test_class.declarator: logger = LoggingToolFactory.createLoggingTool(MDLV2000ReaderTest.class)
test_class.modifier: private static
test_class.original_string: private static ILoggingTool logger = LoggingToolFactory.createLoggingTool(MDLV2000ReaderTest.class);
test_class.type: ILoggingTool
test_class.var_name: logger
test_class.file: storage/ctab/src/test/java/org/openscience/cdk/io/MDLV2000ReaderTest.java
test_class.identifier: MDLV2000ReaderTest
test_class.superclass: extends SimpleChemObjectReaderTest
test_case.body: @Test
      public void seaborgiumAbsMass() throws Exception {
          try (InputStream in = getClass().getResourceAsStream("seaborgium_abs.mol");
               MDLV2000Reader mdlr = new MDLV2000Reader(in, Mode.STRICT)) {
              IAtomContainer mol = mdlr.read(new AtomContainer());
              assertThat(mol.getAtom(0).getMassNumber(), is(261));
          }
      }
test_case.class_method_signature: MDLV2000ReaderTest.seaborgiumAbsMass()
test_case.full_signature: @Test public void seaborgiumAbsMass()
test_case.identifier: seaborgiumAbsMass
test_case.invocations: getResourceAsStream getClass read assertThat getMassNumber getAtom is
test_case.modifiers: @Test public
test_case.parameters: ()
test_case.return: void
test_case.signature: void seaborgiumAbsMass()
focal_class.declarator: input            = null
focal_class.original_string: BufferedReader                   input            = null;
focal_class.type: BufferedReader
focal_class.var_name: input
focal_class.declarator: logger           = LoggingToolFactory.createLoggingTool(MDLV2000Reader.class)
focal_class.modifier: private static
focal_class.original_string: private static ILoggingTool      logger           = LoggingToolFactory.createLoggingTool(MDLV2000Reader.class);
focal_class.type: ILoggingTool
focal_class.var_name: logger
focal_class.declarator: forceReadAs3DCoords
focal_class.modifier: private
focal_class.original_string: private BooleanIOSetting         forceReadAs3DCoords;
focal_class.type: BooleanIOSetting
focal_class.var_name: forceReadAs3DCoords
focal_class.declarator: interpretHydrogenIsotopes
focal_class.modifier: private
focal_class.original_string: private BooleanIOSetting         interpretHydrogenIsotopes;
focal_class.type: BooleanIOSetting
focal_class.var_name: interpretHydrogenIsotopes
focal_class.declarator: addStereoElements
focal_class.modifier: private
focal_class.original_string: private BooleanIOSetting         addStereoElements;
focal_class.type: BooleanIOSetting
focal_class.var_name: addStereoElements
focal_class.declarator: TRAILING_SPACE   = Pattern.compile("\\s+$")
focal_class.modifier: private static final
focal_class.original_string: private static final Pattern     TRAILING_SPACE   = Pattern.compile("\\s+$");
focal_class.type: Pattern
focal_class.var_name: TRAILING_SPACE
focal_class.declarator: RECORD_DELIMITER = "$$$$"
focal_class.modifier: private static final
focal_class.original_string: private static final String      RECORD_DELIMITER = "$$$$";
focal_class.type: String
focal_class.var_name: RECORD_DELIMITER
focal_class.declarator: PSUEDO_LABELS    = ImmutableSet.<String> builder().add("*").add("A").add("Q")
                                                                .add("L").add("LP").add("R") // XXX: not in spec
                                                                .add("R#").build()
focal_class.modifier: private static final
focal_class.original_string: private static final Set<String> PSUEDO_LABELS    = ImmutableSet.<String> builder().add("*").add("A").add("Q")
                                                                .add("L").add("LP").add("R") // XXX: not in spec
                                                                .add("R#").build();
focal_class.type: Set<String>
focal_class.var_name: PSUEDO_LABELS
focal_class.declarator: PSEUDO_LABELS    = ImmutableSet.<String> builder().add("*").add("A").add("Q")
                                                                .add("L").add("LP").add("R") // XXX: not in spec
                                                                .add("R#").build()
focal_class.modifier: private static final
focal_class.original_string: private static final Set<String> PSEUDO_LABELS    = ImmutableSet.<String> builder().add("*").add("A").add("Q")
                                                                .add("L").add("LP").add("R") // XXX: not in spec
                                                                .add("R#").build();
focal_class.type: Set<String>
focal_class.var_name: PSEUDO_LABELS
focal_class.file: storage/ctab/src/main/java/org/openscience/cdk/io/MDLV2000Reader.java
focal_class.identifier: MDLV2000Reader
focal_class.class_method_signature: MDLV2000Reader.MDLV2000Reader()
focal_class.full_signature: public  MDLV2000Reader()
focal_class.identifier: MDLV2000Reader
focal_class.modifiers: public
focal_class.parameters: ()
focal_class.signature:  MDLV2000Reader()
focal_class.class_method_signature: MDLV2000Reader.MDLV2000Reader(InputStream in)
focal_class.full_signature: public  MDLV2000Reader(InputStream in)
focal_class.identifier: MDLV2000Reader
focal_class.modifiers: public
focal_class.parameters: (InputStream in)
focal_class.signature:  MDLV2000Reader(InputStream in)
focal_class.class_method_signature: MDLV2000Reader.MDLV2000Reader(InputStream in, Mode mode)
focal_class.full_signature: public  MDLV2000Reader(InputStream in, Mode mode)
focal_class.identifier: MDLV2000Reader
focal_class.modifiers: public
focal_class.parameters: (InputStream in, Mode mode)
focal_class.signature:  MDLV2000Reader(InputStream in, Mode mode)
focal_class.class_method_signature: MDLV2000Reader.MDLV2000Reader(Reader in)
focal_class.full_signature: public  MDLV2000Reader(Reader in)
focal_class.identifier: MDLV2000Reader
focal_class.modifiers: public
focal_class.parameters: (Reader in)
focal_class.signature:  MDLV2000Reader(Reader in)
focal_class.class_method_signature: MDLV2000Reader.MDLV2000Reader(Reader in, Mode mode)
focal_class.full_signature: public  MDLV2000Reader(Reader in, Mode mode)
focal_class.identifier: MDLV2000Reader
focal_class.modifiers: public
focal_class.parameters: (Reader in, Mode mode)
focal_class.signature:  MDLV2000Reader(Reader in, Mode mode)
focal_class.class_method_signature: MDLV2000Reader.getFormat()
focal_class.full_signature: @Override public IResourceFormat getFormat()
focal_class.identifier: getFormat
focal_class.modifiers: @Override public
focal_class.parameters: ()
focal_class.return: IResourceFormat
focal_class.signature: IResourceFormat getFormat()
focal_class.class_method_signature: MDLV2000Reader.setReader(Reader input)
focal_class.full_signature: @Override public void setReader(Reader input)
focal_class.identifier: setReader
focal_class.modifiers: @Override public
focal_class.parameters: (Reader input)
focal_class.return: void
focal_class.signature: void setReader(Reader input)
focal_class.class_method_signature: MDLV2000Reader.setReader(InputStream input)
focal_class.full_signature: @Override public void setReader(InputStream input)
focal_class.identifier: setReader
focal_class.modifiers: @Override public
focal_class.parameters: (InputStream input)
focal_class.return: void
focal_class.signature: void setReader(InputStream input)
focal_class.class_method_signature: MDLV2000Reader.accepts(Class<? extends IChemObject> classObject)
focal_class.full_signature: @SuppressWarnings("unchecked") @Override public boolean accepts(Class<? extends IChemObject> classObject)
focal_class.identifier: accepts
focal_class.modifiers: @SuppressWarnings("unchecked") @Override public
focal_class.parameters: (Class<? extends IChemObject> classObject)
focal_class.return: boolean
focal_class.signature: boolean accepts(Class<? extends IChemObject> classObject)
focal_class.class_method_signature: MDLV2000Reader.read(T object)
focal_class.full_signature: @SuppressWarnings("unchecked") @Override public T read(T object)
focal_class.identifier: read
focal_class.modifiers: @SuppressWarnings("unchecked") @Override public
focal_class.parameters: (T object)
focal_class.return: T
focal_class.signature: T read(T object)
focal_class.class_method_signature: MDLV2000Reader.readChemModel(IChemModel chemModel)
focal_class.full_signature: private IChemModel readChemModel(IChemModel chemModel)
focal_class.identifier: readChemModel
focal_class.modifiers: private
focal_class.parameters: (IChemModel chemModel)
focal_class.return: IChemModel
focal_class.signature: IChemModel readChemModel(IChemModel chemModel)
focal_class.class_method_signature: MDLV2000Reader.readChemFile(IChemFile chemFile)
focal_class.full_signature: private IChemFile readChemFile(IChemFile chemFile)
focal_class.identifier: readChemFile
focal_class.modifiers: private
focal_class.parameters: (IChemFile chemFile)
focal_class.return: IChemFile
focal_class.signature: IChemFile readChemFile(IChemFile chemFile)
focal_class.class_method_signature: MDLV2000Reader.newModel(final IAtomContainer container)
focal_class.full_signature: private static IChemModel newModel(final IAtomContainer container)
focal_class.identifier: newModel
focal_class.modifiers: private static
focal_class.parameters: (final IAtomContainer container)
focal_class.return: IChemModel
focal_class.signature: IChemModel newModel(final IAtomContainer container)
focal_class.class_method_signature: MDLV2000Reader.readAtomContainer(IAtomContainer molecule)
focal_class.full_signature: private IAtomContainer readAtomContainer(IAtomContainer molecule)
focal_class.identifier: readAtomContainer
focal_class.modifiers: private
focal_class.parameters: (IAtomContainer molecule)
focal_class.return: IAtomContainer
focal_class.signature: IAtomContainer readAtomContainer(IAtomContainer molecule)
focal_class.class_method_signature: MDLV2000Reader.is3Dfile(String program)
focal_class.full_signature: private boolean is3Dfile(String program)
focal_class.identifier: is3Dfile
focal_class.modifiers: private
focal_class.parameters: (String program)
focal_class.return: boolean
focal_class.signature: boolean is3Dfile(String program)
focal_class.class_method_signature: MDLV2000Reader.applyMDLValenceModel(IAtom atom, int explicitValence, int unpaired)
focal_class.full_signature: private void applyMDLValenceModel(IAtom atom, int explicitValence, int unpaired)
focal_class.identifier: applyMDLValenceModel
focal_class.modifiers: private
focal_class.parameters: (IAtom atom, int explicitValence, int unpaired)
focal_class.return: void
focal_class.signature: void applyMDLValenceModel(IAtom atom, int explicitValence, int unpaired)
focal_class.class_method_signature: MDLV2000Reader.fixHydrogenIsotopes(IAtomContainer molecule, IsotopeFactory isotopeFactory)
focal_class.full_signature: private void fixHydrogenIsotopes(IAtomContainer molecule, IsotopeFactory isotopeFactory)
focal_class.identifier: fixHydrogenIsotopes
focal_class.modifiers: private
focal_class.parameters: (IAtomContainer molecule, IsotopeFactory isotopeFactory)
focal_class.return: void
focal_class.signature: void fixHydrogenIsotopes(IAtomContainer molecule, IsotopeFactory isotopeFactory)
focal_class.class_method_signature: MDLV2000Reader.close()
focal_class.full_signature: @Override public void close()
focal_class.identifier: close
focal_class.modifiers: @Override public
focal_class.parameters: ()
focal_class.return: void
focal_class.signature: void close()
focal_class.class_method_signature: MDLV2000Reader.initIOSettings()
focal_class.full_signature: private void initIOSettings()
focal_class.identifier: initIOSettings
focal_class.modifiers: private
focal_class.parameters: ()
focal_class.return: void
focal_class.signature: void initIOSettings()
focal_class.class_method_signature: MDLV2000Reader.customizeJob()
focal_class.full_signature: public void customizeJob()
focal_class.identifier: customizeJob
focal_class.modifiers: public
focal_class.parameters: ()
focal_class.return: void
focal_class.signature: void customizeJob()
focal_class.class_method_signature: MDLV2000Reader.removeNonDigits(String input)
focal_class.full_signature: private String removeNonDigits(String input)
focal_class.identifier: removeNonDigits
focal_class.modifiers: private
focal_class.parameters: (String input)
focal_class.return: String
focal_class.signature: String removeNonDigits(String input)
focal_class.class_method_signature: MDLV2000Reader.readAtomFast(String line, IChemObjectBuilder builder, int lineNum)
focal_class.full_signature:  IAtom readAtomFast(String line, IChemObjectBuilder builder, int lineNum)
focal_class.identifier: readAtomFast
focal_class.parameters: (String line, IChemObjectBuilder builder, int lineNum)
focal_class.return: IAtom
focal_class.signature: IAtom readAtomFast(String line, IChemObjectBuilder builder, int lineNum)
focal_class.class_method_signature: MDLV2000Reader.readAtomFast(String line, IChemObjectBuilder builder, Map<IAtom,Integer> parities, int lineNum, boolean isQuery)
focal_class.full_signature:  IAtom readAtomFast(String line, IChemObjectBuilder builder, Map<IAtom,Integer> parities, int lineNum, boolean isQuery)
focal_class.identifier: readAtomFast
focal_class.parameters: (String line, IChemObjectBuilder builder, Map<IAtom,Integer> parities, int lineNum, boolean isQuery)
focal_class.return: IAtom
focal_class.signature: IAtom readAtomFast(String line, IChemObjectBuilder builder, Map<IAtom,Integer> parities, int lineNum, boolean isQuery)
focal_class.class_method_signature: MDLV2000Reader.readBondFast(String line, IChemObjectBuilder builder, IAtom[] atoms, int[] explicitValence, int lineNum)
focal_class.full_signature:  IBond readBondFast(String line, IChemObjectBuilder builder, IAtom[] atoms, int[] explicitValence, int lineNum)
focal_class.identifier: readBondFast
focal_class.parameters: (String line, IChemObjectBuilder builder, IAtom[] atoms, int[] explicitValence, int lineNum)
focal_class.return: IBond
focal_class.signature: IBond readBondFast(String line, IChemObjectBuilder builder, IAtom[] atoms, int[] explicitValence, int lineNum)
focal_class.class_method_signature: MDLV2000Reader.readBondFast(String line, IChemObjectBuilder builder, IAtom[] atoms, int[] explicitValence, int lineNum,
                         boolean isQuery)
focal_class.full_signature:  IBond readBondFast(String line, IChemObjectBuilder builder, IAtom[] atoms, int[] explicitValence, int lineNum,
                         boolean isQuery)
focal_class.identifier: readBondFast
focal_class.parameters: (String line, IChemObjectBuilder builder, IAtom[] atoms, int[] explicitValence, int lineNum,
                         boolean isQuery)
focal_class.return: IBond
focal_class.signature: IBond readBondFast(String line, IChemObjectBuilder builder, IAtom[] atoms, int[] explicitValence, int lineNum,
                         boolean isQuery)
focal_class.class_method_signature: MDLV2000Reader.readPropertiesFast(final BufferedReader input, final IAtomContainer container, final int nAtoms)
focal_class.full_signature:  void readPropertiesFast(final BufferedReader input, final IAtomContainer container, final int nAtoms)
focal_class.identifier: readPropertiesFast
focal_class.parameters: (final BufferedReader input, final IAtomContainer container, final int nAtoms)
focal_class.return: void
focal_class.signature: void readPropertiesFast(final BufferedReader input, final IAtomContainer container, final int nAtoms)
focal_class.class_method_signature: MDLV2000Reader.ensureSgroup(Map<Integer, Sgroup> map, int idx)
focal_class.full_signature: private Sgroup ensureSgroup(Map<Integer, Sgroup> map, int idx)
focal_class.identifier: ensureSgroup
focal_class.modifiers: private
focal_class.parameters: (Map<Integer, Sgroup> map, int idx)
focal_class.return: Sgroup
focal_class.signature: Sgroup ensureSgroup(Map<Integer, Sgroup> map, int idx)
focal_class.class_method_signature: MDLV2000Reader.toStereo(final int stereo, final int type)
focal_class.full_signature: private IBond.Stereo toStereo(final int stereo, final int type)
focal_class.identifier: toStereo
focal_class.modifiers: private
focal_class.parameters: (final int stereo, final int type)
focal_class.return: IBond.Stereo
focal_class.signature: IBond.Stereo toStereo(final int stereo, final int type)
focal_class.class_method_signature: MDLV2000Reader.length(final String str)
focal_class.full_signature: static int length(final String str)
focal_class.identifier: length
focal_class.modifiers: static
focal_class.parameters: (final String str)
focal_class.return: int
focal_class.signature: int length(final String str)
focal_class.class_method_signature: MDLV2000Reader.createAtom(String symbol, IChemObjectBuilder builder, int lineNum)
focal_class.full_signature: private IAtom createAtom(String symbol, IChemObjectBuilder builder, int lineNum)
focal_class.identifier: createAtom
focal_class.modifiers: private
focal_class.parameters: (String symbol, IChemObjectBuilder builder, int lineNum)
focal_class.return: IAtom
focal_class.signature: IAtom createAtom(String symbol, IChemObjectBuilder builder, int lineNum)
focal_class.class_method_signature: MDLV2000Reader.isPseudoElement(final String symbol)
focal_class.full_signature: static boolean isPseudoElement(final String symbol)
focal_class.identifier: isPseudoElement
focal_class.modifiers: static
focal_class.parameters: (final String symbol)
focal_class.return: boolean
focal_class.signature: boolean isPseudoElement(final String symbol)
focal_class.class_method_signature: MDLV2000Reader.readMDLCoordinate(final String line, int offset)
focal_class.full_signature:  double readMDLCoordinate(final String line, int offset)
focal_class.identifier: readMDLCoordinate
focal_class.parameters: (final String line, int offset)
focal_class.return: double
focal_class.signature: double readMDLCoordinate(final String line, int offset)
focal_class.class_method_signature: MDLV2000Reader.toCharge(final char c)
focal_class.full_signature: private static int toCharge(final char c)
focal_class.identifier: toCharge
focal_class.modifiers: private static
focal_class.parameters: (final char c)
focal_class.return: int
focal_class.signature: int toCharge(final char c)
focal_class.class_method_signature: MDLV2000Reader.sign(final char c)
focal_class.full_signature: private static int sign(final char c)
focal_class.identifier: sign
focal_class.modifiers: private static
focal_class.parameters: (final char c)
focal_class.return: int
focal_class.signature: int sign(final char c)
focal_class.class_method_signature: MDLV2000Reader.toInt(final char c)
focal_class.full_signature: private static int toInt(final char c)
focal_class.identifier: toInt
focal_class.modifiers: private static
focal_class.parameters: (final char c)
focal_class.return: int
focal_class.signature: int toInt(final char c)
focal_class.class_method_signature: MDLV2000Reader.readUInt(final String line, int index, int digits)
focal_class.full_signature: private static int readUInt(final String line, int index, int digits)
focal_class.identifier: readUInt
focal_class.modifiers: private static
focal_class.parameters: (final String line, int index, int digits)
focal_class.return: int
focal_class.signature: int readUInt(final String line, int index, int digits)
focal_class.class_method_signature: MDLV2000Reader.readMolfileInt(final String line, final int index)
focal_class.full_signature: private static int readMolfileInt(final String line, final int index)
focal_class.identifier: readMolfileInt
focal_class.modifiers: private static
focal_class.parameters: (final String line, final int index)
focal_class.return: int
focal_class.signature: int readMolfileInt(final String line, final int index)
focal_class.class_method_signature: MDLV2000Reader.label(final IAtomContainer container, final int index, final String label)
focal_class.full_signature: static void label(final IAtomContainer container, final int index, final String label)
focal_class.identifier: label
focal_class.modifiers: static
focal_class.parameters: (final IAtomContainer container, final int index, final String label)
focal_class.return: void
focal_class.signature: void label(final IAtomContainer container, final int index, final String label)
focal_class.class_method_signature: MDLV2000Reader.readAtomSlow(String line, IChemObjectBuilder builder, int linecount)
focal_class.full_signature: private IAtom readAtomSlow(String line, IChemObjectBuilder builder, int linecount)
focal_class.identifier: readAtomSlow
focal_class.modifiers: private
focal_class.parameters: (String line, IChemObjectBuilder builder, int linecount)
focal_class.return: IAtom
focal_class.signature: IAtom readAtomSlow(String line, IChemObjectBuilder builder, int linecount)
focal_class.class_method_signature: MDLV2000Reader.readBondSlow(String line, IChemObjectBuilder builder, IAtom[] atoms, int[] explicitValence,
              int linecount)
focal_class.full_signature: private IBond readBondSlow(String line, IChemObjectBuilder builder, IAtom[] atoms, int[] explicitValence,
              int linecount)
focal_class.identifier: readBondSlow
focal_class.modifiers: private
focal_class.parameters: (String line, IChemObjectBuilder builder, IAtom[] atoms, int[] explicitValence,
              int linecount)
focal_class.return: IBond
focal_class.signature: IBond readBondSlow(String line, IChemObjectBuilder builder, IAtom[] atoms, int[] explicitValence,
              int linecount)
focal_class.class_method_signature: MDLV2000Reader.readPropertiesSlow(BufferedReader input, IAtomContainer container, int nAtoms, int linecount)
focal_class.full_signature: private void readPropertiesSlow(BufferedReader input, IAtomContainer container, int nAtoms, int linecount)
focal_class.identifier: readPropertiesSlow
focal_class.modifiers: private
focal_class.parameters: (BufferedReader input, IAtomContainer container, int nAtoms, int linecount)
focal_class.return: void
focal_class.signature: void readPropertiesSlow(BufferedReader input, IAtomContainer container, int nAtoms, int linecount)
focal_class.class_method_signature: MDLV2000Reader.readNonStructuralData(final BufferedReader input, final IAtomContainer container)
focal_class.full_signature: static void readNonStructuralData(final BufferedReader input, final IAtomContainer container)
focal_class.identifier: readNonStructuralData
focal_class.modifiers: static
focal_class.parameters: (final BufferedReader input, final IAtomContainer container)
focal_class.return: void
focal_class.signature: void readNonStructuralData(final BufferedReader input, final IAtomContainer container)
focal_class.class_method_signature: MDLV2000Reader.dataHeader(final String line)
focal_class.full_signature: static String dataHeader(final String line)
focal_class.identifier: dataHeader
focal_class.modifiers: static
focal_class.parameters: (final String line)
focal_class.return: String
focal_class.signature: String dataHeader(final String line)
focal_class.class_method_signature: MDLV2000Reader.endOfRecord(final String line)
focal_class.full_signature: private static boolean endOfRecord(final String line)
focal_class.identifier: endOfRecord
focal_class.modifiers: private static
focal_class.parameters: (final String line)
focal_class.return: boolean
focal_class.signature: boolean endOfRecord(final String line)
focal_class.superclass: extends DefaultChemObjectReader
focal_method.body: @SuppressWarnings("unchecked")
      @Override
      public <T extends IChemObject> T read(T object) throws CDKException {
          if (object instanceof IAtomContainer) {
              return (T) readAtomContainer((IAtomContainer) object);
          } else if (object instanceof IChemFile) {
              return (T) readChemFile((IChemFile) object);
          } else if (object instanceof IChemModel) {
              return (T) readChemModel((IChemModel) object);
          } else {
              throw new CDKException("Only supported are ChemFile and Molecule.");
          }
      }
focal_method.class_method_signature: MDLV2000Reader.read(T object)
focal_method.full_signature: @SuppressWarnings("unchecked") @Override public T read(T object)
focal_method.identifier: read
focal_method.invocations: readAtomContainer readChemFile readChemModel
focal_method.modifiers: @SuppressWarnings("unchecked") @Override public
focal_method.parameters: (T object)
focal_method.return: T
focal_method.signature: T read(T object)