/dports/science/openbabel/openbabel-3.1.1/test/ |
H A D | invalidsmarts.cpp | 68 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()
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H A D | smilesmatch.cpp | 82 OBSmartsPattern smarts; in smilesmatch() local 103 smarts.Init(buffer); in smilesmatch() 104 if (smarts.Match(mol)) in smilesmatch()
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/dports/science/rdkit/rdkit-Release_2021_03_5/Code/GraphMol/MolStandardize/FragmentCatalog/ |
H A D | FragmentCatalogUtils.cpp | 49 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()
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/dports/science/rdkit/rdkit-Release_2021_03_5/rdkit/Chem/MolStandardize/ |
H A D | validations.py | 60 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))
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H A D | fragment.py | 29 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)
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H A D | tautomer.py | 36 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):
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/dports/science/rdkit/rdkit-Release_2021_03_5/rdkit/Chem/fmcs/ |
H A D | fmcs.py | 1313 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 …]
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/dports/science/jmol/jmol-14.32.7/src/org/jmol/minimize/forcefield/ |
H A D | ForceFieldUFF.java | 90 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 …]
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/dports/science/openbabel/openbabel-3.1.1/src/ops/ |
H A D | ophighlight.cpp | 78 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()
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/dports/science/cdk/cdk-cdk-2.3/legacy/src/test/java/org/openscience/cdk/smiles/smarts/ |
H A D | SMARTSTest.java | 20 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;
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/dports/science/rdkit/rdkit-Release_2021_03_5/rdkit/Chem/ |
H A D | UnitTestMCS.py | 23 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]',
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H A D | SaltRemover.py | 58 smarts = whitespace.split(line) 59 salt = Chem.MolFromSmarts(smarts[0]) 71 smarts = _smartsFromSmartsLine(line) 72 if smarts: 73 yield smarts
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H A D | EnumerateHeterocycles.py | 65 smarts = row.SMARTS 66 if not smarts: 70 reaction = smarts + '>>' + product
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/dports/science/rdkit/rdkit-Release_2021_03_5/Contrib/mmpa/ |
H A D | mol_transform.py | 52 smarts = Chem.MolToSmiles(mol, isomericSmiles=True) 54 smarts = re.sub(r'\[42', "[", smarts) 57 return smarts
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/dports/science/rdkit/rdkit-Release_2021_03_5/Code/GraphMol/MolChemicalFeatures/ |
H A D | MolChemicalFeatureDef.cpp | 20 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()
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/dports/science/rdkit/rdkit-Release_2021_03_5/Docs/Book/data/ |
H A D | test_multi_colours.py | 39 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')
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/dports/science/rdkit/rdkit-Release_2021_03_5/Code/Demos/RDKit/Basement/xpcom/ |
H A D | IRDKit.h | 41 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)
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/dports/science/rdkit/rdkit-Release_2021_03_5/Code/GraphMol/FragCatalog/ |
H A D | FragCatalogUtils.cpp | 55 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()
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/dports/science/cdk/cdk-cdk-2.3/tool/pcore/src/main/java/org/openscience/cdk/pharmacophore/ |
H A D | PharmacophoreMatcher.java | 47 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()
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/dports/deskutils/calibre/calibre-src-5.34.0/src/calibre/gui2/tweak_book/editor/ |
H A D | text.py | 113 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 …]
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/dports/science/rdkit/rdkit-Release_2021_03_5/Code/Demos/sqlite/ |
H A D | rdk_funcs.cpp | 176 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()
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/dports/science/rdkit/rdkit-Release_2021_03_5/Code/GraphMol/FilterCatalog/ |
H A D | FilterMatchers.cpp | 58 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()
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/dports/science/rdkit/rdkit-Release_2021_03_5/Code/GraphMol/MolEnumerator/ |
H A D | enumerator_catch.cpp | 629 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());
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/dports/science/cdk/.m2/repository/org/openscience/cdk/cdk-smarts/2.3/ |
H A D | _remote.repositories | 3 cdk-smarts-2.3.pom>= 4 cdk-smarts-2.3.jar>=
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/dports/science/cdk/cdk-cdk-2.3/descriptor/qsarmolecular/src/main/java/org/openscience/cdk/qsar/descriptors/molecular/ |
H A D | BasicGroupCountDescriptor.java | 35 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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