Home
last modified time | relevance | path

Searched refs:QueryAtom (Results 1 – 25 of 82) sorted by relevance

1234

/dports/science/rdkit/rdkit-Release_2021_03_5/Code/GraphMol/
H A DQueryAtom.h27 class RDKIT_GRAPHMOL_EXPORT QueryAtom : public Atom {
31 QueryAtom() : Atom(){}; in QueryAtom() function
32 explicit QueryAtom(int num) : Atom(num), dp_query(makeAtomNumQuery(num)){}; in QueryAtom() function
33 explicit QueryAtom(const Atom &other) in QueryAtom() function
49 QueryAtom(const QueryAtom &other) : Atom(other) { in QueryAtom() function
52 QueryAtom &operator=(const QueryAtom &other) {
59 ~QueryAtom();
100 bool QueryMatch(QueryAtom const *what) const;
H A DQueryAtom.cpp17 QueryAtom::~QueryAtom() { in ~QueryAtom()
22 Atom *QueryAtom::copy() const { in copy()
23 auto *res = new QueryAtom(*this); in copy()
27 void QueryAtom::expandQuery(QUERYATOM_QUERY *what, in expandQuery()
75 bool queriesMatch(QueryAtom::QUERYATOM_QUERY const *q1, in queriesMatch()
76 QueryAtom::QUERYATOM_QUERY const *q2) { in queriesMatch()
180 bool QueryAtom::Match(Atom const *what) const { in Match()
185 bool QueryAtom::QueryMatch(QueryAtom const *what) const { in QueryMatch()
H A DAdjustQuery.cpp364 auto *qa = new QueryAtom(); in adjustQueryProperties()
395 auto *qa = new QueryAtom(); in adjustQueryProperties()
409 QueryAtom *qa; in adjustQueryProperties()
411 qa = new QueryAtom(*at); in adjustQueryProperties()
419 qa = static_cast<QueryAtom *>(at); in adjustQueryProperties()
432 QueryAtom *qa; in adjustQueryProperties()
434 qa = new QueryAtom(*at); in adjustQueryProperties()
455 QueryAtom *qa; in adjustQueryProperties()
457 qa = new QueryAtom(*at); in adjustQueryProperties()
477 QueryAtom *qa; in adjustQueryProperties()
[all …]
H A Dquerytest.cpp550 QueryAtom qA; in testQualifiedQueries()
557 QueryAtom qA; in testQualifiedQueries()
564 QueryAtom qA; in testQualifiedQueries()
571 QueryAtom qA; in testQualifiedQueries()
606 QueryAtom qA; in testHasPropMatch()
616 QueryAtom qA; in testHasPropWithValueMatch()
631 QueryAtom qA; in testHasPropWithValueMatch()
666 QueryAtom qA; in testHasPropWithDoubleValueMatch()
692 QueryAtom qA; in testExtraAtomQueries()
708 QueryAtom qA; in testExtraAtomQueries()
[all …]
H A DAtomIterators.h27 class QueryAtom; variable
103 QueryAtom *_qA;
148 QueryAtomIterator_(Mol_ *mol, QueryAtom const *what);
170 QueryAtom *_qA{nullptr};
H A DAtomIterators.cpp167 _qA = new QueryAtom(6); in HeteroatomIterator_()
175 _qA = new QueryAtom(6); in HeteroatomIterator_()
191 _qA = static_cast<QueryAtom *>(other._qA->copy()); in HeteroatomIterator_()
200 _qA = static_cast<QueryAtom *>(other._qA->copy()); in operator =()
389 QueryAtom const *what) { in QueryAtomIterator_()
392 _qA = static_cast<QueryAtom *>(what->copy()); in QueryAtomIterator_()
415 _qA = static_cast<QueryAtom *>(other._qA->copy()); in QueryAtomIterator_()
430 _qA = static_cast<QueryAtom *>(other._qA->copy()); in operator =()
/dports/science/rdkit/rdkit-Release_2021_03_5/Code/GraphMol/Wrap/
H A DQueries.cpp32 QueryAtom *res = new QueryAtom(); \
38 QueryAtom *res = new QueryAtom(); \
45 QueryAtom *res = new QueryAtom(); \
53 QueryAtom *_funcname_(bool negate) { \
54 QueryAtom *res = new QueryAtom(); \
96 auto *res = new QueryAtom(); in HasPropQueryAtom()
220 PropQueryWithTol<Atom, QueryAtom, int>, in wrap()
228 PropQuery<Atom, QueryAtom, bool>, in wrap()
237 PropQuery<Atom, QueryAtom, std::string>, in wrap()
246 PropQueryWithTol<Atom, QueryAtom, double>, in wrap()
[all …]
H A DAtom.cpp30 void expandQuery(QueryAtom *self, const QueryAtom *other, in expandQuery()
33 const QueryAtom::QUERYATOM_QUERY *qry = other->getQuery(); in expandQuery()
38 void setQuery(QueryAtom *self, const QueryAtom *other) { in setQuery()
106 res = SmartsWrite::GetAtomSmarts(static_cast<const QueryAtom *>(atom)); in AtomGetSmarts()
459 python::class_<QueryAtom, python::bases<Atom>>( in wrap()
/dports/science/rdkit/rdkit-Release_2021_03_5/Code/GraphMol/SmilesParse/
H A Dsmarts.yy336 QueryAtom *newQ = new QueryAtom(1);
342 QueryAtom *newQ = new QueryAtom(1);
351 QueryAtom *newQ = new QueryAtom(1);
357 QueryAtom *newQ = new QueryAtom(1);
365 QueryAtom *newQ = new QueryAtom(1);
373 QueryAtom *newQ = new QueryAtom(1);
443 QueryAtom *qA = new QueryAtom();
464 QueryAtom *qA = new QueryAtom();
544 QueryAtom *newQ = new QueryAtom();
552 QueryAtom *newQ = new QueryAtom();
[all …]
H A Dsmarts.ll219 yylval->atom = new QueryAtom();
224 yylval->atom = new QueryAtom();
230 yylval->atom = new QueryAtom();
236 yylval->atom = new QueryAtom();
242 yylval->atom = new QueryAtom();
248 yylval->atom = new QueryAtom();
254 yylval->atom = new QueryAtom();
260 yylval->atom = new QueryAtom();
266 yylval->atom = new QueryAtom();
272 yylval->atom = new QueryAtom();
[all …]
H A DSmartsWrite.h18 class QueryAtom; variable
22 RDKIT_SMILESPARSE_EXPORT std::string GetAtomSmarts(const QueryAtom *qatom);
H A Dsmatest.cpp1845 static_cast<QueryAtom *>(p->getAtomWithIdx(0))); in testGithub544()
1853 static_cast<QueryAtom *>(p->getAtomWithIdx(0))); in testGithub544()
1869 static_cast<QueryAtom *>(p->getAtomWithIdx(0))); in testGithub544()
1878 static_cast<QueryAtom *>(p->getAtomWithIdx(0))); in testGithub544()
2068 static_cast<QueryAtom *>(p->getAtomWithIdx(0))); in testGithub1338()
2079 static_cast<QueryAtom *>(p->getAtomWithIdx(0))); in testGithub1338()
2090 static_cast<QueryAtom *>(p->getAtomWithIdx(0))); in testGithub1338()
2101 static_cast<QueryAtom *>(p->getAtomWithIdx(0))); in testGithub1338()
2112 static_cast<QueryAtom *>(p->getAtomWithIdx(0))); in testGithub1338()
2123 static_cast<QueryAtom *>(p->getAtomWithIdx(0))); in testGithub1338()
[all …]
H A DSmartsWrite.cpp35 std::string _recurseGetSmarts(const QueryAtom *qatom,
36 const QueryAtom::QUERYATOM_QUERY *node,
101 std::string getAtomSmartsSimple(const QueryAtom *qatom, in getAtomSmartsSimple()
315 const QueryAtom::QUERYATOM_QUERY *query) { in getRecursiveStructureQuerySmarts()
410 std::string _recurseGetSmarts(const QueryAtom *qatom, in _recurseGetSmarts()
411 const QueryAtom::QUERYATOM_QUERY *node, in _recurseGetSmarts()
646 auto *qatm = static_cast<QueryAtom *>(msCI.obj.atom); in FragmentSmartsConstruct()
680 std::string getNonQueryAtomSmarts(const QueryAtom *qatom) { in getNonQueryAtomSmarts()
815 std::string GetAtomSmarts(const QueryAtom *qatom) { in GetAtomSmarts()
H A Dsmarts.tab.cpp.cmake2238 QueryAtom *qA = new QueryAtom();
2264 QueryAtom *qA = new QueryAtom();
2403 QueryAtom *newQ = new QueryAtom();
2416 QueryAtom *newQ = new QueryAtom();
2429 QueryAtom *newQ = new QueryAtom();
2440 QueryAtom *newQ = new QueryAtom();
2451 QueryAtom *newQ = new QueryAtom();
2462 QueryAtom *newQ = new QueryAtom();
2473 QueryAtom *newQ = new QueryAtom();
2484 QueryAtom *newQ = new QueryAtom();
[all …]
/dports/science/rdkit/rdkit-Release_2021_03_5/Code/GraphMol/SLNParse/
H A DSLNAttribs.cpp77 QueryAtom::QUERYATOM_QUERY *res = nullptr; in makeQueryFromOp()
135 QueryAtom::QUERYATOM_QUERY *atomQuery = nullptr; in parseAtomAttribs()
139 QueryAtom::QUERYATOM_QUERY *query = nullptr; in parseAtomAttribs()
284 QueryAtom::QUERYATOM_QUERY *tQuery; in parseAtomAttribs()
291 QueryAtom::QUERYATOM_QUERY::CHILD_TYPE(atomQuery)); in parseAtomAttribs()
300 QueryAtom::QUERYATOM_QUERY::CHILD_TYPE(atomQuery)); in parseAtomAttribs()
310 QueryAtom::QUERYATOM_QUERY *newAndQuery; in parseAtomAttribs()
322 QueryAtom::QUERYATOM_QUERY::CHILD_TYPE(tQuery)); in parseAtomAttribs()
330 QueryAtom::QUERYATOM_QUERY::CHILD_TYPE(atomQuery)); in parseAtomAttribs()
359 std::list<QueryAtom::QUERYATOM_QUERY *> q; in parseFinalAtomAttribs()
[all …]
H A Dsln.yy182 newAtom = new RDKit::QueryAtom(1);
230 newAtom = new RDKit::QueryAtom(1);
242 newAtom = new RDKit::QueryAtom(1);
255 newAtom = new RDKit::QueryAtom(1);
267 newAtom = new RDKit::QueryAtom(1);
281 newAtom = new RDKit::QueryAtom(1);
293 newAtom = new RDKit::QueryAtom(1);
329 $$ = new RDKit::QueryAtom(1);
337 $$ = new RDKit::QueryAtom(1);
345 $$ = new RDKit::QueryAtom(1);
[all …]
/dports/science/rdkit/rdkit-Release_2021_03_5/Code/JavaWrappers/
H A DQueryAtom_doc.i34 %typemap(javaimports) RDKit::QueryAtom "
40 %javamethodmodifiers RDKit::QueryAtom::expandQuery ( QUERYATOM_QUERY * what, Queries::Composi…
56 %javamethodmodifiers RDKit::QueryAtom::Match ( Atom const * what ) const "
/dports/science/cdk/cdk-cdk-2.3/base/isomorphism/src/main/java/org/openscience/cdk/isomorphism/matchers/
H A DQueryAtom.java41 public class QueryAtom extends QueryChemObject implements IQueryAtom { class
43 private static ILoggingTool logger = LoggingToolFactory.createLoggingTool(QueryAtom.class);
143 public QueryAtom(String symbol, IChemObjectBuilder builder) { in QueryAtom() method in QueryAtom
149 public QueryAtom(IChemObjectBuilder builder) { in QueryAtom() method in QueryAtom
802 public QueryAtom(Expr expr) { in QueryAtom() method in QueryAtom
816 public QueryAtom (Expr.Type type) { in QueryAtom() method in QueryAtom
831 public QueryAtom(Expr.Type type, int val) { in QueryAtom() method in QueryAtom
H A DQueryAtomContainerCreator.java217 if (!(AtomRef.deref(atom) instanceof QueryAtom)) in suppressQueryHydrogens()
229 QueryAtom qnbor = (QueryAtom) AtomRef.deref(nbor); in suppressQueryHydrogens()
237 QueryAtom qatom = (QueryAtom) AtomRef.deref(atom); in suppressQueryHydrogens()
/dports/science/rdkit/rdkit-Release_2021_03_5/External/FreeSASA/
H A DRDFreeSASA.h111 const RDKit::QueryAtom *query = NULL,
121 RDKIT_FREESASALIB_EXPORT const RDKit::QueryAtom *makeFreeSasaAPolarAtomQuery();
128 RDKIT_FREESASALIB_EXPORT const RDKit::QueryAtom *makeFreeSasaPolarAtomQuery();
H A DRDFreeSASA.cpp182 int confIdx, const RDKit::QueryAtom *query, in calcSASA()
196 const RDKit::QueryAtom *makeFreeSasaAPolarAtomQuery() { in makeFreeSasaAPolarAtomQuery()
197 auto *qa = new QueryAtom; in makeFreeSasaAPolarAtomQuery()
202 const RDKit::QueryAtom *makeFreeSasaPolarAtomQuery() { in makeFreeSasaPolarAtomQuery()
203 auto *qa = new QueryAtom; in makeFreeSasaPolarAtomQuery()
/dports/science/rdkit/rdkit-Release_2021_03_5/Code/GraphMol/Substruct/
H A Dtest1.cpp48 q1->addAtom(new QueryAtom(6), updateLabel, takeOwnership); in test1()
49 q1->addAtom(new QueryAtom(6), updateLabel, takeOwnership); in test1()
268 auto *qA = new QueryAtom(6); in test4()
274 q2->addAtom(new QueryAtom(6), true, true); in test4()
330 auto *qA = new QueryAtom(); in test5()
334 q2->addAtom(new QueryAtom(6), true, true); in test5()
382 auto *qA = new QueryAtom(); in test5QueryRoot()
386 q2->addAtom(new QueryAtom(6), true, true); in test5QueryRoot()
638 auto *qA = new QueryAtom(6); in testRecursiveSerialNumbers()
644 q2->addAtom(new QueryAtom(8), true, true); in testRecursiveSerialNumbers()
[all …]
/dports/science/cdk/cdk-cdk-2.3/legacy/src/main/java/org/openscience/cdk/isomorphism/matchers/smarts/
H A DSMARTSAtom.java24 import org.openscience.cdk.isomorphism.matchers.QueryAtom;
34 public abstract class SMARTSAtom extends QueryAtom implements IQueryAtom {
/dports/science/cdk/cdk-cdk-2.3/base/isomorphism/src/main/java/org/openscience/cdk/isomorphism/
H A DQueryStereoFilter.java38 import org.openscience.cdk.isomorphism.matchers.QueryAtom;
154 return ((QueryAtom)queryAtom).getExpression().matches(targetAtom, 0); in checkTetrahedral()
180 return ((QueryAtom) queryAtom).getExpression() in checkTetrahedral()
183 return ((QueryAtom) queryAtom).getExpression() in checkTetrahedral()
186 return ((QueryAtom) queryAtom).getExpression() in checkTetrahedral()
/dports/science/cdk/cdk-cdk-2.3/legacy/src/main/java/org/openscience/cdk/isomorphism/
H A DSmartsStereoMatch.java36 import org.openscience.cdk.isomorphism.matchers.QueryAtom;
154 return ((QueryAtom)queryAtom).getExpression().matches(targetAtom, 0); in checkTetrahedral()
168 … return ((QueryAtom) queryAtom).getExpression().matches(targetAtom, IStereoElement.LEFT); in checkTetrahedral()
170 … return ((QueryAtom) queryAtom).getExpression().matches(targetAtom, IStereoElement.RIGHT); in checkTetrahedral()
172 return ((QueryAtom) queryAtom).getExpression().matches(targetAtom, 0); in checkTetrahedral()

1234