/dports/science/rdkit/rdkit-Release_2021_03_5/Code/JavaWrappers/ |
H A D | Atom.i | 88 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 = &($self)->getOwningMol(); in getBonds()
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H A D | Bond.i | 68 if(!($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()
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/dports/science/rdkit/rdkit-Release_2021_03_5/Code/GraphMol/MolTransforms/ |
H A D | MolTransforms.cpp | 27 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() [all …]
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/dports/science/rdkit/rdkit-Release_2021_03_5/Code/GraphMol/ |
H A D | QueryOps.h | 88 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() [all …]
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H A D | Atom.cpp | 150 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() [all …]
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H A D | ConjugHybrid.cpp | 44 auto &mol = at->getOwningMol(); in markConjAtomBonds() 81 auto &mol = at->getOwningMol(); in numBondsPlusLonePairs() 114 auto &mol = at->getOwningMol(); in atomHasConjugatedBond()
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H A D | Bond.cpp | 91 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()
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H A D | Aromaticity.cpp | 261 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()
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H A D | ROMol.cpp | 170 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()
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H A D | FindStereo.cpp | 47 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()
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H A D | QueryOps.cpp | 32 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()
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H A D | Conformer.h | 79 ROMol &getOwningMol() const { in getOwningMol() function
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H A D | Canon.cpp | 173 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()
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/dports/science/rdkit/rdkit-Release_2021_03_5/Code/GraphMol/Wrap/ |
H A D | Atom.cpp | 65 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()
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H A D | Bond.cpp | 56 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()
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H A D | Conformer.cpp | 81 .def("GetOwningMol", &Conformer::getOwningMol, in wrap()
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/dports/science/rdkit/rdkit-Release_2021_03_5/Code/GraphMol/MolHash/ |
H A D | hashfunctions.cpp | 383 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() [all …]
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/dports/science/rdkit/rdkit-Release_2021_03_5/Code/GraphMol/Descriptors/ |
H A D | WHIM.cpp | 239 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()
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/dports/science/rdkit/rdkit-Release_2021_03_5/Code/GraphMol/SmilesParse/ |
H A D | SmilesWrite.cpp | 62 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()
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H A D | SmartsWrite.cpp | 291 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()
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/dports/science/rdkit/rdkit-Release_2021_03_5/Code/GraphMol/FileParsers/ |
H A D | MolFileStereochem.cpp | 26 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()
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/dports/science/rdkit/rdkit-Release_2021_03_5/Code/GraphMol/ChemReactions/ |
H A D | Reaction.cpp | 491 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()
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H A D | ReactionUtils.cpp | 197 atom1->getOwningMol().getAtomNeighbors(atom1))) { in getNbrOrder() 198 const auto &nbrAtom = atom1->getOwningMol()[nbri]; in getNbrOrder()
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/dports/science/rdkit/rdkit-Release_2021_03_5/Code/GraphMol/ChemTransforms/ |
H A D | MolFragmenter.cpp | 673 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()
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/dports/science/rdkit/rdkit-Release_2021_03_5/Code/GraphMol/ShapeHelpers/ |
H A D | ShapeEncoder.cpp | 34 const ROMol &mol = conf.getOwningMol(); in EncodeShape()
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