test_class.declarator: smipar = new SmilesParser(SilentChemObjectBuilder.getInstance())
test_class.modifier: private static
test_class.original_string: private static SmilesParser smipar = new SmilesParser(SilentChemObjectBuilder.getInstance());
test_class.type: SmilesParser
test_class.var_name: smipar
test_class.file: app/depict/src/test/java/org/openscience/cdk/depict/AbbreviationsTest.java
test_class.identifier: AbbreviationsTest
test_case.body: @Test
      public void loadFromFile() throws Exception {
          Abbreviations factory = new Abbreviations();
          assertThat(factory.loadFromFile("obabel_superatoms.smi"), is(27));
          assertThat(factory.loadFromFile("/org/openscience/cdk/depict/obabel_superatoms.smi"), is(27));
      }
test_case.class_method_signature: AbbreviationsTest.loadFromFile()
test_case.full_signature: @Test public void loadFromFile()
test_case.identifier: loadFromFile
test_case.invocations: assertThat loadFromFile is assertThat loadFromFile is
test_case.modifiers: @Test public
test_case.parameters: ()
test_case.return: void
test_case.signature: void loadFromFile()
focal_class.declarator: MAX_FRAG = 50
focal_class.modifier: private static final
focal_class.original_string: private static final int MAX_FRAG = 50;
focal_class.type: int
focal_class.var_name: MAX_FRAG
focal_class.declarator: INTERPUNCT = "·";
focal_class.modifier: private static final
focal_class.original_string: private static final String INTERPUNCT = "·";
focal_class.type: String
focal_class.var_name: INTERPUNCT
focal_class.declarator: connectedAbbreviations    = new LinkedHashMap<>()
focal_class.modifier: private final
focal_class.original_string: private final Map<String, String> connectedAbbreviations    = new LinkedHashMap<>();
focal_class.type: Map<String, String>
focal_class.var_name: connectedAbbreviations
focal_class.declarator: disconnectedAbbreviations = new LinkedHashMap<>()
focal_class.modifier: private final
focal_class.original_string: private final Map<String, String> disconnectedAbbreviations = new LinkedHashMap<>();
focal_class.type: Map<String, String>
focal_class.var_name: disconnectedAbbreviations
focal_class.declarator: labels                    = new LinkedHashSet<>()
focal_class.modifier: private final
focal_class.original_string: private final Set<String>         labels                    = new LinkedHashSet<>();
focal_class.type: Set<String>
focal_class.var_name: labels
focal_class.declarator: disabled                  = new HashSet<>()
focal_class.modifier: private final
focal_class.original_string: private final Set<String>         disabled                  = new HashSet<>();
focal_class.type: Set<String>
focal_class.var_name: disabled
focal_class.declarator: usmigen                   = SmilesGenerator.unique()
focal_class.modifier: private final
focal_class.original_string: private final SmilesGenerator     usmigen                   = SmilesGenerator.unique();
focal_class.type: SmilesGenerator
focal_class.var_name: usmigen
focal_class.declarator: smipar = new SmilesParser(SilentChemObjectBuilder.getInstance())
focal_class.modifier: private final
focal_class.original_string: private final SmilesParser smipar = new SmilesParser(SilentChemObjectBuilder.getInstance());
focal_class.type: SmilesParser
focal_class.var_name: smipar
focal_class.declarator: contractOnHetero = true
focal_class.modifier: private
focal_class.original_string: private boolean contractOnHetero = true;
focal_class.type: boolean
focal_class.var_name: contractOnHetero
focal_class.declarator: contractSingleFragments = false
focal_class.modifier: private
focal_class.original_string: private boolean contractSingleFragments = false;
focal_class.type: boolean
focal_class.var_name: contractSingleFragments
focal_class.declarator: CUT_BOND = "cutbond"
focal_class.modifier: private static final
focal_class.original_string: private static final String CUT_BOND = "cutbond";
focal_class.type: String
focal_class.var_name: CUT_BOND
focal_class.file: app/depict/src/main/java/org/openscience/cdk/depict/Abbreviations.java
focal_class.identifier: Abbreviations
focal_class.interfaces: implements Iterable<String>
focal_class.class_method_signature: Abbreviations.Abbreviations()
focal_class.full_signature: public  Abbreviations()
focal_class.identifier: Abbreviations
focal_class.modifiers: public
focal_class.parameters: ()
focal_class.signature:  Abbreviations()
focal_class.class_method_signature: Abbreviations.iterator()
focal_class.full_signature: @Override public Iterator<String> iterator()
focal_class.identifier: iterator
focal_class.modifiers: @Override public
focal_class.parameters: ()
focal_class.return: Iterator<String>
focal_class.signature: Iterator<String> iterator()
focal_class.class_method_signature: Abbreviations.isEnabled(final String label)
focal_class.full_signature: public boolean isEnabled(final String label)
focal_class.identifier: isEnabled
focal_class.modifiers: public
focal_class.parameters: (final String label)
focal_class.return: boolean
focal_class.signature: boolean isEnabled(final String label)
focal_class.class_method_signature: Abbreviations.setEnabled(String label, boolean enabled)
focal_class.full_signature: public boolean setEnabled(String label, boolean enabled)
focal_class.identifier: setEnabled
focal_class.modifiers: public
focal_class.parameters: (String label, boolean enabled)
focal_class.return: boolean
focal_class.signature: boolean setEnabled(String label, boolean enabled)
focal_class.class_method_signature: Abbreviations.setContractOnHetero(boolean val)
focal_class.full_signature: public void setContractOnHetero(boolean val)
focal_class.identifier: setContractOnHetero
focal_class.modifiers: public
focal_class.parameters: (boolean val)
focal_class.return: void
focal_class.signature: void setContractOnHetero(boolean val)
focal_class.class_method_signature: Abbreviations.setContractToSingleLabel(boolean val)
focal_class.full_signature: public void setContractToSingleLabel(boolean val)
focal_class.identifier: setContractToSingleLabel
focal_class.modifiers: public
focal_class.parameters: (boolean val)
focal_class.return: void
focal_class.signature: void setContractToSingleLabel(boolean val)
focal_class.class_method_signature: Abbreviations.findCutBonds(IAtomContainer mol, EdgeToBondMap bmap, int[][] adjlist)
focal_class.full_signature: private static Set<IBond> findCutBonds(IAtomContainer mol, EdgeToBondMap bmap, int[][] adjlist)
focal_class.identifier: findCutBonds
focal_class.modifiers: private static
focal_class.parameters: (IAtomContainer mol, EdgeToBondMap bmap, int[][] adjlist)
focal_class.return: Set<IBond>
focal_class.signature: Set<IBond> findCutBonds(IAtomContainer mol, EdgeToBondMap bmap, int[][] adjlist)
focal_class.class_method_signature: Abbreviations.makeCut(IBond cut, IAtomContainer mol, Map<IAtom, Integer> idx,
                                                  int[][] adjlist)
focal_class.full_signature: private static List<IAtomContainer> makeCut(IBond cut, IAtomContainer mol, Map<IAtom, Integer> idx,
                                                  int[][] adjlist)
focal_class.identifier: makeCut
focal_class.modifiers: private static
focal_class.parameters: (IBond cut, IAtomContainer mol, Map<IAtom, Integer> idx,
                                                  int[][] adjlist)
focal_class.return: List<IAtomContainer>
focal_class.signature: List<IAtomContainer> makeCut(IBond cut, IAtomContainer mol, Map<IAtom, Integer> idx,
                                                  int[][] adjlist)
focal_class.class_method_signature: Abbreviations.generateFragments(IAtomContainer mol)
focal_class.full_signature: private static List<IAtomContainer> generateFragments(IAtomContainer mol)
focal_class.identifier: generateFragments
focal_class.modifiers: private static
focal_class.parameters: (IAtomContainer mol)
focal_class.return: List<IAtomContainer>
focal_class.signature: List<IAtomContainer> generateFragments(IAtomContainer mol)
focal_class.class_method_signature: Abbreviations.generate(final IAtomContainer mol)
focal_class.full_signature: public List<Sgroup> generate(final IAtomContainer mol)
focal_class.identifier: generate
focal_class.modifiers: public
focal_class.parameters: (final IAtomContainer mol)
focal_class.return: List<Sgroup>
focal_class.signature: List<Sgroup> generate(final IAtomContainer mol)
focal_class.class_method_signature: Abbreviations.getAbbr(IAtomContainer part)
focal_class.full_signature: private Sgroup getAbbr(IAtomContainer part)
focal_class.identifier: getAbbr
focal_class.modifiers: private
focal_class.parameters: (IAtomContainer part)
focal_class.return: Sgroup
focal_class.signature: Sgroup getAbbr(IAtomContainer part)
focal_class.class_method_signature: Abbreviations.countUpper(String str)
focal_class.full_signature: private int countUpper(String str)
focal_class.identifier: countUpper
focal_class.modifiers: private
focal_class.parameters: (String str)
focal_class.return: int
focal_class.signature: int countUpper(String str)
focal_class.class_method_signature: Abbreviations.containsChargeChar(String str)
focal_class.full_signature: private boolean containsChargeChar(String str)
focal_class.identifier: containsChargeChar
focal_class.modifiers: private
focal_class.parameters: (String str)
focal_class.return: boolean
focal_class.signature: boolean containsChargeChar(String str)
focal_class.class_method_signature: Abbreviations.digitAtEnd(String str)
focal_class.full_signature: private boolean digitAtEnd(String str)
focal_class.identifier: digitAtEnd
focal_class.modifiers: private
focal_class.parameters: (String str)
focal_class.return: boolean
focal_class.signature: boolean digitAtEnd(String str)
focal_class.class_method_signature: Abbreviations.newSymbol(int atomnum, int hcount, boolean prefix)
focal_class.full_signature: private String newSymbol(int atomnum, int hcount, boolean prefix)
focal_class.identifier: newSymbol
focal_class.modifiers: private
focal_class.parameters: (int atomnum, int hcount, boolean prefix)
focal_class.return: String
focal_class.signature: String newSymbol(int atomnum, int hcount, boolean prefix)
focal_class.class_method_signature: Abbreviations.appendGroup(StringBuilder sb, String group, int coef, boolean useParen)
focal_class.full_signature: private void appendGroup(StringBuilder sb, String group, int coef, boolean useParen)
focal_class.identifier: appendGroup
focal_class.modifiers: private
focal_class.parameters: (StringBuilder sb, String group, int coef, boolean useParen)
focal_class.return: void
focal_class.signature: void appendGroup(StringBuilder sb, String group, int coef, boolean useParen)
focal_class.class_method_signature: Abbreviations.apply(final IAtomContainer mol)
focal_class.full_signature: public int apply(final IAtomContainer mol)
focal_class.identifier: apply
focal_class.modifiers: public
focal_class.parameters: (final IAtomContainer mol)
focal_class.return: int
focal_class.signature: int apply(final IAtomContainer mol)
focal_class.class_method_signature: Abbreviations.matchExact(final IAtomContainer mol, final IAtom atom)
focal_class.full_signature: private IQueryAtom matchExact(final IAtomContainer mol, final IAtom atom)
focal_class.identifier: matchExact
focal_class.modifiers: private
focal_class.parameters: (final IAtomContainer mol, final IAtom atom)
focal_class.return: IQueryAtom
focal_class.signature: IQueryAtom matchExact(final IAtomContainer mol, final IAtom atom)
focal_class.class_method_signature: Abbreviations.matchExact(IAtomContainer mol)
focal_class.full_signature: private IQueryAtomContainer matchExact(IAtomContainer mol)
focal_class.identifier: matchExact
focal_class.modifiers: private
focal_class.parameters: (IAtomContainer mol)
focal_class.return: IQueryAtomContainer
focal_class.signature: IQueryAtomContainer matchExact(IAtomContainer mol)
focal_class.class_method_signature: Abbreviations.addDisconnectedAbbreviation(IAtomContainer mol, String label)
focal_class.full_signature: private boolean addDisconnectedAbbreviation(IAtomContainer mol, String label)
focal_class.identifier: addDisconnectedAbbreviation
focal_class.modifiers: private
focal_class.parameters: (IAtomContainer mol, String label)
focal_class.return: boolean
focal_class.signature: boolean addDisconnectedAbbreviation(IAtomContainer mol, String label)
focal_class.class_method_signature: Abbreviations.addConnectedAbbreviation(IAtomContainer mol, String label)
focal_class.full_signature: private boolean addConnectedAbbreviation(IAtomContainer mol, String label)
focal_class.identifier: addConnectedAbbreviation
focal_class.modifiers: private
focal_class.parameters: (IAtomContainer mol, String label)
focal_class.return: boolean
focal_class.signature: boolean addConnectedAbbreviation(IAtomContainer mol, String label)
focal_class.class_method_signature: Abbreviations.add(String line)
focal_class.full_signature: public boolean add(String line)
focal_class.identifier: add
focal_class.modifiers: public
focal_class.parameters: (String line)
focal_class.return: boolean
focal_class.signature: boolean add(String line)
focal_class.class_method_signature: Abbreviations.add(IAtomContainer mol, String label)
focal_class.full_signature: public boolean add(IAtomContainer mol, String label)
focal_class.identifier: add
focal_class.modifiers: public
focal_class.parameters: (IAtomContainer mol, String label)
focal_class.return: boolean
focal_class.signature: boolean add(IAtomContainer mol, String label)
focal_class.class_method_signature: Abbreviations.getSmilesSuffix(String line)
focal_class.full_signature: private static String getSmilesSuffix(String line)
focal_class.identifier: getSmilesSuffix
focal_class.modifiers: private static
focal_class.parameters: (String line)
focal_class.return: String
focal_class.signature: String getSmilesSuffix(String line)
focal_class.class_method_signature: Abbreviations.getBasicElementSymbol(IAtom atom)
focal_class.full_signature: private static String getBasicElementSymbol(IAtom atom)
focal_class.identifier: getBasicElementSymbol
focal_class.modifiers: private static
focal_class.parameters: (IAtom atom)
focal_class.return: String
focal_class.signature: String getBasicElementSymbol(IAtom atom)
focal_class.class_method_signature: Abbreviations.loadSmiles(final InputStream in)
focal_class.full_signature: private int loadSmiles(final InputStream in)
focal_class.identifier: loadSmiles
focal_class.modifiers: private
focal_class.parameters: (final InputStream in)
focal_class.return: int
focal_class.signature: int loadSmiles(final InputStream in)
focal_class.class_method_signature: Abbreviations.loadFromFile(final String path)
focal_class.full_signature: public int loadFromFile(final String path)
focal_class.identifier: loadFromFile
focal_class.modifiers: public
focal_class.parameters: (final String path)
focal_class.return: int
focal_class.signature: int loadFromFile(final String path)
focal_method.body: public int loadFromFile(final String path) throws IOException {
          InputStream in = null;
          try {
              in = getClass().getResourceAsStream(path);
              if (in != null)
                  return loadSmiles(in);
              File file = new File(path);
              if (file.exists() && file.canRead())
                  return loadSmiles(new FileInputStream(file));
          } finally {
              if (in != null)
                  in.close();
          }
          return 0;
      }
focal_method.class_method_signature: Abbreviations.loadFromFile(final String path)
focal_method.full_signature: public int loadFromFile(final String path)
focal_method.identifier: loadFromFile
focal_method.invocations: getResourceAsStream getClass loadSmiles exists canRead loadSmiles close
focal_method.modifiers: public
focal_method.parameters: (final String path)
focal_method.return: int
focal_method.signature: int loadFromFile(final String path)