test_class.declarator: logger = LoggingToolFactory.createLoggingTool(MDLRXNV2000ReaderTest.class)
test_class.modifier: private static
test_class.original_string: private static ILoggingTool logger = LoggingToolFactory.createLoggingTool(MDLRXNV2000ReaderTest.class);
test_class.type: ILoggingTool
test_class.var_name: logger
test_class.file: storage/ctab/src/test/java/org/openscience/cdk/io/MDLRXNV2000ReaderTest.java
test_class.identifier: MDLRXNV2000ReaderTest
test_class.superclass: extends SimpleChemObjectReaderTest
test_case.body: @Test
      public void testAgentParts() throws Exception {
          try (InputStream in = this.getClass().getResourceAsStream("ethylesterification.mol");
               MDLRXNV2000Reader rdr = new MDLRXNV2000Reader(in);) {
              IReaction reaction = rdr.read(new Reaction());
              assertThat(reaction.getAgents().getAtomContainerCount(), is(1));
          }
      }
test_case.class_method_signature: MDLRXNV2000ReaderTest.testAgentParts()
test_case.full_signature: @Test public void testAgentParts()
test_case.identifier: testAgentParts
test_case.invocations: getResourceAsStream getClass read assertThat getAtomContainerCount getAgents is
test_case.modifiers: @Test public
test_case.parameters: ()
test_case.return: void
test_case.signature: void testAgentParts()
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(MDLRXNV2000Reader.class)
focal_class.modifier: private static
focal_class.original_string: private static ILoggingTool logger = LoggingToolFactory.createLoggingTool(MDLRXNV2000Reader.class);
focal_class.type: ILoggingTool
focal_class.var_name: logger
focal_class.file: storage/ctab/src/main/java/org/openscience/cdk/io/MDLRXNV2000Reader.java
focal_class.identifier: MDLRXNV2000Reader
focal_class.class_method_signature: MDLRXNV2000Reader.MDLRXNV2000Reader(Reader in)
focal_class.full_signature: public  MDLRXNV2000Reader(Reader in)
focal_class.identifier: MDLRXNV2000Reader
focal_class.modifiers: public
focal_class.parameters: (Reader in)
focal_class.signature:  MDLRXNV2000Reader(Reader in)
focal_class.class_method_signature: MDLRXNV2000Reader.MDLRXNV2000Reader(Reader in, Mode mode)
focal_class.full_signature: public  MDLRXNV2000Reader(Reader in, Mode mode)
focal_class.identifier: MDLRXNV2000Reader
focal_class.modifiers: public
focal_class.parameters: (Reader in, Mode mode)
focal_class.signature:  MDLRXNV2000Reader(Reader in, Mode mode)
focal_class.class_method_signature: MDLRXNV2000Reader.MDLRXNV2000Reader(InputStream input)
focal_class.full_signature: public  MDLRXNV2000Reader(InputStream input)
focal_class.identifier: MDLRXNV2000Reader
focal_class.modifiers: public
focal_class.parameters: (InputStream input)
focal_class.signature:  MDLRXNV2000Reader(InputStream input)
focal_class.class_method_signature: MDLRXNV2000Reader.MDLRXNV2000Reader(InputStream input, Mode mode)
focal_class.full_signature: public  MDLRXNV2000Reader(InputStream input, Mode mode)
focal_class.identifier: MDLRXNV2000Reader
focal_class.modifiers: public
focal_class.parameters: (InputStream input, Mode mode)
focal_class.signature:  MDLRXNV2000Reader(InputStream input, Mode mode)
focal_class.class_method_signature: MDLRXNV2000Reader.MDLRXNV2000Reader()
focal_class.full_signature: public  MDLRXNV2000Reader()
focal_class.identifier: MDLRXNV2000Reader
focal_class.modifiers: public
focal_class.parameters: ()
focal_class.signature:  MDLRXNV2000Reader()
focal_class.class_method_signature: MDLRXNV2000Reader.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: MDLRXNV2000Reader.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: MDLRXNV2000Reader.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: MDLRXNV2000Reader.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: MDLRXNV2000Reader.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: MDLRXNV2000Reader.accepts(IChemObject object)
focal_class.full_signature: public boolean accepts(IChemObject object)
focal_class.identifier: accepts
focal_class.modifiers: public
focal_class.parameters: (IChemObject object)
focal_class.return: boolean
focal_class.signature: boolean accepts(IChemObject object)
focal_class.class_method_signature: MDLRXNV2000Reader.readReaction(IChemObjectBuilder builder)
focal_class.full_signature: private IReaction readReaction(IChemObjectBuilder builder)
focal_class.identifier: readReaction
focal_class.modifiers: private
focal_class.parameters: (IChemObjectBuilder builder)
focal_class.return: IReaction
focal_class.signature: IReaction readReaction(IChemObjectBuilder builder)
focal_class.class_method_signature: MDLRXNV2000Reader.processMol(IAtomContainer mol, List<IAtomContainer> components, StringBuilder sb)
focal_class.full_signature: private void processMol(IAtomContainer mol, List<IAtomContainer> components, StringBuilder sb)
focal_class.identifier: processMol
focal_class.modifiers: private
focal_class.parameters: (IAtomContainer mol, List<IAtomContainer> components, StringBuilder sb)
focal_class.return: void
focal_class.signature: void processMol(IAtomContainer mol, List<IAtomContainer> components, StringBuilder sb)
focal_class.class_method_signature: MDLRXNV2000Reader.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.superclass: extends DefaultChemObjectReader
focal_method.body: @Override
      public <T extends IChemObject> T read(T object) throws CDKException {
          if (object instanceof IReaction) {
              return (T) readReaction(object.getBuilder());
          } else if (object instanceof IReactionSet) {
              IReactionSet reactionSet = object.getBuilder().newInstance(IReactionSet.class);
              reactionSet.addReaction(readReaction(object.getBuilder()));
              return (T) reactionSet;
          } else if (object instanceof IChemModel) {
              IChemModel model = object.getBuilder().newInstance(IChemModel.class);
              IReactionSet reactionSet = object.getBuilder().newInstance(IReactionSet.class);
              reactionSet.addReaction(readReaction(object.getBuilder()));
              model.setReactionSet(reactionSet);
              return (T) model;
          } else if (object instanceof IChemFile) {
              IChemFile chemFile = object.getBuilder().newInstance(IChemFile.class);
              IChemSequence sequence = object.getBuilder().newInstance(IChemSequence.class);
              sequence.addChemModel((IChemModel) read(object.getBuilder().newInstance(IChemModel.class)));
              chemFile.addChemSequence(sequence);
              return (T) chemFile;
          } else {
              throw new CDKException("Only supported are Reaction and ChemModel, and not " + object.getClass().getName()
                      + ".");
          }
      }
focal_method.class_method_signature: MDLRXNV2000Reader.read(T object)
focal_method.full_signature: @Override public T read(T object)
focal_method.identifier: read
focal_method.invocations: readReaction getBuilder newInstance getBuilder addReaction readReaction getBuilder newInstance getBuilder newInstance getBuilder addReaction readReaction getBuilder setReactionSet newInstance getBuilder newInstance getBuilder addChemModel read newInstance getBuilder addChemSequence getName getClass
focal_method.modifiers: @Override public
focal_method.parameters: (T object)
focal_method.return: T
focal_method.signature: T read(T object)