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/dports/science/rdkit/rdkit-Release_2021_03_5/Code/GraphMol/Abbreviations/
H A DAbbreviations.h26 std::string smarts; member
31 displayLabelW == other.displayLabelW && smarts == other.smarts;
/dports/science/openbabel/openbabel-3.1.1/src/
H A Dpatty.cpp128 smarts.push_back(vs[0]); in read_rules()
156 smarts.push_back(vs[0]); in assign_rules()
181 errorMsg << typ[i] << " " << smarts[i] << " matched "; in assign_types()
216 errorMsg << typ[i] << " " << smarts[i] << " matched " ; in assign_types()
/dports/science/cdk/cdk-cdk-2.3/legacy/src/main/java/org/openscience/cdk/smiles/smarts/parser/
H A DASTGroup.java18 package org.openscience.cdk.smiles.smarts.parser;
20 import org.openscience.cdk.isomorphism.matchers.smarts.ReactionRoleQueryAtom;
/dports/science/cdk/cdk-cdk-2.3/descriptor/qsarmolecular/src/main/java/org/openscience/cdk/qsar/descriptors/molecular/
H A DAcidicGroupCountDescriptor.java36 import org.openscience.cdk.smarts.SmartsPattern;
68 for (String smarts : SMARTS_STRINGS) { in initialise()
69 tools.add(SmartsPattern.create(smarts)); in initialise()
/dports/science/jmol/jmol-14.32.7/src/org/jmol/symmetry/
H A DCIPDataSmiles.java48 protected BS[] getList(String smarts) throws Exception { in getList() argument
49 return vwr.getSubstructureSetArrayForNodes(smarts, (Node[]) atoms, in getList()
54 protected BS match(String smarts) throws Exception { in match() argument
55 return vwr.getSmartsMatchForNodes(smarts, (Node[]) atoms); in match()
/dports/science/rdkit/rdkit-Release_2021_03_5/Code/GraphMol/SmilesParse/
H A Dsmarts.tab.hpp.cmake102 #line 68 "smarts.yy"
109 #line 110 "/scratch/RDKit_git/Code/GraphMol/SmilesParse/smarts.tab.hpp"
121 #line 63 "smarts.yy"
126 #line 127 "/scratch/RDKit_git/Code/GraphMol/SmilesParse/smarts.tab.hpp"
H A Dsmatest.cpp205 matcher = SmartsToMol(smarts); in _checkMatches()
206 CHECK_INVARIANT(matcher, smarts); in _checkMatches()
211 CHECK_INVARIANT(matcher2, smarts); in _checkMatches()
226 CHECK_INVARIANT(matches, smarts + " " + smiles); in _checkMatches()
235 CHECK_INVARIANT(matches, smarts + " " + smiles); in _checkMatches()
255 matcher = SmartsToMol(smarts); in _checkNoMatches()
256 CHECK_INVARIANT(matcher, smarts); in _checkNoMatches()
261 CHECK_INVARIANT(matcher2, smarts); in _checkNoMatches()
273 CHECK_INVARIANT(!matches, smarts + "|" + smiles); in _checkNoMatches()
2640 std::vector<std::string> smarts = { in testGithub1985() local
[all …]
/dports/science/openbabel/openbabel-3.1.1/src/descriptors/
H A Dsmartsdescriptors.cpp34 SmartsDescriptor(const char* ID, const char* smarts, const char* descr) in SmartsDescriptor() argument
35 : OBDescriptor(ID, false), _smarts(smarts), _descr(descr){} in SmartsDescriptor()
H A Dfilters.cpp84 string smarts; in Compare() local
85 bool matchornegate = ReadStringFromFilter(optionText, smarts); in Compare()
89 if (!sp.Init(smarts)) in Compare()
/dports/science/rdkit/rdkit-Release_2021_03_5/Code/GraphMol/StructChecker/
H A DStructCheckerOptions.cpp633 const std::vector<std::string> &smarts) { in parseSMARTS() argument
635 for (const auto &patt : smarts) { in parseSMARTS()
642 const std::vector<std::string> &smarts) { in parsePatterns() argument
643 parseSMARTS(Patterns, smarts); in parsePatterns()
647 const std::vector<std::string> &smarts) { in parseRotatePatterns() argument
648 parseSMARTS(RotatePatterns, smarts); in parseRotatePatterns()
652 const std::vector<std::string> &smarts) { in parseStereoPatterns() argument
653 parseSMARTS(StereoPatterns, smarts); in parseStereoPatterns()
H A DStructChecker.h177 const std::vector<std::string> &smarts); // can throw RDKit exceptions
183 const std::vector<std::string> &smarts); // can throw RDKit exceptions
189 const std::vector<std::string> &smarts); // can throw RDKit exceptions
/dports/science/rdkit/rdkit-Release_2021_03_5/rdkit/Chem/MolStandardize/
H A Dmetal.py56 for smarts in [self._metal_nof, self._metal_non]:
57 pairs = mol.GetSubstructMatches(smarts)
H A Dcharge.py103 def __init__(self, name, smarts, charge): argument
112 self.smarts_str = smarts
116 def smarts(self): member in ChargeCorrection
176 for match in mol.GetSubstructMatches(cc.smarts):
/dports/science/cdk/cdk-cdk-2.3/legacy/src/test/java/org/openscience/cdk/smiles/smarts/parser/
H A DSMARTSSearchTest.java19 package org.openscience.cdk.smiles.smarts.parser;
45 import org.openscience.cdk.smiles.smarts.SMARTSQueryTool;
88 static SMARTSQueryTool smarts(String smarts) { in smarts() method in SMARTSSearchTest
103 return match(smarts(smarts), smiles(smiles)); in match()
496 SMARTSQueryTool sqt = smarts("[R2]"); in testPropertyR2()
507 SMARTSQueryTool sqt = smarts("[R2]"); in testPropertyR2_essentialRings()
518 SMARTSQueryTool sqt = smarts("[R2]"); in testPropertyR2_relevantRings()
1361 SMARTSQueryTool sqt = smarts("[#7,C;+0,+1]"); in testLogicalOrLowAnd6()
1369 SMARTSQueryTool sqt = smarts("[#7,C;+0,+1]"); in testLogicalOrLowAnd6_cdkAromaticity()
1734 results = match(smarts("[^1]"), smilesAtomTyped("N#N")); in testHybridizationNumber()
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H A DSmartsQueryVisitorTest.java19 package org.openscience.cdk.smiles.smarts.parser;
26 import org.openscience.cdk.smiles.smarts.parser.ASTStart;
27 import org.openscience.cdk.smiles.smarts.parser.SMARTSParser;
28 import org.openscience.cdk.smiles.smarts.parser.SmartsQueryVisitor;
40 public void visit(String smarts) throws Exception { in visit() argument
41 SMARTSParser parser = new SMARTSParser(new StringReader(smarts)); in visit()
/dports/science/rdkit/rdkit-Release_2021_03_5/Code/GraphMol/RGroupDecomposition/Wrap/
H A Dtest_rgroups.py185 smarts = 'C([*:1])N([*:5])O([*:6])'
186 core = Chem.MolFromSmarts(smarts)
198 smarts = 'C([*:4])N([*:5])O([*:6])'
200 core = Chem.MolFromSmarts(smarts)
280 smarts = 'C([*:1])N([*:5])O([*:6])'
281 core = Chem.MolFromSmarts(smarts)
/dports/science/rdkit/rdkit-Release_2021_03_5/Code/GraphMol/FragCatalog/
H A Dtest1.cpp264 for (const auto &smarts : data) { in testWhiteSpaceInSmarts() local
265 std::istringstream input(smarts); in testWhiteSpaceInSmarts()
283 for (const auto &smarts : data) { in testFragmentWithoutSmarts() local
285 std::istringstream input(smarts); in testFragmentWithoutSmarts()
/dports/science/rdkit/rdkit-Release_2021_03_5/Code/GraphMol/MolStandardize/
H A DtestFragment.cpp212 for (const auto& smarts : data) { in testWhiteSpaceInSmarts() local
213 std::istringstream input(smarts); in testWhiteSpaceInSmarts()
231 for (const auto& smarts : data) { in testFragmentWithoutSmarts() local
233 std::istringstream input(smarts); in testFragmentWithoutSmarts()
H A DCharge.h42 ChargeCorrection(std::string name, std::string smarts, int charge) in ChargeCorrection()
43 : Name(name), Smarts(smarts), Charge(charge) {} in ChargeCorrection()
H A DTautomer.cpp83 smarts_mol_holder(const std::string &smarts) : d_smarts(smarts) { in smarts_mol_holder()
84 dp_mol.reset(SmartsToMol(smarts)); in smarts_mol_holder()
95 std::string smarts; member
99 : name(std::move(aname)), smarts(std::move(asmarts)), score(ascore) { in SubstructTerm()
100 matcher = smarts_mol_flyweight(smarts).get().dp_mol; in SubstructTerm()
/dports/science/py-oddt/oddt-0.7/oddt/
H A Dvirtualscreening.py24 def _filter_smarts(mols, smarts, soft_fail=0): argument
30 if isinstance(smarts, six.string_types):
31 compiled_smarts = oddt.toolkit.Smarts(smarts)
35 compiled_smarts = [oddt.toolkit.Smarts(s) for s in smarts]
163 smarts=list(pains_smarts.values()),
/dports/science/cdk/cdk-cdk-2.3/legacy/src/main/jjtree/org/openscience/cdk/smiles/smarts/parser/
H A DSMARTSParser.jjt31 package org.openscience.cdk.smiles.smarts.parser;
39 * <a href="http://www.daylight.com/dayhtml/doc/theory/theory.smarts.html">the
50 * <p>See the cdk.test.smiles.smarts.parser.ParserTest for examples of the implemented
60 * @see org.openscience.cdk.isomorphism.matchers.smarts.SMARTSAtom
66 * @cdk.module smarts
79 public static QueryAtomContainer parse(String smarts, IChemObjectBuilder builder) {
81 StringReader reader = new StringReader(smarts);
85 org.openscience.cdk.smiles.smarts.parser.SmartsQueryVisitor visitor
86 = new org.openscience.cdk.smiles.smarts.parser.SmartsQueryVisitor(builder);
89 throw new IllegalArgumentException("The string " + smarts + " is not a valid" +
/dports/science/rdkit/rdkit-Release_2021_03_5/Code/GraphMol/ForceFieldHelpers/CrystalFF/
H A DTorsionPreferences.cpp55 std::string smarts; member
124 angle.smarts = *token; in ExpTorsionAngleCollection()
133 boost::shared_ptr<const ROMol>(SmartsToMol(angle.smarts)); in ExpTorsionAngleCollection()
251 sstr << param.smarts << ": " << aid1 << " " << aid2 << " " << aid3 in getExperimentalTorsions()
/dports/deskutils/calibre/calibre-src-5.34.0/src/calibre/gui2/tweak_book/editor/smarts/
H A Dpython.py12 from calibre.gui2.tweak_book.editor.smarts import NullSmarts
13 from calibre.gui2.tweak_book.editor.smarts.utils import (
/dports/science/jmol/jmol-14.32.7/src/org/jmol/smiles/
H A DSmilesMatcher.java305 public void getMMFF94AtomTypes(String[] smarts, Node[] atoms, int ac, in getMMFF94AtomTypes() argument
324 for (int i = 0; i < smarts.length; i++) { in getMMFF94AtomTypes()
325 if (smarts[i] == null || smarts[i].length() == 0 in getMMFF94AtomTypes()
326 || smarts[i].startsWith("#")) { in getMMFF94AtomTypes()
332 SmilesParser.cleanPattern(smarts[i]), flags); in getMMFF94AtomTypes()

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