/dports/science/cdk/cdk-cdk-2.3/tool/smarts/src/test/java/org/openscience/cdk/smarts/ |
H A D | SmartsFragmentExtractorTest.java | 24 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() [all …]
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/dports/science/cdk/cdk-cdk-2.3/tool/pcore/src/main/java/org/openscience/cdk/pharmacophore/ |
H A D | PharmacophoreAtom.java | 48 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()
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H A D | PharmacophoreQueryAtom.java | 26 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()
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/dports/science/rdkit/rdkit-Release_2021_03_5/Code/GraphMol/SmilesParse/ |
H A D | smarts.tab.cpp.cmake | 74 #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" [all …]
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H A D | lex.yysmarts.cpp.cmake | 799 #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" [all …]
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H A D | catch_tests.cpp | 131 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 [all …]
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/dports/science/cdk/cdk-cdk-2.3/descriptor/fingerprint/src/test/java/org/openscience/cdk/fingerprint/ |
H A D | StandardSubstructureSetsTest.java | 36 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()
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/dports/science/cdk/cdk-cdk-2.3/legacy/src/main/java/org/openscience/cdk/smiles/smarts/ |
H A D | SmartsPattern.java | 24 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()
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H A D | SMARTSQueryTool.java | 19 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() [all …]
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/dports/science/cdk/cdk-cdk-2.3/descriptor/fingerprint/src/main/java/org/openscience/cdk/fingerprint/ |
H A D | SubstructureFingerprinter.java | 29 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;
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H A D | MACCSFingerprinter.java | 32 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()
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/dports/science/cdk/cdk-cdk-2.3/legacy/src/main/java/org/openscience/cdk/smiles/smarts/parser/ |
H A D | SmartsQueryVisitor.java | 18 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() [all …]
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/dports/science/cdk/cdk-cdk-2.3/tool/smarts/src/main/java/org/openscience/cdk/smarts/ |
H A D | SmartsPattern.java | 24 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()
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/dports/science/cdk/cdk-cdk-2.3/legacy/src/test/java/org/openscience/cdk/smiles/smarts/parser/ |
H A D | SmartsDumpVisitorTest.java | 1 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()
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H A D | SmartsStereoTest.java | 25 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()
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H A D | RecursiveTest.java | 19 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() [all …]
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/dports/science/p5-PerlMol/PerlMol-0.3500/inc/BUNDLES/Chemistry-3DBuilder-0.10/t/ |
H A D | builder.t | 24 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'), [all …]
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/dports/science/p5-Chemistry-3DBuilder/Chemistry-3DBuilder-0.10/t/ |
H A D | builder.t | 24 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'), [all …]
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/dports/science/rdkit/rdkit-Release_2021_03_5/Code/Demos/nacl/GraphMol/SmilesParse/ |
H A D | Makefile | 13 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
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/dports/science/rdkit/rdkit-Release_2021_03_5/Code/GraphMol/Abbreviations/ |
H A D | AbbreviationsUtils.cpp | 137 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()
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/dports/science/rdkit/rdkit-Release_2021_03_5/rdkit/Chem/ |
H A D | FunctionalGroups.py | 47 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,
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H A D | MCS.py | 247 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)
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H A D | UnitTestEnumerateHeterocycles.py | 69 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: [all …]
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/dports/science/rdkit/rdkit-Release_2021_03_5/Code/GraphMol/ |
H A D | catch_adjustquery.cpp | 53 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 [all …]
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/dports/science/rdkit/rdkit-Release_2021_03_5/Code/GraphMol/MolStandardize/TautomerCatalog/ |
H A D | TautomerCatalogUtils.cpp | 40 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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