/dports/science/rdkit/rdkit-Release_2021_03_5/Code/GraphMol/ |
H A D | itertest.cpp | 32 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() [all …]
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H A D | Chirality.cpp | 836 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 [all …]
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H A D | MolPickler.cpp | 993 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() [all …]
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/dports/science/rdkit/rdkit-Release_2021_03_5/Code/GraphMol/StructChecker/ |
H A D | StripSmallFragments.cpp | 103 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()
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/dports/science/rdkit/rdkit-Release_2021_03_5/Code/GraphMol/RGroupDecomposition/ |
H A D | RGroupData.h | 102 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()
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H A D | RGroupUtils.cpp | 109 for (RWMol::ConstAtomIterator atIt = core.beginAtoms(); in hasDummy() local 110 atIt != core.endAtoms(); ++atIt) { in hasDummy() 111 if ((*atIt)->getAtomicNum() == 0) { in hasDummy()
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H A D | RGroupDecompData.h | 360 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()
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/dports/science/rdkit/rdkit-Release_2021_03_5/Code/GraphMol/ReducedGraphs/ |
H A D | ReducedGraphs.cpp | 150 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()
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/dports/science/rdkit/rdkit-Release_2021_03_5/Code/Demos/RDKit/Basement/xpcom/ |
H A D | RDMolImpl.cpp | 29 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()
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/dports/science/rdkit/rdkit-Release_2021_03_5/Code/GraphMol/SmilesParse/ |
H A D | CXSmilesOps.cpp | 738 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() [all …]
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H A D | SmilesParseOps.cpp | 178 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()
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/dports/science/rdkit/rdkit-Release_2021_03_5/Code/GraphMol/Substruct/ |
H A D | SubstructMatch.cpp | 426 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()
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/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 D | TestFetchFailure.java | 111 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()
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/dports/science/rdkit/rdkit-Release_2021_03_5/Code/GraphMol/FileParsers/ |
H A D | Mol2FileParser.cpp | 297 for (ROMol::AtomIterator atIt = res->beginAtoms(); atIt != res->endAtoms(); in cleanUpMol2Substructures() local 298 ++atIt) { in cleanUpMol2Substructures() 300 Atom *at = *atIt; in cleanUpMol2Substructures()
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/dports/science/rdkit/rdkit-Release_2021_03_5/Code/GraphMol/Depictor/ |
H A D | testDepictor.cpp | 785 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()
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