test_class.file: base/isomorphism/src/test/java/org/openscience/cdk/isomorphism/matchers/QueryAtomContainerCreatorTest.java
test_class.identifier: QueryAtomContainerCreatorTest
test_class.superclass: extends CDKTestCase
test_case.body: @Test
      public void test12DimethylBenzene() throws Exception {
          IChemObjectBuilder builder = SilentChemObjectBuilder.getInstance();
          IAtomContainer molecule = builder.newInstance(IAtomContainer.class);
          molecule.addAtom(builder.newInstance(IAtom.class, "C"));
          molecule.addAtom(builder.newInstance(IAtom.class, "C"));
          molecule.addAtom(builder.newInstance(IAtom.class, "C"));
          molecule.addAtom(builder.newInstance(IAtom.class, "C"));
          molecule.addAtom(builder.newInstance(IAtom.class, "C"));
          molecule.addAtom(builder.newInstance(IAtom.class, "C"));
          molecule.addAtom(builder.newInstance(IAtom.class, "C"));
          molecule.addAtom(builder.newInstance(IAtom.class, "C"));
          molecule.addBond(0, 1, IBond.Order.SINGLE);
          molecule.addBond(1, 2, IBond.Order.DOUBLE);
          molecule.addBond(2, 3, IBond.Order.SINGLE);
          molecule.addBond(3, 4, IBond.Order.DOUBLE);
          molecule.addBond(4, 5, IBond.Order.SINGLE);
          molecule.addBond(5, 0, IBond.Order.DOUBLE);
          molecule.addBond(0, 6, IBond.Order.SINGLE);
          molecule.addBond(1, 7, IBond.Order.SINGLE);
  
          // 2,3-dimethyl-1,3-butadiene matches
          IAtomContainer query1 = builder.newInstance(IAtomContainer.class);
          query1.addAtom(builder.newInstance(IAtom.class, "C"));
          query1.addAtom(builder.newInstance(IAtom.class, "C"));
          query1.addAtom(builder.newInstance(IAtom.class, "C"));
          query1.addAtom(builder.newInstance(IAtom.class, "C"));
          query1.addAtom(builder.newInstance(IAtom.class, "C"));
          query1.addAtom(builder.newInstance(IAtom.class, "C"));
          query1.addBond(0, 1, IBond.Order.SINGLE);
          query1.addBond(1, 2, IBond.Order.DOUBLE);
          query1.addBond(3, 0, IBond.Order.DOUBLE);
          query1.addBond(0, 4, IBond.Order.SINGLE);
          query1.addBond(1, 5, IBond.Order.SINGLE);
          QueryAtomContainer queryContainer1 = QueryAtomContainerCreator.createSymbolAndBondOrderQueryContainer(query1);
          Assert.assertTrue(new UniversalIsomorphismTester().isSubgraph(molecule, queryContainer1));
  
          // 2,3-dimethyl-2-butene does not match
          IAtomContainer query2 = builder.newInstance(IAtomContainer.class);
          query2.addAtom(builder.newInstance(IAtom.class, "C"));
          query2.addAtom(builder.newInstance(IAtom.class, "C"));
          query2.addAtom(builder.newInstance(IAtom.class, "C"));
          query2.addAtom(builder.newInstance(IAtom.class, "C"));
          query2.addAtom(builder.newInstance(IAtom.class, "C"));
          query2.addAtom(builder.newInstance(IAtom.class, "C"));
          query2.addBond(0, 1, IBond.Order.DOUBLE);
          query2.addBond(1, 2, IBond.Order.SINGLE);
          query2.addBond(3, 0, IBond.Order.SINGLE);
          query2.addBond(0, 4, IBond.Order.SINGLE);
          query2.addBond(1, 5, IBond.Order.SINGLE);
          QueryAtomContainer queryContainer2 = QueryAtomContainerCreator.createSymbolAndBondOrderQueryContainer(query2);
          Assert.assertFalse(new UniversalIsomorphismTester().isSubgraph(molecule, queryContainer2));
      }
test_case.class_method_signature: QueryAtomContainerCreatorTest.test12DimethylBenzene()
test_case.full_signature: @Test public void test12DimethylBenzene()
test_case.identifier: test12DimethylBenzene
test_case.invocations: getInstance newInstance addAtom newInstance addAtom newInstance addAtom newInstance addAtom newInstance addAtom newInstance addAtom newInstance addAtom newInstance addAtom newInstance addBond addBond addBond addBond addBond addBond addBond addBond newInstance addAtom newInstance addAtom newInstance addAtom newInstance addAtom newInstance addAtom newInstance addAtom newInstance addBond addBond addBond addBond addBond createSymbolAndBondOrderQueryContainer assertTrue isSubgraph newInstance addAtom newInstance addAtom newInstance addAtom newInstance addAtom newInstance addAtom newInstance addAtom newInstance addBond addBond addBond addBond addBond createSymbolAndBondOrderQueryContainer assertFalse isSubgraph
test_case.modifiers: @Test public
test_case.parameters: ()
test_case.return: void
test_case.signature: void test12DimethylBenzene()
focal_class.file: base/isomorphism/src/main/java/org/openscience/cdk/isomorphism/matchers/QueryAtomContainerCreator.java
focal_class.identifier: QueryAtomContainerCreator
focal_class.class_method_signature: QueryAtomContainerCreator.createBasicQueryContainer(IAtomContainer container)
focal_class.full_signature: public static QueryAtomContainer createBasicQueryContainer(IAtomContainer container)
focal_class.identifier: createBasicQueryContainer
focal_class.modifiers: public static
focal_class.parameters: (IAtomContainer container)
focal_class.return: QueryAtomContainer
focal_class.signature: QueryAtomContainer createBasicQueryContainer(IAtomContainer container)
focal_class.class_method_signature: QueryAtomContainerCreator.createSymbolAndBondOrderQueryContainer(IAtomContainer container)
focal_class.full_signature: public static QueryAtomContainer createSymbolAndBondOrderQueryContainer(IAtomContainer container)
focal_class.identifier: createSymbolAndBondOrderQueryContainer
focal_class.modifiers: public static
focal_class.parameters: (IAtomContainer container)
focal_class.return: QueryAtomContainer
focal_class.signature: QueryAtomContainer createSymbolAndBondOrderQueryContainer(IAtomContainer container)
focal_class.class_method_signature: QueryAtomContainerCreator.createSymbolAndChargeQueryContainer(IAtomContainer container)
focal_class.full_signature: public static QueryAtomContainer createSymbolAndChargeQueryContainer(IAtomContainer container)
focal_class.identifier: createSymbolAndChargeQueryContainer
focal_class.modifiers: public static
focal_class.parameters: (IAtomContainer container)
focal_class.return: QueryAtomContainer
focal_class.signature: QueryAtomContainer createSymbolAndChargeQueryContainer(IAtomContainer container)
focal_class.class_method_signature: QueryAtomContainerCreator.createSymbolChargeIDQueryContainer(IAtomContainer container)
focal_class.full_signature: public static QueryAtomContainer createSymbolChargeIDQueryContainer(IAtomContainer container)
focal_class.identifier: createSymbolChargeIDQueryContainer
focal_class.modifiers: public static
focal_class.parameters: (IAtomContainer container)
focal_class.return: QueryAtomContainer
focal_class.signature: QueryAtomContainer createSymbolChargeIDQueryContainer(IAtomContainer container)
focal_class.class_method_signature: QueryAtomContainerCreator.createAnyAtomContainer(IAtomContainer container, boolean aromaticity)
focal_class.full_signature: public static QueryAtomContainer createAnyAtomContainer(IAtomContainer container, boolean aromaticity)
focal_class.identifier: createAnyAtomContainer
focal_class.modifiers: public static
focal_class.parameters: (IAtomContainer container, boolean aromaticity)
focal_class.return: QueryAtomContainer
focal_class.signature: QueryAtomContainer createAnyAtomContainer(IAtomContainer container, boolean aromaticity)
focal_class.class_method_signature: QueryAtomContainerCreator.createAnyAtomAnyBondContainer(IAtomContainer container, boolean aromaticity)
focal_class.full_signature: public static QueryAtomContainer createAnyAtomAnyBondContainer(IAtomContainer container, boolean aromaticity)
focal_class.identifier: createAnyAtomAnyBondContainer
focal_class.modifiers: public static
focal_class.parameters: (IAtomContainer container, boolean aromaticity)
focal_class.return: QueryAtomContainer
focal_class.signature: QueryAtomContainer createAnyAtomAnyBondContainer(IAtomContainer container, boolean aromaticity)
focal_class.class_method_signature: QueryAtomContainerCreator.createAnyAtomForPseudoAtomQueryContainer(IAtomContainer container)
focal_class.full_signature: public static QueryAtomContainer createAnyAtomForPseudoAtomQueryContainer(IAtomContainer container)
focal_class.identifier: createAnyAtomForPseudoAtomQueryContainer
focal_class.modifiers: public static
focal_class.parameters: (IAtomContainer container)
focal_class.return: QueryAtomContainer
focal_class.signature: QueryAtomContainer createAnyAtomForPseudoAtomQueryContainer(IAtomContainer container)
focal_class.class_method_signature: QueryAtomContainerCreator.isSimpleHydrogen(Expr expr)
focal_class.full_signature: static boolean isSimpleHydrogen(Expr expr)
focal_class.identifier: isSimpleHydrogen
focal_class.modifiers: static
focal_class.parameters: (Expr expr)
focal_class.return: boolean
focal_class.signature: boolean isSimpleHydrogen(Expr expr)
focal_class.class_method_signature: QueryAtomContainerCreator.suppressQueryHydrogens(IAtomContainer mol)
focal_class.full_signature: public static IAtomContainer suppressQueryHydrogens(IAtomContainer mol)
focal_class.identifier: suppressQueryHydrogens
focal_class.modifiers: public static
focal_class.parameters: (IAtomContainer mol)
focal_class.return: IAtomContainer
focal_class.signature: IAtomContainer suppressQueryHydrogens(IAtomContainer mol)
focal_method.body: public static QueryAtomContainer createSymbolAndBondOrderQueryContainer(IAtomContainer container) {
          return QueryAtomContainer.create(container,
                                           Expr.Type.ELEMENT,
                                           Expr.Type.ORDER);
      }
focal_method.class_method_signature: QueryAtomContainerCreator.createSymbolAndBondOrderQueryContainer(IAtomContainer container)
focal_method.full_signature: public static QueryAtomContainer createSymbolAndBondOrderQueryContainer(IAtomContainer container)
focal_method.identifier: createSymbolAndBondOrderQueryContainer
focal_method.invocations: create
focal_method.modifiers: public static
focal_method.parameters: (IAtomContainer container)
focal_method.return: QueryAtomContainer
focal_method.signature: QueryAtomContainer createSymbolAndBondOrderQueryContainer(IAtomContainer container)