/dports/science/rdkit/rdkit-Release_2021_03_5/Code/GraphMol/Descriptors/ |
H A D | MolDescriptors.cpp | 26 atomIt != mol.endAtoms(); ++atomIt) { in calcAMW() 27 int atNum = (*atomIt)->getAtomicNum(); in calcAMW() 29 res += (*atomIt)->getMass(); in calcAMW() 47 atomIt != mol.endAtoms(); ++atomIt) { in calcExactMW() 48 int atNum = (*atomIt)->getAtomicNum(); in calcExactMW() 50 if (!(*atomIt)->getIsotope()) { in calcExactMW() 53 res += (*atomIt)->getMass(); in calcExactMW() 123 atomIt != mol.endAtoms(); ++atomIt) { in calcMolFormula() 124 int atNum = (*atomIt)->getAtomicNum(); in calcMolFormula() 144 nHs += (*atomIt)->getTotalNumHs(); in calcMolFormula() [all …]
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/dports/science/rdkit/rdkit-Release_2021_03_5/Code/GraphMol/ChemReactions/ |
H A D | Reaction.cpp | 101 atomIt != (*molIter)->endAtoms(); ++atomIt) { in validate() 116 reactingAtoms[mapNum] = *atomIt; in validate() 137 atomIt != (*molIter)->endAtoms(); ++atomIt) { in validate() 153 atomIt != (*molIter)->endAtoms(); ++atomIt) { in validate() 207 if ((*atomIt)->hasQuery()) { in validate() 209 queries.push_back((*atomIt)->getQuery()); in validate() 222 if ((*atomIt)->getPropIfPresent( in validate() 236 (*atomIt)->setProp( in validate() 254 (*atomIt)->setProp( in validate() 271 (*atomIt)->setProp( in validate() [all …]
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H A D | MDLParser.cpp | 352 for (ROMol::AtomIterator atomIt = (*iter)->beginAtoms(); in RxnDataStreamToChemicalReaction() local 353 atomIt != (*iter)->endAtoms(); ++atomIt) { in RxnDataStreamToChemicalReaction() 354 QueryOps::replaceAtomWithQueryAtom((RWMol *)iter->get(), (*atomIt)); in RxnDataStreamToChemicalReaction() 360 for (ROMol::AtomIterator atomIt = (*iter)->beginAtoms(); in RxnDataStreamToChemicalReaction() local 361 atomIt != (*iter)->endAtoms(); ++atomIt) { in RxnDataStreamToChemicalReaction() 362 QueryOps::replaceAtomWithQueryAtom((RWMol *)iter->get(), (*atomIt)); in RxnDataStreamToChemicalReaction()
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H A D | ReactionUtils.cpp | 348 for (ROMol::AtomIterator atomIt = mol.beginAtoms(); in removeMappingNumbersFromReactionMoleculeTemplate() local 349 atomIt != mol.endAtoms(); ++atomIt) { in removeMappingNumbersFromReactionMoleculeTemplate() 350 if ((*atomIt)->hasProp(common_properties::molAtomMapNumber)) { in removeMappingNumbersFromReactionMoleculeTemplate() 351 (*atomIt)->clearProp(common_properties::molAtomMapNumber); in removeMappingNumbersFromReactionMoleculeTemplate()
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/dports/science/rdkit/rdkit-Release_2021_03_5/Code/GraphMol/SLNParse/ |
H A D | SLNParse.cpp | 84 for (ROMol::AtomIterator atomIt = mol->beginAtoms(); in finalizeQueryMol() local 85 atomIt != mol->endAtoms(); ++atomIt) { in finalizeQueryMol() 87 if ((*atomIt)->getNumExplicitHs()) { in finalizeQueryMol() 88 (*atomIt)->expandQuery( in finalizeQueryMol() 99 for (ROMol::AtomIterator atomIt = mol->beginAtoms(); in finalizeQueryMol() local 100 atomIt != mol->endAtoms(); ++atomIt) { in finalizeQueryMol() 101 SLNParse::parseFinalAtomAttribs(*atomIt, true); in finalizeQueryMol() 108 rootIdx = (*atomIt)->getIdx(); in finalizeQueryMol() 214 for (ROMol::AtomIterator atomIt = res->beginAtoms(); in SLNToMol() local 215 atomIt != res->endAtoms(); ++atomIt) { in SLNToMol() [all …]
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H A D | SLNAttribs.cpp | 481 for (RWMol::AtomIterator atomIt = mol->beginAtoms(); in adjustAtomChiralities() local 482 atomIt != mol->endAtoms(); atomIt++) { in adjustAtomChiralities() 484 if ((*atomIt)->getPropIfPresent(common_properties::_SLN_s, attribVal)) { in adjustAtomChiralities() 494 (*atomIt)->setChiralTag(Atom::CHI_TETRAHEDRAL_CW); in adjustAtomChiralities() 496 (*atomIt)->setChiralTag(Atom::CHI_TETRAHEDRAL_CCW); in adjustAtomChiralities() 500 boost::tie(nbrIdx, endNbrs) = mol->getAtomNeighbors(*atomIt); in adjustAtomChiralities() 502 Bond *nbrBond = mol->getBondBetweenAtoms((*atomIt)->getIdx(), *nbrIdx); in adjustAtomChiralities() 523 int nSwaps = (*atomIt)->getPerturbationOrder(bondOrdering); in adjustAtomChiralities() 526 (*atomIt)->setChiralTag((*atomIt)->getChiralTag() == in adjustAtomChiralities()
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/dports/science/rdkit/rdkit-Release_2021_03_5/Code/GraphMol/ |
H A D | itertest.cpp | 321 Mol::AromaticAtomIterator atomIt; in test7() local 325 for (atomIt = beginP; atomIt != endP; atomIt++) { in test7() 326 TEST_ASSERT((*atomIt)->getIdx() == idx); in test7() 331 atomIt = beginP; in test7() 332 atomIt++; in test7() 333 atomIt--; in test7() 334 TEST_ASSERT((*atomIt)->getIdx() == 0); in test7() 342 for (atomIt = beginP; atomIt != endP; atomIt++) { in test7() 357 Mol::AtomIterator atomIt; in testIssue263() local 359 for (atomIt = m->beginAtoms(); atomIt != m->endAtoms(); ++atomIt) { in testIssue263() [all …]
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H A D | ROMol.cpp | 572 for (AtomIterator atomIt = this->beginAtoms(); atomIt != this->endAtoms(); in updatePropertyCache() local 573 ++atomIt) { in updatePropertyCache() 574 (*atomIt)->updatePropertyCache(strict); in updatePropertyCache() 583 for (ConstAtomIterator atomIt = this->beginAtoms(); in needsUpdatePropertyCache() local 584 atomIt != this->endAtoms(); ++atomIt) { in needsUpdatePropertyCache() 585 if ((*atomIt)->needsUpdatePropertyCache()) { in needsUpdatePropertyCache()
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H A D | MolOps.cpp | 787 for (ROMol::ConstAtomIterator atomIt = mol.beginAtoms(); in getFormalCharge() local 788 atomIt != mol.endAtoms(); ++atomIt) { in getFormalCharge() 789 accum += (*atomIt)->getFormalCharge(); in getFormalCharge()
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/dports/science/lammps/lammps-stable_29Sep2021/lib/atc/ |
H A D | MoleculeSet.cpp | 131 for (SIT atomIt = myAtoms->begin(); atomIt != myAtoms->end(); atomIt++) in atoms_by_global_molecule() local 132 realAtoms.insert(*atomIt); in atoms_by_global_molecule() 284 set<int>::const_iterator atomIt; in remove_proc_ghosts() local 285 for (atomIt = atomSet.begin(); atomIt != atomSet.end(); atomIt++) { in remove_proc_ghosts() 286 if (*atomIt > nlocalIdx) in remove_proc_ghosts() 287 atomSet.erase(atomIt); in remove_proc_ghosts()
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/dports/science/liggghts/LIGGGHTS-PUBLIC-3.8.0-26-g6e873439/lib/atc/ |
H A D | MoleculeSet.cpp | 131 for (SIT atomIt = myAtoms->begin(); atomIt != myAtoms->end(); atomIt++) in atoms_by_global_molecule() local 132 realAtoms.insert(*atomIt); in atoms_by_global_molecule() 284 set<int>::const_iterator atomIt; in remove_proc_ghosts() local 285 for (atomIt = atomSet.begin(); atomIt != atomSet.end(); atomIt++) { in remove_proc_ghosts() 286 if (*atomIt > nlocalIdx) in remove_proc_ghosts() 287 atomSet.erase(atomIt); in remove_proc_ghosts()
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/dports/science/rdkit/rdkit-Release_2021_03_5/Code/Demos/RDKit/Basement/TemplEnum/ |
H A D | TemplEnumTools.cpp | 210 RWMol::AtomIterator atomIt; in markAttachmentPoints() local 215 for (atomIt = mol->beginAtoms(); atomIt != mol->endAtoms(); atomIt++) { in markAttachmentPoints() 218 if ((*atomIt)->hasProp(common_properties::molFileAlias)) { in markAttachmentPoints() 219 (*atomIt)->getProp(common_properties::molFileAlias, attachLabel); in markAttachmentPoints() 220 } else if ((*atomIt)->hasProp(common_properties::dummyLabel)) { in markAttachmentPoints() 221 (*atomIt)->getProp(common_properties::dummyLabel, attachLabel); in markAttachmentPoints() 229 if ((*atomIt)->getDegree() > 1) in markAttachmentPoints() 238 mol->setAtomBookmark(*atomIt, offset); in markAttachmentPoints()
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/dports/science/rdkit/rdkit-Release_2021_03_5/Code/GraphMol/MolChemicalFeatures/ |
H A D | MolChemicalFeature.cpp | 66 for (auto atomIt = d_atoms.begin(); atomIt != d_atoms.end(); in getPos() local 67 atomIt++, weightIt++) { in getPos() 68 const Atom *atom = *atomIt; in getPos()
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/dports/science/rdkit/rdkit-Release_2021_03_5/Code/GraphMol/SmilesParse/ |
H A D | SmilesParseOps.cpp | 384 auto atomIt = bookmark.second.begin(); in CloseMolRings() local 386 while (atomIt != atomsEnd) { in CloseMolRings() 387 Atom *atom1 = *atomIt; in CloseMolRings() 388 ++atomIt; in CloseMolRings() 389 if (!toleratePartials && atomIt == atomsEnd) { in CloseMolRings() 391 } else if (atomIt != atomsEnd && *atomIt == atom1) { in CloseMolRings() 401 (*atomIt)->getIdx()) != nullptr) { in CloseMolRings() 406 bookmark.first % atom1->getIdx() % (*atomIt)->getIdx(); in CloseMolRings() 409 } else if (atomIt != atomsEnd) { in CloseMolRings() 411 Atom *atom2 = *atomIt; in CloseMolRings() [all …]
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/dports/science/rdkit/rdkit-Release_2021_03_5/Code/GraphMol/FileParsers/ |
H A D | PDBWriter.cpp | 219 for (ROMol::ConstAtomIterator atomIt = mol.beginAtoms(); in MolToPDBBody() local 220 atomIt != mol.endAtoms(); ++atomIt) { in MolToPDBBody() 221 last = GetPDBAtomLine(*atomIt, conf, elem); in MolToPDBBody() 244 for (ROMol::ConstAtomIterator atomIt = mol.beginAtoms(); in MolToPDBBody() local 245 atomIt != mol.endAtoms(); ++atomIt) { in MolToPDBBody() 246 res += GetPDBBondLines(*atomIt, all, both, mult, conect_count); in MolToPDBBody()
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H A D | MolFileWriter.cpp | 148 for (ROMol::ConstAtomIterator atomIt = mol.beginAtoms(); in GetMolFileChargeInfo() local 149 atomIt != mol.endAtoms(); ++atomIt) { in GetMolFileChargeInfo() 150 const Atom *atom = *atomIt; in GetMolFileChargeInfo() 277 for (ROMol::ConstAtomIterator atomIt = mol.beginAtoms(); in GetMolFileRGroupInfo() local 278 atomIt != mol.endAtoms(); ++atomIt) { in GetMolFileRGroupInfo() 295 for (ROMol::ConstAtomIterator atomIt = mol.beginAtoms(); in GetMolFileAliasInfo() local 296 atomIt != mol.endAtoms(); ++atomIt) { in GetMolFileAliasInfo() 1253 for (ROMol::ConstAtomIterator atomIt = tmol.beginAtoms(); in outputMolToMolBlock() local 1254 atomIt != tmol.endAtoms(); ++atomIt) { in outputMolToMolBlock() 1288 for (ROMol::ConstAtomIterator atomIt = tmol.beginAtoms(); in outputMolToMolBlock() local [all …]
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H A D | SequenceWriters.cpp | 190 for (ROMol::ConstAtomIterator atomIt = mol.beginAtoms(); in MolToSequence() local 191 atomIt != mol.endAtoms(); ++atomIt) { in MolToSequence() 192 const Atom *atom = *atomIt; in MolToSequence() 553 for (ROMol::ConstAtomIterator atomIt = mol.beginAtoms(); in MolToHELM() local 554 atomIt != mol.endAtoms(); ++atomIt) { in MolToHELM() 555 const Atom *atom = *atomIt; in MolToHELM()
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H A D | PDBParser.cpp | 514 for (ROMol::AtomIterator atomIt = mol->beginAtoms(); in StandardPDBResidueChirality() local 515 atomIt != mol->endAtoms(); ++atomIt) { in StandardPDBResidueChirality() 516 Atom *atom = *atomIt; in StandardPDBResidueChirality()
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/dports/science/rdkit/rdkit-Release_2021_03_5/Code/GraphMol/Basement/FeatTrees/ |
H A D | FeatTreeUtils.cpp | 198 for (ROMol::ConstAtomIterator atomIt = mol.beginAtoms(); in addNonringAtoms() local 199 atomIt != mol.endAtoms(); ++atomIt) { in addNonringAtoms() 200 const Atom *atom = *atomIt; in addNonringAtoms() 220 for (ROMol::ConstAtomIterator atomIt = mol.beginAtoms(); in addBondsFromNonringAtoms() local 221 atomIt != mol.endAtoms(); ++atomIt) { in addBondsFromNonringAtoms() 222 const Atom *atom = *atomIt; in addBondsFromNonringAtoms()
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/dports/science/rdkit/rdkit-Release_2021_03_5/Code/GraphMol/Fingerprints/ |
H A D | RDKitFPGenerator.cpp | 43 for (ROMol::ConstAtomIterator atomIt = mol.beginAtoms(); in getAtomInvariants() local 44 atomIt != mol.endAtoms(); ++atomIt) { in getAtomInvariants() 45 unsigned int aHash = ((*atomIt)->getAtomicNum() % 128) << 1 | in getAtomInvariants() 46 static_cast<unsigned int>((*atomIt)->getIsAromatic()); in getAtomInvariants()
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H A D | FingerprintUtil.cpp | 292 for (ROMol::ConstAtomIterator atomIt = mol.beginAtoms(); in buildDefaultRDKitFingerprintAtomInvariants() local 293 atomIt != mol.endAtoms(); ++atomIt) { in buildDefaultRDKitFingerprintAtomInvariants() 294 unsigned int aHash = ((*atomIt)->getAtomicNum() % 128) << 1 | in buildDefaultRDKitFingerprintAtomInvariants() 295 static_cast<unsigned int>((*atomIt)->getIsAromatic()); in buildDefaultRDKitFingerprintAtomInvariants()
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/dports/science/rdkit/rdkit-Release_2021_03_5/Code/Demos/RDKit/GettingStarted/ |
H A D | sample.cpp | 131 for (INT_VECT_CI atomIt = ringIt->begin(); atomIt != ringIt->end(); in WorkWithRingInfo() local 132 ++atomIt) { in WorkWithRingInfo() 133 if (!mol->getAtomWithIdx(*atomIt)->getIsAromatic()) { in WorkWithRingInfo()
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/dports/science/rdkit/rdkit-Release_2021_03_5/Code/GraphMol/FragCatalog/ |
H A D | FragCatalogEntry.cpp | 169 for (ROMol::AtomIterator atomIt = dp_mol->beginAtoms(); in getDiscrims() local 170 atomIt != dp_mol->endAtoms(); ++atomIt) { in getDiscrims() 171 unsigned int aid = (*atomIt)->getIdx(); in getDiscrims()
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/dports/math/cvc4/CVC4-1.7/src/proof/ |
H A D | resolution_bitvector_proof.cpp | 480 std::set<Node>::iterator atomIt; in printBBDeclarationAndCnf() local 484 for (atomIt = d_atomsInBitblastingProof.begin(); in printBBDeclarationAndCnf() 485 atomIt != d_atomsInBitblastingProof.end(); in printBBDeclarationAndCnf() 486 ++atomIt) in printBBDeclarationAndCnf() 488 Debug("pf::bv") << "\tAtom: " << *atomIt << std::endl; in printBBDeclarationAndCnf()
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/dports/science/rdkit/rdkit-Release_2021_03_5/Code/GraphMol/MolTransforms/ |
H A D | MolTransforms.cpp | 38 ROMol::AtomIterator atomIt; in transformMolsAtoms() local 39 for (atomIt = mol->beginAtoms(); atomIt != mol->endAtoms(); atomIt++) { in transformMolsAtoms() 40 transformAtom(*atomIt, tform); in transformMolsAtoms()
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