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/dports/science/cdk/cdk-cdk-2.3/tool/smarts/src/test/java/org/openscience/cdk/smarts/
H A DSmartsFragmentExtractorTest.java24 package org.openscience.cdk.smarts;
54 String smarts = generate("CC(C)CCC", in methylExact() local
57 assertThat(smarts, is("[CH3v4X4+0]")); in methylExact()
62 String smarts = generate("CC(C)CCC", in methylForJCompoundMap() local
65 assertThat(smarts, is("C*")); in methylForJCompoundMap()
70 String smarts = generate("[nH]1ccc2c1cccc2", in indole() local
78 String smarts = generate("[nH]1ccc2c1cccc2", in indoleForJCompoundMap() local
81 assertThat(smarts, is("n(ccc(a)a)a")); in indoleForJCompoundMap()
86 String smarts = generate("c1ccccc1-c1ccccc1", in biphenylIncludesSingleBond() local
89 assertThat(smarts, containsString("-")); in biphenylIncludesSingleBond()
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/dports/science/cdk/cdk-cdk-2.3/tool/pcore/src/main/java/org/openscience/cdk/pharmacophore/
H A DPharmacophoreAtom.java48 private String smarts; field in PharmacophoreAtom
62 public PharmacophoreAtom(String smarts, String symbol, Point3d coordinates) { in PharmacophoreAtom() argument
63 this.smarts = smarts; in PharmacophoreAtom()
74 this.smarts = pharmacophoreAtom.getSmarts(); in PharmacophoreAtom()
97 public void setSmarts(String smarts) { in setSmarts() argument
98 this.smarts = smarts; in setSmarts()
108 return smarts; in getSmarts()
151 int result = smarts != null ? smarts.hashCode() : 0; in hashCode()
161 return smarts.equals(that.getSmarts()) && symbol.equals(that.getSymbol()) in equals()
H A DPharmacophoreQueryAtom.java26 import org.openscience.cdk.smarts.Smarts;
27 import org.openscience.cdk.smarts.SmartsPattern;
47 private String smarts; field in PharmacophoreQueryAtom
57 public PharmacophoreQueryAtom(String symbol, String smarts) { in PharmacophoreQueryAtom() argument
59 this.smarts = smarts; in PharmacophoreQueryAtom()
63 String[] subSmarts = smarts.split("\\|"); in PharmacophoreQueryAtom()
93 return smarts; in getSmarts()
/dports/science/rdkit/rdkit-Release_2021_03_5/Code/GraphMol/SmilesParse/
H A Dsmarts.tab.cpp.cmake74 #line 1 "smarts.yy"
94 #include "smarts.tab.hpp"
224 #line 68 "smarts.yy"
243 #line 63 "smarts.yy"
1388 #line 103 "smarts.yy"
1394 #line 103 "smarts.yy"
1400 #line 103 "smarts.yy"
1406 #line 103 "smarts.yy"
1412 #line 103 "smarts.yy"
1418 #line 103 "smarts.yy"
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H A Dlex.yysmarts.cpp.cmake799 #line 1 "smarts.ll"
800 #line 6 "smarts.ll"
1166 #line 91 "smarts.ll"
1170 #line 95 "smarts.ll"
1237 #line 104 "smarts.ll"
1239 #line 105 "smarts.ll"
1241 #line 106 "smarts.ll"
1243 #line 107 "smarts.ll"
1246 #line 107 "smarts.ll"
1251 #line 109 "smarts.ll"
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H A Dcatch_tests.cpp131 std::vector<std::string> smarts = { variable
139 for (const auto &sma : smarts) {
150 for (const auto &sma : smarts) {
439 CHECK(smarts == "[#6]");
444 CHECK(smarts == ":");
489 CHECK(smarts == "C[C,N]N");
579 CHECK(smarts == "*!@CCC");
594 CHECK(smarts == "*!@CCC");
610 CHECK(smarts == "*!@CCC");
689 auto smarts = MolToSmarts(*m); variable
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/dports/science/cdk/cdk-cdk-2.3/descriptor/fingerprint/src/test/java/org/openscience/cdk/fingerprint/
H A DStandardSubstructureSetsTest.java36 String[] smarts = null; in testGetFunctionalGroupSubstructureSet() local
37 smarts = StandardSubstructureSets.getFunctionalGroupSMARTS(); in testGetFunctionalGroupSubstructureSet()
38 Assert.assertNotNull(smarts); in testGetFunctionalGroupSubstructureSet()
39 Assert.assertEquals(307, smarts.length); in testGetFunctionalGroupSubstructureSet()
44 String[] smarts = null; in testGetCountableMACCSSMARTSSubstructureSet() local
45 smarts = StandardSubstructureSets.getCountableMACCSSMARTS(); in testGetCountableMACCSSMARTSSubstructureSet()
46 Assert.assertNotNull(smarts); in testGetCountableMACCSSMARTSSubstructureSet()
47 Assert.assertEquals(142, smarts.length); // currently fragment pattern is ignored in testGetCountableMACCSSMARTSSubstructureSet()
/dports/science/cdk/cdk-cdk-2.3/legacy/src/main/java/org/openscience/cdk/smiles/smarts/
H A DSmartsPattern.java24 package org.openscience.cdk.smiles.smarts;
35 import org.openscience.cdk.smarts.Smarts;
102 private SmartsPattern(final String smarts, IChemObjectBuilder builder) throws IOException { in SmartsPattern() argument
104 if (!Smarts.parse(query, smarts)) in SmartsPattern()
105 throw new IOException("Could not parse SMARTS: " + smarts); in SmartsPattern()
181 … public static SmartsPattern create(String smarts, IChemObjectBuilder builder) throws IOException { in create() argument
182 return new SmartsPattern(smarts, builder); in create()
192 public static SmartsPattern create(String smarts) throws IOException { in create() argument
193 return new SmartsPattern(smarts, null); in create()
H A DSMARTSQueryTool.java19 package org.openscience.cdk.smiles.smarts;
39 import org.openscience.cdk.smiles.smarts.parser.SMARTSParser;
40 import org.openscience.cdk.smiles.smarts.parser.TokenMgrError;
115 private String smarts; field in SMARTSQueryTool
213 this.smarts = smarts; in SMARTSQueryTool()
296 return smarts; in getSmarts()
305 public void setSmarts(String smarts) throws CDKException { in setSmarts() argument
306 this.smarts = smarts; in setSmarts()
447 query = cache.get(smarts); in initializeQuery()
449 query = SMARTSParser.parse(smarts, builder); in initializeQuery()
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/dports/science/cdk/cdk-cdk-2.3/descriptor/fingerprint/src/main/java/org/openscience/cdk/fingerprint/
H A DSubstructureFingerprinter.java29 import org.openscience.cdk.smarts.Smarts;
30 import org.openscience.cdk.smarts.SmartsPattern;
375 final String smarts; field in SubstructureFingerprinter.Key
378 public Key(String smarts, Pattern pattern) { in Key() argument
379 this.smarts = smarts; in Key()
391 public SubstructureFingerprinter(String[] smarts) { in SubstructureFingerprinter() argument
392 setSmarts(smarts); in SubstructureFingerprinter()
411 private void setSmarts(String[] smarts) { in setSmarts() argument
413 for (String key : smarts) { in setSmarts()
515 return keys.get(bitIndex).smarts;
H A DMACCSFingerprinter.java32 import org.openscience.cdk.smarts.SmartsPattern;
111 switch (key.smarts) { in getBitFingerprint()
257 private String smarts; field in MACCSFingerprinter.MaccsKey
261 private MaccsKey(String smarts, Pattern pattern, int count) { in MaccsKey() argument
262 this.smarts = smarts; in MaccsKey()
268 return smarts; in getSmarts()
315 private Pattern createPattern(String smarts, IChemObjectBuilder builder) throws IOException { in createPattern() argument
316 SmartsPattern ptrn = SmartsPattern.create(smarts, builder); in createPattern()
/dports/science/cdk/cdk-cdk-2.3/legacy/src/main/java/org/openscience/cdk/smiles/smarts/parser/
H A DSmartsQueryVisitor.java18 package org.openscience.cdk.smiles.smarts.parser;
33 import org.openscience.cdk.isomorphism.matchers.smarts.AnyAtom;
35 import org.openscience.cdk.isomorphism.matchers.smarts.AromaticAtom;
48 import org.openscience.cdk.isomorphism.matchers.smarts.MassAtom;
54 import org.openscience.cdk.isomorphism.matchers.smarts.RingBond;
57 import org.openscience.cdk.isomorphism.matchers.smarts.SMARTSAtom;
58 import org.openscience.cdk.isomorphism.matchers.smarts.SMARTSBond;
60 import org.openscience.cdk.isomorphism.matchers.smarts.StereoBond;
286 ASTSmarts smarts = (ASTSmarts) node.jjtGetChild(i); in visit() local
290 smarts.jjtAccept(this, null); in visit()
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/dports/science/cdk/cdk-cdk-2.3/tool/smarts/src/main/java/org/openscience/cdk/smarts/
H A DSmartsPattern.java24 package org.openscience.cdk.smarts;
97 private SmartsPattern(final String smarts, IChemObjectBuilder builder) { in SmartsPattern() argument
99 if (!Smarts.parse(query, smarts)) in SmartsPattern()
101 smarts + "\n" + in SmartsPattern()
179 public static SmartsPattern create(String smarts, IChemObjectBuilder builder) { in create() argument
180 return new SmartsPattern(smarts, builder); in create()
189 public static SmartsPattern create(String smarts) { in create() argument
190 return new SmartsPattern(smarts, null); in create()
/dports/science/cdk/cdk-cdk-2.3/legacy/src/test/java/org/openscience/cdk/smiles/smarts/parser/
H A DSmartsDumpVisitorTest.java1 package org.openscience.cdk.smiles.smarts.parser;
6 import org.openscience.cdk.smiles.smarts.parser.ASTStart;
7 import org.openscience.cdk.smiles.smarts.parser.SMARTSParser;
8 import org.openscience.cdk.smiles.smarts.parser.SmartsDumpVisitor;
20 public void dump(String smarts) throws Exception { in dump() argument
21 SMARTSParser parser = new SMARTSParser(new StringReader(smarts)); in dump()
H A DSmartsStereoTest.java25 package org.openscience.cdk.smiles.smarts.parser;
33 import org.openscience.cdk.smiles.smarts.SMARTSQueryTool;
146 static void assertMatch(String smarts, String smiles, int hits, int usaHits) throws Exception { in assertMatch() argument
147 assertMatch(smarts(smarts), smiles(smiles), hits, usaHits); in assertMatch()
154 static SMARTSQueryTool smarts(String smarts) { in smarts() method in SmartsStereoTest
155 return new SMARTSQueryTool(smarts, DefaultChemObjectBuilder.getInstance()); in smarts()
H A DRecursiveTest.java19 package org.openscience.cdk.smiles.smarts.parser;
38 import org.openscience.cdk.smiles.smarts.SMARTSQueryTool;
43 import static org.openscience.cdk.smiles.smarts.parser.SMARTSSearchTest.smarts;
328 SMARTSQueryTool sqt = smarts("[NX3;H2,H1;!$(NC=O)]"); in testRecursiveSmarts26()
337 SMARTSQueryTool sqt = smarts("[NX3;H2,H1;!$(NC=O)]"); in testRecursiveSmarts26_cdkAromaticModel()
348 SMARTSQueryTool sqt = smarts("[NX3;H2,H1;!$(NC=O)]"); in testRecursiveSmarts27_cdkAromaticModel()
359 SMARTSQueryTool sqt = smarts("[NX3;H2,H1;!$(NC=O)]"); in testRecursiveSmarts27()
368 SMARTSQueryTool sqt = smarts("[NX3;H2,H1;!$(NC=O)]"); in testRecursive28()
377 SMARTSQueryTool sqt = smarts("[NX3;H2,H1;!$(NC=O)]"); in testRecursive28_cdkAromaticModel()
388 SMARTSQueryTool sqt = smarts("[NX3;H2,H1;!$(NC=O)]"); in testRecursive29()
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/dports/science/p5-PerlMol/PerlMol-0.3500/inc/BUNDLES/Chemistry-3DBuilder-0.10/t/
H A Dbuilder.t24 patt => Chemistry::Pattern->parse('CC', format => 'smarts'),
29 patt => Chemistry::Pattern->parse('*=*', format => 'smarts'),
34 patt => Chemistry::Pattern->parse('*#*', format => 'smarts'),
39 patt => Chemistry::Pattern->parse('*[H]', format => 'smarts'),
48 format => 'smarts'),
53 patt => Chemistry::Pattern->parse('*~[CX3,NX2]~*', format => 'smarts'),
58 patt => Chemistry::Pattern->parse('*~[CX2]~*', format => 'smarts'),
67 format => 'smarts'),
74 format => 'smarts'),
81 format => 'smarts'),
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/dports/science/p5-Chemistry-3DBuilder/Chemistry-3DBuilder-0.10/t/
H A Dbuilder.t24 patt => Chemistry::Pattern->parse('CC', format => 'smarts'),
29 patt => Chemistry::Pattern->parse('*=*', format => 'smarts'),
34 patt => Chemistry::Pattern->parse('*#*', format => 'smarts'),
39 patt => Chemistry::Pattern->parse('*[H]', format => 'smarts'),
48 format => 'smarts'),
53 patt => Chemistry::Pattern->parse('*~[CX3,NX2]~*', format => 'smarts'),
58 patt => Chemistry::Pattern->parse('*~[CX2]~*', format => 'smarts'),
67 format => 'smarts'),
74 format => 'smarts'),
81 format => 'smarts'),
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/dports/science/rdkit/rdkit-Release_2021_03_5/Code/Demos/nacl/GraphMol/SmilesParse/
H A DMakefile13 objs=lex.yysmiles.o smiles.tab.o lex.yysmarts.o smarts.tab.o InputFiller.o SmilesParse.o SmilesPar…
21 smarts.tab.cpp smarts.tab.hpp : smarts.yy
22 bison -p yysmarts_ -d -o smarts.tab.cpp $<
23 lex.yysmarts.cpp: smarts.ll smarts.tab.hpp
/dports/science/rdkit/rdkit-Release_2021_03_5/Code/GraphMol/Abbreviations/
H A DAbbreviationsUtils.cpp137 std::string smarts; in createAbbreviationMol() local
139 smarts = "*" + txt; in createAbbreviationMol()
141 smarts = txt; in createAbbreviationMol()
143 RWMol *q = SmartsToMol(smarts); in createAbbreviationMol()
163 unsigned int nDummies = std::count_if(smarts.begin(), smarts.end(), in createAbbreviationMol()
197 defn.smarts = *field; in parseAbbreviations()
207 defn.smarts, removeExtraDummies, allowConnectionToDummies)); in parseAbbreviations()
/dports/science/rdkit/rdkit-Release_2021_03_5/rdkit/Chem/
H A DFunctionalGroups.py47 smarts = "" variable in FGHierarchyNode
52 def __init__(self, name, patt, smarts="", label="", rxnSmarts="", parent=None): argument
58 self.smarts = smarts
122 smarts = splitL[1]
123 patt = Chem.MolFromSmarts(smarts)
126 'Smarts "%s" (line %d) could not be parsed.' % (smarts, lineNo))
134 node = FGHierarchyNode(name, patt, smarts=smarts, label=label, parent=parent,
H A DMCS.py247 self.smarts = obj.smarts
251 return self.smarts is not None
255 self.numAtoms, self.numBonds, self.smarts, self.completed)
258 msg = "MCS %r has %d atoms and %d bonds" % (self.smarts, self.numAtoms, self.numBonds)
H A DUnitTestEnumerateHeterocycles.py69 smarts = row.SMARTS
70 if not smarts:
73 substruct = Chem.MolFromSmarts(smarts)
77 assert mol.HasSubstructMatch(substruct), "%s not in %s" % (smarts, smiles)
84 … assert not mol.HasSubstructMatch(substruct), "%s should not be in %s" % (smarts, smiles)
97 smarts = row.SMARTS
98 if not smarts:
101 substruct = Chem.MolFromSmarts(smarts)
115 smarts = row.SMARTS
116 if not smarts:
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/dports/science/rdkit/rdkit-Release_2021_03_5/Code/GraphMol/
H A Dcatch_adjustquery.cpp53 return _IsSubstructOf(m, smarts, ps); in IsSubstructOf()
57 return _IsSubstructOf(m, smarts); in IsSubstructOf()
453 auto smarts = MolToSmarts(*qry); variable
454 CHECK(smarts=="[!#1]1:[#6]:[#6]:[#6]:[#6]:1");
456 smarts = MolToSmarts(*qry);
462 auto smarts = MolToSmarts(*qry); variable
463 CHECK(smarts == "[#6]1=[#6]-[#8]-[#6]-[#6]-1");
465 CHECK(MolToSmarts(*qry) == smarts);
469 auto smarts = MolToSmarts(*qry); variable
477 auto smarts = MolToSmarts(*qry); variable
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/dports/science/rdkit/rdkit-Release_2021_03_5/Code/GraphMol/MolStandardize/TautomerCatalog/
H A DTautomerCatalogUtils.cpp40 std::string smarts; in getTautomer() local
52 smarts = result[1]; in getTautomer()
57 smarts = result[1]; in getTautomer()
63 smarts = result[1]; in getTautomer()
68 boost::erase_all(smarts, " "); in getTautomer()
77 ROMol* tautomer = SmartsToMol(smarts); in getTautomer()
78 CHECK_INVARIANT(tautomer, smarts); in getTautomer()

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