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 optionalSdfSeparator() throws Exception {
          String dummyRecord = "ethanol\n" +
                         "  Mrv1810 09251921392D          \n" +
                         "\n" +
                         "  3  2  0  0  0  0            999 V2000\n" +
                         "    1.9520   -1.1270    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0\n" +
                         "    1.2375   -0.7145    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0\n" +
                         "    2.6664   -0.7145    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0\n" +
                         "  1  2  1  0  0  0  0\n" +
                         "  1  3  1  0  0  0  0\n" +
                         "M  END\n" +
                         "$$$$\n";
          StringBuilder sb = new StringBuilder();
          sb.append("$RXN\n");
          sb.append("Test\n\n\n  2  1\n");
          sb.append("$MOL\n");
          sb.append(dummyRecord);
          sb.append("$MOL\n");
          sb.append(dummyRecord);
          sb.append("$MOL\n");
          sb.append(dummyRecord);
  
          IChemObjectBuilder bldr = SilentChemObjectBuilder.getInstance();
          try (MDLRXNV2000Reader reader = new MDLRXNV2000Reader(new StringReader(sb.toString()))) {
              IReaction rxn = reader.read(bldr.newInstance(IReaction.class));
              assertThat(rxn.getReactants().getAtomContainerCount(), is(2));
              assertThat(rxn.getProducts().getAtomContainerCount(), is(1));
              assertThat(rxn.getReactants().getAtomContainer(0).getAtomCount(), is(3));
              assertThat(rxn.getReactants().getAtomContainer(1).getAtomCount(), is(3));
          }
      }
test_case.class_method_signature: MDLRXNV2000ReaderTest.optionalSdfSeparator()
test_case.full_signature: @Test public void optionalSdfSeparator()
test_case.identifier: optionalSdfSeparator
test_case.invocations: append append append append append append append append getInstance toString read newInstance assertThat getAtomContainerCount getReactants is assertThat getAtomContainerCount getProducts is assertThat getAtomCount getAtomContainer getReactants is assertThat getAtomCount getAtomContainer getReactants is
test_case.modifiers: @Test public
test_case.parameters: ()
test_case.return: void
test_case.signature: void optionalSdfSeparator()
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)