLs>o)X)_Y_8AgNF n%qAsvwdC?4_(-ZgBSW8-Ob!IGCX>;WsMBV!@Yho^hc^8`knvur literal 0 HcmV?d00001 diff --git a/cell2mol/test/ACEYOW/cell2mol.out b/cell2mol/test/ACEYOW/cell2mol.out new file mode 100644 index 00000000..c2a1d4fe --- /dev/null +++ b/cell2mol/test/ACEYOW/cell2mol.out @@ -0,0 +1,1470 @@ +cell2mol version 2.0 +INITIATING cell object from info path: ACEYOW.info +Debug level: 2 +######################################### + GETREFS: Generate reference molecules +######################################### +GETREFS: found 2 reference molecules +GETREFS: ['F6-Sb', 'H18-C12-N6-Fe'] +GETREFS: [------------- Cell2mol MOLECULE Object -------------- + Version = 0.1 + Type = specie + Sub-Type = molecule + Number of Atoms = 7 + Formula = F6-Sb + Has Adjacency Matrix = YES +--------------------------------------------------- +, ------------- Cell2mol MOLECULE Object -------------- + Version = 0.1 + Type = specie + Sub-Type = molecule + Number of Atoms = 37 + Formula = H18-C12-N6-Fe + Has Adjacency Matrix = YES + Number of Ligands = 6 + Number of Metals = 1 +--------------------------------------------------- +] +GETREFS: working with F6-Sb +GETREFS: working with H18-C12-N6-Fe + +LIGAND.SPLIT_LIGAND: splitting H3-C2-N into groups +LIGAND.SPLIT_LIGAND: self.indices=[0, 1, 2, 3, 4, 5] +LIGAND.SPLIT_LIGAND: connected_idx=[0] +LIGAND.SPLIT_LIGAND: conn_labels=['N'] +SPILT_SPECIES: Laplacian lap=array([[0]]) +SPILT_SPECIES: graph=<1x1 sparse matrix of type '' + with 0 stored elements in Compressed Sparse Row format> +LIGAND.SPLIT_LIGAND: blocklist=[[0]] +LIGAND.SPLIT_LIGAND: block=[0] +EXTRACT_FROM_LIST. received: entrylist=[0] old_array=[0] +EXTRACT_FROM_LIST. received: idx=0 val=0 old_array[val]=0 +EXTRACT_FROM_LIST. new_array=array([0], dtype=object) +LIGAND.SPLIT_LIGAND: gr_indices=[0] +EXTRACT_FROM_LIST. received: entrylist=[0] old_array=['N'] +EXTRACT_FROM_LIST. received: idx=0 val=0 old_array[val]='N' +EXTRACT_FROM_LIST. new_array=array(['N'], dtype=object) +Entering COORD_CORR_NONHAPTIC: + Coordinating atom label=N with mconnec=1, group index 0 + evaluating coordination with metal Fe + +------------- Cell2mol METAL Object -------------- + Version = 0.1 + Type = atom + Sub-Type = metal + Label = Fe + Atomic Number = 26 + Index in Molecule = 0 + Metal Adjacency (mconnec) = 6 + Regular Adjacencies (connec) = 6 +---------------------------------------------------- + +ADD_ATOM: Metalist length 1 +ADD_ATOM: Ligand Atoms 6 +ADD_ATOM: site= 0 +ADD_ATOM: target ligand atom N +ADD_ATOM: evaluating apos=array([4.78256065, 1.72154327, 6.98727675]) and tgt.coord=[5.67046699, 3.2731909394491323, 5.7855547199999995] +ADD_ATOM: Chosen Metal index 0. H is added at site 0 + connectivity verified for atom N with ligand index 0 +LIGAND.SPLIT_LIGAND: new group is found +LIGAND.SPLIT_LIGAND: found groups ['N'] +[------------- Cell2mol GROUP Object -------------- + Version = 0.1 + Type = specie + Sub-Type = group + Number of Atoms = 1 + Formula = N + Has Adjacency Matrix = YES + Origin = split_ligand + Number of Metals = 1 +--------------------------------------------------- +] + +LIGAND.SPLIT_LIGAND: splitting H3-C2-N into groups +LIGAND.SPLIT_LIGAND: self.indices=[0, 1, 2, 3, 4, 5] +LIGAND.SPLIT_LIGAND: connected_idx=[0] +LIGAND.SPLIT_LIGAND: conn_labels=['N'] +SPILT_SPECIES: Laplacian lap=array([[0]]) +SPILT_SPECIES: graph=<1x1 sparse matrix of type '' + with 0 stored elements in Compressed Sparse Row format> +LIGAND.SPLIT_LIGAND: blocklist=[[0]] +LIGAND.SPLIT_LIGAND: block=[0] +EXTRACT_FROM_LIST. received: entrylist=[0] old_array=[0] +EXTRACT_FROM_LIST. received: idx=0 val=0 old_array[val]=0 +EXTRACT_FROM_LIST. new_array=array([0], dtype=object) +LIGAND.SPLIT_LIGAND: gr_indices=[0] +EXTRACT_FROM_LIST. received: entrylist=[0] old_array=['N'] +EXTRACT_FROM_LIST. received: idx=0 val=0 old_array[val]='N' +EXTRACT_FROM_LIST. new_array=array(['N'], dtype=object) +Entering COORD_CORR_NONHAPTIC: + Coordinating atom label=N with mconnec=1, group index 0 + evaluating coordination with metal Fe + +------------- Cell2mol METAL Object -------------- + Version = 0.1 + Type = atom + Sub-Type = metal + Label = Fe + Atomic Number = 26 + Index in Molecule = 0 + Metal Adjacency (mconnec) = 6 + Regular Adjacencies (connec) = 6 +---------------------------------------------------- + +ADD_ATOM: Metalist length 1 +ADD_ATOM: Ligand Atoms 6 +ADD_ATOM: site= 0 +ADD_ATOM: target ligand atom N +ADD_ATOM: evaluating apos=array([7.45761947, 3.28104738, 6.98727675]) and tgt.coord=[5.67046699, 3.2731909394491323, 5.7855547199999995] +ADD_ATOM: Chosen Metal index 0. H is added at site 0 + connectivity verified for atom N with ligand index 0 +LIGAND.SPLIT_LIGAND: new group is found +LIGAND.SPLIT_LIGAND: found groups ['N'] +[------------- Cell2mol GROUP Object -------------- + Version = 0.1 + Type = specie + Sub-Type = group + Number of Atoms = 1 + Formula = N + Has Adjacency Matrix = YES + Origin = split_ligand + Number of Metals = 1 +--------------------------------------------------- +] + +LIGAND.SPLIT_LIGAND: splitting H3-C2-N into groups +LIGAND.SPLIT_LIGAND: self.indices=[0, 1, 2, 3, 4, 5] +LIGAND.SPLIT_LIGAND: connected_idx=[0] +LIGAND.SPLIT_LIGAND: conn_labels=['N'] +SPILT_SPECIES: Laplacian lap=array([[0]]) +SPILT_SPECIES: graph=<1x1 sparse matrix of type '' + with 0 stored elements in Compressed Sparse Row format> +LIGAND.SPLIT_LIGAND: blocklist=[[0]] +LIGAND.SPLIT_LIGAND: block=[0] +EXTRACT_FROM_LIST. received: entrylist=[0] old_array=[0] +EXTRACT_FROM_LIST. received: idx=0 val=0 old_array[val]=0 +EXTRACT_FROM_LIST. new_array=array([0], dtype=object) +LIGAND.SPLIT_LIGAND: gr_indices=[0] +EXTRACT_FROM_LIST. received: entrylist=[0] old_array=['N'] +EXTRACT_FROM_LIST. received: idx=0 val=0 old_array[val]='N' +EXTRACT_FROM_LIST. new_array=array(['N'], dtype=object) +Entering COORD_CORR_NONHAPTIC: + Coordinating atom label=N with mconnec=1, group index 0 + evaluating coordination with metal Fe + +------------- Cell2mol METAL Object -------------- + Version = 0.1 + Type = atom + Sub-Type = metal + Label = Fe + Atomic Number = 26 + Index in Molecule = 0 + Metal Adjacency (mconnec) = 6 + Regular Adjacencies (connec) = 6 +---------------------------------------------------- + +ADD_ATOM: Metalist length 1 +ADD_ATOM: Ligand Atoms 6 +ADD_ATOM: site= 0 +ADD_ATOM: target ligand atom N +ADD_ATOM: evaluating apos=array([6.57027445, 1.72907563, 4.5849957 ]) and tgt.coord=[5.67046699, 3.2731909394491323, 5.7855547199999995] +ADD_ATOM: Chosen Metal index 0. H is added at site 0 + connectivity verified for atom N with ligand index 0 +LIGAND.SPLIT_LIGAND: new group is found +LIGAND.SPLIT_LIGAND: found groups ['N'] +[------------- Cell2mol GROUP Object -------------- + Version = 0.1 + Type = specie + Sub-Type = group + Number of Atoms = 1 + Formula = N + Has Adjacency Matrix = YES + Origin = split_ligand + Number of Metals = 1 +--------------------------------------------------- +] + +LIGAND.SPLIT_LIGAND: splitting H3-C2-N into groups +LIGAND.SPLIT_LIGAND: self.indices=[0, 1, 2, 3, 4, 5] +LIGAND.SPLIT_LIGAND: connected_idx=[0] +LIGAND.SPLIT_LIGAND: conn_labels=['N'] +SPILT_SPECIES: Laplacian lap=array([[0]]) +SPILT_SPECIES: graph=<1x1 sparse matrix of type '' + with 0 stored elements in Compressed Sparse Row format> +LIGAND.SPLIT_LIGAND: blocklist=[[0]] +LIGAND.SPLIT_LIGAND: block=[0] +EXTRACT_FROM_LIST. received: entrylist=[0] old_array=[0] +EXTRACT_FROM_LIST. received: idx=0 val=0 old_array[val]=0 +EXTRACT_FROM_LIST. new_array=array([0], dtype=object) +LIGAND.SPLIT_LIGAND: gr_indices=[0] +EXTRACT_FROM_LIST. received: entrylist=[0] old_array=['N'] +EXTRACT_FROM_LIST. received: idx=0 val=0 old_array[val]='N' +EXTRACT_FROM_LIST. new_array=array(['N'], dtype=object) +Entering COORD_CORR_NONHAPTIC: + Coordinating atom label=N with mconnec=1, group index 0 + evaluating coordination with metal Fe + +------------- Cell2mol METAL Object -------------- + Version = 0.1 + Type = atom + Sub-Type = metal + Label = Fe + Atomic Number = 26 + Index in Molecule = 0 + Metal Adjacency (mconnec) = 6 + Regular Adjacencies (connec) = 6 +---------------------------------------------------- + +ADD_ATOM: Metalist length 1 +ADD_ATOM: Ligand Atoms 6 +ADD_ATOM: site= 0 +ADD_ATOM: target ligand atom N +ADD_ATOM: evaluating apos=array([6.55723368, 4.82549659, 4.5849957 ]) and tgt.coord=[5.67046699, 3.2731909394491323, 5.7855547199999995] +ADD_ATOM: Chosen Metal index 0. H is added at site 0 + connectivity verified for atom N with ligand index 0 +LIGAND.SPLIT_LIGAND: new group is found +LIGAND.SPLIT_LIGAND: found groups ['N'] +[------------- Cell2mol GROUP Object -------------- + Version = 0.1 + Type = specie + Sub-Type = group + Number of Atoms = 1 + Formula = N + Has Adjacency Matrix = YES + Origin = split_ligand + Number of Metals = 1 +--------------------------------------------------- +] + +LIGAND.SPLIT_LIGAND: splitting H3-C2-N into groups +LIGAND.SPLIT_LIGAND: self.indices=[0, 1, 2, 3, 4, 5] +LIGAND.SPLIT_LIGAND: connected_idx=[0] +LIGAND.SPLIT_LIGAND: conn_labels=['N'] +SPILT_SPECIES: Laplacian lap=array([[0]]) +SPILT_SPECIES: graph=<1x1 sparse matrix of type '' + with 0 stored elements in Compressed Sparse Row format> +LIGAND.SPLIT_LIGAND: blocklist=[[0]] +LIGAND.SPLIT_LIGAND: block=[0] +EXTRACT_FROM_LIST. received: entrylist=[0] old_array=[0] +EXTRACT_FROM_LIST. received: idx=0 val=0 old_array[val]=0 +EXTRACT_FROM_LIST. new_array=array([0], dtype=object) +LIGAND.SPLIT_LIGAND: gr_indices=[0] +EXTRACT_FROM_LIST. received: entrylist=[0] old_array=['N'] +EXTRACT_FROM_LIST. received: idx=0 val=0 old_array[val]='N' +EXTRACT_FROM_LIST. new_array=array(['N'], dtype=object) +Entering COORD_CORR_NONHAPTIC: + Coordinating atom label=N with mconnec=1, group index 0 + evaluating coordination with metal Fe + +------------- Cell2mol METAL Object -------------- + Version = 0.1 + Type = atom + Sub-Type = metal + Label = Fe + Atomic Number = 26 + Index in Molecule = 0 + Metal Adjacency (mconnec) = 6 + Regular Adjacencies (connec) = 6 +---------------------------------------------------- + +ADD_ATOM: Metalist length 1 +ADD_ATOM: Ligand Atoms 6 +ADD_ATOM: site= 0 +ADD_ATOM: target ligand atom N +ADD_ATOM: evaluating apos=array([3.88217486, 3.26599247, 4.5849957 ]) and tgt.coord=[5.67046699, 3.2731909394491323, 5.7855547199999995] +ADD_ATOM: Chosen Metal index 0. H is added at site 0 + connectivity verified for atom N with ligand index 0 +LIGAND.SPLIT_LIGAND: new group is found +LIGAND.SPLIT_LIGAND: found groups ['N'] +[------------- Cell2mol GROUP Object -------------- + Version = 0.1 + Type = specie + Sub-Type = group + Number of Atoms = 1 + Formula = N + Has Adjacency Matrix = YES + Origin = split_ligand + Number of Metals = 1 +--------------------------------------------------- +] + +LIGAND.SPLIT_LIGAND: splitting H3-C2-N into groups +LIGAND.SPLIT_LIGAND: self.indices=[0, 1, 2, 3, 4, 5] +LIGAND.SPLIT_LIGAND: connected_idx=[0] +LIGAND.SPLIT_LIGAND: conn_labels=['N'] +SPILT_SPECIES: Laplacian lap=array([[0]]) +SPILT_SPECIES: graph=<1x1 sparse matrix of type '' + with 0 stored elements in Compressed Sparse Row format> +LIGAND.SPLIT_LIGAND: blocklist=[[0]] +LIGAND.SPLIT_LIGAND: block=[0] +EXTRACT_FROM_LIST. received: entrylist=[0] old_array=[0] +EXTRACT_FROM_LIST. received: idx=0 val=0 old_array[val]=0 +EXTRACT_FROM_LIST. new_array=array([0], dtype=object) +LIGAND.SPLIT_LIGAND: gr_indices=[0] +EXTRACT_FROM_LIST. received: entrylist=[0] old_array=['N'] +EXTRACT_FROM_LIST. received: idx=0 val=0 old_array[val]='N' +EXTRACT_FROM_LIST. new_array=array(['N'], dtype=object) +Entering COORD_CORR_NONHAPTIC: + Coordinating atom label=N with mconnec=1, group index 0 + evaluating coordination with metal Fe + +------------- Cell2mol METAL Object -------------- + Version = 0.1 + Type = atom + Sub-Type = metal + Label = Fe + Atomic Number = 26 + Index in Molecule = 0 + Metal Adjacency (mconnec) = 6 + Regular Adjacencies (connec) = 6 +---------------------------------------------------- + +ADD_ATOM: Metalist length 1 +ADD_ATOM: Ligand Atoms 6 +ADD_ATOM: site= 0 +ADD_ATOM: target ligand atom N +ADD_ATOM: evaluating apos=array([4.76951988, 4.81796422, 6.98727675]) and tgt.coord=[5.67046699, 3.2731909394491323, 5.7855547199999995] +ADD_ATOM: Chosen Metal index 0. H is added at site 0 + connectivity verified for atom N with ligand index 0 +LIGAND.SPLIT_LIGAND: new group is found +LIGAND.SPLIT_LIGAND: found groups ['N'] +[------------- Cell2mol GROUP Object -------------- + Version = 0.1 + Type = specie + Sub-Type = group + Number of Atoms = 1 + Formula = N + Has Adjacency Matrix = YES + Origin = split_ligand + Number of Metals = 1 +--------------------------------------------------- +] +LIGAND.Get_denticity: checking connectivity of ligand H3-C2-N +LIGAND.Get_denticity: initial connectivity is 1 +LIGAND.Get_denticity: final connectivity of ligand H3-C2-N is 1 +LIGAND.Get_denticity: checking connectivity of ligand H3-C2-N +LIGAND.Get_denticity: initial connectivity is 1 +LIGAND.Get_denticity: final connectivity of ligand H3-C2-N is 1 +LIGAND.Get_denticity: checking connectivity of ligand H3-C2-N +LIGAND.Get_denticity: initial connectivity is 1 +LIGAND.Get_denticity: final connectivity of ligand H3-C2-N is 1 +LIGAND.Get_denticity: checking connectivity of ligand H3-C2-N +LIGAND.Get_denticity: initial connectivity is 1 +LIGAND.Get_denticity: final connectivity of ligand H3-C2-N is 1 +LIGAND.Get_denticity: checking connectivity of ligand H3-C2-N +LIGAND.Get_denticity: initial connectivity is 1 +LIGAND.Get_denticity: final connectivity of ligand H3-C2-N is 1 +LIGAND.Get_denticity: checking connectivity of ligand H3-C2-N +LIGAND.Get_denticity: initial connectivity is 1 +LIGAND.Get_denticity: final connectivity of ligand H3-C2-N is 1 + +METAL.Get_coord_geometry: Fe +METAL.Get_coord_geometry: +coord_group=[------------- Cell2mol GROUP Object -------------- + Version = 0.1 + Type = specie + Sub-Type = group + Number of Atoms = 1 + Formula = N + Has Adjacency Matrix = YES + Origin = split_ligand + Number of Metals = 1 +--------------------------------------------------- +, ------------- Cell2mol GROUP Object -------------- + Version = 0.1 + Type = specie + Sub-Type = group + Number of Atoms = 1 + Formula = N + Has Adjacency Matrix = YES + Origin = split_ligand + Number of Metals = 1 +--------------------------------------------------- +, ------------- Cell2mol GROUP Object -------------- + Version = 0.1 + Type = specie + Sub-Type = group + Number of Atoms = 1 + Formula = N + Has Adjacency Matrix = YES + Origin = split_ligand + Number of Metals = 1 +--------------------------------------------------- +, ------------- Cell2mol GROUP Object -------------- + Version = 0.1 + Type = specie + Sub-Type = group + Number of Atoms = 1 + Formula = N + Has Adjacency Matrix = YES + Origin = split_ligand + Number of Metals = 1 +--------------------------------------------------- +, ------------- Cell2mol GROUP Object -------------- + Version = 0.1 + Type = specie + Sub-Type = group + Number of Atoms = 1 + Formula = N + Has Adjacency Matrix = YES + Origin = split_ligand + Number of Metals = 1 +--------------------------------------------------- +, ------------- Cell2mol GROUP Object -------------- + Version = 0.1 + Type = specie + Sub-Type = group + Number of Atoms = 1 + Formula = N + Has Adjacency Matrix = YES + Origin = split_ligand + Number of Metals = 1 +--------------------------------------------------- +] +METAL.Get_coord_geometry: coord_nr=6 +SHAPE_MEASURE: symbols=['Fe', 'N', 'N', 'N', 'N', 'N', 'N'] +SHAPE_MEASURE: positions=[[5.67046699, 3.2731909394491323, 5.7855547199999995], [4.78256065, 1.7215432693832378, 6.987276752], [7.457619470000001, 3.281047383348201, 6.987276752], [6.570274450100001, 1.7290756349714687, 4.5849957008], [6.557233680100001, 4.8254965866915756, 4.5849957008], [3.882174860100002, 3.265992472726612, 4.5849957008], [4.7695198800000025, 4.8179642211033435, 6.987276752]] +SHAPE_MEASURE: coordination number of metal center 6 +SHAPE_MEASURE: connectivity of metal center(1) [[1, 2], [1, 3], [1, 4], [1, 5], [1, 6], [1, 7]] +DEFINE_coordination_geometry: The number of coordinating points: 6 +DEFINE_coordination_geometry: {'Hexagon': 31.102, 'Pentagonal pyramidal': 29.369, 'Octahedral': 0.057, 'Trigonal prismatic': 16.556} +DEFINE_coordination_geometry: The type of hapticity : [] +DEFINE_coordination_geometry: The most likely geometry is 'Octahedral' with deviation value 0.057 +METAL.Get_coord_geometry: self.coord_geometry='Octahedral' self.geom_deviation=0.057 +METAL.Get_relative_metal_radius: diff_list=[1.444, 1.444, 1.443, 1.443, 1.444, 1.445] +METAL.Get_relative_metal_radius: average=1.444 +METAL.Get_coord_geometry: self.rel_metal_radius=1.094 + +################## +Checking Missing H +################## +Not a Single Molecule has Missing H atoms (apparently) +------------------------------- +Errors in Reference Molecules +------------------------------- +Cell2mol terminated with error number 0. Message: +No Errors Found +SAVING cell2mol CELL object to /Users/ycho/cell2mol/cell2mol/test/ACEYOW/Ref_Cell_ACEYOW.cell +ENTERING cell2mol with debug=2 +Entered CELL.MOLECLIST with debug=2 +CELL.MOLECLIST passed initial checks +SPILT_SPECIES: Laplacian lap=array([[ 0, 0, 0, ..., 0, 0, 0], + [ 0, -1, 0, ..., 0, 0, 0], + [ 0, 0, -1, ..., 0, 0, 0], + ..., + [ 0, 0, 0, ..., -1, 0, 0], + [ 0, 0, 0, ..., 0, -1, 0], + [ 0, 0, 0, ..., 0, 0, -1]]) +SPILT_SPECIES: graph=<51x51 sparse matrix of type '' + with 134 stored elements in Compressed Sparse Row format> +CELL.MOLECLIST: found 9 blocks +CELL.MOLECLIST: blocklist=[[38, 40, 41, 43, 46, 47, 49], [37, 39, 42, 44, 45, 48, 50], [1, 7, 13, 19, 25, 31], [6, 12, 18, 24, 30, 36], [5, 11, 17, 23, 29, 35], [4, 10, 16, 22, 28, 34], [3, 9, 15, 21, 27, 33], [2, 8, 14, 20, 26, 32], [0]] +CELL.MOLECLIST: doing block=[38, 40, 41, 43, 46, 47, 49] +CELL.MOLECLIST: doing block=[37, 39, 42, 44, 45, 48, 50] +CELL.MOLECLIST: doing block=[1, 7, 13, 19, 25, 31] +CELL.MOLECLIST: doing block=[6, 12, 18, 24, 30, 36] +CELL.MOLECLIST: doing block=[5, 11, 17, 23, 29, 35] +CELL.MOLECLIST: doing block=[4, 10, 16, 22, 28, 34] +CELL.MOLECLIST: doing block=[3, 9, 15, 21, 27, 33] +CELL.MOLECLIST: doing block=[2, 8, 14, 20, 26, 32] +CELL.MOLECLIST: doing block=[0] +CLASSIFY_FRAGMENTS. 9 Blocks sorted as (Molec, Frag, H): 2 7 0 + +############################################## +FRAG_RECONSTRUCT. 7 molecules submitted to SEQUENTIAL with Heavy +############################################## +FINISHED succesfully +FRAG_RECONSTRUCT. 1 molecules and 0 fragments out of SEQUENTIAL with Heavy + +Cell Reconstruction Finished Normally. Total execution time: 0.59 seconds +Getting unique species in cell +Molecule 0 formula=F6-Sb +New molecule found with: formula=F6-Sb and added in position 0 +Molecule 1 formula=F6-Sb +Molecule 1 is the same with 0 in typelist +Molecule 2 formula=H18-C12-N6-Fe +New ligand found with: formula H3-C2-N added in position 1 +ligand 1 is the same with 0 in typelist +ligand 2 is the same with 0 in typelist +ligand 3 is the same with 0 in typelist +ligand 4 is the same with 0 in typelist +ligand 5 is the same with 0 in typelist +New Metal Center found with: labels Fe and added in position 2 +3 Species (Metal or Ligand or Molecules) to Characterize + POSCHARGE: doing empty PROTONATION for this specie + CREATED EMPTY PROTONATION ------------- Cell2mol Protonation ---------------- + Status = True + Labels = ['Sb', 'F', 'F', 'F', 'F', 'F', 'F'] + Type = Empty + Atoms added in positions = [0, 0, 0, 0, 0, 0, 0] + Atoms blocked (no atoms added) = [0, 0, 0, 0, 0, 0, 0] +--------------------------------------------------- + + POSCHARGE will try charges [0, -1, 1, -2, 2, -3, 3] + POSCHARGE: charge 0 with smiles F[Sb-](F)(F)(F)(F)F + POSCHARGE: charge 0 with smiles F[Sb-](F)(F)(F)(F)F + POSCHARGE: charge 0 with smiles F[Sb-](F)(F)(F)(F)F + POSCHARGE: charge 0 with smiles F[Sb-](F)(F)(F)(F)F + POSCHARGE: charge 0 with smiles F[Sb-](F)(F)(F)(F)F + POSCHARGE: charge 0 with smiles F[Sb-](F)(F)(F)(F)F + POSCHARGE: charge 0 with smiles F[Sb-](F)(F)(F)(F)F + NEW SELECT FUNCTION: uncorr_total: [-1, -1, -1, -1, -1, -1, -1] + NEW SELECT FUNCTION: uncorr_abs_total: [1, 1, 1, 1, 1, 1, 1] + NEW SELECT FUNCTION: uncorr_abs_atcharge: [1, 1, 1, 1, 1, 1, 1] + NEW SELECT FUNCTION: uncorr_zwitt: [False, False, False, False, False, False, False] + NEW SELECT FUNCTION: coincide: [False, True, False, False, False, False, False] + NEW SELECT FUNCTION: listofmintot: [0, 1, 2, 3, 4, 5, 6] + NEW SELECT FUNCTION: listofminabs: [0, 1, 2, 3, 4, 5, 6] + NEW SELECT FUNCTION: tmplist: [1], including: + NEW SELECT FUNCTION: Corr_charge=-1 + NEW SELECT FUNCTION: Smiles=F[Sb-](F)(F)(F)(F)F + NEW SELECT FUNCTION: found corr_charges=[-1] + NEW SELECT FUNCTION: doing tgt_charge=-1 + NEW SELECT FUNCTION: charge_state added + NEW SELECT FUNCTION: Case 1, only one entry for -1 in tmplist + GET_PROTONATION_STATES: Evaluating group N with parent_indices [0] + GET_PROTONATION_STATES: evaluating non-haptic group with index 0 and label N + GET_PROTONATION_STATES: adj=0 Fe + GET_PROTONATION_STATES: adj=8 C + GET_PROTONATION_STATES: will be sent to nonlocal due to N atom + + GET_PROTONATION_STATES: Enters non-local with: + GET_PROTONATION_STATES: block: [0 0 0 0 0 0] + GET_PROTONATION_STATES: addedlist: [0 0 0 0 0 0] + GET_PROTONATION_STATES: 1 non_local_groups groups found + + GET_PROTONATION_STATES: doing combination 0 + GET_PROTONATION_STATES: Protonation SAVED with 0 atoms added to ligand. status=True + + GET_PROTONATION_STATES: doing combination 1 + GET_PROTONATION_STATES: Added H to atom 0 with: a.mconnec=1 and label=N + GET_PROTONATION_STATES: Protonation SAVED with 1 atoms added to ligand. status=True + GET_PROTONATION_STATES:protonation_states=[------------- Cell2mol Protonation ---------------- + Status = True + Labels = ['N', 'C', 'C', 'H', 'H', 'H'] + Type = Non-local + Atoms added in positions = [0 0 0 0 0 0] + Atoms blocked (no atoms added) = [0 0 0 0 0 0] +--------------------------------------------------- +, ------------- Cell2mol Protonation ---------------- + Status = True + Labels = ['N', 'C', 'C', 'H', 'H', 'H', 'H'] + Type = Non-local + Atoms added in positions = [1 0 0 0 0 0] + Atoms blocked (no atoms added) = [0 0 0 0 0 0] +--------------------------------------------------- +] + POSCHARGE will try charges [0, -1, 1, -2, 2] + POSCHARGE: charge 0 with smiles [H]C([H])([H])C#N + POSCHARGE: charge 0 with smiles [H]C([H])([H])C[N-2] + POSCHARGE: charge 0 with smiles [H]C([H])([H])C[N-2] + POSCHARGE: charge 0 with smiles [H]C([H])([H])C[N-2] + POSCHARGE: charge 0 with smiles [H]C([H])([H])C[N-2] + POSCHARGE will try charges [0, -1, 1, -2, 2] + POSCHARGE: charge 0 with smiles [H][N-]CC([H])([H])[H] + POSCHARGE: charge 0 with smiles [H]N=[C-]C([H])([H])[H] + POSCHARGE: charge 0 with smiles [H][N+]#CC([H])([H])[H] + POSCHARGE: charge 0 with smiles [H][N-]CC([H])([H])[H] + POSCHARGE: charge 0 with smiles [H][N-]CC([H])([H])[H] + NEW SELECT FUNCTION: uncorr_total: [-1, -1, 1, -1, -1] + NEW SELECT FUNCTION: uncorr_abs_total: [1, 1, 1, 1, 1] + NEW SELECT FUNCTION: uncorr_abs_atcharge: [1, 1, 1, 1, 1] + NEW SELECT FUNCTION: uncorr_zwitt: [False, False, False, False, False] + NEW SELECT FUNCTION: coincide: [False, True, True, False, False] + NEW SELECT FUNCTION: listofmintot: [0, 1, 2, 3, 4] + NEW SELECT FUNCTION: listofminabs: [0, 1, 2, 3, 4] + NEW SELECT FUNCTION: tmplist: [1, 2], including: + NEW SELECT FUNCTION: Corr_charge=-2 + NEW SELECT FUNCTION: Smiles=[H]N=[C-]C([H])([H])[H] + NEW SELECT FUNCTION: Corr_charge=0 + NEW SELECT FUNCTION: Smiles=[H][N+]#CC([H])([H])[H] + NEW SELECT FUNCTION: found corr_charges=[-2, 0] + NEW SELECT FUNCTION: doing tgt_charge=-2 + NEW SELECT FUNCTION: charge_state added + NEW SELECT FUNCTION: Case 1, only one entry for -2 in tmplist + NEW SELECT FUNCTION: doing tgt_charge=0 + NEW SELECT FUNCTION: charge_state added + NEW SELECT FUNCTION: Case 1, only one entry for 0 in tmplist +BALANCE: iterlist [[-1], [-2, 0], [2, 3]] +BALANCE: unique_indices [0, 0, 1, 1, 1, 1, 1, 1, 2] +BALANCE: tmpdistr [(-1, -2, 2), (-1, -2, 3), (-1, 0, 2), (-1, 0, 3)] +BALANCE: alldistr added: [-1, -1, -2, -2, -2, -2, -2, -2, 2] +BALANCE: distribution=[-1, -1, -2, -2, -2, -2, -2, -2, 2] +BALANCE: alldistr added: [-1, -1, -2, -2, -2, -2, -2, -2, 3] +BALANCE: distribution=[-1, -1, -2, -2, -2, -2, -2, -2, 2] +BALANCE: distribution=[-1, -1, -2, -2, -2, -2, -2, -2, 3] +BALANCE: alldistr added: [-1, -1, 0, 0, 0, 0, 0, 0, 2] +BALANCE: distribution=[-1, -1, -2, -2, -2, -2, -2, -2, 2] +BALANCE: distribution=[-1, -1, -2, -2, -2, -2, -2, -2, 3] +BALANCE: distribution=[-1, -1, 0, 0, 0, 0, 0, 0, 2] +BALANCE: alldistr added: [-1, -1, 0, 0, 0, 0, 0, 0, 3] +BALANCE: distribution=[-1, -1, -2, -2, -2, -2, -2, -2, 2] +BALANCE: distribution=[-1, -1, -2, -2, -2, -2, -2, -2, 3] +BALANCE: distribution=[-1, -1, 0, 0, 0, 0, 0, 0, 2] +BALANCE: distribution=[-1, -1, 0, 0, 0, 0, 0, 0, 3] + +FINAL Charge Distribution: [[-1, -1, 0, 0, 0, 0, 0, 0, 2]] + +######################################### +Assigning Charges and Preparing Molecules +######################################### +SET_TARGET_CHARGE: ------------- Cell2mol MOLECULE Object -------------- + Version = 0.1 + Type = specie + Sub-Type = molecule + Number of Atoms = 7 + Formula = F6-Sb + Has Adjacency Matrix = YES + Origin = cell.reconstruct +--------------------------------------------------- + [0, 1] -1 +SET_TARGET_CHARGE: Target charge -1 of F6-Sb exists in [-1]. +SET_TARGET_CHARGE: F6-Sb + POSCHARGE: doing empty PROTONATION for this specie + CREATED EMPTY PROTONATION ------------- Cell2mol Protonation ---------------- + Status = True + Labels = ['Sb', 'F', 'F', 'F', 'F', 'F', 'F'] + Type = Empty + Atoms added in positions = [0, 0, 0, 0, 0, 0, 0] + Atoms blocked (no atoms added) = [0, 0, 0, 0, 0, 0, 0] +--------------------------------------------------- + + POSCHARGE will try charges [0, -1, 1, -2, 2, -3, 3] + POSCHARGE: charge 0 with smiles F[Sb-](F)(F)(F)(F)F + POSCHARGE: charge 0 with smiles F[Sb-](F)(F)(F)(F)F + POSCHARGE: charge 0 with smiles F[Sb-](F)(F)(F)(F)F + POSCHARGE: charge 0 with smiles F[Sb-](F)(F)(F)(F)F + POSCHARGE: charge 0 with smiles F[Sb-](F)(F)(F)(F)F + POSCHARGE: charge 0 with smiles F[Sb-](F)(F)(F)(F)F + POSCHARGE: charge 0 with smiles F[Sb-](F)(F)(F)(F)F + NEW SELECT FUNCTION: uncorr_total: [-1, -1, -1, -1, -1, -1, -1] + NEW SELECT FUNCTION: uncorr_abs_total: [1, 1, 1, 1, 1, 1, 1] + NEW SELECT FUNCTION: uncorr_abs_atcharge: [1, 1, 1, 1, 1, 1, 1] + NEW SELECT FUNCTION: uncorr_zwitt: [False, False, False, False, False, False, False] + NEW SELECT FUNCTION: coincide: [False, True, False, False, False, False, False] + NEW SELECT FUNCTION: listofmintot: [0, 1, 2, 3, 4, 5, 6] + NEW SELECT FUNCTION: listofminabs: [0, 1, 2, 3, 4, 5, 6] + NEW SELECT FUNCTION: tmplist: [1], including: + NEW SELECT FUNCTION: Corr_charge=-1 + NEW SELECT FUNCTION: Smiles=F[Sb-](F)(F)(F)(F)F + NEW SELECT FUNCTION: found corr_charges=[-1] + NEW SELECT FUNCTION: doing tgt_charge=-1 + NEW SELECT FUNCTION: charge_state added + NEW SELECT FUNCTION: Case 1, only one entry for -1 in tmplist +SET_TARGET_CHARGE: Target charge -1 of F6-Sb exists in [-1]. +SET_TARGET_CHARGE: ------------- Cell2mol MOLECULE Object -------------- + Version = 0.1 + Type = specie + Sub-Type = molecule + Number of Atoms = 7 + Formula = F6-Sb + Has Adjacency Matrix = YES + Total Charge = -1 + Smiles = F[Sb-](F)(F)(F)(F)F + Origin = cell.reconstruct +--------------------------------------------------- + [0, 1] -1 +SET_TARGET_CHARGE: Target charge -1 of F6-Sb exists in [-1]. +SET_TARGET_CHARGE: F6-Sb + POSCHARGE: doing empty PROTONATION for this specie + CREATED EMPTY PROTONATION ------------- Cell2mol Protonation ---------------- + Status = True + Labels = ['Sb', 'F', 'F', 'F', 'F', 'F', 'F'] + Type = Empty + Atoms added in positions = [0, 0, 0, 0, 0, 0, 0] + Atoms blocked (no atoms added) = [0, 0, 0, 0, 0, 0, 0] +--------------------------------------------------- + + POSCHARGE will try charges [0, -1, 1, -2, 2, -3, 3] + POSCHARGE: charge 0 with smiles F[Sb-](F)(F)(F)(F)F + POSCHARGE: charge 0 with smiles F[Sb-](F)(F)(F)(F)F + POSCHARGE: charge 0 with smiles F[Sb-](F)(F)(F)(F)F + POSCHARGE: charge 0 with smiles F[Sb-](F)(F)(F)(F)F + POSCHARGE: charge 0 with smiles F[Sb-](F)(F)(F)(F)F + POSCHARGE: charge 0 with smiles F[Sb-](F)(F)(F)(F)F + POSCHARGE: charge 0 with smiles F[Sb-](F)(F)(F)(F)F + NEW SELECT FUNCTION: uncorr_total: [-1, -1, -1, -1, -1, -1, -1] + NEW SELECT FUNCTION: uncorr_abs_total: [1, 1, 1, 1, 1, 1, 1] + NEW SELECT FUNCTION: uncorr_abs_atcharge: [1, 1, 1, 1, 1, 1, 1] + NEW SELECT FUNCTION: uncorr_zwitt: [False, False, False, False, False, False, False] + NEW SELECT FUNCTION: coincide: [False, True, False, False, False, False, False] + NEW SELECT FUNCTION: listofmintot: [0, 1, 2, 3, 4, 5, 6] + NEW SELECT FUNCTION: listofminabs: [0, 1, 2, 3, 4, 5, 6] + NEW SELECT FUNCTION: tmplist: [1], including: + NEW SELECT FUNCTION: Corr_charge=-1 + NEW SELECT FUNCTION: Smiles=F[Sb-](F)(F)(F)(F)F + NEW SELECT FUNCTION: found corr_charges=[-1] + NEW SELECT FUNCTION: doing tgt_charge=-1 + NEW SELECT FUNCTION: charge_state added + NEW SELECT FUNCTION: Case 1, only one entry for -1 in tmplist +SET_TARGET_CHARGE: Target charge -1 of F6-Sb exists in [-1]. +SET_TARGET_CHARGE: ------------- Cell2mol LIGAND Object -------------- + Version = 0.1 + Type = specie + Sub-Type = ligand + Number of Atoms = 6 + Formula = H3-C2-N + Has Adjacency Matrix = YES + Origin = split_complex + Number of Groups = 1 +--------------------------------------------------- + [2, 3, 4, 5, 6, 7] 0 +SET_TARGET_CHARGE: Target charge 0 of H3-C2-N exists in [-2, 0]. +SET_TARGET_CHARGE: H3-C2-N + GET_PROTONATION_STATES: Evaluating group N with parent_indices [0] + GET_PROTONATION_STATES: evaluating non-haptic group with index 0 and label N + GET_PROTONATION_STATES: adj=0 Fe + GET_PROTONATION_STATES: adj=8 C + GET_PROTONATION_STATES: will be sent to nonlocal due to N atom + + GET_PROTONATION_STATES: Enters non-local with: + GET_PROTONATION_STATES: block: [0 0 0 0 0 0] + GET_PROTONATION_STATES: addedlist: [0 0 0 0 0 0] + GET_PROTONATION_STATES: 1 non_local_groups groups found + + GET_PROTONATION_STATES: doing combination 0 + GET_PROTONATION_STATES: Protonation SAVED with 0 atoms added to ligand. status=True + + GET_PROTONATION_STATES: doing combination 1 + GET_PROTONATION_STATES: Added H to atom 0 with: a.mconnec=1 and label=N + GET_PROTONATION_STATES: Protonation SAVED with 1 atoms added to ligand. status=True + GET_PROTONATION_STATES:protonation_states=[------------- Cell2mol Protonation ---------------- + Status = True + Labels = ['N', 'C', 'C', 'H', 'H', 'H'] + Type = Non-local + Atoms added in positions = [0 0 0 0 0 0] + Atoms blocked (no atoms added) = [0 0 0 0 0 0] +--------------------------------------------------- +, ------------- Cell2mol Protonation ---------------- + Status = True + Labels = ['N', 'C', 'C', 'H', 'H', 'H', 'H'] + Type = Non-local + Atoms added in positions = [1 0 0 0 0 0] + Atoms blocked (no atoms added) = [0 0 0 0 0 0] +--------------------------------------------------- +] + POSCHARGE will try charges [0, -1, 1, -2, 2] + POSCHARGE: charge 0 with smiles [H]C([H])([H])C#N + POSCHARGE: charge 0 with smiles [H]C([H])([H])C[N-2] + POSCHARGE: charge 0 with smiles [H]C([H])([H])C[N-2] + POSCHARGE: charge 0 with smiles [H]C([H])([H])C[N-2] + POSCHARGE: charge 0 with smiles [H]C([H])([H])C[N-2] + POSCHARGE will try charges [0, -1, 1, -2, 2] + POSCHARGE: charge 0 with smiles [H][N-]CC([H])([H])[H] + POSCHARGE: charge 0 with smiles [H]N=[C-]C([H])([H])[H] + POSCHARGE: charge 0 with smiles [H][N+]#CC([H])([H])[H] + POSCHARGE: charge 0 with smiles [H][N-]CC([H])([H])[H] + POSCHARGE: charge 0 with smiles [H][N-]CC([H])([H])[H] + NEW SELECT FUNCTION: uncorr_total: [-1, -1, 1, -1, -1] + NEW SELECT FUNCTION: uncorr_abs_total: [1, 1, 1, 1, 1] + NEW SELECT FUNCTION: uncorr_abs_atcharge: [1, 1, 1, 1, 1] + NEW SELECT FUNCTION: uncorr_zwitt: [False, False, False, False, False] + NEW SELECT FUNCTION: coincide: [False, True, True, False, False] + NEW SELECT FUNCTION: listofmintot: [0, 1, 2, 3, 4] + NEW SELECT FUNCTION: listofminabs: [0, 1, 2, 3, 4] + NEW SELECT FUNCTION: tmplist: [1, 2], including: + NEW SELECT FUNCTION: Corr_charge=-2 + NEW SELECT FUNCTION: Smiles=[H]N=[C-]C([H])([H])[H] + NEW SELECT FUNCTION: Corr_charge=0 + NEW SELECT FUNCTION: Smiles=[H][N+]#CC([H])([H])[H] + NEW SELECT FUNCTION: found corr_charges=[-2, 0] + NEW SELECT FUNCTION: doing tgt_charge=-2 + NEW SELECT FUNCTION: charge_state added + NEW SELECT FUNCTION: Case 1, only one entry for -2 in tmplist + NEW SELECT FUNCTION: doing tgt_charge=0 + NEW SELECT FUNCTION: charge_state added + NEW SELECT FUNCTION: Case 1, only one entry for 0 in tmplist +SET_TARGET_CHARGE: Target charge 0 of H3-C2-N exists in [-2, 0]. +SET_TARGET_CHARGE: ------------- Cell2mol LIGAND Object -------------- + Version = 0.1 + Type = specie + Sub-Type = ligand + Number of Atoms = 6 + Formula = H3-C2-N + Has Adjacency Matrix = YES + Total Charge = 0 + Smiles = [H][N+]#CC([H])([H])[H] + Origin = split_complex + Number of Groups = 1 +--------------------------------------------------- + [2, 3, 4, 5, 6, 7] 0 +SET_TARGET_CHARGE: Target charge 0 of H3-C2-N exists in [-2, 0]. +SET_TARGET_CHARGE: H3-C2-N + GET_PROTONATION_STATES: Evaluating group N with parent_indices [0] + GET_PROTONATION_STATES: evaluating non-haptic group with index 0 and label N + GET_PROTONATION_STATES: adj=0 Fe + GET_PROTONATION_STATES: adj=14 C + GET_PROTONATION_STATES: will be sent to nonlocal due to N atom + + GET_PROTONATION_STATES: Enters non-local with: + GET_PROTONATION_STATES: block: [0 0 0 0 0 0] + GET_PROTONATION_STATES: addedlist: [0 0 0 0 0 0] + GET_PROTONATION_STATES: 1 non_local_groups groups found + + GET_PROTONATION_STATES: doing combination 0 + GET_PROTONATION_STATES: Protonation SAVED with 0 atoms added to ligand. status=True + + GET_PROTONATION_STATES: doing combination 1 + GET_PROTONATION_STATES: Added H to atom 0 with: a.mconnec=1 and label=N + GET_PROTONATION_STATES: Protonation SAVED with 1 atoms added to ligand. status=True + GET_PROTONATION_STATES:protonation_states=[------------- Cell2mol Protonation ---------------- + Status = True + Labels = ['N', 'C', 'C', 'H', 'H', 'H'] + Type = Non-local + Atoms added in positions = [0 0 0 0 0 0] + Atoms blocked (no atoms added) = [0 0 0 0 0 0] +--------------------------------------------------- +, ------------- Cell2mol Protonation ---------------- + Status = True + Labels = ['N', 'C', 'C', 'H', 'H', 'H', 'H'] + Type = Non-local + Atoms added in positions = [1 0 0 0 0 0] + Atoms blocked (no atoms added) = [0 0 0 0 0 0] +--------------------------------------------------- +] + POSCHARGE will try charges [0, -1, 1, -2, 2] + POSCHARGE: charge 0 with smiles [H]C([H])([H])C#N + POSCHARGE: charge 0 with smiles [H]C([H])([H])C[N-2] + POSCHARGE: charge 0 with smiles [H]C([H])([H])C[N-2] + POSCHARGE: charge 0 with smiles [H]C([H])([H])C[N-2] + POSCHARGE: charge 0 with smiles [H]C([H])([H])C[N-2] + POSCHARGE will try charges [0, -1, 1, -2, 2] + POSCHARGE: charge 0 with smiles [H][N-]CC([H])([H])[H] + POSCHARGE: charge 0 with smiles [H]N=[C-]C([H])([H])[H] + POSCHARGE: charge 0 with smiles [H][N+]#CC([H])([H])[H] + POSCHARGE: charge 0 with smiles [H][N-]CC([H])([H])[H] + POSCHARGE: charge 0 with smiles [H][N-]CC([H])([H])[H] + NEW SELECT FUNCTION: uncorr_total: [-1, -1, 1, -1, -1] + NEW SELECT FUNCTION: uncorr_abs_total: [1, 1, 1, 1, 1] + NEW SELECT FUNCTION: uncorr_abs_atcharge: [1, 1, 1, 1, 1] + NEW SELECT FUNCTION: uncorr_zwitt: [False, False, False, False, False] + NEW SELECT FUNCTION: coincide: [False, True, True, False, False] + NEW SELECT FUNCTION: listofmintot: [0, 1, 2, 3, 4] + NEW SELECT FUNCTION: listofminabs: [0, 1, 2, 3, 4] + NEW SELECT FUNCTION: tmplist: [1, 2], including: + NEW SELECT FUNCTION: Corr_charge=-2 + NEW SELECT FUNCTION: Smiles=[H]N=[C-]C([H])([H])[H] + NEW SELECT FUNCTION: Corr_charge=0 + NEW SELECT FUNCTION: Smiles=[H][N+]#CC([H])([H])[H] + NEW SELECT FUNCTION: found corr_charges=[-2, 0] + NEW SELECT FUNCTION: doing tgt_charge=-2 + NEW SELECT FUNCTION: charge_state added + NEW SELECT FUNCTION: Case 1, only one entry for -2 in tmplist + NEW SELECT FUNCTION: doing tgt_charge=0 + NEW SELECT FUNCTION: charge_state added + NEW SELECT FUNCTION: Case 1, only one entry for 0 in tmplist +SET_TARGET_CHARGE: Target charge 0 of H3-C2-N exists in [-2, 0]. +SET_TARGET_CHARGE: ------------- Cell2mol LIGAND Object -------------- + Version = 0.1 + Type = specie + Sub-Type = ligand + Number of Atoms = 6 + Formula = H3-C2-N + Has Adjacency Matrix = YES + Total Charge = 0 + Smiles = [H][N+]#CC([H])([H])[H] + Origin = split_complex + Number of Groups = 1 +--------------------------------------------------- + [2, 3, 4, 5, 6, 7] 0 +SET_TARGET_CHARGE: Target charge 0 of H3-C2-N exists in [-2, 0]. +SET_TARGET_CHARGE: H3-C2-N + GET_PROTONATION_STATES: Evaluating group N with parent_indices [0] + GET_PROTONATION_STATES: evaluating non-haptic group with index 0 and label N + GET_PROTONATION_STATES: adj=0 Fe + GET_PROTONATION_STATES: adj=20 C + GET_PROTONATION_STATES: will be sent to nonlocal due to N atom + + GET_PROTONATION_STATES: Enters non-local with: + GET_PROTONATION_STATES: block: [0 0 0 0 0 0] + GET_PROTONATION_STATES: addedlist: [0 0 0 0 0 0] + GET_PROTONATION_STATES: 1 non_local_groups groups found + + GET_PROTONATION_STATES: doing combination 0 + GET_PROTONATION_STATES: Protonation SAVED with 0 atoms added to ligand. status=True + + GET_PROTONATION_STATES: doing combination 1 + GET_PROTONATION_STATES: Added H to atom 0 with: a.mconnec=1 and label=N + GET_PROTONATION_STATES: Protonation SAVED with 1 atoms added to ligand. status=True + GET_PROTONATION_STATES:protonation_states=[------------- Cell2mol Protonation ---------------- + Status = True + Labels = ['N', 'C', 'C', 'H', 'H', 'H'] + Type = Non-local + Atoms added in positions = [0 0 0 0 0 0] + Atoms blocked (no atoms added) = [0 0 0 0 0 0] +--------------------------------------------------- +, ------------- Cell2mol Protonation ---------------- + Status = True + Labels = ['N', 'C', 'C', 'H', 'H', 'H', 'H'] + Type = Non-local + Atoms added in positions = [1 0 0 0 0 0] + Atoms blocked (no atoms added) = [0 0 0 0 0 0] +--------------------------------------------------- +] + POSCHARGE will try charges [0, -1, 1, -2, 2] + POSCHARGE: charge 0 with smiles [H]C([H])([H])C#N + POSCHARGE: charge 0 with smiles [H]C([H])([H])C[N-2] + POSCHARGE: charge 0 with smiles [H]C([H])([H])C[N-2] + POSCHARGE: charge 0 with smiles [H]C([H])([H])C[N-2] + POSCHARGE: charge 0 with smiles [H]C([H])([H])C[N-2] + POSCHARGE will try charges [0, -1, 1, -2, 2] + POSCHARGE: charge 0 with smiles [H][N-]CC([H])([H])[H] + POSCHARGE: charge 0 with smiles [H]N=[C-]C([H])([H])[H] + POSCHARGE: charge 0 with smiles [H][N+]#CC([H])([H])[H] + POSCHARGE: charge 0 with smiles [H][N-]CC([H])([H])[H] + POSCHARGE: charge 0 with smiles [H][N-]CC([H])([H])[H] + NEW SELECT FUNCTION: uncorr_total: [-1, -1, 1, -1, -1] + NEW SELECT FUNCTION: uncorr_abs_total: [1, 1, 1, 1, 1] + NEW SELECT FUNCTION: uncorr_abs_atcharge: [1, 1, 1, 1, 1] + NEW SELECT FUNCTION: uncorr_zwitt: [False, False, False, False, False] + NEW SELECT FUNCTION: coincide: [False, True, True, False, False] + NEW SELECT FUNCTION: listofmintot: [0, 1, 2, 3, 4] + NEW SELECT FUNCTION: listofminabs: [0, 1, 2, 3, 4] + NEW SELECT FUNCTION: tmplist: [1, 2], including: + NEW SELECT FUNCTION: Corr_charge=-2 + NEW SELECT FUNCTION: Smiles=[H]N=[C-]C([H])([H])[H] + NEW SELECT FUNCTION: Corr_charge=0 + NEW SELECT FUNCTION: Smiles=[H][N+]#CC([H])([H])[H] + NEW SELECT FUNCTION: found corr_charges=[-2, 0] + NEW SELECT FUNCTION: doing tgt_charge=-2 + NEW SELECT FUNCTION: charge_state added + NEW SELECT FUNCTION: Case 1, only one entry for -2 in tmplist + NEW SELECT FUNCTION: doing tgt_charge=0 + NEW SELECT FUNCTION: charge_state added + NEW SELECT FUNCTION: Case 1, only one entry for 0 in tmplist +SET_TARGET_CHARGE: Target charge 0 of H3-C2-N exists in [-2, 0]. +SET_TARGET_CHARGE: ------------- Cell2mol LIGAND Object -------------- + Version = 0.1 + Type = specie + Sub-Type = ligand + Number of Atoms = 6 + Formula = H3-C2-N + Has Adjacency Matrix = YES + Total Charge = 0 + Smiles = [H][N+]#CC([H])([H])[H] + Origin = split_complex + Number of Groups = 1 +--------------------------------------------------- + [2, 3, 4, 5, 6, 7] 0 +SET_TARGET_CHARGE: Target charge 0 of H3-C2-N exists in [-2, 0]. +SET_TARGET_CHARGE: H3-C2-N + GET_PROTONATION_STATES: Evaluating group N with parent_indices [0] + GET_PROTONATION_STATES: evaluating non-haptic group with index 0 and label N + GET_PROTONATION_STATES: adj=0 Fe + GET_PROTONATION_STATES: adj=26 C + GET_PROTONATION_STATES: will be sent to nonlocal due to N atom + + GET_PROTONATION_STATES: Enters non-local with: + GET_PROTONATION_STATES: block: [0 0 0 0 0 0] + GET_PROTONATION_STATES: addedlist: [0 0 0 0 0 0] + GET_PROTONATION_STATES: 1 non_local_groups groups found + + GET_PROTONATION_STATES: doing combination 0 + GET_PROTONATION_STATES: Protonation SAVED with 0 atoms added to ligand. status=True + + GET_PROTONATION_STATES: doing combination 1 + GET_PROTONATION_STATES: Added H to atom 0 with: a.mconnec=1 and label=N + GET_PROTONATION_STATES: Protonation SAVED with 1 atoms added to ligand. status=True + GET_PROTONATION_STATES:protonation_states=[------------- Cell2mol Protonation ---------------- + Status = True + Labels = ['N', 'C', 'C', 'H', 'H', 'H'] + Type = Non-local + Atoms added in positions = [0 0 0 0 0 0] + Atoms blocked (no atoms added) = [0 0 0 0 0 0] +--------------------------------------------------- +, ------------- Cell2mol Protonation ---------------- + Status = True + Labels = ['N', 'C', 'C', 'H', 'H', 'H', 'H'] + Type = Non-local + Atoms added in positions = [1 0 0 0 0 0] + Atoms blocked (no atoms added) = [0 0 0 0 0 0] +--------------------------------------------------- +] + POSCHARGE will try charges [0, -1, 1, -2, 2] + POSCHARGE: charge 0 with smiles [H]C([H])([H])C#N + POSCHARGE: charge 0 with smiles [H]C([H])([H])C[N-2] + POSCHARGE: charge 0 with smiles [H]C([H])([H])C[N-2] + POSCHARGE: charge 0 with smiles [H]C([H])([H])C[N-2] + POSCHARGE: charge 0 with smiles [H]C([H])([H])C[N-2] + POSCHARGE will try charges [0, -1, 1, -2, 2] + POSCHARGE: charge 0 with smiles [H][N-]CC([H])([H])[H] + POSCHARGE: charge 0 with smiles [H]N=[C-]C([H])([H])[H] + POSCHARGE: charge 0 with smiles [H][N+]#CC([H])([H])[H] + POSCHARGE: charge 0 with smiles [H][N-]CC([H])([H])[H] + POSCHARGE: charge 0 with smiles [H][N-]CC([H])([H])[H] + NEW SELECT FUNCTION: uncorr_total: [-1, -1, 1, -1, -1] + NEW SELECT FUNCTION: uncorr_abs_total: [1, 1, 1, 1, 1] + NEW SELECT FUNCTION: uncorr_abs_atcharge: [1, 1, 1, 1, 1] + NEW SELECT FUNCTION: uncorr_zwitt: [False, False, False, False, False] + NEW SELECT FUNCTION: coincide: [False, True, True, False, False] + NEW SELECT FUNCTION: listofmintot: [0, 1, 2, 3, 4] + NEW SELECT FUNCTION: listofminabs: [0, 1, 2, 3, 4] + NEW SELECT FUNCTION: tmplist: [1, 2], including: + NEW SELECT FUNCTION: Corr_charge=-2 + NEW SELECT FUNCTION: Smiles=[H]N=[C-]C([H])([H])[H] + NEW SELECT FUNCTION: Corr_charge=0 + NEW SELECT FUNCTION: Smiles=[H][N+]#CC([H])([H])[H] + NEW SELECT FUNCTION: found corr_charges=[-2, 0] + NEW SELECT FUNCTION: doing tgt_charge=-2 + NEW SELECT FUNCTION: charge_state added + NEW SELECT FUNCTION: Case 1, only one entry for -2 in tmplist + NEW SELECT FUNCTION: doing tgt_charge=0 + NEW SELECT FUNCTION: charge_state added + NEW SELECT FUNCTION: Case 1, only one entry for 0 in tmplist +SET_TARGET_CHARGE: Target charge 0 of H3-C2-N exists in [-2, 0]. +SET_TARGET_CHARGE: ------------- Cell2mol LIGAND Object -------------- + Version = 0.1 + Type = specie + Sub-Type = ligand + Number of Atoms = 6 + Formula = H3-C2-N + Has Adjacency Matrix = YES + Total Charge = 0 + Smiles = [H][N+]#CC([H])([H])[H] + Origin = split_complex + Number of Groups = 1 +--------------------------------------------------- + [2, 3, 4, 5, 6, 7] 0 +SET_TARGET_CHARGE: Target charge 0 of H3-C2-N exists in [-2, 0]. +SET_TARGET_CHARGE: H3-C2-N + GET_PROTONATION_STATES: Evaluating group N with parent_indices [0] + GET_PROTONATION_STATES: evaluating non-haptic group with index 0 and label N + GET_PROTONATION_STATES: adj=0 Fe + GET_PROTONATION_STATES: adj=32 C + GET_PROTONATION_STATES: will be sent to nonlocal due to N atom + + GET_PROTONATION_STATES: Enters non-local with: + GET_PROTONATION_STATES: block: [0 0 0 0 0 0] + GET_PROTONATION_STATES: addedlist: [0 0 0 0 0 0] + GET_PROTONATION_STATES: 1 non_local_groups groups found + + GET_PROTONATION_STATES: doing combination 0 + GET_PROTONATION_STATES: Protonation SAVED with 0 atoms added to ligand. status=True + + GET_PROTONATION_STATES: doing combination 1 + GET_PROTONATION_STATES: Added H to atom 0 with: a.mconnec=1 and label=N + GET_PROTONATION_STATES: Protonation SAVED with 1 atoms added to ligand. status=True + GET_PROTONATION_STATES:protonation_states=[------------- Cell2mol Protonation ---------------- + Status = True + Labels = ['N', 'C', 'C', 'H', 'H', 'H'] + Type = Non-local + Atoms added in positions = [0 0 0 0 0 0] + Atoms blocked (no atoms added) = [0 0 0 0 0 0] +--------------------------------------------------- +, ------------- Cell2mol Protonation ---------------- + Status = True + Labels = ['N', 'C', 'C', 'H', 'H', 'H', 'H'] + Type = Non-local + Atoms added in positions = [1 0 0 0 0 0] + Atoms blocked (no atoms added) = [0 0 0 0 0 0] +--------------------------------------------------- +] + POSCHARGE will try charges [0, -1, 1, -2, 2] + POSCHARGE: charge 0 with smiles [H]C([H])([H])C#N + POSCHARGE: charge 0 with smiles [H]C([H])([H])C[N-2] + POSCHARGE: charge 0 with smiles [H]C([H])([H])C[N-2] + POSCHARGE: charge 0 with smiles [H]C([H])([H])C[N-2] + POSCHARGE: charge 0 with smiles [H]C([H])([H])C[N-2] + POSCHARGE will try charges [0, -1, 1, -2, 2] + POSCHARGE: charge 0 with smiles [H][N-]CC([H])([H])[H] + POSCHARGE: charge 0 with smiles [H]N=[C-]C([H])([H])[H] + POSCHARGE: charge 0 with smiles [H][N+]#CC([H])([H])[H] + POSCHARGE: charge 0 with smiles [H][N-]CC([H])([H])[H] + POSCHARGE: charge 0 with smiles [H][N-]CC([H])([H])[H] + NEW SELECT FUNCTION: uncorr_total: [-1, -1, 1, -1, -1] + NEW SELECT FUNCTION: uncorr_abs_total: [1, 1, 1, 1, 1] + NEW SELECT FUNCTION: uncorr_abs_atcharge: [1, 1, 1, 1, 1] + NEW SELECT FUNCTION: uncorr_zwitt: [False, False, False, False, False] + NEW SELECT FUNCTION: coincide: [False, True, True, False, False] + NEW SELECT FUNCTION: listofmintot: [0, 1, 2, 3, 4] + NEW SELECT FUNCTION: listofminabs: [0, 1, 2, 3, 4] + NEW SELECT FUNCTION: tmplist: [1, 2], including: + NEW SELECT FUNCTION: Corr_charge=-2 + NEW SELECT FUNCTION: Smiles=[H]N=[C-]C([H])([H])[H] + NEW SELECT FUNCTION: Corr_charge=0 + NEW SELECT FUNCTION: Smiles=[H][N+]#CC([H])([H])[H] + NEW SELECT FUNCTION: found corr_charges=[-2, 0] + NEW SELECT FUNCTION: doing tgt_charge=-2 + NEW SELECT FUNCTION: charge_state added + NEW SELECT FUNCTION: Case 1, only one entry for -2 in tmplist + NEW SELECT FUNCTION: doing tgt_charge=0 + NEW SELECT FUNCTION: charge_state added + NEW SELECT FUNCTION: Case 1, only one entry for 0 in tmplist +SET_TARGET_CHARGE: Target charge 0 of H3-C2-N exists in [-2, 0]. +SET_TARGET_CHARGE: ------------- Cell2mol LIGAND Object -------------- + Version = 0.1 + Type = specie + Sub-Type = ligand + Number of Atoms = 6 + Formula = H3-C2-N + Has Adjacency Matrix = YES + Total Charge = 0 + Smiles = [H][N+]#CC([H])([H])[H] + Origin = split_complex + Number of Groups = 1 +--------------------------------------------------- + [2, 3, 4, 5, 6, 7] 0 +SET_TARGET_CHARGE: Target charge 0 of H3-C2-N exists in [-2, 0]. +SET_TARGET_CHARGE: H3-C2-N + GET_PROTONATION_STATES: Evaluating group N with parent_indices [0] + GET_PROTONATION_STATES: evaluating non-haptic group with index 0 and label N + GET_PROTONATION_STATES: adj=0 Fe + GET_PROTONATION_STATES: adj=2 C + GET_PROTONATION_STATES: will be sent to nonlocal due to N atom + + GET_PROTONATION_STATES: Enters non-local with: + GET_PROTONATION_STATES: block: [0 0 0 0 0 0] + GET_PROTONATION_STATES: addedlist: [0 0 0 0 0 0] + GET_PROTONATION_STATES: 1 non_local_groups groups found + + GET_PROTONATION_STATES: doing combination 0 + GET_PROTONATION_STATES: Protonation SAVED with 0 atoms added to ligand. status=True + + GET_PROTONATION_STATES: doing combination 1 + GET_PROTONATION_STATES: Added H to atom 0 with: a.mconnec=1 and label=N + GET_PROTONATION_STATES: Protonation SAVED with 1 atoms added to ligand. status=True + GET_PROTONATION_STATES:protonation_states=[------------- Cell2mol Protonation ---------------- + Status = True + Labels = ['N', 'C', 'C', 'H', 'H', 'H'] + Type = Non-local + Atoms added in positions = [0 0 0 0 0 0] + Atoms blocked (no atoms added) = [0 0 0 0 0 0] +--------------------------------------------------- +, ------------- Cell2mol Protonation ---------------- + Status = True + Labels = ['N', 'C', 'C', 'H', 'H', 'H', 'H'] + Type = Non-local + Atoms added in positions = [1 0 0 0 0 0] + Atoms blocked (no atoms added) = [0 0 0 0 0 0] +--------------------------------------------------- +] + POSCHARGE will try charges [0, -1, 1, -2, 2] + POSCHARGE: charge 0 with smiles [H]C([H])([H])C#N + POSCHARGE: charge 0 with smiles [H]C([H])([H])C[N-2] + POSCHARGE: charge 0 with smiles [H]C([H])([H])C[N-2] + POSCHARGE: charge 0 with smiles [H]C([H])([H])C[N-2] + POSCHARGE: charge 0 with smiles [H]C([H])([H])C[N-2] + POSCHARGE will try charges [0, -1, 1, -2, 2] + POSCHARGE: charge 0 with smiles [H][N-]CC([H])([H])[H] + POSCHARGE: charge 0 with smiles [H]N=[C-]C([H])([H])[H] + POSCHARGE: charge 0 with smiles [H][N+]#CC([H])([H])[H] + POSCHARGE: charge 0 with smiles [H][N-]CC([H])([H])[H] + POSCHARGE: charge 0 with smiles [H][N-]CC([H])([H])[H] + NEW SELECT FUNCTION: uncorr_total: [-1, -1, 1, -1, -1] + NEW SELECT FUNCTION: uncorr_abs_total: [1, 1, 1, 1, 1] + NEW SELECT FUNCTION: uncorr_abs_atcharge: [1, 1, 1, 1, 1] + NEW SELECT FUNCTION: uncorr_zwitt: [False, False, False, False, False] + NEW SELECT FUNCTION: coincide: [False, True, True, False, False] + NEW SELECT FUNCTION: listofmintot: [0, 1, 2, 3, 4] + NEW SELECT FUNCTION: listofminabs: [0, 1, 2, 3, 4] + NEW SELECT FUNCTION: tmplist: [1, 2], including: + NEW SELECT FUNCTION: Corr_charge=-2 + NEW SELECT FUNCTION: Smiles=[H]N=[C-]C([H])([H])[H] + NEW SELECT FUNCTION: Corr_charge=0 + NEW SELECT FUNCTION: Smiles=[H][N+]#CC([H])([H])[H] + NEW SELECT FUNCTION: found corr_charges=[-2, 0] + NEW SELECT FUNCTION: doing tgt_charge=-2 + NEW SELECT FUNCTION: charge_state added + NEW SELECT FUNCTION: Case 1, only one entry for -2 in tmplist + NEW SELECT FUNCTION: doing tgt_charge=0 + NEW SELECT FUNCTION: charge_state added + NEW SELECT FUNCTION: Case 1, only one entry for 0 in tmplist +SET_TARGET_CHARGE: Target charge 0 of H3-C2-N exists in [-2, 0]. +SET_TARGET_CHARGE: ------------- Cell2mol METAL Object -------------- + Version = 0.1 + Type = atom + Sub-Type = metal + Label = Fe + Atomic Number = 26 + Index in Molecule = 0 + Metal Adjacency (mconnec) = 6 + Regular Adjacencies (connec) = 6 + Possible Charges = [2, 3] +---------------------------------------------------- + [8] 2 +SET_TARGET_CHARGE: Target charge 2 of Fe exists in [2, 3]. +SET_TARGET_CHARGE: Fe +SET_TARGET_CHARGE: Target charge 2 of Fe exists in [2, 3]. +CELL.CREATE_BONDS: Creating Bonds for molecule F6-Sb +CREATE_bonds_specie: specie.formula='F6-Sb', specie.subtype='molecule' + Number of atoms in molecule object and RDKit object are equal: 7 7 + idx=0 Sb Number of bonds : 6 + BOND CREATED 0 0 1 1.0 Sb F + BOND CREATED 0 0 2 1.0 Sb F + BOND CREATED 0 0 3 1.0 Sb F + BOND CREATED 0 0 4 1.0 Sb F + BOND CREATED 0 0 5 1.0 Sb F + BOND CREATED 0 0 6 1.0 Sb F + BONDS [('Sb', 'F', 1.0, 1.839), ('Sb', 'F', 1.0, 1.839), ('Sb', 'F', 1.0, 1.839), ('Sb', 'F', 1.0, 1.854), ('Sb', 'F', 1.0, 1.854), ('Sb', 'F', 1.0, 1.854)] + idx=1 F Number of bonds : 1 + BOND CREATED 1 1 0 1.0 F Sb + BONDS [('F', 'Sb', 1.0, 1.839)] + idx=2 F Number of bonds : 1 + BOND CREATED 2 2 0 1.0 F Sb + BONDS [('F', 'Sb', 1.0, 1.839)] + idx=3 F Number of bonds : 1 + BOND CREATED 3 3 0 1.0 F Sb + BONDS [('F', 'Sb', 1.0, 1.839)] + idx=4 F Number of bonds : 1 + BOND CREATED 4 4 0 1.0 F Sb + BONDS [('F', 'Sb', 1.0, 1.854)] + idx=5 F Number of bonds : 1 + BOND CREATED 5 5 0 1.0 F Sb + BONDS [('F', 'Sb', 1.0, 1.854)] + idx=6 F Number of bonds : 1 + BOND CREATED 6 6 0 1.0 F Sb + BONDS [('F', 'Sb', 1.0, 1.854)] +CELL.CREATE_BONDS: Creating Bonds for molecule F6-Sb +CREATE_bonds_specie: specie.formula='F6-Sb', specie.subtype='molecule' + Number of atoms in molecule object and RDKit object are equal: 7 7 + idx=0 Sb Number of bonds : 6 + BOND CREATED 0 0 1 1.0 Sb F + BOND CREATED 0 0 2 1.0 Sb F + BOND CREATED 0 0 3 1.0 Sb F + BOND CREATED 0 0 4 1.0 Sb F + BOND CREATED 0 0 5 1.0 Sb F + BOND CREATED 0 0 6 1.0 Sb F + BONDS [('Sb', 'F', 1.0, 1.839), ('Sb', 'F', 1.0, 1.839), ('Sb', 'F', 1.0, 1.839), ('Sb', 'F', 1.0, 1.854), ('Sb', 'F', 1.0, 1.854), ('Sb', 'F', 1.0, 1.854)] + idx=1 F Number of bonds : 1 + BOND CREATED 1 1 0 1.0 F Sb + BONDS [('F', 'Sb', 1.0, 1.839)] + idx=2 F Number of bonds : 1 + BOND CREATED 2 2 0 1.0 F Sb + BONDS [('F', 'Sb', 1.0, 1.839)] + idx=3 F Number of bonds : 1 + BOND CREATED 3 3 0 1.0 F Sb + BONDS [('F', 'Sb', 1.0, 1.839)] + idx=4 F Number of bonds : 1 + BOND CREATED 4 4 0 1.0 F Sb + BONDS [('F', 'Sb', 1.0, 1.854)] + idx=5 F Number of bonds : 1 + BOND CREATED 5 5 0 1.0 F Sb + BONDS [('F', 'Sb', 1.0, 1.854)] + idx=6 F Number of bonds : 1 + BOND CREATED 6 6 0 1.0 F Sb + BONDS [('F', 'Sb', 1.0, 1.854)] +CELL.CREATE_BONDS: Creating Bonds for molecule H18-C12-N6-Fe +CREATE_bonds_specie: specie.formula='H3-C2-N', specie.subtype='ligand' + Number of atoms in ligand object and RDKit object are different: 6 7 + [(0, 'N'), (1, 'C'), (2, 'C'), (3, 'H'), (4, 'H'), (5, 'H')] + [(0, 'N'), (1, 'C'), (2, 'C'), (3, 'H'), (4, 'H'), (5, 'H'), (6, 'H')] + NON_BONDED_ATOMS [6] + idx=0 N Number of bonds : 2 + BOND CREATED 0 0 1 3.0 N C + NO BOND CREATED bond_startatom=0 or bond_endatom=6 is not in the specie.atoms. It belongs to non_bonded_atoms=[6]. + BONDS [('N', 'C', 3.0, 1.129)] + idx=1 C Number of bonds : 2 + BOND CREATED 1 1 0 3.0 C N + BOND CREATED 1 1 2 1.0 C C + BONDS [('C', 'N', 3.0, 1.129), ('C', 'C', 1.0, 1.455)] + idx=2 C Number of bonds : 4 + BOND CREATED 2 2 1 1.0 C C + BOND CREATED 2 2 3 1.0 C H + BOND CREATED 2 2 4 1.0 C H + BOND CREATED 2 2 5 1.0 C H + BONDS [('C', 'C', 1.0, 1.455), ('C', 'H', 1.0, 0.979), ('C', 'H', 1.0, 0.98), ('C', 'H', 1.0, 0.981)] + idx=3 H Number of bonds : 1 + BOND CREATED 3 3 2 1.0 H C + BONDS [('H', 'C', 1.0, 0.979)] + idx=4 H Number of bonds : 1 + BOND CREATED 4 4 2 1.0 H C + BONDS [('H', 'C', 1.0, 0.98)] + idx=5 H Number of bonds : 1 + BOND CREATED 5 5 2 1.0 H C + BONDS [('H', 'C', 1.0, 0.981)] + idx=6 H Number of bonds : 1 + NO BOND CREATED bond_startatom=0 or bond_endatom=6 is not in the specie.atoms. It belongs to non_bonded_atoms=[6]. + NO BONDS for H with ligand RDKit object index 6 because it is an added atom +CREATE_bonds_specie: specie.formula='H3-C2-N', specie.subtype='ligand' + Number of atoms in ligand object and RDKit object are different: 6 7 + [(0, 'N'), (1, 'C'), (2, 'C'), (3, 'H'), (4, 'H'), (5, 'H')] + [(0, 'N'), (1, 'C'), (2, 'C'), (3, 'H'), (4, 'H'), (5, 'H'), (6, 'H')] + NON_BONDED_ATOMS [6] + idx=0 N Number of bonds : 2 + BOND CREATED 0 0 1 3.0 N C + NO BOND CREATED bond_startatom=0 or bond_endatom=6 is not in the specie.atoms. It belongs to non_bonded_atoms=[6]. + BONDS [('N', 'C', 3.0, 1.129)] + idx=1 C Number of bonds : 2 + BOND CREATED 1 1 0 3.0 C N + BOND CREATED 1 1 2 1.0 C C + BONDS [('C', 'N', 3.0, 1.129), ('C', 'C', 1.0, 1.455)] + idx=2 C Number of bonds : 4 + BOND CREATED 2 2 1 1.0 C C + BOND CREATED 2 2 3 1.0 C H + BOND CREATED 2 2 4 1.0 C H + BOND CREATED 2 2 5 1.0 C H + BONDS [('C', 'C', 1.0, 1.455), ('C', 'H', 1.0, 0.979), ('C', 'H', 1.0, 0.98), ('C', 'H', 1.0, 0.981)] + idx=3 H Number of bonds : 1 + BOND CREATED 3 3 2 1.0 H C + BONDS [('H', 'C', 1.0, 0.979)] + idx=4 H Number of bonds : 1 + BOND CREATED 4 4 2 1.0 H C + BONDS [('H', 'C', 1.0, 0.98)] + idx=5 H Number of bonds : 1 + BOND CREATED 5 5 2 1.0 H C + BONDS [('H', 'C', 1.0, 0.981)] + idx=6 H Number of bonds : 1 + NO BOND CREATED bond_startatom=0 or bond_endatom=6 is not in the specie.atoms. It belongs to non_bonded_atoms=[6]. + NO BONDS for H with ligand RDKit object index 6 because it is an added atom +CREATE_bonds_specie: specie.formula='H3-C2-N', specie.subtype='ligand' + Number of atoms in ligand object and RDKit object are different: 6 7 + [(0, 'N'), (1, 'C'), (2, 'C'), (3, 'H'), (4, 'H'), (5, 'H')] + [(0, 'N'), (1, 'C'), (2, 'C'), (3, 'H'), (4, 'H'), (5, 'H'), (6, 'H')] + NON_BONDED_ATOMS [6] + idx=0 N Number of bonds : 2 + BOND CREATED 0 0 1 3.0 N C + NO BOND CREATED bond_startatom=0 or bond_endatom=6 is not in the specie.atoms. It belongs to non_bonded_atoms=[6]. + BONDS [('N', 'C', 3.0, 1.129)] + idx=1 C Number of bonds : 2 + BOND CREATED 1 1 0 3.0 C N + BOND CREATED 1 1 2 1.0 C C + BONDS [('C', 'N', 3.0, 1.129), ('C', 'C', 1.0, 1.455)] + idx=2 C Number of bonds : 4 + BOND CREATED 2 2 1 1.0 C C + BOND CREATED 2 2 3 1.0 C H + BOND CREATED 2 2 4 1.0 C H + BOND CREATED 2 2 5 1.0 C H + BONDS [('C', 'C', 1.0, 1.455), ('C', 'H', 1.0, 0.979), ('C', 'H', 1.0, 0.98), ('C', 'H', 1.0, 0.981)] + idx=3 H Number of bonds : 1 + BOND CREATED 3 3 2 1.0 H C + BONDS [('H', 'C', 1.0, 0.979)] + idx=4 H Number of bonds : 1 + BOND CREATED 4 4 2 1.0 H C + BONDS [('H', 'C', 1.0, 0.98)] + idx=5 H Number of bonds : 1 + BOND CREATED 5 5 2 1.0 H C + BONDS [('H', 'C', 1.0, 0.981)] + idx=6 H Number of bonds : 1 + NO BOND CREATED bond_startatom=0 or bond_endatom=6 is not in the specie.atoms. It belongs to non_bonded_atoms=[6]. + NO BONDS for H with ligand RDKit object index 6 because it is an added atom +CREATE_bonds_specie: specie.formula='H3-C2-N', specie.subtype='ligand' + Number of atoms in ligand object and RDKit object are different: 6 7 + [(0, 'N'), (1, 'C'), (2, 'C'), (3, 'H'), (4, 'H'), (5, 'H')] + [(0, 'N'), (1, 'C'), (2, 'C'), (3, 'H'), (4, 'H'), (5, 'H'), (6, 'H')] + NON_BONDED_ATOMS [6] + idx=0 N Number of bonds : 2 + BOND CREATED 0 0 1 3.0 N C + NO BOND CREATED bond_startatom=0 or bond_endatom=6 is not in the specie.atoms. It belongs to non_bonded_atoms=[6]. + BONDS [('N', 'C', 3.0, 1.129)] + idx=1 C Number of bonds : 2 + BOND CREATED 1 1 0 3.0 C N + BOND CREATED 1 1 2 1.0 C C + BONDS [('C', 'N', 3.0, 1.129), ('C', 'C', 1.0, 1.455)] + idx=2 C Number of bonds : 4 + BOND CREATED 2 2 1 1.0 C C + BOND CREATED 2 2 3 1.0 C H + BOND CREATED 2 2 4 1.0 C H + BOND CREATED 2 2 5 1.0 C H + BONDS [('C', 'C', 1.0, 1.455), ('C', 'H', 1.0, 0.979), ('C', 'H', 1.0, 0.98), ('C', 'H', 1.0, 0.981)] + idx=3 H Number of bonds : 1 + BOND CREATED 3 3 2 1.0 H C + BONDS [('H', 'C', 1.0, 0.979)] + idx=4 H Number of bonds : 1 + BOND CREATED 4 4 2 1.0 H C + BONDS [('H', 'C', 1.0, 0.98)] + idx=5 H Number of bonds : 1 + BOND CREATED 5 5 2 1.0 H C + BONDS [('H', 'C', 1.0, 0.981)] + idx=6 H Number of bonds : 1 + NO BOND CREATED bond_startatom=0 or bond_endatom=6 is not in the specie.atoms. It belongs to non_bonded_atoms=[6]. + NO BONDS for H with ligand RDKit object index 6 because it is an added atom +CREATE_bonds_specie: specie.formula='H3-C2-N', specie.subtype='ligand' + Number of atoms in ligand object and RDKit object are different: 6 7 + [(0, 'N'), (1, 'C'), (2, 'C'), (3, 'H'), (4, 'H'), (5, 'H')] + [(0, 'N'), (1, 'C'), (2, 'C'), (3, 'H'), (4, 'H'), (5, 'H'), (6, 'H')] + NON_BONDED_ATOMS [6] + idx=0 N Number of bonds : 2 + BOND CREATED 0 0 1 3.0 N C + NO BOND CREATED bond_startatom=0 or bond_endatom=6 is not in the specie.atoms. It belongs to non_bonded_atoms=[6]. + BONDS [('N', 'C', 3.0, 1.129)] + idx=1 C Number of bonds : 2 + BOND CREATED 1 1 0 3.0 C N + BOND CREATED 1 1 2 1.0 C C + BONDS [('C', 'N', 3.0, 1.129), ('C', 'C', 1.0, 1.455)] + idx=2 C Number of bonds : 4 + BOND CREATED 2 2 1 1.0 C C + BOND CREATED 2 2 3 1.0 C H + BOND CREATED 2 2 4 1.0 C H + BOND CREATED 2 2 5 1.0 C H + BONDS [('C', 'C', 1.0, 1.455), ('C', 'H', 1.0, 0.979), ('C', 'H', 1.0, 0.98), ('C', 'H', 1.0, 0.981)] + idx=3 H Number of bonds : 1 + BOND CREATED 3 3 2 1.0 H C + BONDS [('H', 'C', 1.0, 0.979)] + idx=4 H Number of bonds : 1 + BOND CREATED 4 4 2 1.0 H C + BONDS [('H', 'C', 1.0, 0.98)] + idx=5 H Number of bonds : 1 + BOND CREATED 5 5 2 1.0 H C + BONDS [('H', 'C', 1.0, 0.981)] + idx=6 H Number of bonds : 1 + NO BOND CREATED bond_startatom=0 or bond_endatom=6 is not in the specie.atoms. It belongs to non_bonded_atoms=[6]. + NO BONDS for H with ligand RDKit object index 6 because it is an added atom +CREATE_bonds_specie: specie.formula='H3-C2-N', specie.subtype='ligand' + Number of atoms in ligand object and RDKit object are different: 6 7 + [(0, 'N'), (1, 'C'), (2, 'C'), (3, 'H'), (4, 'H'), (5, 'H')] + [(0, 'N'), (1, 'C'), (2, 'C'), (3, 'H'), (4, 'H'), (5, 'H'), (6, 'H')] + NON_BONDED_ATOMS [6] + idx=0 N Number of bonds : 2 + BOND CREATED 0 0 1 3.0 N C + NO BOND CREATED bond_startatom=0 or bond_endatom=6 is not in the specie.atoms. It belongs to non_bonded_atoms=[6]. + BONDS [('N', 'C', 3.0, 1.129)] + idx=1 C Number of bonds : 2 + BOND CREATED 1 1 0 3.0 C N + BOND CREATED 1 1 2 1.0 C C + BONDS [('C', 'N', 3.0, 1.129), ('C', 'C', 1.0, 1.455)] + idx=2 C Number of bonds : 4 + BOND CREATED 2 2 1 1.0 C C + BOND CREATED 2 2 3 1.0 C H + BOND CREATED 2 2 4 1.0 C H + BOND CREATED 2 2 5 1.0 C H + BONDS [('C', 'C', 1.0, 1.455), ('C', 'H', 1.0, 0.979), ('C', 'H', 1.0, 0.98), ('C', 'H', 1.0, 0.981)] + idx=3 H Number of bonds : 1 + BOND CREATED 3 3 2 1.0 H C + BONDS [('H', 'C', 1.0, 0.979)] + idx=4 H Number of bonds : 1 + BOND CREATED 4 4 2 1.0 H C + BONDS [('H', 'C', 1.0, 0.98)] + idx=5 H Number of bonds : 1 + BOND CREATED 5 5 2 1.0 H C + BONDS [('H', 'C', 1.0, 0.981)] + idx=6 H Number of bonds : 1 + NO BOND CREATED bond_startatom=0 or bond_endatom=6 is not in the specie.atoms. It belongs to non_bonded_atoms=[6]. + NO BONDS for H with ligand RDKit object index 6 because it is an added atom +ligand.formula='H3-C2-N' smiles='[H]C([H])([H])C#N' + +ligand.formula='H3-C2-N' smiles='[H]C([H])([H])C#N' + +ligand.formula='H3-C2-N' smiles='[H]C([H])([H])C#N' + +ligand.formula='H3-C2-N' smiles='[H]C([H])([H])C#N' + +ligand.formula='H3-C2-N' smiles='[H]C([H])([H])C#N' + +ligand.formula='H3-C2-N' smiles='[H]C([H])([H])C#N' + +Charge Assignment Finished Normally. Total execution time: 0.48 seconds +######################################### + Assigning Spin multiplicity +######################################### +GET_SPIN: Spin multiplicity of the complex F6-Sb is assigned as 1 + +GET_SPIN: Spin multiplicity of the complex F6-Sb is assigned as 1 + +GENERATE_feature_vector: Fe +GENERATE_feature_vector: elem_nr=26 m_ox=2.0 valence_elec=6.0 +GENERATE_feature_vector: metal.coord_nr=6 metal.coord_geometry='Octahedral' geom_nr=14 +GENERATE_feature_vector: metal.rel_metal_radius=1.094 +GENERATE_feature_vector: hapticity=0 +GENERATE_feature_vector: feature=array([[26. , 2. , 6. , 6. , 14. , 1.094, 0. ]]) +ASSIGN_SPIN_METAL: Spin multiplicity of the metal Fe is predicted as 5 using Random Forest model +GET_SPIN: Spin multiplicity of the metal Fe is assigned as 5 +GET_SPIN: Spin multiplicity of the complex H18-C12-N6-Fe is assigned as 5 + + +Total execution time for Spin Assignment: 2.83 seconds +------------------------------- +Errors in Unit Cell +------------------------------- +Cell2mol terminated with error number 0. Message: +No Errors Found +SAVING cell2mol CELL object to /Users/ycho/cell2mol/cell2mol/test/ACEYOW/Cell_ACEYOW.cell diff --git a/cell2mol/test/ACEYOW/cif2cell.err b/cell2mol/test/ACEYOW/cif2cell.err new file mode 100644 index 00000000..e69de29b diff --git a/cell2mol/test/ACEYOW/error_0.out b/cell2mol/test/ACEYOW/error_0.out new file mode 100644 index 00000000..1ed2c65b --- /dev/null +++ b/cell2mol/test/ACEYOW/error_0.out @@ -0,0 +1,2 @@ +Cell2mol terminated with error number 0. 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zSN4imRos>G+E$&F$}7#gqV3zNXGP=a?0jw2*<9ZIeP`o}@mpsg_CxEutg6!3pQ~oi z#eQ2g`>ie1u|L~lX4RC({*3*$YBKQILhX)2_qx2*Ie+)Mym6x6r^7((w@-)nj?UUv zKNf%Tu$`a(+0Oke^LlmZQh2Z0G#{EK>0*Aa zXNmda)TaHKYLcpC*+1X&X>A$d^0xK5T)cdaoa_*2te#PSWbLf!4NZqN)fAq!!{F8- zrdcq~G%uPaUzpRoOP9l%3ilXYZK1)uSx}f)6wRNSZ(OskwqZ(r!|WNg^YYWD?AElP kaSbb(S>Mo5KkLY%V72_*xwGd^nO577Z%Vq%pE~aU1AvpgVE_OC literal 0 HcmV?d00001 diff --git a/cell2mol/test/YETBUV/YETBUV.cif b/cell2mol/test/YETBUV/YETBUV.cif new file mode 100644 index 00000000..aa906538 --- /dev/null +++ b/cell2mol/test/YETBUV/YETBUV.cif @@ -0,0 +1,224 @@ + +####################################################################### +# +# Cambridge Crystallographic Data Centre +# CCDC +# +####################################################################### +# +# If this CIF has been generated from an entry in the Cambridge +# Structural Database, then it will include bibliographic, chemical, +# crystal, experimental, refinement or atomic coordinate data resulting +# from the CCDC's data processing and validation procedures. +# +####################################################################### + +data_CSD_CIF_YETBUV +_audit_creation_date 2007-04-11 +_audit_creation_method CSD-ConQuest-V1 +_database_code_CSD YETBUV +_database_code_depnum_ccdc_archive 'CCDC 618532' +_chemical_formula_sum 'C14 H36 Cl3 Co1 O4 P4' +_chemical_formula_moiety +; +C14 H36 Cl2 Co1 P4 1+,Cl1 O4 1- +; +_journal_coden_Cambridge 222 +_journal_year 2007 +_journal_page_first 308 +_journal_name_full 'Dalton Trans. ' +loop_ +_publ_author_name +"T.Suzuki" +"K.Fujiiwara" +"H.D.Takagi" +"K.Kashiwabara" +_chemical_name_systematic +; +trans-Dichloro-bis(1,3-bis(dimethylphosphino)propane-P,P')-cobalt(iii) +perchlorate +; +_cell_volume 2382.832 +_exptl_crystal_colour 'green' +_exptl_crystal_density_diffrn 1.554 +_exptl_crystal_description 'block' +_exptl_crystal_preparation 'acetonitrile/diethyl ether' +_diffrn_ambient_temperature 296 +#These two values have been output from a single CSD field. +_refine_ls_R_factor_gt 0.0427 +_refine_ls_wR_factor_gt 0.0427 +_symmetry_cell_setting tetragonal +_symmetry_space_group_name_H-M 'P 42/n b c' +_symmetry_Int_Tables_number 133 +loop_ +_symmetry_equiv_pos_site_id +_symmetry_equiv_pos_as_xyz +1 x,y,z +2 1/2-y,x,1/2+z +3 y,1/2-x,1/2+z +4 y,x,1/2-z +5 x,1/2-y,-z +6 1/2-y,1/2-x,1/2-z +7 1/2-x,y,-z +8 1/2-x,1/2-y,z +9 -x,-y,-z +10 -1/2+y,-x,-1/2-z +11 -y,-1/2+x,-1/2-z +12 -y,-x,-1/2+z +13 -x,-1/2+y,z +14 -1/2+y,-1/2+x,-1/2+z +15 -1/2+x,-y,z +16 -1/2+x,-1/2+y,-z +_cell_length_a 11.4228(15) +_cell_length_b 11.4228(15) +_cell_length_c 18.262(3) +_cell_angle_alpha 90 +_cell_angle_beta 90 +_cell_angle_gamma 90 +_cell_formula_units_Z 4 +loop_ +_atom_type_symbol +_atom_type_radius_bond +C 0.68 +H 0.23 +Cl 0.99 +Co 1.33 +O 0.68 +P 1.05 +loop_ +_atom_site_label +_atom_site_type_symbol +_atom_site_fract_x +_atom_site_fract_y +_atom_site_fract_z +Co1 Co 0.75000 0.25000 0.50000 +Cl1 Cl 0.94746(7) 0.25000 0.50000 +Cl2 Cl 0.25000 0.25000 0.25000 +P1 P 0.76355(5) 0.10723(6) 0.41267(4) +O1 O 0.1566(7) 0.2452(7) 0.2917(5) +C1 C 0.8621(3) 0.1351(3) 0.33638(17) +H1 H 0.93600 0.16250 0.35470 +H2 H 0.82860 0.19350 0.30490 +H3 H 0.87380 0.06410 0.30920 +C2 C 0.6304(3) 0.0570(3) 0.36794(18) +H4 H 0.58980 0.12270 0.34730 +H5 H 0.58100 0.01890 0.40320 +H6 H 0.65020 0.00270 0.32970 +C3 C 0.8280(3) -0.0273(2) 0.44813(17) +H7 H 0.84940 -0.07650 0.40690 +H8 H 0.89950 -0.00740 0.47390 +C4 C 0.75000 -0.0991(3) 0.50000 +H9 H 0.70010 -0.14940 0.47070 +H10 H 0.79990 -0.14940 0.52930 +Cl1F Cl 0.55254(7) 0.25000 0.50000 +P1F P 0.73645(5) 0.10723(6) 0.58733(4) +P1D P 0.76355(5) 0.39277(6) 0.58733(4) +P1G P 0.73645(5) 0.39277(6) 0.41267(4) +O1C O 0.2452(7) 0.1566(7) 0.2083(5) +O1E O 0.2548(7) 0.3434(7) 0.2083(5) +O1G O 0.3434(7) 0.2548(7) 0.2917(5) +C1D C 0.8621(3) 0.3649(3) 0.66362(17) +C1G C 0.6379(3) 0.3649(3) 0.33638(17) +C1F C 0.6379(3) 0.1351(3) 0.66362(17) +H1D H 0.93600 0.33750 0.64530 +H1G H 0.56400 0.33750 0.35470 +H1F H 0.56400 0.16250 0.64530 +H2D H 0.82860 0.30650 0.69510 +H2G H 0.67140 0.30650 0.30490 +H2F H 0.67140 0.19350 0.69510 +H3D H 0.87380 0.43590 0.69080 +H3G H 0.62620 0.43590 0.30920 +H3F H 0.62620 0.06410 0.69080 +C2D C 0.6304(3) 0.4430(3) 0.63206(18) +C2G C 0.8696(3) 0.4430(3) 0.36794(18) +C2F C 0.8696(3) 0.0570(3) 0.63206(18) +H4D H 0.58980 0.37730 0.65270 +H4G H 0.91020 0.37730 0.34730 +H4F H 0.91020 0.12270 0.65270 +H5D H 0.58100 0.48110 0.59680 +H5G H 0.91900 0.48110 0.40320 +H5F H 0.91900 0.01890 0.59680 +H6D H 0.65020 0.49730 0.67030 +H6G H 0.84980 0.49730 0.32970 +H6F H 0.84980 0.00270 0.67030 +C3F C 0.6720(3) -0.0273(2) 0.55187(17) +C3D C 0.8280(3) 0.5273(2) 0.55187(17) +C3G C 0.6720(3) 0.5273(2) 0.44813(17) +H7D H 0.84940 0.57650 0.59310 +H7G H 0.65060 0.57650 0.40690 +H7F H 0.65060 -0.07650 0.59310 +H8D H 0.89950 0.50740 0.52610 +H8G H 0.60050 0.50740 0.47390 +H8F H 0.60050 -0.00740 0.52610 +C4D C 0.75000 0.5991(3) 0.50000 +H9D H 0.70010 0.64940 0.52930 +H9G H 0.79990 0.64940 0.47070 +loop_ +_geom_bond_atom_site_label_1 +_geom_bond_atom_site_label_2 +_geom_bond_distance +_geom_bond_site_symmetry_1 +_geom_bond_site_symmetry_2 +Co1 Cl1 2.256 1_555 1_555 +Cl2 O1 1.312 1_555 1_555 +P1 Co1 2.286 1_555 1_555 +C1 P1 1.819 1_555 1_555 +H1 C1 0.960 1_555 1_555 +H2 C1 0.960 1_555 1_555 +H3 C1 0.960 1_555 1_555 +C2 P1 1.819 1_555 1_555 +H4 C2 0.959 1_555 1_555 +H5 C2 0.960 1_555 1_555 +H6 C2 0.961 1_555 1_555 +C3 P1 1.823 1_555 1_555 +H7 C3 0.971 1_555 1_555 +H8 C3 0.970 1_555 1_555 +C4 C3 1.537 1_555 1_555 +H9 C4 0.970 1_555 1_555 +H10 C4 0.970 1_555 1_555 +Cl1F Co1 2.256 1_555 1_555 +P1F Co1 2.286 1_555 1_555 +P1D Co1 2.286 1_555 1_555 +P1G Co1 2.286 1_555 1_555 +O1C Cl2 1.312 1_555 1_555 +O1E Cl2 1.312 1_555 1_555 +O1G Cl2 1.312 1_555 1_555 +C1D P1D 1.819 1_555 1_555 +C1G P1G 1.819 1_555 1_555 +C1F P1F 1.819 1_555 1_555 +H1D C1D 0.960 1_555 1_555 +H1G C1G 0.960 1_555 1_555 +H1F C1F 0.960 1_555 1_555 +H2D C1D 0.960 1_555 1_555 +H2G C1G 0.960 1_555 1_555 +H2F C1F 0.960 1_555 1_555 +H3D C1D 0.960 1_555 1_555 +H3G C1G 0.960 1_555 1_555 +H3F C1F 0.960 1_555 1_555 +C2D P1D 1.819 1_555 1_555 +C2G P1G 1.819 1_555 1_555 +C2F P1F 1.819 1_555 1_555 +H4D C2D 0.959 1_555 1_555 +H4G C2G 0.959 1_555 1_555 +H4F C2F 0.959 1_555 1_555 +H5D C2D 0.960 1_555 1_555 +H5G C2G 0.960 1_555 1_555 +H5F C2F 0.960 1_555 1_555 +H6D C2D 0.961 1_555 1_555 +H6G C2G 0.961 1_555 1_555 +H6F C2F 0.961 1_555 1_555 +C3F C4 1.537 1_555 1_555 +C3D P1D 1.823 1_555 1_555 +C3G P1G 1.823 1_555 1_555 +H7D C3D 0.971 1_555 1_555 +H7G C3G 0.971 1_555 1_555 +H7F C3F 0.971 1_555 1_555 +H8D C3D 0.970 1_555 1_555 +H8G C3G 0.970 1_555 1_555 +H8F C3F 0.970 1_555 1_555 +C4D C3D 1.537 1_555 1_555 +H9D C4D 0.970 1_555 1_555 +H9G C4D 0.970 1_555 1_555 +P1F C3F 1.823 1_555 1_555 +C3G C4D 1.537 1_555 1_555 +#END diff --git a/cell2mol/test/YETBUV/YETBUV.info b/cell2mol/test/YETBUV/YETBUV.info new file mode 100644 index 00000000..af25cf66 --- /dev/null +++ b/cell2mol/test/YETBUV/YETBUV.info @@ -0,0 +1,1077 @@ +CIF2CELL 2.0.0 +2024-04-25 15:45 +Output for None (trans-Dichloro-bis(1,3-bis(dimethylphosphino)propane-P,P')-cobalt(iii) +perchlorate) +CIF file exported from Cambridge Structural Database. +Database reference code: YETBUV. + BIBLIOGRAPHIC INFORMATION +T.Suzuki et al., Dalton Trans. , 308- (2007) + INPUT CELL INFORMATION +Symmetry information: +Tetragonal crystal system. +Space group number : 133 +Hall symbol : P 4n 2c -1n +Hermann-Mauguin symbol : P42/nbc + +Lattice parameters: + a b c + 11.4228000 11.4228000 18.2620000 + alpha beta gamma + 90.0000000 90.0000000 90.0000000 +Representative sites : +Atom x y z +Co 0.7500000 0.2500000 0.5000000 +Cl 0.9474600 0.2500000 0.5000000 +Cl 0.2500000 0.2500000 0.2500000 +P 0.7635500 0.1072300 0.4126700 +O 0.1566000 0.2452000 0.2917000 +C 0.8621000 0.1351000 0.3363800 +H 0.9360000 0.1625000 0.3547000 +H 0.8286000 0.1935000 0.3049000 +H 0.8738000 0.0641000 0.3092000 +C 0.6304000 0.0570000 0.3679400 +H 0.5898000 0.1227000 0.3473000 +H 0.5810000 0.0189000 0.4032000 +H 0.6502000 0.0027000 0.3297000 +C 0.8280000 -0.0273000 0.4481300 +H 0.8494000 -0.0765000 0.4069000 +H 0.8995000 -0.0074000 0.4739000 +C 0.7500000 -0.0991000 0.5000000 +H 0.7001000 -0.1494000 0.4707000 +H 0.7999000 -0.1494000 0.5293000 +Cl 0.5525400 0.2500000 0.5000000 +P 0.7364500 0.1072300 0.5873300 +P 0.7635500 0.3927700 0.5873300 +P 0.7364500 0.3927700 0.4126700 +O 0.2452000 0.1566000 0.2083000 +O 0.2548000 0.3434000 0.2083000 +O 0.3434000 0.2548000 0.2917000 +C 0.8621000 0.3649000 0.6636200 +C 0.6379000 0.3649000 0.3363800 +C 0.6379000 0.1351000 0.6636200 +H 0.9360000 0.3375000 0.6453000 +H 0.5640000 0.3375000 0.3547000 +H 0.5640000 0.1625000 0.6453000 +H 0.8286000 0.3065000 0.6951000 +H 0.6714000 0.3065000 0.3049000 +H 0.6714000 0.1935000 0.6951000 +H 0.8738000 0.4359000 0.6908000 +H 0.6262000 0.4359000 0.3092000 +H 0.6262000 0.0641000 0.6908000 +C 0.6304000 0.4430000 0.6320600 +C 0.8696000 0.4430000 0.3679400 +C 0.8696000 0.0570000 0.6320600 +H 0.5898000 0.3773000 0.6527000 +H 0.9102000 0.3773000 0.3473000 +H 0.9102000 0.1227000 0.6527000 +H 0.5810000 0.4811000 0.5968000 +H 0.9190000 0.4811000 0.4032000 +H 0.9190000 0.0189000 0.5968000 +H 0.6502000 0.4973000 0.6703000 +H 0.8498000 0.4973000 0.3297000 +H 0.8498000 0.0027000 0.6703000 +C 0.6720000 -0.0273000 0.5518700 +C 0.8280000 0.5273000 0.5518700 +C 0.6720000 0.5273000 0.4481300 +H 0.8494000 0.5765000 0.5931000 +H 0.6506000 0.5765000 0.4069000 +H 0.6506000 -0.0765000 0.5931000 +H 0.8995000 0.5074000 0.5261000 +H 0.6005000 0.5074000 0.4739000 +H 0.6005000 -0.0074000 0.5261000 +C 0.7500000 0.5991000 0.5000000 +H 0.7001000 0.6494000 0.5293000 +H 0.7999000 0.6494000 0.4707000 + + OUTPUT CELL INFORMATION +Symmetry information: +Tetragonal crystal system. +Space group number : 133 +Hall symbol : P 4n 2c -1n +Hermann-Mauguin symbol : P42/nbc + +Bravais lattice vectors : + 11.4228000 0.0000000 0.0000000 + 0.0000000 11.4228000 0.0000000 + 0.0000000 0.0000000 18.2620000 +All sites, (cartesian coordinates): +Atom x y z +Co 8.5671000 2.8557000 9.1310000 +Co 2.8557000 2.8557000 0.0000000 +Co 8.5671000 2.8557000 0.0000000 +Co 8.5671000 8.5671000 0.0000000 +Co 2.8557000 8.5671000 9.1310000 +Co 2.8557000 2.8557000 9.1310000 +Co 8.5671000 8.5671000 9.1310000 +Co 2.8557000 8.5671000 0.0000000 +Cl 10.8226461 2.8557000 9.1310000 +Cl 0.6001539 2.8557000 0.0000000 +Cl 8.5671000 0.6001539 0.0000000 +Cl 6.3115539 2.8557000 0.0000000 +Cl 8.5671000 6.3115539 0.0000000 +Cl 0.6001539 8.5671000 9.1310000 +Cl 2.8557000 0.6001539 9.1310000 +Cl 2.8557000 6.3115539 9.1310000 +Cl 6.3115539 8.5671000 9.1310000 +Cl 8.5671000 10.8226461 9.1310000 +Cl 10.8226461 8.5671000 0.0000000 +Cl 2.8557000 10.8226461 0.0000000 +Cl 2.8557000 5.1112461 0.0000000 +Cl 5.1112461 8.5671000 0.0000000 +Cl 8.5671000 5.1112461 9.1310000 +Cl 5.1112461 2.8557000 9.1310000 +Cl 2.8557000 2.8557000 4.5655000 +Cl 8.5671000 2.8557000 4.5655000 +Cl 8.5671000 8.5671000 13.6965000 +Cl 8.5671000 2.8557000 13.6965000 +Cl 8.5671000 8.5671000 4.5655000 +Cl 2.8557000 8.5671000 13.6965000 +Cl 2.8557000 2.8557000 13.6965000 +Cl 2.8557000 8.5671000 4.5655000 +P 8.7218789 1.2248668 7.5361795 +P 2.7009211 1.2248668 1.5948205 +P 10.1979332 2.7009211 16.6671795 +P 8.4123211 4.4865332 1.5948205 +P 6.9362668 8.4123211 16.6671795 +P 2.7009211 10.1979332 7.5361795 +P 1.2248668 2.7009211 10.7258205 +P 4.4865332 8.4123211 10.7258205 +P 8.4123211 6.9362668 7.5361795 +P 10.1979332 8.7218789 10.7258205 +P 8.7218789 10.1979332 1.5948205 +P 1.2248668 8.7218789 16.6671795 +P 4.4865332 3.0104789 16.6671795 +P 3.0104789 6.9362668 1.5948205 +P 6.9362668 3.0104789 10.7258205 +P 3.0104789 4.4865332 7.5361795 +O 1.7888105 2.8008706 5.3270254 +O 9.6339895 2.8008706 3.8039746 +O 8.6219294 9.6339895 14.4580254 +O 3.9225895 2.9105294 3.8039746 +O 8.5122706 3.9225895 14.4580254 +O 9.6339895 8.6219294 5.3270254 +O 2.8008706 9.6339895 12.9349746 +O 2.9105294 3.9225895 12.9349746 +O 3.9225895 8.5122706 5.3270254 +O 8.6219294 1.7888105 12.9349746 +O 1.7888105 8.6219294 3.8039746 +O 2.8008706 1.7888105 14.4580254 +O 2.9105294 7.5002105 14.4580254 +O 7.5002105 8.5122706 3.8039746 +O 8.5122706 7.5002105 12.9349746 +O 7.5002105 2.9105294 5.3270254 +C 9.8475959 1.5432203 6.1429716 +C 1.5752041 1.5432203 2.9880284 +C 9.8795797 1.5752041 15.2739716 +C 7.2866041 4.1681797 2.9880284 +C 7.2546203 7.2866041 15.2739716 +C 1.5752041 9.8795797 6.1429716 +C 1.5432203 1.5752041 12.1190284 +C 4.1681797 7.2866041 12.1190284 +C 7.2866041 7.2546203 6.1429716 +C 9.8795797 9.8475959 12.1190284 +C 9.8475959 9.8795797 2.9880284 +C 1.5432203 9.8475959 15.2739716 +C 4.1681797 4.1361959 15.2739716 +C 4.1361959 7.2546203 2.9880284 +C 7.2546203 4.1361959 12.1190284 +C 4.1361959 4.1681797 6.1429716 +H 10.6917408 1.8562050 6.4775314 +H 0.7310592 1.8562050 2.6534686 +H 9.5665950 0.7310592 15.6085314 +H 6.4424592 3.8551950 2.6534686 +H 7.5676050 6.4424592 15.6085314 +H 0.7310592 9.5665950 6.4775314 +H 1.8562050 0.7310592 11.7844686 +H 3.8551950 6.4424592 11.7844686 +H 6.4424592 7.5676050 6.4775314 +H 9.5665950 10.6917408 11.7844686 +H 10.6917408 9.5665950 2.6534686 +H 1.8562050 10.6917408 15.6085314 +H 3.8551950 4.9803408 15.6085314 +H 4.9803408 7.5676050 2.6534686 +H 7.5676050 4.9803408 11.7844686 +H 4.9803408 3.8551950 6.4775314 +H 9.4649321 2.2103118 5.5680838 +H 1.9578679 2.2103118 3.5629162 +H 9.2124882 1.9578679 14.6990838 +H 7.6692679 3.5010882 3.5629162 +H 7.9217118 7.6692679 14.6990838 +H 1.9578679 9.2124882 5.5680838 +H 2.2103118 1.9578679 12.6939162 +H 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+H 1.7202737 6.5852442 16.5618078 +H 4.8375558 1.7202737 1.7001922 +H 7.4316737 10.5489558 16.5618078 +H 0.8738442 7.4316737 1.7001922 +H 1.7202737 4.8375558 10.8311922 +H 6.5852442 1.7202737 7.4308078 +H 10.5489558 7.4316737 7.4308078 +H 7.4316737 0.8738442 10.8311922 +H 4.8375558 9.7025263 7.4308078 +H 9.7025263 4.8375558 16.5618078 +H 6.5852442 9.7025263 1.7001922 +H 10.5489558 3.9911263 1.7001922 +H 3.9911263 0.8738442 16.5618078 +H 0.8738442 3.9911263 7.4308078 +H 3.9911263 10.5489558 10.8311922 +H 7.4316737 6.5852442 7.4308078 +H 3.9911263 6.5852442 1.7001922 +H 4.8375558 3.9911263 16.5618078 +H 9.7025263 10.5489558 1.7001922 +H 0.8738442 9.7025263 16.5618078 +H 3.9911263 4.8375558 7.4308078 +H 6.5852442 3.9911263 10.8311922 +H 10.5489558 9.7025263 10.8311922 +H 9.7025263 0.8738442 7.4308078 +H 4.8375558 7.4316737 10.8311922 +H 7.4316737 4.8375558 1.7001922 +H 6.5852442 7.4316737 16.5618078 +H 10.5489558 1.7202737 16.5618078 +H 1.7202737 0.8738442 1.7001922 +H 0.8738442 1.7202737 10.8311922 +H 1.7202737 10.5489558 7.4308078 +H 7.4316737 10.5489558 10.8311922 +H 3.9911263 10.5489558 16.5618078 +H 0.8738442 3.9911263 1.7001922 +H 9.7025263 6.5852442 16.5618078 +H 4.8375558 9.7025263 1.7001922 +H 3.9911263 0.8738442 10.8311922 +H 10.5489558 3.9911263 7.4308078 +H 6.5852442 9.7025263 7.4308078 +H 9.7025263 4.8375558 10.8311922 +H 0.8738442 7.4316737 7.4308078 +H 7.4316737 0.8738442 16.5618078 +H 10.5489558 7.4316737 1.7001922 +H 6.5852442 1.7202737 1.7001922 +H 1.7202737 4.8375558 16.5618078 +H 4.8375558 1.7202737 7.4308078 +H 1.7202737 6.5852442 10.8311922 +H 10.2748086 5.7959287 9.6076382 +H 1.1479914 5.7959287 17.7853618 +H 5.6268713 1.1479914 0.4766382 +H 6.8593914 11.3382713 17.7853618 +H 0.0845287 6.8593914 0.4766382 +H 1.1479914 5.6268713 9.6076382 +H 5.7959287 1.1479914 8.6543618 +H 11.3382713 6.8593914 8.6543618 +H 6.8593914 0.0845287 9.6076382 +H 5.6268713 10.2748086 8.6543618 +H 10.2748086 5.6268713 17.7853618 +H 5.7959287 10.2748086 0.4766382 +H 11.3382713 4.5634086 0.4766382 +H 4.5634086 0.0845287 17.7853618 +H 0.0845287 4.5634086 8.6543618 +H 4.5634086 11.3382713 9.6076382 +H 6.8593914 5.7959287 8.6543618 +H 4.5634086 5.7959287 0.4766382 +H 5.6268713 4.5634086 17.7853618 +H 10.2748086 11.3382713 0.4766382 +H 0.0845287 10.2748086 17.7853618 +H 4.5634086 5.6268713 8.6543618 +H 5.7959287 4.5634086 9.6076382 +H 11.3382713 10.2748086 9.6076382 +H 10.2748086 0.0845287 8.6543618 +H 5.6268713 6.8593914 9.6076382 +H 6.8593914 5.6268713 0.4766382 +H 5.7959287 6.8593914 17.7853618 +H 11.3382713 1.1479914 17.7853618 +H 1.1479914 0.0845287 0.4766382 +H 0.0845287 1.1479914 9.6076382 +H 1.1479914 11.3382713 8.6543618 +H 6.8593914 11.3382713 9.6076382 +H 4.5634086 11.3382713 17.7853618 +H 0.0845287 4.5634086 0.4766382 +H 10.2748086 5.7959287 17.7853618 +H 5.6268713 10.2748086 0.4766382 +H 4.5634086 0.0845287 9.6076382 +H 11.3382713 4.5634086 8.6543618 +H 5.7959287 10.2748086 8.6543618 +H 10.2748086 5.6268713 9.6076382 +H 0.0845287 6.8593914 8.6543618 +H 6.8593914 0.0845287 17.7853618 +H 11.3382713 6.8593914 0.4766382 +H 5.7959287 1.1479914 0.4766382 +H 1.1479914 5.6268713 17.7853618 +H 5.6268713 1.1479914 8.6543618 +H 1.1479914 5.7959287 9.6076382 +C 8.5671000 6.8433995 9.1310000 +C 2.8557000 6.8433995 0.0000000 +C 4.5794005 2.8557000 0.0000000 +C 8.5671000 10.2908005 0.0000000 +C 1.1319995 8.5671000 0.0000000 +C 2.8557000 4.5794005 9.1310000 +C 6.8433995 2.8557000 9.1310000 +C 10.2908005 8.5671000 9.1310000 +C 8.5671000 1.1319995 9.1310000 +C 4.5794005 8.5671000 9.1310000 +C 8.5671000 4.5794005 0.0000000 +C 6.8433995 8.5671000 0.0000000 +C 10.2908005 2.8557000 0.0000000 +C 2.8557000 1.1319995 0.0000000 +C 1.1319995 2.8557000 9.1310000 +C 2.8557000 10.2908005 9.1310000 +H 7.9971023 7.4179663 9.6660766 +H 3.4256977 7.4179663 17.7269234 +H 4.0048337 3.4256977 0.5350766 +H 9.1370977 9.7162337 17.7269234 +H 1.7065663 9.1370977 0.5350766 +H 3.4256977 4.0048337 9.6660766 +H 7.4179663 3.4256977 8.5959234 +H 9.7162337 9.1370977 8.5959234 +H 9.1370977 1.7065663 9.6660766 +H 4.0048337 7.9971023 8.5959234 +H 7.9971023 4.0048337 17.7269234 +H 7.4179663 7.9971023 0.5350766 +H 9.7162337 2.2857023 0.5350766 +H 2.2857023 1.7065663 17.7269234 +H 1.7065663 2.2857023 8.5959234 +H 2.2857023 9.7162337 9.6660766 +H 9.1370977 7.4179663 8.5959234 +H 2.2857023 7.4179663 0.5350766 +H 4.0048337 2.2857023 17.7269234 +H 7.9971023 9.7162337 0.5350766 +H 1.7065663 7.9971023 17.7269234 +H 2.2857023 4.0048337 8.5959234 +H 7.4179663 2.2857023 9.6660766 +H 9.7162337 7.9971023 9.6660766 +H 7.9971023 1.7065663 8.5959234 +H 4.0048337 9.1370977 9.6660766 +H 9.1370977 4.0048337 0.5350766 +H 7.4179663 9.1370977 17.7269234 +H 9.7162337 3.4256977 17.7269234 +H 3.4256977 1.7065663 0.5350766 +H 1.7065663 3.4256977 9.6660766 +H 3.4256977 9.7162337 8.5959234 diff --git a/cell2mol/test/YETBUV/YETBUV_ref.xyz b/cell2mol/test/YETBUV/YETBUV_ref.xyz new file mode 100644 index 00000000..3049eaa5 --- /dev/null +++ b/cell2mol/test/YETBUV/YETBUV_ref.xyz @@ -0,0 +1,64 @@ +62 + +Co 0.7500000 0.2500000 0.5000000 +Cl 0.9474600 0.2500000 0.5000000 +Cl 0.2500000 0.2500000 0.2500000 +P 0.7635500 0.1072300 0.4126700 +O 0.1566000 0.2452000 0.2917000 +C 0.8621000 0.1351000 0.3363800 +H 0.9360000 0.1625000 0.3547000 +H 0.8286000 0.1935000 0.3049000 +H 0.8738000 0.0641000 0.3092000 +C 0.6304000 0.0570000 0.3679400 +H 0.5898000 0.1227000 0.3473000 +H 0.5810000 0.0189000 0.4032000 +H 0.6502000 0.0027000 0.3297000 +C 0.8280000 -0.0273000 0.4481300 +H 0.8494000 -0.0765000 0.4069000 +H 0.8995000 -0.0074000 0.4739000 +C 0.7500000 -0.0991000 0.5000000 +H 0.7001000 -0.1494000 0.4707000 +H 0.7999000 -0.1494000 0.5293000 +Cl 0.5525400 0.2500000 0.5000000 +P 0.7364500 0.1072300 0.5873300 +P 0.7635500 0.3927700 0.5873300 +P 0.7364500 0.3927700 0.4126700 +O 0.2452000 0.1566000 0.2083000 +O 0.2548000 0.3434000 0.2083000 +O 0.3434000 0.2548000 0.2917000 +C 0.8621000 0.3649000 0.6636200 +C 0.6379000 0.3649000 0.3363800 +C 0.6379000 0.1351000 0.6636200 +H 0.9360000 0.3375000 0.6453000 +H 0.5640000 0.3375000 0.3547000 +H 0.5640000 0.1625000 0.6453000 +H 0.8286000 0.3065000 0.6951000 +H 0.6714000 0.3065000 0.3049000 +H 0.6714000 0.1935000 0.6951000 +H 0.8738000 0.4359000 0.6908000 +H 0.6262000 0.4359000 0.3092000 +H 0.6262000 0.0641000 0.6908000 +C 0.6304000 0.4430000 0.6320600 +C 0.8696000 0.4430000 0.3679400 +C 0.8696000 0.0570000 0.6320600 +H 0.5898000 0.3773000 0.6527000 +H 0.9102000 0.3773000 0.3473000 +H 0.9102000 0.1227000 0.6527000 +H 0.5810000 0.4811000 0.5968000 +H 0.9190000 0.4811000 0.4032000 +H 0.9190000 0.0189000 0.5968000 +H 0.6502000 0.4973000 0.6703000 +H 0.8498000 0.4973000 0.3297000 +H 0.8498000 0.0027000 0.6703000 +C 0.6720000 -0.0273000 0.5518700 +C 0.8280000 0.5273000 0.5518700 +C 0.6720000 0.5273000 0.4481300 +H 0.8494000 0.5765000 0.5931000 +H 0.6506000 0.5765000 0.4069000 +H 0.6506000 -0.0765000 0.5931000 +H 0.8995000 0.5074000 0.5261000 +H 0.6005000 0.5074000 0.4739000 +H 0.6005000 -0.0074000 0.5261000 +C 0.7500000 0.5991000 0.5000000 +H 0.7001000 0.6494000 0.5293000 +H 0.7999000 0.6494000 0.4707000 diff --git a/cell2mol/test/YETBUV/cell2mol.out b/cell2mol/test/YETBUV/cell2mol.out new file mode 100644 index 00000000..bc22ec91 --- /dev/null +++ b/cell2mol/test/YETBUV/cell2mol.out @@ -0,0 +1,457 @@ +cell2mol version 2.0 +INITIATING cell object from info path: /Users/ycho/cell2mol/cell2mol/test/YETBUV/YETBUV.info +Debug level: 2 +######################################### + GETREFS: Generate reference molecules +######################################### +GETREFS: found 2 reference molecules +GETREFS: ['O4-Cl', 'H36-C14-P4-Cl2-Co'] +GETREFS: [------------- Cell2mol MOLECULE Object -------------- + Version = 0.1 + Type = specie + Sub-Type = molecule + Number of Atoms = 5 + Formula = O4-Cl + Has Adjacency Matrix = YES +--------------------------------------------------- +, ------------- Cell2mol MOLECULE Object -------------- + Version = 0.1 + Type = specie + Sub-Type = molecule + Number of Atoms = 57 + Formula = H36-C14-P4-Cl2-Co + Has Adjacency Matrix = YES + Number of Ligands = 4 + Number of Metals = 1 +--------------------------------------------------- +] +GETREFS: working with O4-Cl +GETREFS: working with H36-C14-P4-Cl2-Co + +LIGAND.SPLIT_LIGAND: splitting H18-C7-P2 into groups +LIGAND.SPLIT_LIGAND: self.indices=[0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26] +LIGAND.SPLIT_LIGAND: connected_idx=[0, 15] +LIGAND.SPLIT_LIGAND: conn_labels=['P', 'P'] +SPILT_SPECIES: Laplacian lap=array([[0, 0], + [0, 0]]) +SPILT_SPECIES: graph=<2x2 sparse matrix of type '' + with 0 stored elements in Compressed Sparse Row format> +LIGAND.SPLIT_LIGAND: blocklist=[[1], [0]] +LIGAND.SPLIT_LIGAND: block=[1] +EXTRACT_FROM_LIST. received: entrylist=[1] old_array=[0, 15] +EXTRACT_FROM_LIST. received: idx=0 val=1 old_array[val]=15 +EXTRACT_FROM_LIST. new_array=array([15], dtype=object) +LIGAND.SPLIT_LIGAND: gr_indices=[15] +EXTRACT_FROM_LIST. received: entrylist=[1] old_array=['P', 'P'] +EXTRACT_FROM_LIST. received: idx=0 val=1 old_array[val]='P' +EXTRACT_FROM_LIST. new_array=array(['P'], dtype=object) +Entering COORD_CORR_NONHAPTIC: + Coordinating atom label=P with mconnec=1, group index 0 + evaluating coordination with metal Co + +------------- Cell2mol METAL Object -------------- + Version = 0.1 + Type = atom + Sub-Type = metal + Label = Co + Atomic Number = 27 + Index in Molecule = 0 + Metal Adjacency (mconnec) = 6 + Regular Adjacencies (connec) = 6 +---------------------------------------------------- + +ADD_ATOM: Metalist length 1 +ADD_ATOM: Ligand Atoms 27 +ADD_ATOM: site= 15 +ADD_ATOM: target ligand atom P +ADD_ATOM: evaluating apos=array([ 8.41232106, 1.22486684, 10.72582046]) and tgt.coord=[8.5671, 2.8557000000000006, 9.131] +ADD_ATOM: Chosen Metal index 0. H is added at site 15 + connectivity verified for atom P with ligand index 15 +LIGAND.SPLIT_LIGAND: new group is found +LIGAND.SPLIT_LIGAND: block=[0] +EXTRACT_FROM_LIST. received: entrylist=[0] old_array=[0, 15] +EXTRACT_FROM_LIST. received: idx=0 val=0 old_array[val]=0 +EXTRACT_FROM_LIST. new_array=array([0], dtype=object) +LIGAND.SPLIT_LIGAND: gr_indices=[0] +EXTRACT_FROM_LIST. received: entrylist=[0] old_array=['P', 'P'] +EXTRACT_FROM_LIST. received: idx=0 val=0 old_array[val]='P' +EXTRACT_FROM_LIST. new_array=array(['P'], dtype=object) +Entering COORD_CORR_NONHAPTIC: + Coordinating atom label=P with mconnec=1, group index 0 + evaluating coordination with metal Co + +------------- Cell2mol METAL Object -------------- + Version = 0.1 + Type = atom + Sub-Type = metal + Label = Co + Atomic Number = 27 + Index in Molecule = 0 + Metal Adjacency (mconnec) = 6 + Regular Adjacencies (connec) = 6 +---------------------------------------------------- + +ADD_ATOM: Metalist length 1 +ADD_ATOM: Ligand Atoms 27 +ADD_ATOM: site= 0 +ADD_ATOM: target ligand atom P +ADD_ATOM: evaluating apos=array([8.72187894, 1.22486684, 7.53617954]) and tgt.coord=[8.5671, 2.8557000000000006, 9.131] +ADD_ATOM: Chosen Metal index 0. H is added at site 0 + connectivity verified for atom P with ligand index 0 +LIGAND.SPLIT_LIGAND: new group is found +LIGAND.SPLIT_LIGAND: found groups ['P', 'P'] +[------------- Cell2mol GROUP Object -------------- + Version = 0.1 + Type = specie + Sub-Type = group + Number of Atoms = 1 + Formula = P + Has Adjacency Matrix = YES + Origin = split_ligand + Number of Metals = 1 +--------------------------------------------------- +, ------------- Cell2mol GROUP Object -------------- + Version = 0.1 + Type = specie + Sub-Type = group + Number of Atoms = 1 + Formula = P + Has Adjacency Matrix = YES + Origin = split_ligand + Number of Metals = 1 +--------------------------------------------------- +] + +LIGAND.SPLIT_LIGAND: splitting H18-C7-P2 into groups +LIGAND.SPLIT_LIGAND: self.indices=[0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26] +LIGAND.SPLIT_LIGAND: connected_idx=[0, 1] +LIGAND.SPLIT_LIGAND: conn_labels=['P', 'P'] +SPILT_SPECIES: Laplacian lap=array([[0, 0], + [0, 0]]) +SPILT_SPECIES: graph=<2x2 sparse matrix of type '' + with 0 stored elements in Compressed Sparse Row format> +LIGAND.SPLIT_LIGAND: blocklist=[[1], [0]] +LIGAND.SPLIT_LIGAND: block=[1] +EXTRACT_FROM_LIST. received: entrylist=[1] old_array=[0, 1] +EXTRACT_FROM_LIST. received: idx=0 val=1 old_array[val]=1 +EXTRACT_FROM_LIST. new_array=array([1], dtype=object) +LIGAND.SPLIT_LIGAND: gr_indices=[1] +EXTRACT_FROM_LIST. received: entrylist=[1] old_array=['P', 'P'] +EXTRACT_FROM_LIST. received: idx=0 val=1 old_array[val]='P' +EXTRACT_FROM_LIST. new_array=array(['P'], dtype=object) +Entering COORD_CORR_NONHAPTIC: + Coordinating atom label=P with mconnec=1, group index 0 + evaluating coordination with metal Co + +------------- Cell2mol METAL Object -------------- + Version = 0.1 + Type = atom + Sub-Type = metal + Label = Co + Atomic Number = 27 + Index in Molecule = 0 + Metal Adjacency (mconnec) = 6 + Regular Adjacencies (connec) = 6 +---------------------------------------------------- + +ADD_ATOM: Metalist length 1 +ADD_ATOM: Ligand Atoms 27 +ADD_ATOM: site= 1 +ADD_ATOM: target ligand atom P +ADD_ATOM: evaluating apos=array([8.41232106, 4.48653316, 7.53617954]) and tgt.coord=[8.5671, 2.8557000000000006, 9.131] +ADD_ATOM: Chosen Metal index 0. H is added at site 1 + connectivity verified for atom P with ligand index 1 +LIGAND.SPLIT_LIGAND: new group is found +LIGAND.SPLIT_LIGAND: block=[0] +EXTRACT_FROM_LIST. received: entrylist=[0] old_array=[0, 1] +EXTRACT_FROM_LIST. received: idx=0 val=0 old_array[val]=0 +EXTRACT_FROM_LIST. new_array=array([0], dtype=object) +LIGAND.SPLIT_LIGAND: gr_indices=[0] +EXTRACT_FROM_LIST. received: entrylist=[0] old_array=['P', 'P'] +EXTRACT_FROM_LIST. received: idx=0 val=0 old_array[val]='P' +EXTRACT_FROM_LIST. new_array=array(['P'], dtype=object) +Entering COORD_CORR_NONHAPTIC: + Coordinating atom label=P with mconnec=1, group index 0 + evaluating coordination with metal Co + +------------- Cell2mol METAL Object -------------- + Version = 0.1 + Type = atom + Sub-Type = metal + Label = Co + Atomic Number = 27 + Index in Molecule = 0 + Metal Adjacency (mconnec) = 6 + Regular Adjacencies (connec) = 6 +---------------------------------------------------- + +ADD_ATOM: Metalist length 1 +ADD_ATOM: Ligand Atoms 27 +ADD_ATOM: site= 0 +ADD_ATOM: target ligand atom P +ADD_ATOM: evaluating apos=array([ 8.72187894, 4.48653316, 10.72582046]) and tgt.coord=[8.5671, 2.8557000000000006, 9.131] +ADD_ATOM: Chosen Metal index 0. H is added at site 0 + connectivity verified for atom P with ligand index 0 +LIGAND.SPLIT_LIGAND: new group is found +LIGAND.SPLIT_LIGAND: found groups ['P', 'P'] +[------------- Cell2mol GROUP Object -------------- + Version = 0.1 + Type = specie + Sub-Type = group + Number of Atoms = 1 + Formula = P + Has Adjacency Matrix = YES + Origin = split_ligand + Number of Metals = 1 +--------------------------------------------------- +, ------------- Cell2mol GROUP Object -------------- + Version = 0.1 + Type = specie + Sub-Type = group + Number of Atoms = 1 + Formula = P + Has Adjacency Matrix = YES + Origin = split_ligand + Number of Metals = 1 +--------------------------------------------------- +] + +LIGAND.SPLIT_LIGAND: splitting Cl into groups +LIGAND.SPLIT_LIGAND: self.indices=[0] +LIGAND.SPLIT_LIGAND: connected_idx=[0] +LIGAND.SPLIT_LIGAND: conn_labels=['Cl'] +SPILT_SPECIES: Laplacian lap=array([[0]]) +SPILT_SPECIES: graph=<1x1 sparse matrix of type '' + with 0 stored elements in Compressed Sparse Row format> +LIGAND.SPLIT_LIGAND: blocklist=[[0]] +LIGAND.SPLIT_LIGAND: block=[0] +EXTRACT_FROM_LIST. received: entrylist=[0] old_array=[0] +EXTRACT_FROM_LIST. received: idx=0 val=0 old_array[val]=0 +EXTRACT_FROM_LIST. new_array=array([0], dtype=object) +LIGAND.SPLIT_LIGAND: gr_indices=[0] +EXTRACT_FROM_LIST. received: entrylist=[0] old_array=['Cl'] +EXTRACT_FROM_LIST. received: idx=0 val=0 old_array[val]='Cl' +EXTRACT_FROM_LIST. new_array=array(['Cl'], dtype=object) +Entering COORD_CORR_NONHAPTIC: + Coordinating atom label=Cl with mconnec=1, group index 0 + evaluating coordination with metal Co + +------------- Cell2mol METAL Object -------------- + Version = 0.1 + Type = atom + Sub-Type = metal + Label = Co + Atomic Number = 27 + Index in Molecule = 0 + Metal Adjacency (mconnec) = 6 + Regular Adjacencies (connec) = 6 +---------------------------------------------------- + +ADD_ATOM: Metalist length 1 +ADD_ATOM: Ligand Atoms 1 +ADD_ATOM: site= 0 +ADD_ATOM: target ligand atom Cl +ADD_ATOM: evaluating apos=array([6.31155391, 2.8557 , 9.131 ]) and tgt.coord=[8.5671, 2.8557000000000006, 9.131] +ADD_ATOM: Chosen Metal index 0. H is added at site 0 + connectivity verified for atom Cl with ligand index 0 +LIGAND.SPLIT_LIGAND: new group is found +LIGAND.SPLIT_LIGAND: found groups ['Cl'] +[------------- Cell2mol GROUP Object -------------- + Version = 0.1 + Type = specie + Sub-Type = group + Number of Atoms = 1 + Formula = Cl + Has Adjacency Matrix = YES + Origin = split_ligand + Number of Metals = 1 +--------------------------------------------------- +] + +LIGAND.SPLIT_LIGAND: splitting Cl into groups +LIGAND.SPLIT_LIGAND: self.indices=[0] +LIGAND.SPLIT_LIGAND: connected_idx=[0] +LIGAND.SPLIT_LIGAND: conn_labels=['Cl'] +SPILT_SPECIES: Laplacian lap=array([[0]]) +SPILT_SPECIES: graph=<1x1 sparse matrix of type '' + with 0 stored elements in Compressed Sparse Row format> +LIGAND.SPLIT_LIGAND: blocklist=[[0]] +LIGAND.SPLIT_LIGAND: block=[0] +EXTRACT_FROM_LIST. received: entrylist=[0] old_array=[0] +EXTRACT_FROM_LIST. received: idx=0 val=0 old_array[val]=0 +EXTRACT_FROM_LIST. new_array=array([0], dtype=object) +LIGAND.SPLIT_LIGAND: gr_indices=[0] +EXTRACT_FROM_LIST. received: entrylist=[0] old_array=['Cl'] +EXTRACT_FROM_LIST. received: idx=0 val=0 old_array[val]='Cl' +EXTRACT_FROM_LIST. new_array=array(['Cl'], dtype=object) +Entering COORD_CORR_NONHAPTIC: + Coordinating atom label=Cl with mconnec=1, group index 0 + evaluating coordination with metal Co + +------------- Cell2mol METAL Object -------------- + Version = 0.1 + Type = atom + Sub-Type = metal + Label = Co + Atomic Number = 27 + Index in Molecule = 0 + Metal Adjacency (mconnec) = 6 + Regular Adjacencies (connec) = 6 +---------------------------------------------------- + +ADD_ATOM: Metalist length 1 +ADD_ATOM: Ligand Atoms 1 +ADD_ATOM: site= 0 +ADD_ATOM: target ligand atom Cl +ADD_ATOM: evaluating apos=array([10.82264609, 2.8557 , 9.131 ]) and tgt.coord=[8.5671, 2.8557000000000006, 9.131] +ADD_ATOM: Chosen Metal index 0. H is added at site 0 + connectivity verified for atom Cl with ligand index 0 +LIGAND.SPLIT_LIGAND: new group is found +LIGAND.SPLIT_LIGAND: found groups ['Cl'] +[------------- Cell2mol GROUP Object -------------- + Version = 0.1 + Type = specie + Sub-Type = group + Number of Atoms = 1 + Formula = Cl + Has Adjacency Matrix = YES + Origin = split_ligand + Number of Metals = 1 +--------------------------------------------------- +] +LIGAND.Get_denticity: checking connectivity of ligand H18-C7-P2 +LIGAND.Get_denticity: initial connectivity is 2 +LIGAND.Get_denticity: final connectivity of ligand H18-C7-P2 is 2 +LIGAND.Get_denticity: checking connectivity of ligand H18-C7-P2 +LIGAND.Get_denticity: initial connectivity is 2 +LIGAND.Get_denticity: final connectivity of ligand H18-C7-P2 is 2 +LIGAND.Get_denticity: checking connectivity of ligand Cl +LIGAND.Get_denticity: initial connectivity is 1 +LIGAND.Get_denticity: final connectivity of ligand Cl is 1 +LIGAND.Get_denticity: checking connectivity of ligand Cl +LIGAND.Get_denticity: initial connectivity is 1 +LIGAND.Get_denticity: final connectivity of ligand Cl is 1 + +METAL.Get_coord_geometry: Co +METAL.Get_coord_geometry: +coord_group=[------------- Cell2mol GROUP Object -------------- + Version = 0.1 + Type = specie + Sub-Type = group + Number of Atoms = 1 + Formula = P + Has Adjacency Matrix = YES + Origin = split_ligand + Number of Metals = 1 +--------------------------------------------------- +, ------------- Cell2mol GROUP Object -------------- + Version = 0.1 + Type = specie + Sub-Type = group + Number of Atoms = 1 + Formula = P + Has Adjacency Matrix = YES + Origin = split_ligand + Number of Metals = 1 +--------------------------------------------------- +, ------------- Cell2mol GROUP Object -------------- + Version = 0.1 + Type = specie + Sub-Type = group + Number of Atoms = 1 + Formula = P + Has Adjacency Matrix = YES + Origin = split_ligand + Number of Metals = 1 +--------------------------------------------------- +, ------------- Cell2mol GROUP Object -------------- + Version = 0.1 + Type = specie + Sub-Type = group + Number of Atoms = 1 + Formula = P + Has Adjacency Matrix = YES + Origin = split_ligand + Number of Metals = 1 +--------------------------------------------------- +, ------------- Cell2mol GROUP Object -------------- + Version = 0.1 + Type = specie + Sub-Type = group + Number of Atoms = 1 + Formula = Cl + Has Adjacency Matrix = YES + Origin = split_ligand + Number of Metals = 1 +--------------------------------------------------- +, ------------- Cell2mol GROUP Object -------------- + Version = 0.1 + Type = specie + Sub-Type = group + Number of Atoms = 1 + Formula = Cl + Has Adjacency Matrix = YES + Origin = split_ligand + Number of Metals = 1 +--------------------------------------------------- +] +METAL.Get_coord_geometry: coord_nr=6 +SHAPE_MEASURE: symbols=['Co', 'P', 'P', 'P', 'P', 'Cl', 'Cl'] +SHAPE_MEASURE: positions=[[8.5671, 2.8557000000000006, 9.131], [8.412321060000002, 1.2248668440000008, 10.725820460000001], [8.72187894, 1.2248668440000006, 7.53617954], [8.412321060000002, 4.486533156000001, 7.53617954], [8.72187894, 4.486533156000001, 10.725820460000001], [6.311553912000002, 2.8557000000000006, 9.131], [10.822646088, 2.8557000000000006, 9.131]] +SHAPE_MEASURE: coordination number of metal center 6 +SHAPE_MEASURE: connectivity of metal center(1) [[1, 2], [1, 3], [1, 4], [1, 5], [1, 6], [1, 7]] +DEFINE_coordination_geometry: The number of coordinating points: 6 +DEFINE_coordination_geometry: {'Hexagon': 33.049, 'Pentagonal pyramidal': 27.536, 'Octahedral': 0.319, 'Trigonal prismatic': 14.615} +DEFINE_coordination_geometry: The type of hapticity : [] +DEFINE_coordination_geometry: The most likely geometry is 'Octahedral' with deviation value 0.319 +METAL.Get_coord_geometry: self.coord_geometry='Octahedral' self.geom_deviation=0.319 +METAL.Get_relative_metal_radius: diff_list=[1.216, 1.216, 1.216, 1.216, 1.236, 1.236] +METAL.Get_relative_metal_radius: average=1.223 +METAL.Get_coord_geometry: self.rel_metal_radius=0.971 + +################## +Checking Missing H +################## +Not a Single Molecule has Missing H atoms (apparently) +------------------------------- +Errors in Reference Molecules +------------------------------- +Cell2mol terminated with error number 0. Message: +No Errors Found + +SAVING cell2mol CELL object to /Users/ycho/cell2mol/cell2mol/test/YETBUV/Ref_Cell_YETBUV.cell +ENTERING cell2mol with debug=2 +Entered CELL.MOLECLIST with debug=2 +CELL.MOLECLIST passed initial checks +Adjacency Matrix: Distance 0.062 smaller than clash for atoms 179 762 H H +Adjacency Matrix: Distance 0.062 smaller than clash for atoms 180 763 H H +Adjacency Matrix: Distance 0.062 smaller than clash for atoms 183 761 H H +Adjacency Matrix: Distance 0.062 smaller than clash for atoms 184 752 H H +Adjacency Matrix: Distance 0.062 smaller than clash for atoms 188 754 H H +Adjacency Matrix: Distance 0.062 smaller than clash for atoms 189 753 H H +Adjacency Matrix: Distance 0.062 smaller than clash for atoms 190 758 H H +Adjacency Matrix: Distance 0.062 smaller than clash for atoms 191 757 H H +Adjacency Matrix: Distance 0.169 smaller than clash for atoms 227 906 H H +Adjacency Matrix: Distance 0.169 smaller than clash for atoms 228 907 H H +Adjacency Matrix: Distance 0.169 smaller than clash for atoms 231 905 H H +Adjacency Matrix: Distance 0.169 smaller than clash for atoms 232 896 H H +Adjacency Matrix: Distance 0.169 smaller than clash for atoms 236 898 H H +Adjacency Matrix: Distance 0.169 smaller than clash for atoms 237 897 H H +Adjacency Matrix: Distance 0.169 smaller than clash for atoms 238 902 H H +Adjacency Matrix: Distance 0.169 smaller than clash for atoms 239 901 H H +Adjacency Matrix: Distance 0.062 smaller than clash for atoms 736 776 H H +Adjacency Matrix: Distance 0.062 smaller than clash for atoms 737 781 H H +Adjacency Matrix: Distance 0.062 smaller than clash for atoms 738 780 H H +Adjacency Matrix: Distance 0.062 smaller than clash for atoms 741 783 H H +Adjacency Matrix: Distance 0.062 smaller than clash for atoms 742 782 H H +Adjacency Matrix: Distance 0.062 smaller than clash for atoms 745 775 H H +Adjacency Matrix: Distance 0.062 smaller than clash for atoms 746 771 H H +Adjacency Matrix: Distance 0.062 smaller than clash for atoms 747 772 H H +Adjacency Matrix: Distance 0.169 smaller than clash for atoms 880 920 H H +Adjacency Matrix: Distance 0.169 smaller than clash for atoms 881 925 H H +Adjacency Matrix: Distance 0.169 smaller than clash for atoms 882 924 H H +Adjacency Matrix: Distance 0.169 smaller than clash for atoms 885 927 H H +Adjacency Matrix: Distance 0.169 smaller than clash for atoms 886 926 H H +Adjacency Matrix: Distance 0.169 smaller than clash for atoms 889 919 H H +Adjacency Matrix: Distance 0.169 smaller than clash for atoms 890 915 H H +Adjacency Matrix: Distance 0.169 smaller than clash for atoms 891 916 H H diff --git a/cell2mol/test/YETBUV/cif2cell.err b/cell2mol/test/YETBUV/cif2cell.err new file mode 100644 index 00000000..e69de29b