test_class.declarator: logger = LoggingToolFactory.createLoggingTool(MDLV3000ReaderTest.class)
test_class.modifier: private static
test_class.original_string: private static ILoggingTool logger = LoggingToolFactory.createLoggingTool(MDLV3000ReaderTest.class);
test_class.type: ILoggingTool
test_class.var_name: logger
test_class.file: storage/ctab/src/test/java/org/openscience/cdk/io/MDLV3000ReaderTest.java
test_class.identifier: MDLV3000ReaderTest
test_class.superclass: extends SimpleChemObjectReaderTest
test_case.body: @Test public void positionalVariation() throws Exception {
          try (MDLV3000Reader reader = new MDLV3000Reader(getClass().getResourceAsStream("multicenterBond.mol"))) {
              IAtomContainer container = reader.read(new org.openscience.cdk.AtomContainer(0, 0, 0, 0));
              assertThat(container.getBondCount(), is(8));
              List<Sgroup> sgroups = container.getProperty(CDKConstants.CTAB_SGROUPS);
              assertNotNull(sgroups);
              assertThat(sgroups.size(), is(1));
              assertThat(sgroups.get(0).getType(), is(SgroupType.ExtMulticenter));
          }
      }
test_case.class_method_signature: MDLV3000ReaderTest.positionalVariation()
test_case.full_signature: @Test public void positionalVariation()
test_case.identifier: positionalVariation
test_case.invocations: getResourceAsStream getClass read assertThat getBondCount is getProperty assertNotNull assertThat size is assertThat getType get is
test_case.modifiers: @Test public
test_case.parameters: ()
test_case.return: void
test_case.signature: void positionalVariation()
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(MDLV3000Reader.class)
focal_class.modifier: private static
focal_class.original_string: private static ILoggingTool logger = LoggingToolFactory.createLoggingTool(MDLV3000Reader.class);
focal_class.type: ILoggingTool
focal_class.var_name: logger
focal_class.declarator: keyValueTuple
focal_class.modifier: private
focal_class.original_string: private Pattern             keyValueTuple;
focal_class.type: Pattern
focal_class.var_name: keyValueTuple
focal_class.declarator: keyValueTuple2
focal_class.modifier: private
focal_class.original_string: private Pattern             keyValueTuple2;
focal_class.type: Pattern
focal_class.var_name: keyValueTuple2
focal_class.declarator: lineNumber
focal_class.modifier: private
focal_class.original_string: private int                 lineNumber;
focal_class.type: int
focal_class.var_name: lineNumber
focal_class.file: storage/ctab/src/main/java/org/openscience/cdk/io/MDLV3000Reader.java
focal_class.identifier: MDLV3000Reader
focal_class.class_method_signature: MDLV3000Reader.MDLV3000Reader(Reader in)
focal_class.full_signature: public  MDLV3000Reader(Reader in)
focal_class.identifier: MDLV3000Reader
focal_class.modifiers: public
focal_class.parameters: (Reader in)
focal_class.signature:  MDLV3000Reader(Reader in)
focal_class.class_method_signature: MDLV3000Reader.MDLV3000Reader(Reader in, Mode mode)
focal_class.full_signature: public  MDLV3000Reader(Reader in, Mode mode)
focal_class.identifier: MDLV3000Reader
focal_class.modifiers: public
focal_class.parameters: (Reader in, Mode mode)
focal_class.signature:  MDLV3000Reader(Reader in, Mode mode)
focal_class.class_method_signature: MDLV3000Reader.MDLV3000Reader(InputStream input)
focal_class.full_signature: public  MDLV3000Reader(InputStream input)
focal_class.identifier: MDLV3000Reader
focal_class.modifiers: public
focal_class.parameters: (InputStream input)
focal_class.signature:  MDLV3000Reader(InputStream input)
focal_class.class_method_signature: MDLV3000Reader.MDLV3000Reader(InputStream input, Mode mode)
focal_class.full_signature: public  MDLV3000Reader(InputStream input, Mode mode)
focal_class.identifier: MDLV3000Reader
focal_class.modifiers: public
focal_class.parameters: (InputStream input, Mode mode)
focal_class.signature:  MDLV3000Reader(InputStream input, Mode mode)
focal_class.class_method_signature: MDLV3000Reader.MDLV3000Reader()
focal_class.full_signature: public  MDLV3000Reader()
focal_class.identifier: MDLV3000Reader
focal_class.modifiers: public
focal_class.parameters: ()
focal_class.signature:  MDLV3000Reader()
focal_class.class_method_signature: MDLV3000Reader.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: MDLV3000Reader.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: MDLV3000Reader.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: MDLV3000Reader.accepts(Class<? extends IChemObject> classObject)
focal_class.full_signature: @Override public boolean accepts(Class<? extends IChemObject> classObject)
focal_class.identifier: accepts
focal_class.modifiers: @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: MDLV3000Reader.read(T object)
focal_class.full_signature: @Override public T read(T object)
focal_class.identifier: read
focal_class.modifiers: @Override public
focal_class.parameters: (T object)
focal_class.return: T
focal_class.signature: T read(T object)
focal_class.class_method_signature: MDLV3000Reader.readMolecule(IChemObjectBuilder builder)
focal_class.full_signature: public IAtomContainer readMolecule(IChemObjectBuilder builder)
focal_class.identifier: readMolecule
focal_class.modifiers: public
focal_class.parameters: (IChemObjectBuilder builder)
focal_class.return: IAtomContainer
focal_class.signature: IAtomContainer readMolecule(IChemObjectBuilder builder)
focal_class.class_method_signature: MDLV3000Reader.readConnectionTable(IChemObjectBuilder builder)
focal_class.full_signature: public IAtomContainer readConnectionTable(IChemObjectBuilder builder)
focal_class.identifier: readConnectionTable
focal_class.modifiers: public
focal_class.parameters: (IChemObjectBuilder builder)
focal_class.return: IAtomContainer
focal_class.signature: IAtomContainer readConnectionTable(IChemObjectBuilder builder)
focal_class.class_method_signature: MDLV3000Reader.readHeader(IAtomContainer readData)
focal_class.full_signature: public String readHeader(IAtomContainer readData)
focal_class.identifier: readHeader
focal_class.modifiers: public
focal_class.parameters: (IAtomContainer readData)
focal_class.return: String
focal_class.signature: String readHeader(IAtomContainer readData)
focal_class.class_method_signature: MDLV3000Reader.readAtomBlock(IAtomContainer readData)
focal_class.full_signature: public void readAtomBlock(IAtomContainer readData)
focal_class.identifier: readAtomBlock
focal_class.modifiers: public
focal_class.parameters: (IAtomContainer readData)
focal_class.return: void
focal_class.signature: void readAtomBlock(IAtomContainer readData)
focal_class.class_method_signature: MDLV3000Reader.readBondBlock(IAtomContainer readData)
focal_class.full_signature: public void readBondBlock(IAtomContainer readData)
focal_class.identifier: readBondBlock
focal_class.modifiers: public
focal_class.parameters: (IAtomContainer readData)
focal_class.return: void
focal_class.signature: void readBondBlock(IAtomContainer readData)
focal_class.class_method_signature: MDLV3000Reader.readSGroup(IAtomContainer readData)
focal_class.full_signature: public void readSGroup(IAtomContainer readData)
focal_class.identifier: readSGroup
focal_class.modifiers: public
focal_class.parameters: (IAtomContainer readData)
focal_class.return: void
focal_class.signature: void readSGroup(IAtomContainer readData)
focal_class.class_method_signature: MDLV3000Reader.readCommand(String line)
focal_class.full_signature: private String readCommand(String line)
focal_class.identifier: readCommand
focal_class.modifiers: private
focal_class.parameters: (String line)
focal_class.return: String
focal_class.signature: String readCommand(String line)
focal_class.class_method_signature: MDLV3000Reader.parseOptions(String string)
focal_class.full_signature: private Map<String, String> parseOptions(String string)
focal_class.identifier: parseOptions
focal_class.modifiers: private
focal_class.parameters: (String string)
focal_class.return: Map<String, String>
focal_class.signature: Map<String, String> parseOptions(String string)
focal_class.class_method_signature: MDLV3000Reader.exhaustStringTokenizer(StringTokenizer tokenizer)
focal_class.full_signature: public String exhaustStringTokenizer(StringTokenizer tokenizer)
focal_class.identifier: exhaustStringTokenizer
focal_class.modifiers: public
focal_class.parameters: (StringTokenizer tokenizer)
focal_class.return: String
focal_class.signature: String exhaustStringTokenizer(StringTokenizer tokenizer)
focal_class.class_method_signature: MDLV3000Reader.readLine()
focal_class.full_signature: public String readLine()
focal_class.identifier: readLine
focal_class.modifiers: public
focal_class.parameters: ()
focal_class.return: String
focal_class.signature: String readLine()
focal_class.class_method_signature: MDLV3000Reader.isReady()
focal_class.full_signature: public boolean isReady()
focal_class.identifier: isReady
focal_class.modifiers: public
focal_class.parameters: ()
focal_class.return: boolean
focal_class.signature: boolean isReady()
focal_class.class_method_signature: MDLV3000Reader.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: MDLV3000Reader.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: MDLV3000Reader.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.superclass: extends DefaultChemObjectReader
focal_method.body: @Override
      public <T extends IChemObject> T read(T object) throws CDKException {
          if (object instanceof IAtomContainer) {
              return (T) readMolecule(object.getBuilder());
          }
          throw new CDKException("Only supports AtomContainer objects.");
      }
focal_method.class_method_signature: MDLV3000Reader.read(T object)
focal_method.full_signature: @Override public T read(T object)
focal_method.identifier: read
focal_method.invocations: readMolecule getBuilder
focal_method.modifiers: @Override public
focal_method.parameters: (T object)
focal_method.return: T
focal_method.signature: T read(T object)