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/dports/science/openbabel/openbabel-3.1.1/test/
H A Dinvalidsmarts.cpp68 OBSmartsPattern smarts; in invalidsmarts() local
82 if (smarts.Init(pattern)) in invalidsmarts()
103 if (smarts.Init(pattern)) in invalidsmarts()
123 if (smarts.Init(pattern)) in invalidsmarts()
143 if (smarts.Init(pattern)) in invalidsmarts()
H A Dsmilesmatch.cpp82 OBSmartsPattern smarts; in smilesmatch() local
103 smarts.Init(buffer); in smilesmatch()
104 if (smarts.Match(mol)) in smilesmatch()
/dports/science/rdkit/rdkit-Release_2021_03_5/Code/GraphMol/MolStandardize/FragmentCatalog/
H A DFragmentCatalogUtils.cpp49 std::string smarts = *token; in getSmarts() local
50 boost::erase_all(smarts, " "); in getSmarts()
53 mol = SmartsToMol(smarts); in getSmarts()
54 CHECK_INVARIANT(mol, smarts); in getSmarts()
56 mol->setProp(common_properties::_fragSMARTS, smarts); in getSmarts()
/dports/science/rdkit/rdkit-Release_2021_03_5/rdkit/Chem/MolStandardize/
H A Dvalidations.py60 self._smarts = Chem.MolFromSmarts(self.smarts)
63 def smarts(self): member in SmartsValidation
69 self.log.log(self.level, self.message, {'smarts': self.smarts})
75 self.log.log(self.level, self.message, {'smarts': self.smarts})
116 smarts = '[Cl]-[#6]-[#6]-[Cl]' variable in DichloroethaneValidation
133 matches = frozenset(frozenset(match) for match in mol.GetSubstructMatches(fp.smarts))
H A Dfragment.py29 def __init__(self, name, smarts): argument
36 self.smarts_str = smarts
39 def smarts(self): member in FragmentPattern
173 removed = Chem.DeleteSubstructs(mol, frag.smarts, onlyFrags=True)
H A Dtautomer.py36 def __init__(self, name, smarts, bonds=(), charges=(), radicals=()): argument
51 self.tautomer_str = smarts
70 def __init__(self, name, smarts, score): argument
78 self.smarts_str = smarts
82 def smarts(self): member in TautomerScore
209 for match in t.GetSubstructMatches(tscore.smarts):
/dports/science/rdkit/rdkit-Release_2021_03_5/rdkit/Chem/fmcs/
H A Dfmcs.py1313 return smarts
1329 return smarts
1549 self[smarts] = False
1561 self[smarts] = False
1566 self[smarts] = True
1615 self.cache[smarts] = True
1680 self.best_smarts = smarts
1698 self.smarts = smarts
2360 smarts = mcs.smarts
2362 smarts = "-"
[all …]
/dports/science/jmol/jmol-14.32.7/src/org/jmol/minimize/forcefield/
H A DForceFieldUFF.java90 String smarts = data[0]; in setAtomTypes() local
91 if (smarts == null) in setAtomTypes()
93 BS search = getSearch(smarts, elemnoMax, bsElements); in setAtomTypes()
125 private BS getSearch(String smarts, int elemnoMax, BS bsElements) { in getSearch() argument
139 int len = smarts.length(); in getSearch()
141 int n = smarts.charAt(len - 2) - '0'; in getSearch()
146 if (smarts.charAt(1) == '#') { in getSearch()
147 elemNo = PT.parseInt(smarts.substring(2, len - 1)); in getSearch()
149 String s = smarts.substring(1, (n > 0 ? len - 3 : len - 1)); in getSearch()
162 switch (smarts.charAt(len - 3)) { in getSearch()
[all …]
/dports/science/openbabel/openbabel-3.1.1/src/ops/
H A Dophighlight.cpp78 std::string smarts = vec[vecIdx]; in Do() local
81 string msg = "No color specified for SMARTS string: " + smarts; in Do()
100 bool addHydrogens = (smarts.find("#1]")!=string::npos); in Do()
102 if(!sp.Init(smarts)) in Do()
104 string msg = smarts + " cannot be interpreted as a valid SMARTS "; in Do()
/dports/science/cdk/cdk-cdk-2.3/legacy/src/test/java/org/openscience/cdk/smiles/smarts/
H A DSMARTSTest.java20 package org.openscience.cdk.smiles.smarts;
40 import org.openscience.cdk.isomorphism.matchers.smarts.AnyAtom;
41 import org.openscience.cdk.isomorphism.matchers.smarts.AnyOrderQueryBond;
42 import org.openscience.cdk.isomorphism.matchers.smarts.ImplicitHCountAtom;
43 import org.openscience.cdk.isomorphism.matchers.smarts.LogicalOperatorAtom;
44 import org.openscience.cdk.isomorphism.matchers.smarts.MassAtom;
45 import org.openscience.cdk.isomorphism.matchers.smarts.SMARTSAtom;
49 import org.openscience.cdk.smiles.smarts.parser.SMARTSParser;
/dports/science/rdkit/rdkit-Release_2021_03_5/rdkit/Chem/
H A DUnitTestMCS.py23 def assert_search(self, smiles, numAtoms, numBonds, smarts=_ignore, verbose=False, **kwargs): argument
27 self.assert_result(result, canceled=False, numAtoms=numAtoms, numBonds=numBonds, smarts=smarts)
30 smarts=_ignore): argument
37 if smarts is not _ignore:
38 self.assertEqual(result.smartsString, smarts)
95 self.assert_search(atomtype_mols, 4, 3, smarts='[#6](:[#6]:[#6]):[#6]',
99 self.assert_search(atomtype_mols, 4, 3, smarts='[#6](:[#6]:[#6]):[#6]',
H A DSaltRemover.py58 smarts = whitespace.split(line)
59 salt = Chem.MolFromSmarts(smarts[0])
71 smarts = _smartsFromSmartsLine(line)
72 if smarts:
73 yield smarts
H A DEnumerateHeterocycles.py65 smarts = row.SMARTS
66 if not smarts:
70 reaction = smarts + '>>' + product
/dports/science/rdkit/rdkit-Release_2021_03_5/Contrib/mmpa/
H A Dmol_transform.py52 smarts = Chem.MolToSmiles(mol, isomericSmiles=True)
54 smarts = re.sub(r'\[42', "[", smarts)
57 return smarts
/dports/science/rdkit/rdkit-Release_2021_03_5/Code/GraphMol/MolChemicalFeatures/
H A DMolChemicalFeatureDef.cpp20 MolChemicalFeatureDef::MolChemicalFeatureDef(const std::string &smarts, in MolChemicalFeatureDef() argument
23 : d_family(std::move(family)), d_type(std::move(type)), d_smarts(smarts) { in MolChemicalFeatureDef()
24 auto *mol = static_cast<ROMol *>(SmartsToMol(smarts)); in MolChemicalFeatureDef()
/dports/science/rdkit/rdkit-Release_2021_03_5/Docs/Book/data/
H A Dtest_multi_colours.py39 def do_a_picture(smi, smarts, filename, label, fmt='svg'): argument
50 for i, smt in enumerate(smarts):
75 smarts = ['CONN', 'N#CC~CO', 'C=CON', 'CONNCN'] variable
76 do_a_picture(smi, smarts, 'atom_highlights_3.png', '', fmt='png')
/dports/science/rdkit/rdkit-Release_2021_03_5/Code/Demos/RDKit/Basement/xpcom/
H A DIRDKit.h41 NS_IMETHOD GetSmartsMatchCount(const char *smarts, PRUint32 *_retval) = 0;
58 NS_IMETHOD GetSmartsMatchCount(const char *smarts, PRUint32 *_retval); \
69 NS_IMETHOD GetSmartsMatchCount(const char *smarts, PRUint32 *_retval) { \
70 return _to GetSmartsMatchCount(smarts, _retval); \
88 NS_IMETHOD GetSmartsMatchCount(const char *smarts, PRUint32 *_retval) { \
90 : _to->GetSmartsMatchCount(smarts, _retval); \
153 NS_IMETHODIMP _MYCLASS_::GetSmartsMatchCount(const char *smarts, PRUint32 *_retval)
/dports/science/rdkit/rdkit-Release_2021_03_5/Code/GraphMol/FragCatalog/
H A DFragCatalogUtils.cpp55 std::string smarts = *token; in getSmarts() local
56 boost::erase_all(smarts, " "); in getSmarts()
59 mol = SmartsToMol(smarts); in getSmarts()
60 CHECK_INVARIANT(mol, smarts); in getSmarts()
62 mol->setProp(common_properties::_fragSMARTS, smarts); in getSmarts()
/dports/science/cdk/cdk-cdk-2.3/tool/pcore/src/main/java/org/openscience/cdk/pharmacophore/
H A DPharmacophoreMatcher.java47 import org.openscience.cdk.smarts.SmartsPattern;
375 final String smarts = qatom.getSmarts(); in getPharmacophoreMolecule() local
396 uniqueAtoms.add(newPCoreAtom(input, qatom, smarts, mapping)); in getPharmacophoreMolecule()
400 logger.debug("\tFound " + count + " unique matches for " + smarts); in getPharmacophoreMolecule()
486 …om newPCoreAtom(IAtomContainer input, PharmacophoreQueryAtom qatom, String smarts, int[] mapping) { in newPCoreAtom() argument
488 PharmacophoreAtom patom = new PharmacophoreAtom(smarts, qatom.getSymbol(), coords); in newPCoreAtom()
557 String smarts = pqatom.getSmarts(); in checkQuery() local
560 map.put(label, smarts); in checkQuery()
562 if (!map.get(label).equals(smarts)) return false; in checkQuery()
/dports/deskutils/calibre/calibre-src-5.34.0/src/calibre/gui2/tweak_book/editor/
H A Dtext.py113 self.smarts = NullSmarts(self)
277 self.smarts = sclass(self)
506 if hasattr(self.smarts, 'find_text'):
927 if hasattr(self.smarts, 'insert_tag'):
928 self.smarts.insert_tag(self, tag)
931 if hasattr(self.smarts, 'remove_tag'):
932 self.smarts.remove_tag(self)
935 if hasattr(self.smarts, 'split_tag'):
936 self.smarts.split_tag(self)
950 if self.smarts.handle_key_press(ev, self):
[all …]
/dports/science/rdkit/rdkit-Release_2021_03_5/Code/Demos/sqlite/
H A Drdk_funcs.cpp176 std::string smarts = stringFromTextArg(argv[1]); in molHasSubstruct() local
182 if (molMap.find(smarts) != molMap.end()) { in molHasSubstruct()
183 patt = boost::any_cast<RDKit::ROMOL_SPTR>(molMap[smarts]).get(); in molHasSubstruct()
185 patt = static_cast<RDKit::ROMol *>(RDKit::SmartsToMol(smarts)); in molHasSubstruct()
186 molMap[smarts] = boost::any(RDKit::ROMOL_SPTR(patt)); in molHasSubstruct()
210 std::string smarts = stringFromTextArg(argv[1]); in molSubstructCount() local
216 if (molMap.find(smarts) != molMap.end()) { in molSubstructCount()
217 patt = boost::any_cast<RDKit::ROMOL_SPTR>(molMap[smarts]).get(); in molSubstructCount()
219 patt = static_cast<RDKit::ROMol *>(RDKit::SmartsToMol(smarts)); in molSubstructCount()
220 molMap[smarts] = boost::any(RDKit::ROMOL_SPTR(patt)); in molSubstructCount()
/dports/science/rdkit/rdkit-Release_2021_03_5/Code/GraphMol/FilterCatalog/
H A DFilterMatchers.cpp58 SmartsMatcher::SmartsMatcher(const std::string &name, const std::string &smarts, in SmartsMatcher() argument
61 d_pattern(SmartsToMol(smarts, debugParse, mergeHs)), in SmartsMatcher()
72 void SmartsMatcher::setPattern(const std::string &smarts) { in setPattern() argument
73 d_pattern.reset(SmartsToMol(smarts, debugParse, mergeHs)); in setPattern()
/dports/science/rdkit/rdkit-Release_2021_03_5/Code/GraphMol/MolEnumerator/
H A Denumerator_catch.cpp629 auto smarts = MolToSmarts(*molp); variable
630 CHECK(std::find(tsmas.begin(), tsmas.end(), smarts) != tsmas.end());
667 auto smarts = MolToSmarts(*molp); variable
668 CHECK(std::find(tsmas.begin(), tsmas.end(), smarts) != tsmas.end());
705 auto smarts = MolToSmarts(*molp); variable
706 CHECK(std::find(tsmas.begin(), tsmas.end(), smarts) != tsmas.end());
746 auto smarts = MolToSmarts(*molp); variable
747 CHECK(std::find(tsmas.begin(), tsmas.end(), smarts) != tsmas.end());
/dports/science/cdk/.m2/repository/org/openscience/cdk/cdk-smarts/2.3/
H A D_remote.repositories3 cdk-smarts-2.3.pom>=
4 cdk-smarts-2.3.jar>=
/dports/science/cdk/cdk-cdk-2.3/descriptor/qsarmolecular/src/main/java/org/openscience/cdk/qsar/descriptors/molecular/
H A DBasicGroupCountDescriptor.java35 import org.openscience.cdk.smarts.SmartsPattern;
63 for (String smarts : SMARTS_STRINGS) { in initialise()
64 tools.add(SmartsPattern.create(smarts)); in initialise()

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