| /dports/science/py-pymol/pymol-open-source-2.4.0/contrib/uiuc/plugins/molfile_plugin/src/ |
| H A D | mol2plugin.cpp | 56 float *bondorder; member
110 mol2->bondorder = NULL; in open_mol2_read()
252 *bondorderptr = mol2->bondorder; in read_mol2_bonds_aux()
461 if (data->bondorder != NULL) { in write_mol2_timestep()
463 (int)data->bondorder[i]); in write_mol2_timestep()
497 data->bondorder[i]=bondorderptr[i]; in write_mol2_bonds()
513 if (data->bondorder != NULL) free(data->bondorder); in close_mol2_write()
514 data->bondorder = NULL; in close_mol2_write()
531 if (mol2->bondorder != NULL) free(mol2->bondorder); in close_mol2_read()
532 mol2->bondorder = NULL; in close_mol2_read()
[all …]
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| H A D | bgfplugin.cpp | 40 float *bondorder; member
92 bgf->bondorder = NULL; in open_bgf_read()
411 bgf->bondorder[i]=1.0; in read_bgf_bonds_aux()
431 *bondorderptr = bgf->bondorder; in read_bgf_bonds_aux()
456 *bondorderptr = bgf->bondorder; in read_bgf_bonds()
515 if (data->bondorder != NULL) in write_bgf_timestep()
516 o=data->bondorder[i]; in write_bgf_timestep()
614 if (data->bondorder != NULL) free(data->bondorder); in close_bgf_write()
615 data->bondorder = NULL; in close_bgf_write()
631 if (bgf->bondorder != NULL) free(bgf->bondorder); in close_bgf_read()
[all …]
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| H A D | xbgfplugin.cpp | 42 float *bondorder; member
116 bgf->bondorder = NULL; in open_xbgf_read()
446 bgf->bondorder[i]=orders[l]; in read_xbgf_bonds_aux()
448 bgf->bondorder[i]=1.0; in read_xbgf_bonds_aux()
467 *bondorderptr = bgf->bondorder; // not implemented yet in read_xbgf_bonds_aux()
550 if (data->bondorder != NULL) in write_xbgf_timestep()
551 o=data->bondorder[i]; in write_xbgf_timestep()
624 data->bondorder[i]=bondorderptr[i]; in write_xbgf_bonds()
643 if (data->bondorder != NULL) free(data->bondorder); in close_xbgf_write()
644 data->bondorder = NULL; in close_xbgf_write()
[all …]
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| /dports/science/jmol/jmol-14.32.7/src/org/jmol/minimize/forcefield/ |
| H A D | UFFAngleCalc.java | 41 double bondorder = bond.order; in setData() local
43 bondorder = 1.5; in setData()
45 bondorder = 1.41; in setData()
46 …R_R], calcs.parA.dVal[CalculationsUFF.PAR_XI], calcs.parB.dVal[CalculationsUFF.PAR_XI], bondorder); in setData()
49 bondorder = bond.order; in setData()
51 bondorder = 1.5; in setData()
53 bondorder = 1.41; in setData()
55 … calcs.parB.dVal[CalculationsUFF.PAR_XI], calcs.parC.dVal[CalculationsUFF.PAR_XI], bondorder); in setData()
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| H A D | CalculationsUFF.java | 171 double bondorder) { in calculateR0() argument
174 double rbo = -0.1332 * (ri + rj) * Math.log(bondorder); in calculateR0()
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| /dports/science/openkim-models/openkim-models-2021-01-28/model-drivers/ThreeBodyBondOrder_KDS__MD_697985444380_000/ |
| H A D | kimprovenance.edn | 5 "bondorder.inc" "5a16da4fb9719ad06751aed6ace3e3d8ca39394b"
17 "bondorder.inc" "5a16da4fb9719ad06751aed6ace3e3d8ca39394b"
29 "bondorder.inc" "5a16da4fb9719ad06751aed6ace3e3d8ca39394b"
|
| /dports/science/cdk/cdk-cdk-2.3/storage/io/src/main/java/org/openscience/cdk/io/ |
| H A D | GhemicalMMReader.java | 140 IBond.Order[] bondorder = new IBond.Order[1]; in readChemModel() local
184 bondorder = new IBond.Order[numberOfAtoms]; in readChemModel()
193 bondorder[i] = IBond.Order.DOUBLE; in readChemModel()
195 bondorder[i] = IBond.Order.SINGLE; in readChemModel()
197 bondorder[i] = IBond.Order.TRIPLE; in readChemModel()
201 bondorder[i] = IBond.Order.SINGLE; in readChemModel()
261 container.addBond(bondatomid1[i], bondatomid2[i], bondorder[i]); in readChemModel()
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| /dports/science/xdrawchem/xdrawchem-a3f74c34eb09fa72ee16848ec6901049ca5309d5/xdrawchem/ |
| H A D | molecule_tools_1.cpp | 549 if ((alt_pt1->baseElement() == "N") && (tmp_pt->bondorder[0] == 3)) { in CalcKOW()
553 if ((alt_pt1->baseElement() == "O") && (tmp_pt->bondorder[0] == 2)) { in CalcKOW()
557 if ((alt_pt2->baseElement() == "N") && (tmp_pt->bondorder[1] == 3)) { in CalcKOW()
561 if ((alt_pt2->baseElement() == "O") && (tmp_pt->bondorder[1] == 2)) { in CalcKOW()
590 if (tmp_pt->bondorder[0] == 2) in CalcKOW()
595 if (tmp_pt->bondorder[1] == 2) in CalcKOW()
600 if (tmp_pt->bondorder[2] == 2) in CalcKOW()
657 if ((tmp_pt->bondorder[0] + tmp_pt->bondorder[1]) == 2) in CalcKOW()
661 if ((tmp_pt->bondorder[0] + tmp_pt->bondorder[1]) == 3) in CalcKOW()
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| H A D | dpoint.h | 63 QVector<int> bondorder; variable
125 bondorder.resize(6); in DPoint()
141 bondorder.resize(6); in init()
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| H A D | molecule_obmol.cpp | 136 int bondorder = bond->GetBondOrder(); in convertFromOBMol() local
155 addBond(s, e, 1, bondorder, QColor("black"), true); in convertFromOBMol()
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| H A D | ioiface.cpp | 173 int bondorder = bond->GetBondOrder(); in convertToChemData() local
199 chemdata->addBond(s, e, 1, bondorder, QColor("black"), true); in convertToChemData()
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| H A D | molecule_smiles.cpp | 83 tmp_pt->bondorder[(tmp_pt->neighbors.count() - 1)] = tmp_bond->Order(); in SDG()
103 atoms[c1].bondTable[c2] = tmp_pt->bondorder[c2]; in SDG()
|
| /dports/science/py-MDAnalysis/MDAnalysis-0.19.2/MDAnalysis/topology/ |
| H A D | DMSParser.py | 156 bondorder = {}
160 bondorder[desc] = b['order']
162 attrs['bondorder'] = bondorder
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| H A D | MOL2Parser.py | 170 bondorder = []
176 bondorder.append(bond_type)
178 attrs.append(Bonds(bonds, order=bondorder))
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| /dports/science/gromacs/gromacs-2021.4/src/external/vmd_molfile/ |
| H A D | molfile_plugin.h | 569 int (*read_bonds)(void *, int *nbonds, int **from, int **to, float **bondorder,
572 int (*read_bonds)(void *, int *nbonds, int **from, int **to, float **bondorder);
683 int (* write_bonds)(void *, int nbonds, int *from, int *to, float *bondorder,
686 int (* write_bonds)(void *, int nbonds, int *from, int *to, float *bondorder);
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| /dports/science/openkim-models/openkim-models-2021-01-28/model-drivers/ThreeBodyBondOrder_WR__MD_817691861922_000/ |
| H A D | kimprovenance.edn | 5 "bondorder.inc" "84a40be1956e8cbbfbe41529eca8c22cab55c00e"
17 "bondorder.inc" "84a40be1956e8cbbfbe41529eca8c22cab55c00e"
|
| /dports/science/openkim-models/openkim-models-2021-01-28/model-drivers/ThreeBodyBondOrder_PPM__MD_184422512875_000/ |
| H A D | kimprovenance.edn | 5 "bondorder.inc" "c3478a30d9d600f717dab83fe8af49ffcf23a5df"
17 "bondorder.inc" "c3478a30d9d600f717dab83fe8af49ffcf23a5df"
|
| /dports/science/py-rmf/rmf-1.3.1/plugins/vmd/include/ |
| H A D | molfile_plugin.h | 628 float **bondorder, int **bondtype, int *nbondtypes,
632 float **bondorder);
743 int (*write_bonds)(void *, int nbonds, int *from, int *to, float *bondorder,
746 int (*write_bonds)(void *, int nbonds, int *from, int *to, float *bondorder);
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| /dports/science/rmf/rmf-1.3.1/plugins/vmd/include/ |
| H A D | molfile_plugin.h | 628 float **bondorder, int **bondtype, int *nbondtypes,
632 float **bondorder);
743 int (*write_bonds)(void *, int nbonds, int *from, int *to, float *bondorder,
746 int (*write_bonds)(void *, int nbonds, int *from, int *to, float *bondorder);
|
| /dports/science/openbabel/openbabel-3.1.1/src/formats/ |
| H A D | yasaraformat.cpp | 489 int /*samenames,reslen,*/bondorder,flags; in WriteMolecule() local
552 bondorder=(*iter)->GetBondOrder(); in WriteMolecule()
554 if (bondorder==4) bondorder=MOB_LINKQUADRUPLE; in WriteMolecule()
555 else if (bondorder==5) bondorder=MOB_LINKRESONANCE50; in WriteMolecule()
556 buffer[3]=bondorder; in WriteMolecule()
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| /dports/science/openbabel/openbabel-3.1.1/src/forcefields/ |
| H A D | forcefielduff.cpp | 744 double bondorder; in SetupCalculations() local
933 bondorder = bond->GetBondOrder(); in SetupCalculations()
935 bondorder = 1.5; in SetupCalculations()
940 bondorder = 1.5; in SetupCalculations()
942 bondorder = 1.41; in SetupCalculations()
946 bondcalc.bt = bondorder; in SetupCalculations()
1150 bondorder = bondPtr->GetBondOrder(); in SetupCalculations()
1152 bondorder = 1.5; in SetupCalculations()
1154 bondorder = 1.41; in SetupCalculations()
1160 bondorder = 1.5; in SetupCalculations()
[all …]
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| /dports/science/py-qcelemental/qcelemental-0.24.0/qcelemental/molparse/ |
| H A D | from_arrays.py | 465 for (at1, at2, bondorder) in connectivity:
470 if bondorder < 0 or bondorder > 5:
471 … raise ValidationError("""Connectivity bond order should be float [0, 5]: {}""".format(bondorder))
472 conn.append((int(min(at1, at2)), int(max(at1, at2)), float(bondorder)))
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| /dports/science/py-pymol/pymol-open-source-2.4.0/contrib/uiuc/plugins/include/ |
| H A D | molfile_plugin.h | 661 int (*read_bonds)(void *, int *nbonds, int **from, int **to, float **bondorder,
774 int (* write_bonds)(void *, int nbonds, int *from, int *to, float *bondorder,
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| /dports/science/plumed/plumed2-2.7.2/src/molfile/ |
| H A D | molfile_plugin.h | 702 int (*read_bonds)(void *, int *nbonds, int **from, int **to, float **bondorder,
815 int (* write_bonds)(void *, int nbonds, int *from, int *to, float *bondorder,
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| /dports/science/lammps/lammps-stable_29Sep2021/lib/molfile/ |
| H A D | molfile_plugin.h | 706 int (*read_bonds)(void *, int *nbonds, int **from, int **to, float **bondorder,
819 int (* write_bonds)(void *, int nbonds, int *from, int *to, float *bondorder,
|