/dports/science/openbabel/openbabel-3.1.1/src/descriptors/ |
H A D | filters.cpp | 37 if (!pmol) in Predict() 39 return pmol->GetMolWt(); in Predict() 51 if (!pmol) in Predict() 53 return pmol->NumRotors(); in Predict() 80 OBMol *pmol = dynamic_cast<OBMol *>(pOb); in Compare() local 81 if (!pmol) in Compare() 121 if (!pmol) in Compare() 124 string title(pmol->GetTitle()); in Compare() 131 if (pmol) in GetStringValue() 132 svalue = pmol->GetTitle(); in GetStringValue() [all …]
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/dports/science/openbabel/openbabel-3.1.1/src/ops/ |
H A D | opalign.cpp | 92 OBMol* pmol = dynamic_cast<OBMol*>(pOb); in Do() local 93 if(!pmol) in Do() 125 pgen->Do(pmol); in Do() 132 if(pmol->GetDimension()==0) in Do() 138 pgen->Do(pmol); in Do() 149 pgen->Do(pmol); in Do() 157 _refMol = *pmol; in Do() 240 pmol->GetAtom(i)->SetVector(tmpvec); in Do() 245 _align.SetTargetMol(*pmol); in Do() 248 _align.UpdateCoords(pmol); in Do() [all …]
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H A D | ophighlight.cpp | 55 bool AddDataToSubstruct(OBMol* pmol, 67 OBMol* pmol = dynamic_cast<OBMol*>(pOb); in Do() local 68 if(!pmol) in Do() 83 delete pmol; in Do() 84 pmol = nullptr; in Do() 106 delete pmol; in Do() 107 pmol = nullptr; in Do() 113 pmol->AddHydrogens(false,false); in Do() 130 bool OpHighlight::AddDataToSubstruct(OBMol* pmol, in AddDataToSubstruct() argument 138 OBAtom* pAtom = pmol->GetAtom(atomIdxs[j]); in AddDataToSubstruct() [all …]
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H A D | opisomorph.cpp | 35 bool AddDataToSubstruct(OBMol* pmol, in AddDataToSubstruct() argument 54 for(pBond = pmol->BeginBond(i); pBond; pBond = pmol->NextBond(i)) in AddDataToSubstruct() 76 for(int i = pmol->NumAtoms(); i; --i) in ExtractSubstruct() 78 pmol->DeleteAtom(pmol->GetAtom(i)); in ExtractSubstruct() 168 if(!pmol) in Do() 256 delete pmol; in Do() 257 pmol = nullptr; in Do() 281 delete pmol; in Do() 336 pmol->AddHydrogens(false,false); in Do() 354 delete pmol; in Do() [all …]
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H A D | gen2D.cpp | 51 OBMol* pmol = dynamic_cast<OBMol*>(pOb); in Do() local 52 if(!pmol) in Do() 63 if (pmol->GetDimension() == 0) { in Do() 64 pmol->UnsetFlag(OB_CHIRALITY_MOL); in Do() 65 StereoFrom0D(pmol); in Do() 68 generateDiagram(pmol); in Do() 69 pmol->SetDimension(2); in Do()
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H A D | readconformers.cpp | 74 OBMol* pmol = dynamic_cast<OBMol*>(*iter); in ProcessVec() local 75 if(!pmol) in ProcessVec() 77 smiles = smconv.WriteString(pmol); in ProcessVec() 83 double *confCoord = new double [pmol->NumAtoms() * 3]; in ProcessVec() 84 memcpy((char*)confCoord,(char*)pmol->GetCoordinates(),sizeof(double)*3*pmol->NumAtoms()); in ProcessVec() 86 delete pmol; in ProcessVec() 91 stored_pmol = pmol; in ProcessVec()
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/dports/science/openbabel/openbabel-3.1.1/src/ |
H A D | obmolecformat.cpp | 42 OBMol* pmol = new OBMol; in ReadChemObjectImpl() local 98 delete pmol; in ReadChemObjectImpl() 109 || pmol->IsReaction() in ReadChemObjectImpl() 110 || (pFormat->Flags()&ZEROATOMSOK && (*pmol->GetTitle() || pmol->HasData(1))))) in ReadChemObjectImpl() 129 delete pmol; in ReadChemObjectImpl() 158 if(pmol) in WriteChemObjectImpl() 196 if(pmol) { in DoOutputOptions() 205 pmol->SetConformer(c); in DoOutputOptions() 242 delete pmol; in DeferMolOutput() 269 delete pmol; in DeferMolOutput() [all …]
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/dports/science/py-pyscf/pyscf-2.0.1/pyscf/scf/test/ |
H A D | test_uhf.py | 172 pmol.build() 188 pmol.charge = 1 189 pmol.spin = 1 201 pmol.charge = 1 202 pmol.spin = 1 208 pmol.charge = 1 209 pmol.spin = 1 223 pmol.spin = 2 235 pmol.spin = 2 261 pmol.spin = 2 [all …]
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/dports/science/openbabel/openbabel-3.1.1/src/formats/ |
H A D | cofformat.cpp | 70 if (pmol == nullptr) in ReadMolecule() 114 pmol->SetTitle(name); in ReadMolecule() 118 pmol->BeginModify(); in ReadMolecule() 242 for (patom = pmol->BeginAtom(apos); patom; patom = pmol->NextAtom(apos)) in ReadMolecule() 245 for (pbond = pmol->BeginBond(bpos); pbond; pbond = pmol->NextBond(bpos)) in ReadMolecule() 253 for (pbond = pmol->BeginBond(bpos); pbond; pbond = pmol->NextBond(bpos)) in ReadMolecule() 262 bool ok = OBKekulize(pmol); in ReadMolecule() 273 pmol->SetData(dd); in ReadMolecule() 276 pmol->EndModify(); in ReadMolecule() 285 if (pmol == nullptr) in WriteMolecule() [all …]
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H A D | fastaformat.cpp | 98 OBMol* pmol; in WriteMolecule() local 101 pmol = dynamic_cast<OBMol*>(pOb); in WriteMolecule() 102 if (pmol == nullptr) in WriteMolecule() 107 FOR_RESIDUES_OF_MOL(res,pmol) { in WriteMolecule() 118 if (strlen(pmol->GetTitle()) > 0) in WriteMolecule() 119 ofs << ">" << pmol->GetTitle(); in WriteMolecule() 347 OBBond * bond = pmol->NewBond(); in add_bond() 550 pmol->SetChainsPerceived(); in ReadFASTASequence() 558 if (pmol == nullptr) in ReadMolecule() 560 pmol->BeginModify(); in ReadMolecule() [all …]
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H A D | moldenformat.cpp | 126 pmol->BeginModify(); in ReadMolecule() 127 pmol->SetDimension( 3 ); in ReadMolecule() 182 if (pmol->NumAtoms() != 0 && pmol->NumAtoms() != natoms) { in ReadMolecule() 305 if ( pmol->NumAtoms() == 0 ) { in ReadMolecule() 306 pmol->EndModify(); in ReadMolecule() 324 pmol->SetData(vd); in ReadMolecule() 328 pmol->SetEnergies(energies); in ReadMolecule() 343 pmol->SetConformer(pmol->NumConformers()); in ReadMolecule() 352 pmol->EndModify(); in ReadMolecule() 360 if (pmol == nullptr) in WriteMolecule() [all …]
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H A D | maeformat.cpp | 160 OBMol* pmol = pOb->CastAndClear<OBMol>(); in ReadMolecule() local 161 if (pmol == nullptr) in ReadMolecule() 166 pmol->BeginModify(); in ReadMolecule() 167 pmol->SetDimension(3); in ReadMolecule() 179 pmol->ReserveAtoms(natoms); in ReadMolecule() 182 OBAtom* patom = pmol->NewAtom(); in ReadMolecule() 208 pmol->EndModify(); in ReadMolecule() 236 const auto num_atoms = pmol->NumAtoms(); in TranslateAtomBlock() 292 const auto num_atoms = pmol->NumAtoms(); in TranslateBondBlock() 311 OBMol* pmol = dynamic_cast<OBMol*>(pOb); in WriteMolecule() local [all …]
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H A D | castepformat.cpp | 83 if (pmol == nullptr) in ReadMolecule() 101 pmol->BeginModify(); in ReadMolecule() 130 FOR_ATOMS_OF_MOL(a, *pmol) in ReadMolecule() 185 FOR_ATOMS_OF_MOL(atom, pmol) { in ReadMolecule() 220 pmol->SetData(opd_enthalpy); in ReadMolecule() 221 pmol->SetData(opd_enthalpy_pv); in ReadMolecule() 222 pmol->SetData(opd_enthalpy_ev); in ReadMolecule() 224 pmol->SetEnergy(energy); in ReadMolecule() 228 pmol->SetEnergy(enthalpy); in ReadMolecule() 233 pmol->SetData(cell); in ReadMolecule() [all …]
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H A D | groformat.cpp | 143 if (pmol == nullptr) in ReadMolecule() 148 pmol->BeginModify(); in ReadMolecule() 189 pmol->SetTitle(title); in ReadMolecule() 191 pmol->SetTitle(title); in ReadMolecule() 210 pmol->ReserveAtoms(natoms); in ReadMolecule() 226 atom = pmol->NewAtom(); in ReadMolecule() 354 pmol->SetData(cell); in ReadMolecule() 357 pmol->EndModify(); in ReadMolecule() 361 pmol->ConnectTheDots(); in ReadMolecule() 366 pmol->SetChainsPerceived(); in ReadMolecule() [all …]
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H A D | exampleformat.cpp | 151 OBMol* pmol = pOb->CastAndClear<OBMol>(); in ReadMolecule() local 152 if(pmol==nullptr) in ReadMolecule() 157 pmol->BeginModify(); in ReadMolecule() 170 pmol->SetDimension(dim); in ReadMolecule() 172 pmol->EndModify(); in ReadMolecule() 190 OBMol* pmol = dynamic_cast<OBMol*>(pOb); in WriteMolecule() local 191 if(pmol==nullptr) in WriteMolecule() 200 ofs << "Title = " << pmol->GetTitle() << endl; in WriteMolecule()
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H A D | gulpformat.cpp | 82 if (pmol == nullptr) in ReadMolecule() 98 pmol->BeginModify(); in ReadMolecule() 163 FOR_ATOMS_OF_MOL(a, *pmol) in ReadMolecule() 232 FOR_ATOMS_OF_MOL(a, *pmol) in ReadMolecule() 344 FOR_ATOMS_OF_MOL(atom, pmol) { in ReadMolecule() 369 pmol->SetData(enthalpyPD); in ReadMolecule() 370 pmol->SetData(enthalpyPD_pv); in ReadMolecule() 371 pmol->SetData(enthalpyPD_eV); in ReadMolecule() 372 pmol->SetData(enthalpyPD_pv_eV); in ReadMolecule() 376 pmol->SetData(cell); in ReadMolecule() [all …]
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H A D | rxnformat.cpp | 98 if (pmol == nullptr) in ReadMolecule() 120 pmol->SetTitle(Trim(ln)); in ReadMolecule() 154 OBReactionFacade rxnfacade(pmol); in ReadMolecule() 219 pmol->SetIsReaction(); in ReadMolecule() 261 if (pmol->NumAtoms() == 1) { in WriteMolFile() 262 OBAtom *atm = pmol->GetFirstAtom(); in WriteMolFile() 264 pmol->DeleteAtom(atm); in WriteMolFile() 266 pformat->WriteMolecule(pmol, pconv); in WriteMolFile() 282 if (pmol == nullptr || !pmol->IsReaction()) in WriteMolecule() 294 OBReactionFacade rxnfacade(pmol); in WriteMolecule() [all …]
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H A D | acrformat.cpp | 85 OBMol* pmol = pOb->CastAndClear<OBMol>(); in ReadMolecule() local 86 if (pmol == nullptr) in ReadMolecule() 91 pmol->BeginModify(); in ReadMolecule() 144 OBAtom* a = pmol->NewAtom(); in ReadMolecule() 152 if (!pmol->AddBond(atoi((char*)vs[0].c_str()) + 1, atoi((char*)vs[1].c_str()) + 1, in ReadMolecule() 162 if ( pmol->NumBonds() != bonds ) { in ReadMolecule() 166 } else if ( pmol->NumAtoms() != atoms ) { in ReadMolecule() 171 pmol->PerceiveBondOrders(); in ReadMolecule() 173 pmol->EndModify(); in ReadMolecule()
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/dports/science/openbabel/openbabel-3.1.1/src/formats/json/ |
H A D | chemdoodlejsonformat.cpp | 86 pmol->BeginModify(); in ReadMolecule() 229 pmol->SetDimension(dim); in ReadMolecule() 281 (unsigned) end > pmol->NumAtoms() || pmol->GetBond(begin, end)) { in ReadMolecule() 304 pbond->Set(pbond->GetIdx(), pmol->GetAtom(begin), pmol->GetAtom(end), order, flag); in ReadMolecule() 338 pmol->EndModify(); in ReadMolecule() 340 if (pmol->Has3D()) { in ReadMolecule() 342 StereoFrom3D(pmol); in ReadMolecule() 358 } else if (pmol->Has2D()) { in ReadMolecule() 369 if (pmol == nullptr) in WriteMolecule() 379 PerceiveStereo(pmol); in WriteMolecule() [all …]
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H A D | pubchemjsonformat.cpp | 91 pmol->BeginModify(); in ReadMolecule() 153 pmol->SetTitle(title); in ReadMolecule() 158 pmol->SetData(cid); in ReadMolecule() 165 pmol->SetTitle(title); in ReadMolecule() 170 pmol->SetData(sid); in ReadMolecule() 546 pmol->EndModify(); in ReadMolecule() 638 if (pmol->Has3D()) { in ReadMolecule() 640 StereoFrom3D(pmol); in ReadMolecule() 672 if (pmol == nullptr) in WriteMolecule() 686 pmol->AddHydrogens(); in WriteMolecule() [all …]
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/dports/science/py-pyscf/pyscf-2.0.1/pyscf/lo/ |
H A D | iao.py | 60 pmol = reference_mol(mol, minao) 75 s2 = pmol.intor_symmetric('int1e_ovlp') 77 s12 = gto.mole.intor_cross('int1e_ovlp', mol, pmol) 113 pmol = mol.copy() 117 if len(pmol.atom) != len(atoms): 121 if getattr(pmol, 'rcut', None) is not None: 122 pmol.rcut = None 123 pmol.build(False, False, basis=minao) 124 return pmol 138 pmol = reference_mol(mol) [all …]
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/dports/science/py-pyscf/pyscf-2.0.1/pyscf/hessian/test/ |
H A D | test_rks.py | 44 pmol = mol.copy() 45 e1 = g_scanner(pmol.set_geom_('O 0. 0. 0.0001; 1 0. -0.757 0.587; 1 0. 0.757 0.587'))[1] 46 e2 = g_scanner(pmol.set_geom_('O 0. 0. -.0001; 1 0. -0.757 0.587; 1 0. 0.757 0.587'))[1] 58 pmol = mol.copy() 59 e1 = g_scanner(pmol.set_geom_('O 0. 0. 0.0001; 1 0. -0.757 0.587; 1 0. 0.757 0.587'))[1] 60 e2 = g_scanner(pmol.set_geom_('O 0. 0. -.0001; 1 0. -0.757 0.587; 1 0. 0.757 0.587'))[1] 72 pmol = mol.copy() 73 e1 = g_scanner(pmol.set_geom_('O 0. 0. 0.0001; 1 0. -0.757 0.587; 1 0. 0.757 0.587'))[1] 74 e2 = g_scanner(pmol.set_geom_('O 0. 0. -.0001; 1 0. -0.757 0.587; 1 0. 0.757 0.587'))[1]
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H A D | test_uks.py | 46 pmol = mol.copy() 47 e1 = g_scanner(pmol.set_geom_('O 0. 0. 0.0001; 1 0. -0.757 0.587; 1 0. 0.757 0.587'))[1] 48 e2 = g_scanner(pmol.set_geom_('O 0. 0. -.0001; 1 0. -0.757 0.587; 1 0. 0.757 0.587'))[1] 60 pmol = mol.copy() 61 e1 = g_scanner(pmol.set_geom_('O 0. 0. 0.0001; 1 0. -0.757 0.587; 1 0. 0.757 0.587'))[1] 62 e2 = g_scanner(pmol.set_geom_('O 0. 0. -.0001; 1 0. -0.757 0.587; 1 0. 0.757 0.587'))[1] 74 pmol = mol.copy() 75 e1 = g_scanner(pmol.set_geom_('O 0. 0. 0.0001; 1 0. -0.757 0.587; 1 0. 0.757 0.587'))[1] 76 e2 = g_scanner(pmol.set_geom_('O 0. 0. -.0001; 1 0. -0.757 0.587; 1 0. 0.757 0.587'))[1]
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/dports/science/py-pyscf/pyscf-2.0.1/pyscf/df/test/ |
H A D | test_df_jk.py | 65 pmol = mol.copy() 66 pmol.cart = True 71 pmol = mol.copy() 72 pmol.charge = 1 73 pmol.spin = 1 74 pmol.build(False, False) 79 pmol = mol.copy() 94 pmol = mol.copy() 95 pmol.charge = 1 96 pmol.spin = 1 [all …]
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/dports/science/py-pyscf/pyscf-2.0.1/pyscf/grad/test/ |
H A D | test_tduks_grad.py | 37 pmol = mol.copy() variable 44 global mol, pmol 46 del mol, pmol 56 e1 = td_solver(pmol.set_geom_('H 0 0 1.805; F 0 0 0', unit='B')) 57 e2 = td_solver(pmol.set_geom_('H 0 0 1.803; F 0 0 0', unit='B')) 67 e1 = td_solver(pmol.set_geom_('H 0 0 1.805; F 0 0 0', unit='B')) 68 e2 = td_solver(pmol.set_geom_('H 0 0 1.803; F 0 0 0', unit='B')) 78 e1 = td_solver(pmol.set_geom_('H 0 0 1.805; F 0 0 0', unit='B')) 79 e2 = td_solver(pmol.set_geom_('H 0 0 1.803; F 0 0 0', unit='B')) 92 e1 = td_solver(pmol.set_geom_('H 0 0 1.805; F 0 0 0', unit='B')) [all …]
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