/dports/science/rdkit/rdkit-Release_2021_03_5/Code/GraphMol/ |
H A D | QueryAtom.h | 27 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;
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H A D | QueryAtom.cpp | 17 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()
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H A D | AdjustQuery.cpp | 364 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 …]
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H A D | querytest.cpp | 550 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 …]
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H A D | AtomIterators.h | 27 class QueryAtom; variable 103 QueryAtom *_qA; 148 QueryAtomIterator_(Mol_ *mol, QueryAtom const *what); 170 QueryAtom *_qA{nullptr};
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H A D | AtomIterators.cpp | 167 _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 =()
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/dports/science/rdkit/rdkit-Release_2021_03_5/Code/GraphMol/Wrap/ |
H A D | Queries.cpp | 32 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 …]
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H A D | Atom.cpp | 30 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()
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/dports/science/rdkit/rdkit-Release_2021_03_5/Code/GraphMol/SmilesParse/ |
H A D | smarts.yy | 336 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 …]
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H A D | smarts.ll | 219 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 …]
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H A D | SmartsWrite.h | 18 class QueryAtom; variable 22 RDKIT_SMILESPARSE_EXPORT std::string GetAtomSmarts(const QueryAtom *qatom);
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H A D | smatest.cpp | 1845 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 …]
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H A D | SmartsWrite.cpp | 35 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()
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H A D | smarts.tab.cpp.cmake | 2238 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 …]
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/dports/science/rdkit/rdkit-Release_2021_03_5/Code/GraphMol/SLNParse/ |
H A D | SLNAttribs.cpp | 77 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 …]
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H A D | sln.yy | 182 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 …]
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/dports/science/rdkit/rdkit-Release_2021_03_5/Code/JavaWrappers/ |
H A D | QueryAtom_doc.i | 34 %typemap(javaimports) RDKit::QueryAtom " 40 %javamethodmodifiers RDKit::QueryAtom::expandQuery ( QUERYATOM_QUERY * what, Queries::Composi… 56 %javamethodmodifiers RDKit::QueryAtom::Match ( Atom const * what ) const "
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/dports/science/cdk/cdk-cdk-2.3/base/isomorphism/src/main/java/org/openscience/cdk/isomorphism/matchers/ |
H A D | QueryAtom.java | 41 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
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H A D | QueryAtomContainerCreator.java | 217 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()
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/dports/science/rdkit/rdkit-Release_2021_03_5/External/FreeSASA/ |
H A D | RDFreeSASA.h | 111 const RDKit::QueryAtom *query = NULL, 121 RDKIT_FREESASALIB_EXPORT const RDKit::QueryAtom *makeFreeSasaAPolarAtomQuery(); 128 RDKIT_FREESASALIB_EXPORT const RDKit::QueryAtom *makeFreeSasaPolarAtomQuery();
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H A D | RDFreeSASA.cpp | 182 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()
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/dports/science/rdkit/rdkit-Release_2021_03_5/Code/GraphMol/Substruct/ |
H A D | test1.cpp | 48 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 …]
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/dports/science/cdk/cdk-cdk-2.3/legacy/src/main/java/org/openscience/cdk/isomorphism/matchers/smarts/ |
H A D | SMARTSAtom.java | 24 import org.openscience.cdk.isomorphism.matchers.QueryAtom; 34 public abstract class SMARTSAtom extends QueryAtom implements IQueryAtom {
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/dports/science/cdk/cdk-cdk-2.3/base/isomorphism/src/main/java/org/openscience/cdk/isomorphism/ |
H A D | QueryStereoFilter.java | 38 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()
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/dports/science/cdk/cdk-cdk-2.3/legacy/src/main/java/org/openscience/cdk/isomorphism/ |
H A D | SmartsStereoMatch.java | 36 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()
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