test_class.declarator: conformers = null
test_class.modifier: public static
test_class.original_string: public static ConformerContainer conformers = null;
test_class.type: ConformerContainer
test_class.var_name: conformers
test_class.file: tool/pcore/src/test/java/org/openscience/cdk/pharmacophore/PharmacophoreMatcherTest.java
test_class.identifier: PharmacophoreMatcherTest
test_case.body: @Test
      public void testAngleMatch2() throws Exception {
          String filename = "data/mdl/cnssmarts.sdf";
          InputStream ins = PharmacophoreMatcherTest.class.getClassLoader().getResourceAsStream(filename);
          IteratingSDFReader reader = new IteratingSDFReader(ins, SilentChemObjectBuilder.getInstance());
  
          PharmacophoreQuery query = new PharmacophoreQuery();
          PharmacophoreQueryAtom n1 = new PharmacophoreQueryAtom("BasicAmine", "[NX3;h2,h1,H1,H2;!$(NC=O)]");
          PharmacophoreQueryAtom n2 = new PharmacophoreQueryAtom("BasicAmine", "[NX3;h2,h1,H1,H2;!$(NC=O)]");
          PharmacophoreQueryAtom n3 = new PharmacophoreQueryAtom("BasicAmine", "[NX3;h2,h1,H1,H2;!$(NC=O)]");
          PharmacophoreQueryAngleBond b1 = new PharmacophoreQueryAngleBond(n1, n2, n3, 89.14);
          query.addAtom(n1);
          query.addAtom(n2);
          query.addAtom(n3);
          query.addBond(b1);
  
          reader.hasNext();
          IAtomContainer mol = (IAtomContainer) reader.next();
          reader.close();
  
          PharmacophoreMatcher matcher = new PharmacophoreMatcher(query);
          boolean status = matcher.matches(mol);
          Assert.assertTrue(status);
      }
test_case.class_method_signature: PharmacophoreMatcherTest.testAngleMatch2()
test_case.full_signature: @Test public void testAngleMatch2()
test_case.identifier: testAngleMatch2
test_case.invocations: getResourceAsStream getClassLoader getInstance addAtom addAtom addAtom addBond hasNext next close matches assertTrue
test_case.modifiers: @Test public
test_case.parameters: ()
test_case.return: void
test_case.signature: void testAngleMatch2()
focal_class.declarator: logger                = LoggingToolFactory
                                                                          .createLoggingTool(PharmacophoreMatcher.class)
focal_class.modifier: private
focal_class.original_string: private ILoggingTool                  logger                = LoggingToolFactory
                                                                          .createLoggingTool(PharmacophoreMatcher.class);
focal_class.type: ILoggingTool
focal_class.var_name: logger
focal_class.declarator: pharmacophoreQuery    = null
focal_class.modifier: private
focal_class.original_string: private PharmacophoreQuery            pharmacophoreQuery    = null;
focal_class.type: PharmacophoreQuery
focal_class.var_name: pharmacophoreQuery
focal_class.declarator: pharmacophoreMolecule = null
focal_class.modifier: private
focal_class.original_string: private IAtomContainer                pharmacophoreMolecule = null;
focal_class.type: IAtomContainer
focal_class.var_name: pharmacophoreMolecule
focal_class.declarator: mappings = null
focal_class.modifier: private
focal_class.original_string: private Mappings mappings = null;
focal_class.type: Mappings
focal_class.var_name: mappings
focal_class.file: tool/pcore/src/main/java/org/openscience/cdk/pharmacophore/PharmacophoreMatcher.java
focal_class.identifier: PharmacophoreMatcher
focal_class.class_method_signature: PharmacophoreMatcher.PharmacophoreMatcher()
focal_class.full_signature: public  PharmacophoreMatcher()
focal_class.identifier: PharmacophoreMatcher
focal_class.modifiers: public
focal_class.parameters: ()
focal_class.signature:  PharmacophoreMatcher()
focal_class.class_method_signature: PharmacophoreMatcher.PharmacophoreMatcher(PharmacophoreQuery pharmacophoreQuery)
focal_class.full_signature: public  PharmacophoreMatcher(PharmacophoreQuery pharmacophoreQuery)
focal_class.identifier: PharmacophoreMatcher
focal_class.modifiers: public
focal_class.parameters: (PharmacophoreQuery pharmacophoreQuery)
focal_class.signature:  PharmacophoreMatcher(PharmacophoreQuery pharmacophoreQuery)
focal_class.class_method_signature: PharmacophoreMatcher.matches(IAtomContainer atomContainer)
focal_class.full_signature: public boolean matches(IAtomContainer atomContainer)
focal_class.identifier: matches
focal_class.modifiers: public
focal_class.parameters: (IAtomContainer atomContainer)
focal_class.return: boolean
focal_class.signature: boolean matches(IAtomContainer atomContainer)
focal_class.class_method_signature: PharmacophoreMatcher.matches(IAtomContainer atomContainer, boolean initializeTarget)
focal_class.full_signature: public boolean matches(IAtomContainer atomContainer, boolean initializeTarget)
focal_class.identifier: matches
focal_class.modifiers: public
focal_class.parameters: (IAtomContainer atomContainer, boolean initializeTarget)
focal_class.return: boolean
focal_class.signature: boolean matches(IAtomContainer atomContainer, boolean initializeTarget)
focal_class.class_method_signature: PharmacophoreMatcher.getMatchingPharmacophoreBonds()
focal_class.full_signature: public List<List<IBond>> getMatchingPharmacophoreBonds()
focal_class.identifier: getMatchingPharmacophoreBonds
focal_class.modifiers: public
focal_class.parameters: ()
focal_class.return: List<List<IBond>>
focal_class.signature: List<List<IBond>> getMatchingPharmacophoreBonds()
focal_class.class_method_signature: PharmacophoreMatcher.getTargetQueryBondMappings()
focal_class.full_signature: public List<HashMap<IBond, IBond>> getTargetQueryBondMappings()
focal_class.identifier: getTargetQueryBondMappings
focal_class.modifiers: public
focal_class.parameters: ()
focal_class.return: List<HashMap<IBond, IBond>>
focal_class.signature: List<HashMap<IBond, IBond>> getTargetQueryBondMappings()
focal_class.class_method_signature: PharmacophoreMatcher.getMatchingPharmacophoreAtoms()
focal_class.full_signature: public List<List<PharmacophoreAtom>> getMatchingPharmacophoreAtoms()
focal_class.identifier: getMatchingPharmacophoreAtoms
focal_class.modifiers: public
focal_class.parameters: ()
focal_class.return: List<List<PharmacophoreAtom>>
focal_class.signature: List<List<PharmacophoreAtom>> getMatchingPharmacophoreAtoms()
focal_class.class_method_signature: PharmacophoreMatcher.getUniqueMatchingPharmacophoreAtoms()
focal_class.full_signature: public List<List<PharmacophoreAtom>> getUniqueMatchingPharmacophoreAtoms()
focal_class.identifier: getUniqueMatchingPharmacophoreAtoms
focal_class.modifiers: public
focal_class.parameters: ()
focal_class.return: List<List<PharmacophoreAtom>>
focal_class.signature: List<List<PharmacophoreAtom>> getUniqueMatchingPharmacophoreAtoms()
focal_class.class_method_signature: PharmacophoreMatcher.getPCoreAtoms(Mappings mappings)
focal_class.full_signature: private List<List<PharmacophoreAtom>> getPCoreAtoms(Mappings mappings)
focal_class.identifier: getPCoreAtoms
focal_class.modifiers: private
focal_class.parameters: (Mappings mappings)
focal_class.return: List<List<PharmacophoreAtom>>
focal_class.signature: List<List<PharmacophoreAtom>> getPCoreAtoms(Mappings mappings)
focal_class.class_method_signature: PharmacophoreMatcher.getPharmacophoreQuery()
focal_class.full_signature: public PharmacophoreQuery getPharmacophoreQuery()
focal_class.identifier: getPharmacophoreQuery
focal_class.modifiers: public
focal_class.parameters: ()
focal_class.return: PharmacophoreQuery
focal_class.signature: PharmacophoreQuery getPharmacophoreQuery()
focal_class.class_method_signature: PharmacophoreMatcher.setPharmacophoreQuery(PharmacophoreQuery query)
focal_class.full_signature: public void setPharmacophoreQuery(PharmacophoreQuery query)
focal_class.identifier: setPharmacophoreQuery
focal_class.modifiers: public
focal_class.parameters: (PharmacophoreQuery query)
focal_class.return: void
focal_class.signature: void setPharmacophoreQuery(PharmacophoreQuery query)
focal_class.class_method_signature: PharmacophoreMatcher.getPharmacophoreMolecule(IAtomContainer input)
focal_class.full_signature: private IAtomContainer getPharmacophoreMolecule(IAtomContainer input)
focal_class.identifier: getPharmacophoreMolecule
focal_class.modifiers: private
focal_class.parameters: (IAtomContainer input)
focal_class.return: IAtomContainer
focal_class.signature: IAtomContainer getPharmacophoreMolecule(IAtomContainer input)
focal_class.class_method_signature: PharmacophoreMatcher.newPCoreAtom(IAtomContainer input, PharmacophoreQueryAtom qatom, String smarts, int[] mapping)
focal_class.full_signature: private PharmacophoreAtom newPCoreAtom(IAtomContainer input, PharmacophoreQueryAtom qatom, String smarts, int[] mapping)
focal_class.identifier: newPCoreAtom
focal_class.modifiers: private
focal_class.parameters: (IAtomContainer input, PharmacophoreQueryAtom qatom, String smarts, int[] mapping)
focal_class.return: PharmacophoreAtom
focal_class.signature: PharmacophoreAtom newPCoreAtom(IAtomContainer input, PharmacophoreQueryAtom qatom, String smarts, int[] mapping)
focal_class.class_method_signature: PharmacophoreMatcher.prepareInput(IAtomContainer input)
focal_class.full_signature: private void prepareInput(IAtomContainer input)
focal_class.identifier: prepareInput
focal_class.modifiers: private
focal_class.parameters: (IAtomContainer input)
focal_class.return: void
focal_class.signature: void prepareInput(IAtomContainer input)
focal_class.class_method_signature: PharmacophoreMatcher.hasDistanceConstraints(IQueryAtomContainer query)
focal_class.full_signature: private boolean hasDistanceConstraints(IQueryAtomContainer query)
focal_class.identifier: hasDistanceConstraints
focal_class.modifiers: private
focal_class.parameters: (IQueryAtomContainer query)
focal_class.return: boolean
focal_class.signature: boolean hasDistanceConstraints(IQueryAtomContainer query)
focal_class.class_method_signature: PharmacophoreMatcher.hasAngleConstraints(IQueryAtomContainer query)
focal_class.full_signature: private boolean hasAngleConstraints(IQueryAtomContainer query)
focal_class.identifier: hasAngleConstraints
focal_class.modifiers: private
focal_class.parameters: (IQueryAtomContainer query)
focal_class.return: boolean
focal_class.signature: boolean hasAngleConstraints(IQueryAtomContainer query)
focal_class.class_method_signature: PharmacophoreMatcher.intIndices(List<Integer> atomIndices)
focal_class.full_signature: private int[] intIndices(List<Integer> atomIndices)
focal_class.identifier: intIndices
focal_class.modifiers: private
focal_class.parameters: (List<Integer> atomIndices)
focal_class.return: int[]
focal_class.signature: int[] intIndices(List<Integer> atomIndices)
focal_class.class_method_signature: PharmacophoreMatcher.getEffectiveCoordinates(IAtomContainer atomContainer, List<Integer> atomIndices)
focal_class.full_signature: private Point3d getEffectiveCoordinates(IAtomContainer atomContainer, List<Integer> atomIndices)
focal_class.identifier: getEffectiveCoordinates
focal_class.modifiers: private
focal_class.parameters: (IAtomContainer atomContainer, List<Integer> atomIndices)
focal_class.return: Point3d
focal_class.signature: Point3d getEffectiveCoordinates(IAtomContainer atomContainer, List<Integer> atomIndices)
focal_class.class_method_signature: PharmacophoreMatcher.getEffectiveCoordinates(IAtomContainer atomContainer, int[] atomIndices)
focal_class.full_signature: private Point3d getEffectiveCoordinates(IAtomContainer atomContainer, int[] atomIndices)
focal_class.identifier: getEffectiveCoordinates
focal_class.modifiers: private
focal_class.parameters: (IAtomContainer atomContainer, int[] atomIndices)
focal_class.return: Point3d
focal_class.signature: Point3d getEffectiveCoordinates(IAtomContainer atomContainer, int[] atomIndices)
focal_class.class_method_signature: PharmacophoreMatcher.checkQuery(IQueryAtomContainer query)
focal_class.full_signature: private boolean checkQuery(IQueryAtomContainer query)
focal_class.identifier: checkQuery
focal_class.modifiers: private
focal_class.parameters: (IQueryAtomContainer query)
focal_class.return: boolean
focal_class.signature: boolean checkQuery(IQueryAtomContainer query)
focal_method.body: public boolean matches(IAtomContainer atomContainer) throws CDKException {
          return matches(atomContainer, true);
      }
focal_method.class_method_signature: PharmacophoreMatcher.matches(IAtomContainer atomContainer)
focal_method.full_signature: public boolean matches(IAtomContainer atomContainer)
focal_method.identifier: matches
focal_method.invocations: matches
focal_method.modifiers: public
focal_method.parameters: (IAtomContainer atomContainer)
focal_method.return: boolean
focal_method.signature: boolean matches(IAtomContainer atomContainer)