Home
last modified time | relevance | path

Searched refs:atomIt (Results 1 – 25 of 31) sorted by relevance

12

/dports/science/rdkit/rdkit-Release_2021_03_5/Code/GraphMol/Descriptors/
H A DMolDescriptors.cpp26 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 …]
/dports/science/rdkit/rdkit-Release_2021_03_5/Code/GraphMol/ChemReactions/
H A DReaction.cpp101 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 …]
H A DMDLParser.cpp352 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()
H A DReactionUtils.cpp348 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()
/dports/science/rdkit/rdkit-Release_2021_03_5/Code/GraphMol/SLNParse/
H A DSLNParse.cpp84 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 …]
H A DSLNAttribs.cpp481 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()
/dports/science/rdkit/rdkit-Release_2021_03_5/Code/GraphMol/
H A Ditertest.cpp321 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 …]
H A DROMol.cpp572 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()
H A DMolOps.cpp787 for (ROMol::ConstAtomIterator atomIt = mol.beginAtoms(); in getFormalCharge() local
788 atomIt != mol.endAtoms(); ++atomIt) { in getFormalCharge()
789 accum += (*atomIt)->getFormalCharge(); in getFormalCharge()
/dports/science/lammps/lammps-stable_29Sep2021/lib/atc/
H A DMoleculeSet.cpp131 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()
/dports/science/liggghts/LIGGGHTS-PUBLIC-3.8.0-26-g6e873439/lib/atc/
H A DMoleculeSet.cpp131 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()
/dports/science/rdkit/rdkit-Release_2021_03_5/Code/Demos/RDKit/Basement/TemplEnum/
H A DTemplEnumTools.cpp210 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()
/dports/science/rdkit/rdkit-Release_2021_03_5/Code/GraphMol/MolChemicalFeatures/
H A DMolChemicalFeature.cpp66 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()
/dports/science/rdkit/rdkit-Release_2021_03_5/Code/GraphMol/SmilesParse/
H A DSmilesParseOps.cpp384 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 …]
/dports/science/rdkit/rdkit-Release_2021_03_5/Code/GraphMol/FileParsers/
H A DPDBWriter.cpp219 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()
H A DMolFileWriter.cpp148 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 …]
H A DSequenceWriters.cpp190 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()
H A DPDBParser.cpp514 for (ROMol::AtomIterator atomIt = mol->beginAtoms(); in StandardPDBResidueChirality() local
515 atomIt != mol->endAtoms(); ++atomIt) { in StandardPDBResidueChirality()
516 Atom *atom = *atomIt; in StandardPDBResidueChirality()
/dports/science/rdkit/rdkit-Release_2021_03_5/Code/GraphMol/Basement/FeatTrees/
H A DFeatTreeUtils.cpp198 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()
/dports/science/rdkit/rdkit-Release_2021_03_5/Code/GraphMol/Fingerprints/
H A DRDKitFPGenerator.cpp43 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()
H A DFingerprintUtil.cpp292 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()
/dports/science/rdkit/rdkit-Release_2021_03_5/Code/Demos/RDKit/GettingStarted/
H A Dsample.cpp131 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()
/dports/science/rdkit/rdkit-Release_2021_03_5/Code/GraphMol/FragCatalog/
H A DFragCatalogEntry.cpp169 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()
/dports/math/cvc4/CVC4-1.7/src/proof/
H A Dresolution_bitvector_proof.cpp480 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()
/dports/science/rdkit/rdkit-Release_2021_03_5/Code/GraphMol/MolTransforms/
H A DMolTransforms.cpp38 ROMol::AtomIterator atomIt; in transformMolsAtoms() local
39 for (atomIt = mol->beginAtoms(); atomIt != mol->endAtoms(); atomIt++) { in transformMolsAtoms()
40 transformAtom(*atomIt, tform); in transformMolsAtoms()

12