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Searched refs:atIt (Results 1 – 15 of 15) sorted by relevance

/dports/science/rdkit/rdkit-Release_2021_03_5/Code/GraphMol/
H A Ditertest.cpp32 for (atIt = m->beginAtoms(); atIt != m->endAtoms(); atIt++) { in test1()
43 atIt++; in test1()
56 atIt--; in test1()
57 --atIt; in test1()
61 atIt++; in test1()
62 ++atIt; in test1()
66 atIt = atIt + 2; in test1()
67 atIt = atIt - 2; in test1()
253 for (atIt = m->beginAtoms(); atIt != m->endAtoms(); atIt++) { in _test6Help()
287 atIt = atIt + 2; in _test6Help()
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H A DChirality.cpp836 for (ROMol::ConstAtomIterator atIt = mol.beginAtoms(); atIt != mol.endAtoms(); in buildCIPInvariants() local
837 ++atIt) { in buildCIPInvariants()
1490 for (ROMol::AtomIterator atIt = mol.beginAtoms(); atIt != mol.endAtoms(); in assignAtomChiralCodes() local
1491 ++atIt) { in assignAtomChiralCodes()
1492 Atom *atom = *atIt; in assignAtomChiralCodes()
1868 for (ROMol::AtomIterator atIt = mol.beginAtoms(); atIt != mol.endAtoms(); in assignStereochemistry() local
1869 ++atIt) { in assignStereochemistry()
1960 for (ROMol::AtomIterator atIt = mol.beginAtoms(); atIt != mol.endAtoms(); in assignStereochemistry() local
1961 ++atIt) { in assignStereochemistry()
2596 for (ROMol::AtomIterator atIt = mol.beginAtoms(); atIt != mol.endAtoms(); in removeStereochemistry() local
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H A DMolPickler.cpp993 ROMol::ConstAtomIterator atIt; in _pickle() local
995 for (atIt = mol->beginAtoms(); atIt != mol->endAtoms(); ++atIt) { in _pickle()
996 _pickleAtom<T>(ss, *atIt); in _pickle()
1084 atIt != mol->endAtoms(); ++atIt) { in _pickle()
1235 atIt != mol->endAtoms(); ++atIt) { in _depickle()
1247 atIt != mol->endAtoms(); ++atIt) { in _depickle()
1267 for (ROMol::AtomIterator atIt = mol->beginAtoms(); atIt != mol->endAtoms(); in _depickle() local
1268 ++atIt) { in _depickle()
1269 Atom *atom = *atIt; in _depickle()
2244 for (atIt = mol->beginAtoms(); atIt != mol->endAtoms(); ++atIt) { in _pickleV1()
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/dports/science/rdkit/rdkit-Release_2021_03_5/Code/GraphMol/StructChecker/
H A DStripSmallFragments.cpp103 for (ROMol::AtomIterator atIt = copy.beginAtoms(); in StripSmallFragments() local
104 atIt != copy.endAtoms(); ++atIt) { in StripSmallFragments()
105 if ((*atIt)->hasProp(common_properties::_ChiralityPossible)) { in StripSmallFragments()
116 for (ROMol::AtomIterator atIt = mol.beginAtoms(); atIt != mol.endAtoms(); in StripSmallFragments() local
117 ++atIt) { in StripSmallFragments()
118 if ((*atIt)->getChiralTag() == Atom::CHI_TETRAHEDRAL_CW || in StripSmallFragments()
119 (*atIt)->getChiralTag() == Atom::CHI_TETRAHEDRAL_CCW) { in StripSmallFragments()
/dports/science/rdkit/rdkit-Release_2021_03_5/Code/GraphMol/RGroupDecomposition/
H A DRGroupData.h102 for (ROMol::AtomIterator atIt = combinedMol->beginAtoms(); in getNumBondsToRlabels() local
103 atIt != combinedMol->endAtoms(); ++atIt) { in getNumBondsToRlabels()
104 Atom *atom = *atIt; in getNumBondsToRlabels()
136 for (ROMol::AtomIterator atIt = mol.beginAtoms(); atIt != mol.endAtoms(); in isMolHydrogen() local
137 ++atIt) { in isMolHydrogen()
138 if ((*atIt)->getAtomicNum() > 1) { in isMolHydrogen()
H A DRGroupUtils.cpp109 for (RWMol::ConstAtomIterator atIt = core.beginAtoms(); in hasDummy() local
110 atIt != core.endAtoms(); ++atIt) { in hasDummy()
111 if ((*atIt)->getAtomicNum() == 0) { in hasDummy()
H A DRGroupDecompData.h360 for (RWMol::AtomIterator atIt = mol.beginAtoms(); atIt != mol.endAtoms(); in relabelRGroup() local
361 ++atIt) { in relabelRGroup()
362 Atom *atom = *atIt; in relabelRGroup()
408 for (RWMol::AtomIterator atIt = mol.beginAtoms(); atIt != mol.endAtoms(); in relabelRGroup() local
409 ++atIt) { in relabelRGroup()
410 Atom *atom = *atIt; in relabelRGroup()
/dports/science/rdkit/rdkit-Release_2021_03_5/Code/GraphMol/ReducedGraphs/
H A DReducedGraphs.cpp150 for (ROMol::ConstAtomIterator atIt = mol.beginAtoms(); atIt != mol.endAtoms(); in generateErGFingerprintForReducedGraph() local
151 ++atIt) { in generateErGFingerprintForReducedGraph()
153 (*atIt)->getProp<std::vector<int>>("_ErGAtomTypes"); in generateErGFingerprintForReducedGraph()
215 for (ROMol::AtomIterator atIt = res->beginAtoms(); atIt != res->endAtoms(); in generateMolExtendedReducedGraph() local
216 ++atIt) { in generateMolExtendedReducedGraph()
220 if ((*atomTypes)[i][(*atIt)->getIdx()]) { in generateMolExtendedReducedGraph()
224 (*atIt)->setProp("_ErGAtomTypes", tv); in generateMolExtendedReducedGraph()
/dports/science/rdkit/rdkit-Release_2021_03_5/Code/Demos/RDKit/Basement/xpcom/
H A DRDMolImpl.cpp29 for (RDKit::ROMol::AtomIterator atIt = dp_mol->beginAtoms(); in GetMW() local
30 atIt != dp_mol->endAtoms(); atIt++) { in GetMW()
31 *_retval += (*atIt)->getMass() + in GetMW()
32 (*atIt)->getNumImplicitHs() * pt->getAtomicWeight(1); in GetMW()
/dports/science/rdkit/rdkit-Release_2021_03_5/Code/GraphMol/SmilesParse/
H A DCXSmilesOps.cpp738 for (RDKit::ROMol::AtomIterator atIt = mol.beginAtoms(); in processCXSmilesLabels() local
739 atIt != mol.endAtoms(); ++atIt) { in processCXSmilesLabels()
747 addquery(makeQAtomQuery(), symb, mol, (*atIt)->getIdx()); in processCXSmilesLabels()
749 addquery(makeQHAtomQuery(), symb, mol, (*atIt)->getIdx()); in processCXSmilesLabels()
758 addquery(makeAHAtomQuery(), symb, mol, (*atIt)->getIdx()); in processCXSmilesLabels()
760 addquery(makeXAtomQuery(), symb, mol, (*atIt)->getIdx()); in processCXSmilesLabels()
762 addquery(makeXHAtomQuery(), symb, mol, (*atIt)->getIdx()); in processCXSmilesLabels()
764 addquery(makeMAtomQuery(), symb, mol, (*atIt)->getIdx()); in processCXSmilesLabels()
766 addquery(makeMHAtomQuery(), symb, mol, (*atIt)->getIdx()); in processCXSmilesLabels()
768 } else if ((*atIt)->getAtomicNum() == 0 && (*atIt)->getSymbol() == "*") { in processCXSmilesLabels()
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H A DSmilesParseOps.cpp178 for (auto atIt : *frag->getAtomBookmarks()) { in AddFragToMol()
181 if (couldBeRingClosure(atIt.first)) { in AddFragToMol()
182 for (auto at2 : atIt.second) { in AddFragToMol()
184 mol->setAtomBookmark(mol->getAtomWithIdx(newIdx), atIt.first); in AddFragToMol()
185 while (frag->hasBondBookmark(atIt.first)) { in AddFragToMol()
186 Bond *b = frag->getBondWithBookmark(atIt.first); in AddFragToMol()
190 mol->setBondBookmark(b, atIt.first); in AddFragToMol()
191 frag->clearBondBookmark(atIt.first, b); in AddFragToMol()
/dports/science/rdkit/rdkit-Release_2021_03_5/Code/GraphMol/Substruct/
H A DSubstructMatch.cpp426 ROMol::ConstAtomIterator atIt; in SubstructMatch() local
427 for (atIt = query.beginAtoms(); atIt != query.endAtoms(); atIt++) { in SubstructMatch()
428 if ((*atIt)->getQuery()) { in SubstructMatch()
430 detail::MatchSubqueries(mol, (*atIt)->getQuery(), params, subqueryMap, in SubstructMatch()
567 ROMol::ConstAtomIterator atIt; in RecursiveMatcher() local
568 for (atIt = query.beginAtoms(); atIt != query.endAtoms(); atIt++) { in RecursiveMatcher()
569 if ((*atIt)->getQuery()) { in RecursiveMatcher()
570 MatchSubqueries(mol, (*atIt)->getQuery(), params, subqueryMap, locked); in RecursiveMatcher()
/dports/devel/hadoop2/hadoop-2.7.2-src/hadoop-mapreduce-project/hadoop-mapreduce-client/hadoop-mapreduce-client-app/src/test/java/org/apache/hadoop/mapreduce/v2/app/
H A DTestFetchFailure.java111 Iterator<TaskAttempt> atIt = mapTask.getAttempts().values().iterator(); in testFetchFailure() local
112 atIt.next(); in testFetchFailure()
113 TaskAttempt mapAttempt2 = atIt.next(); in testFetchFailure()
348 Iterator<TaskAttempt> atIt = mapTask.getAttempts().values().iterator(); in testFetchFailureMultipleReduces() local
349 atIt.next(); in testFetchFailureMultipleReduces()
350 TaskAttempt mapAttempt2 = atIt.next(); in testFetchFailureMultipleReduces()
/dports/science/rdkit/rdkit-Release_2021_03_5/Code/GraphMol/FileParsers/
H A DMol2FileParser.cpp297 for (ROMol::AtomIterator atIt = res->beginAtoms(); atIt != res->endAtoms(); in cleanUpMol2Substructures() local
298 ++atIt) { in cleanUpMol2Substructures()
300 Atom *at = *atIt; in cleanUpMol2Substructures()
/dports/science/rdkit/rdkit-Release_2021_03_5/Code/GraphMol/Depictor/
H A DtestDepictor.cpp785 for (RWMol::AtomIterator atIt = m->beginAtoms(); atIt != m->endAtoms(); in testGitHubIssue910() local
786 ++atIt) { in testGitHubIssue910()
787 if ((*atIt)->getChiralTag() == Atom::CHI_TETRAHEDRAL_CCW || in testGitHubIssue910()
788 (*atIt)->getChiralTag() == Atom::CHI_TETRAHEDRAL_CW) { in testGitHubIssue910()
789 chiralAts.push_back((*atIt)->getIdx()); in testGitHubIssue910()