test_class.declarator: INSTANCE = new MmffAtomTypeMatcher()
test_class.modifier: static
test_class.original_string: static MmffAtomTypeMatcher INSTANCE = new MmffAtomTypeMatcher();
test_class.type: MmffAtomTypeMatcher
test_class.var_name: INSTANCE
test_class.file: tool/forcefield/src/test/java/org/openscience/cdk/forcefield/mmff/MmffAtomTypeMatcherTest.java
test_class.identifier: MmffAtomTypeMatcherTest
test_case.body: @Test
      public void hydroxyurea() {
          IAtomContainer container = new AtomContainer(9, 8, 0, 0);
          container.addAtom(atom("H", 0));
          container.addAtom(atom("O", 0));
          container.addAtom(atom("N", 0));
          container.addAtom(atom("H", 0));
          container.addAtom(atom("C", 0));
          container.addAtom(atom("O", 0));
          container.addAtom(atom("N", 0));
          container.addAtom(atom("H", 0));
          container.addAtom(atom("H", 0));
          container.addBond(0, 1, IBond.Order.SINGLE);
          container.addBond(1, 2, IBond.Order.SINGLE);
          container.addBond(2, 3, IBond.Order.SINGLE);
          container.addBond(2, 4, IBond.Order.SINGLE);
          container.addBond(4, 5, IBond.Order.DOUBLE);
          container.addBond(4, 6, IBond.Order.SINGLE);
          container.addBond(6, 7, IBond.Order.SINGLE);
          container.addBond(6, 8, IBond.Order.SINGLE);
          String[] expected = {"HO", "-O-", "NC=O", "HNCO", "CONN", "O=CN", "NC=O", "HNCO", "HNCO"};
          String[] actual = INSTANCE.symbolicTypes(container);
          Assert.assertArrayEquals(expected, actual);
      }
test_case.class_method_signature: MmffAtomTypeMatcherTest.hydroxyurea()
test_case.full_signature: @Test public void hydroxyurea()
test_case.identifier: hydroxyurea
test_case.invocations: addAtom atom addAtom atom addAtom atom addAtom atom addAtom atom addAtom atom addAtom atom addAtom atom addAtom atom addBond addBond addBond addBond addBond addBond addBond addBond symbolicTypes assertArrayEquals
test_case.modifiers: @Test public
test_case.parameters: ()
test_case.return: void
test_case.signature: void hydroxyurea()
focal_class.declarator: aromaticTypes = new MmffAromaticTypeMapping()
focal_class.modifier: private final
focal_class.original_string: private final MmffAromaticTypeMapping aromaticTypes = new MmffAromaticTypeMapping();
focal_class.type: MmffAromaticTypeMapping
focal_class.var_name: aromaticTypes
focal_class.declarator: patterns
focal_class.modifier: private final
focal_class.original_string: private final AtomTypePattern[]       patterns;
focal_class.type: AtomTypePattern[]
focal_class.var_name: patterns
focal_class.declarator: hydrogenMap
focal_class.modifier: private final
focal_class.original_string: private final Map<String, String>     hydrogenMap;
focal_class.type: Map<String, String>
focal_class.var_name: hydrogenMap
focal_class.file: tool/forcefield/src/main/java/org/openscience/cdk/forcefield/mmff/MmffAtomTypeMatcher.java
focal_class.identifier: MmffAtomTypeMatcher
focal_class.class_method_signature: MmffAtomTypeMatcher.MmffAtomTypeMatcher()
focal_class.full_signature:   MmffAtomTypeMatcher()
focal_class.identifier: MmffAtomTypeMatcher
focal_class.parameters: ()
focal_class.signature:  MmffAtomTypeMatcher()
focal_class.class_method_signature: MmffAtomTypeMatcher.symbolicTypes(final IAtomContainer container)
focal_class.full_signature:  String[] symbolicTypes(final IAtomContainer container)
focal_class.identifier: symbolicTypes
focal_class.parameters: (final IAtomContainer container)
focal_class.return: String[]
focal_class.signature: String[] symbolicTypes(final IAtomContainer container)
focal_class.class_method_signature: MmffAtomTypeMatcher.symbolicTypes(final IAtomContainer container, final int[][] graph, final EdgeToBondMap bonds, final Set<IBond> mmffArom)
focal_class.full_signature:  String[] symbolicTypes(final IAtomContainer container, final int[][] graph, final EdgeToBondMap bonds, final Set<IBond> mmffArom)
focal_class.identifier: symbolicTypes
focal_class.parameters: (final IAtomContainer container, final int[][] graph, final EdgeToBondMap bonds, final Set<IBond> mmffArom)
focal_class.return: String[]
focal_class.signature: String[] symbolicTypes(final IAtomContainer container, final int[][] graph, final EdgeToBondMap bonds, final Set<IBond> mmffArom)
focal_class.class_method_signature: MmffAtomTypeMatcher.fixNCNTypes(String[] symbs, int[][] graph)
focal_class.full_signature: private void fixNCNTypes(String[] symbs, int[][] graph)
focal_class.identifier: fixNCNTypes
focal_class.modifiers: private
focal_class.parameters: (String[] symbs, int[][] graph)
focal_class.return: void
focal_class.signature: void fixNCNTypes(String[] symbs, int[][] graph)
focal_class.class_method_signature: MmffAtomTypeMatcher.checkPreconditions(IAtomContainer container)
focal_class.full_signature: private void checkPreconditions(IAtomContainer container)
focal_class.identifier: checkPreconditions
focal_class.modifiers: private
focal_class.parameters: (IAtomContainer container)
focal_class.return: void
focal_class.signature: void checkPreconditions(IAtomContainer container)
focal_class.class_method_signature: MmffAtomTypeMatcher.assignHydrogenTypes(IAtomContainer container, String[] symbs, int[][] graph)
focal_class.full_signature: private void assignHydrogenTypes(IAtomContainer container, String[] symbs, int[][] graph)
focal_class.identifier: assignHydrogenTypes
focal_class.modifiers: private
focal_class.parameters: (IAtomContainer container, String[] symbs, int[][] graph)
focal_class.return: void
focal_class.signature: void assignHydrogenTypes(IAtomContainer container, String[] symbs, int[][] graph)
focal_class.class_method_signature: MmffAtomTypeMatcher.assignPreliminaryTypes(IAtomContainer container, String[] symbs)
focal_class.full_signature: private void assignPreliminaryTypes(IAtomContainer container, String[] symbs)
focal_class.identifier: assignPreliminaryTypes
focal_class.modifiers: private
focal_class.parameters: (IAtomContainer container, String[] symbs)
focal_class.return: void
focal_class.signature: void assignPreliminaryTypes(IAtomContainer container, String[] symbs)
focal_class.class_method_signature: MmffAtomTypeMatcher.loadPatterns(InputStream smaIn)
focal_class.full_signature: static AtomTypePattern[] loadPatterns(InputStream smaIn)
focal_class.identifier: loadPatterns
focal_class.modifiers: static
focal_class.parameters: (InputStream smaIn)
focal_class.return: AtomTypePattern[]
focal_class.signature: AtomTypePattern[] loadPatterns(InputStream smaIn)
focal_class.class_method_signature: MmffAtomTypeMatcher.loadHydrogenDefinitions(InputStream hdefIn)
focal_class.full_signature: private Map<String, String> loadHydrogenDefinitions(InputStream hdefIn)
focal_class.identifier: loadHydrogenDefinitions
focal_class.modifiers: private
focal_class.parameters: (InputStream hdefIn)
focal_class.return: Map<String, String>
focal_class.signature: Map<String, String> loadHydrogenDefinitions(InputStream hdefIn)
focal_class.class_method_signature: MmffAtomTypeMatcher.skipLine(String line)
focal_class.full_signature: private static boolean skipLine(String line)
focal_class.identifier: skipLine
focal_class.modifiers: private static
focal_class.parameters: (String line)
focal_class.return: boolean
focal_class.signature: boolean skipLine(String line)
focal_class.class_method_signature: MmffAtomTypeMatcher.close(InputStream in)
focal_class.full_signature: private static void close(InputStream in)
focal_class.identifier: close
focal_class.modifiers: private static
focal_class.parameters: (InputStream in)
focal_class.return: void
focal_class.signature: void close(InputStream in)
focal_method.body: String[] symbolicTypes(final IAtomContainer container) {
          EdgeToBondMap bonds = EdgeToBondMap.withSpaceFor(container);
          int[][] graph = GraphUtil.toAdjList(container, bonds);
          return symbolicTypes(container, graph, bonds, new HashSet<IBond>());
      }
focal_method.class_method_signature: MmffAtomTypeMatcher.symbolicTypes(final IAtomContainer container)
focal_method.full_signature:  String[] symbolicTypes(final IAtomContainer container)
focal_method.identifier: symbolicTypes
focal_method.invocations: withSpaceFor toAdjList symbolicTypes
focal_method.parameters: (final IAtomContainer container)
focal_method.return: String[]
focal_method.signature: String[] symbolicTypes(final IAtomContainer container)