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Searched refs:pmol (Results 1 – 25 of 248) sorted by relevance

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/dports/science/openbabel/openbabel-3.1.1/src/descriptors/
H A Dfilters.cpp37 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()
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/dports/science/openbabel/openbabel-3.1.1/src/ops/
H A Dopalign.cpp92 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()
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H A Dophighlight.cpp55 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()
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H A Dopisomorph.cpp35 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()
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H A Dgen2D.cpp51 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()
H A Dreadconformers.cpp74 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()
/dports/science/openbabel/openbabel-3.1.1/src/
H A Dobmolecformat.cpp42 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()
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/dports/science/py-pyscf/pyscf-2.0.1/pyscf/scf/test/
H A Dtest_uhf.py172 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
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/dports/science/openbabel/openbabel-3.1.1/src/formats/
H A Dcofformat.cpp70 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()
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H A Dfastaformat.cpp98 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()
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H A Dmoldenformat.cpp126 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()
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H A Dmaeformat.cpp160 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
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H A Dcastepformat.cpp83 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()
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H A Dgroformat.cpp143 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()
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H A Dexampleformat.cpp151 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()
H A Dgulpformat.cpp82 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()
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H A Drxnformat.cpp98 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()
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H A Dacrformat.cpp85 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()
/dports/science/openbabel/openbabel-3.1.1/src/formats/json/
H A Dchemdoodlejsonformat.cpp86 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()
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H A Dpubchemjsonformat.cpp91 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()
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/dports/science/py-pyscf/pyscf-2.0.1/pyscf/lo/
H A Diao.py60 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)
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/dports/science/py-pyscf/pyscf-2.0.1/pyscf/hessian/test/
H A Dtest_rks.py44 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]
H A Dtest_uks.py46 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]
/dports/science/py-pyscf/pyscf-2.0.1/pyscf/df/test/
H A Dtest_df_jk.py65 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
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/dports/science/py-pyscf/pyscf-2.0.1/pyscf/grad/test/
H A Dtest_tduks_grad.py37 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'))
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