test_class.file: legacy/src/test/java/org/openscience/cdk/smiles/smarts/parser/SmartsQueryVisitorTest.java
test_class.identifier: SmartsQueryVisitorTest
test_class.superclass: extends CDKTestCase
test_case.body: @Test
      public void testPattern182() throws Exception { // Unfused benzene ring
          visit("[cR1]1[cR1][cR1][cR1][cR1][cR1]1");
      }
test_case.class_method_signature: SmartsQueryVisitorTest.testPattern182()
test_case.full_signature: @Test public void testPattern182()
test_case.identifier: testPattern182
test_case.invocations: visit
test_case.modifiers: @Test public
test_case.parameters: ()
test_case.return: void
test_case.signature: void testPattern182()
focal_class.declarator: ringAtoms
focal_class.modifier: private
focal_class.original_string: private RingIdentifierAtom[]                ringAtoms;
focal_class.type: RingIdentifierAtom[]
focal_class.var_name: ringAtoms
focal_class.declarator: query
focal_class.modifier: private
focal_class.original_string: private IQueryAtomContainer                 query;
focal_class.type: IQueryAtomContainer
focal_class.var_name: query
focal_class.declarator: builder
focal_class.modifier: private final
focal_class.original_string: private final IChemObjectBuilder            builder;
focal_class.type: IChemObjectBuilder
focal_class.var_name: builder
focal_class.declarator: neighbors      = new HashMap<IAtom, List<IAtom>>()
focal_class.modifier: private
focal_class.original_string: private Map<IAtom, List<IAtom>>             neighbors      = new HashMap<IAtom, List<IAtom>>();
focal_class.type: Map<IAtom, List<IAtom>>
focal_class.var_name: neighbors
focal_class.declarator: tetrahedral    = new BitSet()
focal_class.modifier: private
focal_class.original_string: private BitSet                              tetrahedral    = new BitSet();
focal_class.type: BitSet
focal_class.var_name: tetrahedral
focal_class.declarator: stereoBonds    = new ArrayList<IBond>()
focal_class.modifier: private
focal_class.original_string: private List<IBond>                         stereoBonds    = new ArrayList<IBond>();
focal_class.type: List<IBond>
focal_class.var_name: stereoBonds
focal_class.declarator: doubleBonds    = new ArrayList<IBond>()
focal_class.modifier: private
focal_class.original_string: private List<IBond>                         doubleBonds    = new ArrayList<IBond>();
focal_class.type: List<IBond>
focal_class.var_name: doubleBonds
focal_class.declarator: logger = LoggingToolFactory.createLoggingTool(SmartsQueryVisitor.class)
focal_class.modifier: private final static
focal_class.original_string: private final static ILoggingTool logger = LoggingToolFactory.createLoggingTool(SmartsQueryVisitor.class);
focal_class.type: ILoggingTool
focal_class.var_name: logger
focal_class.file: legacy/src/main/java/org/openscience/cdk/smiles/smarts/parser/SmartsQueryVisitor.java
focal_class.identifier: SmartsQueryVisitor
focal_class.interfaces: implements SMARTSParserVisitor
focal_class.class_method_signature: SmartsQueryVisitor.SmartsQueryVisitor(IChemObjectBuilder builder)
focal_class.full_signature: public  SmartsQueryVisitor(IChemObjectBuilder builder)
focal_class.identifier: SmartsQueryVisitor
focal_class.modifiers: public
focal_class.parameters: (IChemObjectBuilder builder)
focal_class.signature:  SmartsQueryVisitor(IChemObjectBuilder builder)
focal_class.class_method_signature: SmartsQueryVisitor.visit(ASTRingIdentifier node, Object data)
focal_class.full_signature: public Object visit(ASTRingIdentifier node, Object data)
focal_class.identifier: visit
focal_class.modifiers: public
focal_class.parameters: (ASTRingIdentifier node, Object data)
focal_class.return: Object
focal_class.signature: Object visit(ASTRingIdentifier node, Object data)
focal_class.class_method_signature: SmartsQueryVisitor.visit(ASTAtom node, Object data)
focal_class.full_signature: public Object visit(ASTAtom node, Object data)
focal_class.identifier: visit
focal_class.modifiers: public
focal_class.parameters: (ASTAtom node, Object data)
focal_class.return: Object
focal_class.signature: Object visit(ASTAtom node, Object data)
focal_class.class_method_signature: SmartsQueryVisitor.handleRingClosure(IQueryAtom atom, ASTRingIdentifier ringIdentifier)
focal_class.full_signature: private void handleRingClosure(IQueryAtom atom, ASTRingIdentifier ringIdentifier)
focal_class.identifier: handleRingClosure
focal_class.modifiers: private
focal_class.parameters: (IQueryAtom atom, ASTRingIdentifier ringIdentifier)
focal_class.return: void
focal_class.signature: void handleRingClosure(IQueryAtom atom, ASTRingIdentifier ringIdentifier)
focal_class.class_method_signature: SmartsQueryVisitor.visit(SimpleNode node, Object data)
focal_class.full_signature: public Object visit(SimpleNode node, Object data)
focal_class.identifier: visit
focal_class.modifiers: public
focal_class.parameters: (SimpleNode node, Object data)
focal_class.return: Object
focal_class.signature: Object visit(SimpleNode node, Object data)
focal_class.class_method_signature: SmartsQueryVisitor.visit(ASTStart node, Object data)
focal_class.full_signature: public Object visit(ASTStart node, Object data)
focal_class.identifier: visit
focal_class.modifiers: public
focal_class.parameters: (ASTStart node, Object data)
focal_class.return: Object
focal_class.signature: Object visit(ASTStart node, Object data)
focal_class.class_method_signature: SmartsQueryVisitor.visit(ASTReaction node, Object data)
focal_class.full_signature: public Object visit(ASTReaction node, Object data)
focal_class.identifier: visit
focal_class.modifiers: public
focal_class.parameters: (ASTReaction node, Object data)
focal_class.return: Object
focal_class.signature: Object visit(ASTReaction node, Object data)
focal_class.class_method_signature: SmartsQueryVisitor.visit(ASTGroup node, Object data)
focal_class.full_signature: public Object visit(ASTGroup node, Object data)
focal_class.identifier: visit
focal_class.modifiers: public
focal_class.parameters: (ASTGroup node, Object data)
focal_class.return: Object
focal_class.signature: Object visit(ASTGroup node, Object data)
focal_class.class_method_signature: SmartsQueryVisitor.findStereoBond(IAtom atom)
focal_class.full_signature: private StereoBond findStereoBond(IAtom atom)
focal_class.identifier: findStereoBond
focal_class.modifiers: private
focal_class.parameters: (IAtom atom)
focal_class.return: StereoBond
focal_class.signature: StereoBond findStereoBond(IAtom atom)
focal_class.class_method_signature: SmartsQueryVisitor.visit(ASTSmarts node, Object data)
focal_class.full_signature: public Object visit(ASTSmarts node, Object data)
focal_class.identifier: visit
focal_class.modifiers: public
focal_class.parameters: (ASTSmarts node, Object data)
focal_class.return: Object
focal_class.signature: Object visit(ASTSmarts node, Object data)
focal_class.class_method_signature: SmartsQueryVisitor.visit(ASTNotBond node, Object data)
focal_class.full_signature: public Object visit(ASTNotBond node, Object data)
focal_class.identifier: visit
focal_class.modifiers: public
focal_class.parameters: (ASTNotBond node, Object data)
focal_class.return: Object
focal_class.signature: Object visit(ASTNotBond node, Object data)
focal_class.class_method_signature: SmartsQueryVisitor.visit(ASTImplicitHighAndBond node, Object data)
focal_class.full_signature: public Object visit(ASTImplicitHighAndBond node, Object data)
focal_class.identifier: visit
focal_class.modifiers: public
focal_class.parameters: (ASTImplicitHighAndBond node, Object data)
focal_class.return: Object
focal_class.signature: Object visit(ASTImplicitHighAndBond node, Object data)
focal_class.class_method_signature: SmartsQueryVisitor.visit(ASTLowAndBond node, Object data)
focal_class.full_signature: public Object visit(ASTLowAndBond node, Object data)
focal_class.identifier: visit
focal_class.modifiers: public
focal_class.parameters: (ASTLowAndBond node, Object data)
focal_class.return: Object
focal_class.signature: Object visit(ASTLowAndBond node, Object data)
focal_class.class_method_signature: SmartsQueryVisitor.visit(ASTOrBond node, Object data)
focal_class.full_signature: public Object visit(ASTOrBond node, Object data)
focal_class.identifier: visit
focal_class.modifiers: public
focal_class.parameters: (ASTOrBond node, Object data)
focal_class.return: Object
focal_class.signature: Object visit(ASTOrBond node, Object data)
focal_class.class_method_signature: SmartsQueryVisitor.visit(ASTExplicitHighAndBond node, Object data)
focal_class.full_signature: public Object visit(ASTExplicitHighAndBond node, Object data)
focal_class.identifier: visit
focal_class.modifiers: public
focal_class.parameters: (ASTExplicitHighAndBond node, Object data)
focal_class.return: Object
focal_class.signature: Object visit(ASTExplicitHighAndBond node, Object data)
focal_class.class_method_signature: SmartsQueryVisitor.visit(ASTSimpleBond node, Object data)
focal_class.full_signature: public Object visit(ASTSimpleBond node, Object data)
focal_class.identifier: visit
focal_class.modifiers: public
focal_class.parameters: (ASTSimpleBond node, Object data)
focal_class.return: Object
focal_class.signature: Object visit(ASTSimpleBond node, Object data)
focal_class.class_method_signature: SmartsQueryVisitor.visit(ASTRecursiveSmartsExpression node, Object data)
focal_class.full_signature: public Object visit(ASTRecursiveSmartsExpression node, Object data)
focal_class.identifier: visit
focal_class.modifiers: public
focal_class.parameters: (ASTRecursiveSmartsExpression node, Object data)
focal_class.return: Object
focal_class.signature: Object visit(ASTRecursiveSmartsExpression node, Object data)
focal_class.class_method_signature: SmartsQueryVisitor.getRoot(Node node)
focal_class.full_signature: public ASTStart getRoot(Node node)
focal_class.identifier: getRoot
focal_class.modifiers: public
focal_class.parameters: (Node node)
focal_class.return: ASTStart
focal_class.signature: ASTStart getRoot(Node node)
focal_class.class_method_signature: SmartsQueryVisitor.visit(ASTElement node, Object data)
focal_class.full_signature: public Object visit(ASTElement node, Object data)
focal_class.identifier: visit
focal_class.modifiers: public
focal_class.parameters: (ASTElement node, Object data)
focal_class.return: Object
focal_class.signature: Object visit(ASTElement node, Object data)
focal_class.class_method_signature: SmartsQueryVisitor.visit(ASTTotalHCount node, Object data)
focal_class.full_signature: public Object visit(ASTTotalHCount node, Object data)
focal_class.identifier: visit
focal_class.modifiers: public
focal_class.parameters: (ASTTotalHCount node, Object data)
focal_class.return: Object
focal_class.signature: Object visit(ASTTotalHCount node, Object data)
focal_class.class_method_signature: SmartsQueryVisitor.visit(ASTImplicitHCount node, Object data)
focal_class.full_signature: public Object visit(ASTImplicitHCount node, Object data)
focal_class.identifier: visit
focal_class.modifiers: public
focal_class.parameters: (ASTImplicitHCount node, Object data)
focal_class.return: Object
focal_class.signature: Object visit(ASTImplicitHCount node, Object data)
focal_class.class_method_signature: SmartsQueryVisitor.visit(ASTExplicitConnectivity node, Object data)
focal_class.full_signature: public Object visit(ASTExplicitConnectivity node, Object data)
focal_class.identifier: visit
focal_class.modifiers: public
focal_class.parameters: (ASTExplicitConnectivity node, Object data)
focal_class.return: Object
focal_class.signature: Object visit(ASTExplicitConnectivity node, Object data)
focal_class.class_method_signature: SmartsQueryVisitor.visit(ASTAtomicNumber node, Object data)
focal_class.full_signature: public Object visit(ASTAtomicNumber node, Object data)
focal_class.identifier: visit
focal_class.modifiers: public
focal_class.parameters: (ASTAtomicNumber node, Object data)
focal_class.return: Object
focal_class.signature: Object visit(ASTAtomicNumber node, Object data)
focal_class.class_method_signature: SmartsQueryVisitor.visit(ASTHybrdizationNumber node, Object data)
focal_class.full_signature: public Object visit(ASTHybrdizationNumber node, Object data)
focal_class.identifier: visit
focal_class.modifiers: public
focal_class.parameters: (ASTHybrdizationNumber node, Object data)
focal_class.return: Object
focal_class.signature: Object visit(ASTHybrdizationNumber node, Object data)
focal_class.class_method_signature: SmartsQueryVisitor.visit(ASTCharge node, Object data)
focal_class.full_signature: public Object visit(ASTCharge node, Object data)
focal_class.identifier: visit
focal_class.modifiers: public
focal_class.parameters: (ASTCharge node, Object data)
focal_class.return: Object
focal_class.signature: Object visit(ASTCharge node, Object data)
focal_class.class_method_signature: SmartsQueryVisitor.visit(ASTRingConnectivity node, Object data)
focal_class.full_signature: public Object visit(ASTRingConnectivity node, Object data)
focal_class.identifier: visit
focal_class.modifiers: public
focal_class.parameters: (ASTRingConnectivity node, Object data)
focal_class.return: Object
focal_class.signature: Object visit(ASTRingConnectivity node, Object data)
focal_class.class_method_signature: SmartsQueryVisitor.visit(ASTPeriodicGroupNumber node, Object data)
focal_class.full_signature: public Object visit(ASTPeriodicGroupNumber node, Object data)
focal_class.identifier: visit
focal_class.modifiers: public
focal_class.parameters: (ASTPeriodicGroupNumber node, Object data)
focal_class.return: Object
focal_class.signature: Object visit(ASTPeriodicGroupNumber node, Object data)
focal_class.class_method_signature: SmartsQueryVisitor.visit(ASTTotalConnectivity node, Object data)
focal_class.full_signature: public Object visit(ASTTotalConnectivity node, Object data)
focal_class.identifier: visit
focal_class.modifiers: public
focal_class.parameters: (ASTTotalConnectivity node, Object data)
focal_class.return: Object
focal_class.signature: Object visit(ASTTotalConnectivity node, Object data)
focal_class.class_method_signature: SmartsQueryVisitor.visit(ASTValence node, Object data)
focal_class.full_signature: public Object visit(ASTValence node, Object data)
focal_class.identifier: visit
focal_class.modifiers: public
focal_class.parameters: (ASTValence node, Object data)
focal_class.return: Object
focal_class.signature: Object visit(ASTValence node, Object data)
focal_class.class_method_signature: SmartsQueryVisitor.visit(ASTRingMembership node, Object data)
focal_class.full_signature: public Object visit(ASTRingMembership node, Object data)
focal_class.identifier: visit
focal_class.modifiers: public
focal_class.parameters: (ASTRingMembership node, Object data)
focal_class.return: Object
focal_class.signature: Object visit(ASTRingMembership node, Object data)
focal_class.class_method_signature: SmartsQueryVisitor.visit(ASTSmallestRingSize node, Object data)
focal_class.full_signature: public Object visit(ASTSmallestRingSize node, Object data)
focal_class.identifier: visit
focal_class.modifiers: public
focal_class.parameters: (ASTSmallestRingSize node, Object data)
focal_class.return: Object
focal_class.signature: Object visit(ASTSmallestRingSize node, Object data)
focal_class.class_method_signature: SmartsQueryVisitor.visit(ASTAliphatic node, Object data)
focal_class.full_signature: public Object visit(ASTAliphatic node, Object data)
focal_class.identifier: visit
focal_class.modifiers: public
focal_class.parameters: (ASTAliphatic node, Object data)
focal_class.return: Object
focal_class.signature: Object visit(ASTAliphatic node, Object data)
focal_class.class_method_signature: SmartsQueryVisitor.visit(ASTNonCHHeavyAtom node, Object data)
focal_class.full_signature: public Object visit(ASTNonCHHeavyAtom node, Object data)
focal_class.identifier: visit
focal_class.modifiers: public
focal_class.parameters: (ASTNonCHHeavyAtom node, Object data)
focal_class.return: Object
focal_class.signature: Object visit(ASTNonCHHeavyAtom node, Object data)
focal_class.class_method_signature: SmartsQueryVisitor.visit(ASTAromatic node, Object data)
focal_class.full_signature: public Object visit(ASTAromatic node, Object data)
focal_class.identifier: visit
focal_class.modifiers: public
focal_class.parameters: (ASTAromatic node, Object data)
focal_class.return: Object
focal_class.signature: Object visit(ASTAromatic node, Object data)
focal_class.class_method_signature: SmartsQueryVisitor.visit(ASTAnyAtom node, Object data)
focal_class.full_signature: public Object visit(ASTAnyAtom node, Object data)
focal_class.identifier: visit
focal_class.modifiers: public
focal_class.parameters: (ASTAnyAtom node, Object data)
focal_class.return: Object
focal_class.signature: Object visit(ASTAnyAtom node, Object data)
focal_class.class_method_signature: SmartsQueryVisitor.visit(ASTAtomicMass node, Object data)
focal_class.full_signature: public Object visit(ASTAtomicMass node, Object data)
focal_class.identifier: visit
focal_class.modifiers: public
focal_class.parameters: (ASTAtomicMass node, Object data)
focal_class.return: Object
focal_class.signature: Object visit(ASTAtomicMass node, Object data)
focal_class.class_method_signature: SmartsQueryVisitor.visit(ASTChirality node, Object data)
focal_class.full_signature: public Object visit(ASTChirality node, Object data)
focal_class.identifier: visit
focal_class.modifiers: public
focal_class.parameters: (ASTChirality node, Object data)
focal_class.return: Object
focal_class.signature: Object visit(ASTChirality node, Object data)
focal_class.class_method_signature: SmartsQueryVisitor.visit(ASTLowAndExpression node, Object data)
focal_class.full_signature: public Object visit(ASTLowAndExpression node, Object data)
focal_class.identifier: visit
focal_class.modifiers: public
focal_class.parameters: (ASTLowAndExpression node, Object data)
focal_class.return: Object
focal_class.signature: Object visit(ASTLowAndExpression node, Object data)
focal_class.class_method_signature: SmartsQueryVisitor.visit(ASTOrExpression node, Object data)
focal_class.full_signature: public Object visit(ASTOrExpression node, Object data)
focal_class.identifier: visit
focal_class.modifiers: public
focal_class.parameters: (ASTOrExpression node, Object data)
focal_class.return: Object
focal_class.signature: Object visit(ASTOrExpression node, Object data)
focal_class.class_method_signature: SmartsQueryVisitor.visit(ASTNotExpression node, Object data)
focal_class.full_signature: public Object visit(ASTNotExpression node, Object data)
focal_class.identifier: visit
focal_class.modifiers: public
focal_class.parameters: (ASTNotExpression node, Object data)
focal_class.return: Object
focal_class.signature: Object visit(ASTNotExpression node, Object data)
focal_class.class_method_signature: SmartsQueryVisitor.visit(ASTExplicitHighAndExpression node, Object data)
focal_class.full_signature: public Object visit(ASTExplicitHighAndExpression node, Object data)
focal_class.identifier: visit
focal_class.modifiers: public
focal_class.parameters: (ASTExplicitHighAndExpression node, Object data)
focal_class.return: Object
focal_class.signature: Object visit(ASTExplicitHighAndExpression node, Object data)
focal_class.class_method_signature: SmartsQueryVisitor.visit(ASTImplicitHighAndExpression node, Object data)
focal_class.full_signature: public Object visit(ASTImplicitHighAndExpression node, Object data)
focal_class.identifier: visit
focal_class.modifiers: public
focal_class.parameters: (ASTImplicitHighAndExpression node, Object data)
focal_class.return: Object
focal_class.signature: Object visit(ASTImplicitHighAndExpression node, Object data)
focal_class.class_method_signature: SmartsQueryVisitor.visit(ASTExplicitAtom node, Object data)
focal_class.full_signature: public Object visit(ASTExplicitAtom node, Object data)
focal_class.identifier: visit
focal_class.modifiers: public
focal_class.parameters: (ASTExplicitAtom node, Object data)
focal_class.return: Object
focal_class.signature: Object visit(ASTExplicitAtom node, Object data)
focal_method.body: public Object visit(ASTRingIdentifier node, Object data) {
          IQueryAtom atom = (IQueryAtom) data;
          RingIdentifierAtom ringIdAtom = new RingIdentifierAtom(builder);
          ringIdAtom.setAtom(atom);
          IQueryBond bond;
          if (node.jjtGetNumChildren() == 0) { // implicit bond
              bond = null;
          } else {
              bond = (IQueryBond) node.jjtGetChild(0).jjtAccept(this, data);
          }
          ringIdAtom.setRingBond(bond);
          return ringIdAtom;
      }
focal_method.class_method_signature: SmartsQueryVisitor.visit(ASTRingIdentifier node, Object data)
focal_method.full_signature: public Object visit(ASTRingIdentifier node, Object data)
focal_method.identifier: visit
focal_method.invocations: setAtom jjtGetNumChildren jjtAccept jjtGetChild setRingBond
focal_method.modifiers: public
focal_method.parameters: (ASTRingIdentifier node, Object data)
focal_method.return: Object
focal_method.signature: Object visit(ASTRingIdentifier node, Object data)