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Searched refs:getOwningMol (Results 1 – 25 of 48) sorted by relevance

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/dports/science/rdkit/rdkit-Release_2021_03_5/Code/JavaWrappers/
H A DAtom.i88 if(!($self)->getOwningMol().getRingInfo()->isInitialized()){ in IsInRing()
89 RDKit::MolOps::findSSSR(($self)->getOwningMol()); in IsInRing()
91 return ($self)->getOwningMol().getRingInfo()->numAtomRings(($self)->getIdx())!=0; in IsInRing()
95 if(!($self)->getOwningMol().getRingInfo()->isInitialized()){ in IsInRingSize()
96 RDKit::MolOps::findSSSR(($self)->getOwningMol()); in IsInRingSize()
98 return ($self)->getOwningMol().getRingInfo()->isAtomInRingOfSize(($self)->getIdx(),size); in IsInRingSize()
103 RDKit::ROMol *parent = &($self)->getOwningMol(); in getBonds()
H A DBond.i68 if(!($self)->getOwningMol().getRingInfo()->isInitialized()){ in IsInRing()
69 RDKit::MolOps::findSSSR(($self)->getOwningMol()); in IsInRing()
71 return ($self)->getOwningMol().getRingInfo()->numBondRings(($self)->getIdx())!=0; in IsInRing()
75 if(!($self)->getOwningMol().getRingInfo()->isInitialized()){ in IsInRingSize()
76 RDKit::MolOps::findSSSR(($self)->getOwningMol()); in IsInRingSize()
78 return ($self)->getOwningMol().getRingInfo()->isBondInRingOfSize(($self)->getIdx(),size); in IsInRingSize()
/dports/science/rdkit/rdkit-Release_2021_03_5/Code/GraphMol/MolTransforms/
H A DMolTransforms.cpp27 ROMol &mol = atom->getOwningMol(); in transformAtom()
46 const ROMol &mol = conf.getOwningMol(); in computeCentroid()
70 const ROMol &mol = conf.getOwningMol(); in computeCovarianceTerms()
125 const ROMol &mol = conf.getOwningMol(); in computeInertiaTerms()
161 conf.getOwningMol().getProp(axesPropName, axes); in computePrincipalAxesAndMoments()
165 const ROMol &mol = conf.getOwningMol(); in computePrincipalAxesAndMoments()
216 conf.getOwningMol().getProp(axesPropName, axes); in computePrincipalAxesAndMomentsFromGyrationMatrix()
220 const ROMol &mol = conf.getOwningMol(); in computePrincipalAxesAndMomentsFromGyrationMatrix()
435 ROMol &mol = conf.getOwningMol(); in setBondLength()
483 ROMol &mol = conf.getOwningMol(); in setAngleRad()
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/dports/science/rdkit/rdkit-Release_2021_03_5/Code/GraphMol/
H A DQueryOps.h88 const auto nbr = at->getOwningMol()[nbri]; in queryAtomNonHydrogenDegree()
101 const auto nbr = at->getOwningMol()[nbri]; in queryAtomHeavyAtomDegree()
187 const Atom *nbr = at->getOwningMol()[*nbrIdx]; in queryAtomHasHeteroatomNbrs()
201 const Atom *nbr = at->getOwningMol()[*nbrIdx]; in queryAtomNumHeteroatomNbrs()
214 const Atom *nbr = at->getOwningMol()[*nbrIdx]; in queryAtomHasAliphaticHeteroatomNbrs()
229 const Atom *nbr = at->getOwningMol()[*nbrIdx]; in queryAtomNumAliphaticHeteroatomNbrs()
288 at->getOwningMol().getTopology()[*atomBonds.first]->getIdx(); in queryAtomHasRingBond()
289 if (at->getOwningMol().getRingInfo()->numBondRings(bondIdx)) { in queryAtomHasRingBond()
314 at->getOwningMol().getTopology()[*atomBonds.first]->getIdx(); in queryAtomRingBondCount()
315 if (at->getOwningMol().getRingInfo()->numBondRings(bondIdx)) { in queryAtomRingBondCount()
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H A DAtom.cpp150 return getOwningMol().getAtomDegree(this); in getDegree()
170 const ROMol *parent = &getOwningMol(); in getTotalNumHs()
217 boost::make_iterator_range(getOwningMol().getAtomBonds(this))) { in calcExplicitValence()
218 const auto bnd = getOwningMol()[nbri]; in calcExplicitValence()
337 boost::make_iterator_range(getOwningMol().getAtomBonds(this))) { in calcImplicitValence()
338 const auto bnd = getOwningMol()[nbri]; in calcImplicitValence()
535 this->getOwningMol().getRingInfo()->isInitialized() && in Match()
536 what->getOwningMol().getRingInfo()->isInitialized() && in Match()
537 this->getOwningMol().getRingInfo()->numAtomRings(d_index) > in Match()
588 boost::tie(beg, end) = getOwningMol().getAtomBonds(this); in getPerturbationOrder()
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H A DConjugHybrid.cpp44 auto &mol = at->getOwningMol(); in markConjAtomBonds()
81 auto &mol = at->getOwningMol(); in numBondsPlusLonePairs()
114 auto &mol = at->getOwningMol(); in atomHasConjugatedBond()
H A DBond.cpp91 URANGE_CHECK(what, getOwningMol().getNumAtoms()); in setBeginAtomIdx()
98 URANGE_CHECK(what, getOwningMol().getNumAtoms()); in setEndAtomIdx()
246 getOwningMol().getBondBetweenAtoms(getBeginAtomIdx(), bgnIdx) != nullptr, in setStereoAtoms()
249 getOwningMol().getBondBetweenAtoms(getEndAtomIdx(), endIdx) != nullptr, in setStereoAtoms()
H A DAromaticity.cpp261 const ROMol &mol = at->getOwningMol(); in incidentNonCyclicMultipleBond()
278 const ROMol &mol = at->getOwningMol(); in incidentCyclicMultipleBond()
296 boost::tie(beg, end) = at->getOwningMol().getAtomBonds(at); in incidentMultipleBond()
298 Bond *bond = at->getOwningMol()[*beg]; in incidentMultipleBond()
507 const ROMol &mol = at->getOwningMol(); in isAtomCandForArom()
541 const ROMol &mol = at->getOwningMol(); in isAtomCandForArom()
569 const ROMol &mol = at->getOwningMol(); in getAtomDonorTypeArom()
650 boost::tie(beg, end) = at->getOwningMol().getAtomBonds(at); in countAtomElec()
652 Bond *bond = at->getOwningMol()[*beg]; in countAtomElec()
H A DROMol.cpp170 PRECONDITION(&at->getOwningMol() == this, in getAtomDegree()
369 PRECONDITION(&at->getOwningMol() == this, in getAtomNeighbors()
377 PRECONDITION(&at->getOwningMol() == this, in getAtomBonds()
393 &atom_pin->getOwningMol() == this, in addAtom()
419 &bond_pin->getOwningMol() == this, in addBond()
H A DFindStereo.cpp47 const auto &mol = bond->getOwningMol(); in getStereoInfo()
138 const auto &mol = atom->getOwningMol(); in getStereoInfo()
204 const auto ri = bond->getOwningMol().getRingInfo(); in isBondPotentialStereoBond()
223 const auto &mol = atom->getOwningMol(); in isAtomPotentialTetrahedralCenter()
H A DQueryOps.cpp32 const auto &mol = at->getOwningMol(); in queryIsAtomBridgehead()
238 boost::tie(beg, end) = at->getOwningMol().getAtomBonds(at); in queryAtomBondProduct()
242 firstThousandPrimes[at->getOwningMol()[*beg]->getBondType()]); in queryAtomBondProduct()
250 boost::tie(beg, end) = at->getOwningMol().getAtomBonds(at); in queryAtomAllBondProduct()
254 firstThousandPrimes[at->getOwningMol()[*beg]->getBondType()]); in queryAtomAllBondProduct()
H A DConformer.h79 ROMol &getOwningMol() const { in getOwningMol() function
H A DCanon.cpp173 ROMol &mol = dblBond->getOwningMol(); in canonicalizeDoubleBond()
635 } else if (theBond->getOwningMol().getRingInfo()->numBondRings( in dfsFindCycles()
811 if (theBond->getOwningMol().getRingInfo()->numBondRings( in dfsBuildStack()
927 PRECONDITION(&refBond->getOwningMol() == &mol, "bad bond"); in clearBondDirs()
929 PRECONDITION(&fromAtom->getOwningMol() == &mol, "bad bond"); in clearBondDirs()
/dports/science/rdkit/rdkit-Release_2021_03_5/Code/GraphMol/Wrap/
H A DAtom.cpp65 const ROMol *parent = &atom->getOwningMol(); in AtomGetNeighbors()
77 const ROMol *parent = &atom->getOwningMol(); in AtomGetBonds()
89 if (!atom->getOwningMol().getRingInfo()->isInitialized()) { in AtomIsInRing()
90 MolOps::findSSSR(atom->getOwningMol()); in AtomIsInRing()
92 return atom->getOwningMol().getRingInfo()->numAtomRings(atom->getIdx()) != 0; in AtomIsInRing()
95 if (!atom->getOwningMol().getRingInfo()->isInitialized()) { in AtomIsInRingSize()
96 MolOps::findSSSR(atom->getOwningMol()); in AtomIsInRingSize()
98 return atom->getOwningMol().getRingInfo()->isAtomInRingOfSize(atom->getIdx(), in AtomIsInRingSize()
240 .def("GetOwningMol", &Atom::getOwningMol, in wrap()
H A DBond.cpp56 if (!bond->getOwningMol().getRingInfo()->isInitialized()) { in BondIsInRing()
57 MolOps::findSSSR(bond->getOwningMol()); in BondIsInRing()
59 return bond->getOwningMol().getRingInfo()->numBondRings(bond->getIdx()) != 0; in BondIsInRing()
63 if (!bond->getOwningMol().getRingInfo()->isInitialized()) { in BondIsInRingSize()
64 MolOps::findSSSR(bond->getOwningMol()); in BondIsInRingSize()
66 return bond->getOwningMol().getRingInfo()->isBondInRingOfSize(bond->getIdx(), in BondIsInRingSize()
93 .def("GetOwningMol", &Bond::getOwningMol, in wrap()
H A DConformer.cpp81 .def("GetOwningMol", &Conformer::getOwningMol, in wrap()
/dports/science/rdkit/rdkit-Release_2021_03_5/Code/GraphMol/MolHash/
H A Dhashfunctions.cpp383 atom->getOwningMol().getAtomNeighbors(atom))) { in TraverseForRing()
384 auto nptr = atom->getOwningMol()[nbri]; in TraverseForRing()
419 atom->getOwningMol().getAtomNeighbors(atom))) { in IsInScaffold()
420 auto nptr = atom->getOwningMol()[nbri]; in IsInScaffold()
432 aptr->getOwningMol().getAtomNeighbors(aptr))) { in HasNbrInScaffold()
433 auto nptr = aptr->getOwningMol()[nbri]; in HasNbrInScaffold()
487 aptr->getOwningMol().getAtomBonds(aptr))) { in MurckoScaffoldHash()
488 auto bptr = (aptr->getOwningMol())[nbri]; in MurckoScaffoldHash()
569 auto bptr = (atom->getOwningMol())[nbri]; in HasDoubleBond()
625 boost::make_iterator_range(atm->getOwningMol().getAtomBonds(atm))) { in ClearEZStereo()
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/dports/science/rdkit/rdkit-Release_2021_03_5/Code/GraphMol/Descriptors/
H A DWHIM.cpp239 weightvector = moldata3D.GetRelativeMW(conf.getOwningMol()); in GetWHIMs()
242 weightvector = moldata3D.GetRelativeVdW(conf.getOwningMol()); in GetWHIMs()
245 weightvector = moldata3D.GetRelativeENeg(conf.getOwningMol()); in GetWHIMs()
248 weightvector = moldata3D.GetRelativePol(conf.getOwningMol()); in GetWHIMs()
251 weightvector = moldata3D.GetRelativeIonPol(conf.getOwningMol()); in GetWHIMs()
254 weightvector = moldata3D.GetIState(conf.getOwningMol()); in GetWHIMs()
293 moldata3D.GetCustomAtomProp(conf.getOwningMol(), customAtomPropName); in GetWHIMsCustom()
/dports/science/rdkit/rdkit-Release_2021_03_5/Code/GraphMol/SmilesParse/
H A DSmilesWrite.cpp62 atom->getOwningMol().hasProp(common_properties::_doIsoSmiles))) { in GetAtomSmiles()
109 atom->getOwningMol().hasProp( in GetAtomSmiles()
122 atom->getOwningMol().hasProp( in GetAtomSmiles()
188 auto a1 = bond->getOwningMol().getAtomWithIdx(atomToLeftIdx); in GetBondSmiles()
189 auto a2 = bond->getOwningMol().getAtomWithIdx( in GetBondSmiles()
210 bond->getOwningMol().hasProp( in GetBondSmiles()
217 bond->getOwningMol().hasProp( in GetBondSmiles()
256 bond->getOwningMol().hasProp( in GetBondSmiles()
263 bond->getOwningMol().hasProp( in GetBondSmiles()
H A DSmartsWrite.cpp291 qatom->getOwningMol().hasProp(common_properties::_doIsoSmiles)) { in getAtomSmartsSimple()
399 bond->getOwningMol().hasProp(common_properties::_doIsoSmiles); in getBondSmartsSimple()
698 qatom->getOwningMol().hasProp(common_properties::_doIsoSmiles)) { in getNonQueryAtomSmarts()
761 qbond->getOwningMol().hasProp(common_properties::_doIsoSmiles); in getNonQueryBondSmarts()
/dports/science/rdkit/rdkit-Release_2021_03_5/Code/GraphMol/FileParsers/
H A DMolFileStereochem.cpp26 PRECONDITION(&conf->getOwningMol() == &bond->getOwningMol(), in WedgeBond()
227 const ROMol *mol = &(bond->getOwningMol()); in DetermineBondWedgeState()
361 PRECONDITION(&(conf->getOwningMol()) == &mol, in DetectAtomStereoChemistry()
380 PRECONDITION(&(conf->getOwningMol()) == &mol, in DetectBondStereoChemistry()
/dports/science/rdkit/rdkit-Release_2021_03_5/Code/GraphMol/ChemReactions/
H A DReaction.cpp491 rAtom.getOwningMol().getAtomNeighbors(&rAtom))) { in isChangedAtom()
492 const Atom *nbr = rAtom.getOwningMol()[nbrIdx]; in isChangedAtom()
495 reactantBonds[mapNum] = rAtom.getOwningMol().getBondBetweenAtoms( in isChangedAtom()
504 pAtom.getOwningMol().getAtomNeighbors(&pAtom))) { in isChangedAtom()
505 const Atom *nbr = pAtom.getOwningMol()[nbrIdx]; in isChangedAtom()
514 const Bond *pBond = pAtom.getOwningMol().getBondBetweenAtoms( in isChangedAtom()
H A DReactionUtils.cpp197 atom1->getOwningMol().getAtomNeighbors(atom1))) { in getNbrOrder()
198 const auto &nbrAtom = atom1->getOwningMol()[nbri]; in getNbrOrder()
/dports/science/rdkit/rdkit-Release_2021_03_5/Code/GraphMol/ChemTransforms/
H A DMolFragmenter.cpp673 auto &m = a->getOwningMol(); in get_other_atom()
724 if (!a->getOwningMol().getBondBetweenAtoms(a->getIdx(), b->getIdx())) { in bond()
725 CHECK_INVARIANT(&a->getOwningMol() == &newmol, in bond()
768 for (auto *bond : a->getOwningMol().bonds()) { in restore_chirality()
791 auto &m = chiral_atom->getOwningMol(); in mark()
801 auto &m = chiral_atom->getOwningMol(); in mark()
836 auto &m = chiral_atom->getOwningMol(); in restore()
/dports/science/rdkit/rdkit-Release_2021_03_5/Code/GraphMol/ShapeHelpers/
H A DShapeEncoder.cpp34 const ROMol &mol = conf.getOwningMol(); in EncodeShape()

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