test_class.file: storage/ctab/src/test/java/org/openscience/cdk/io/MDLV3000WriterTest.java
test_class.identifier: MDLV3000WriterTest
test_case.body: @Test
      public void writeDimensionField() throws Exception {
          IChemObjectBuilder builder = SilentChemObjectBuilder.getInstance();
          IAtomContainer mol = builder.newAtomContainer();
          IAtom atom = builder.newAtom();
          atom.setSymbol("C");
          atom.setImplicitHydrogenCount(4);
          atom.setPoint2d(new Point2d(0.5, 0.5));
          mol.addAtom(atom);
          StringWriter sw = new StringWriter();
          try (MDLV3000Writer mdlw = new MDLV3000Writer(sw)) {
              mdlw.write(mol);
          }
          assertThat(sw.toString(), containsString("2D"));
      }
test_case.class_method_signature: MDLV3000WriterTest.writeDimensionField()
test_case.full_signature: @Test public void writeDimensionField()
test_case.identifier: writeDimensionField
test_case.invocations: getInstance newAtomContainer newAtom setSymbol setImplicitHydrogenCount setPoint2d addAtom write assertThat toString containsString
test_case.modifiers: @Test public
test_case.parameters: ()
test_case.return: void
test_case.signature: void writeDimensionField()
focal_class.declarator: R_GRP_NUM = Pattern.compile("R(\\d+)")
focal_class.modifier: private static final
focal_class.original_string: private static final Pattern         R_GRP_NUM = Pattern.compile("R(\\d+)");
focal_class.type: Pattern
focal_class.var_name: R_GRP_NUM
focal_class.declarator: writer
focal_class.modifier: private
focal_class.original_string: private              V30LineWriter   writer;
focal_class.type: V30LineWriter
focal_class.var_name: writer
focal_class.declarator: programNameOpt
focal_class.modifier: private
focal_class.original_string: private              StringIOSetting programNameOpt;
focal_class.type: StringIOSetting
focal_class.var_name: programNameOpt
focal_class.file: storage/ctab/src/main/java/org/openscience/cdk/io/MDLV3000Writer.java
focal_class.identifier: MDLV3000Writer
focal_class.class_method_signature: MDLV3000Writer.MDLV3000Writer(Writer writer)
focal_class.full_signature: public  MDLV3000Writer(Writer writer)
focal_class.identifier: MDLV3000Writer
focal_class.modifiers: public
focal_class.parameters: (Writer writer)
focal_class.signature:  MDLV3000Writer(Writer writer)
focal_class.class_method_signature: MDLV3000Writer.MDLV3000Writer(OutputStream out)
focal_class.full_signature: public  MDLV3000Writer(OutputStream out)
focal_class.identifier: MDLV3000Writer
focal_class.modifiers: public
focal_class.parameters: (OutputStream out)
focal_class.signature:  MDLV3000Writer(OutputStream out)
focal_class.class_method_signature: MDLV3000Writer.MDLV3000Writer()
focal_class.full_signature: public  MDLV3000Writer()
focal_class.identifier: MDLV3000Writer
focal_class.modifiers: public
focal_class.parameters: ()
focal_class.signature:  MDLV3000Writer()
focal_class.class_method_signature: MDLV3000Writer.nullAsZero(Integer x)
focal_class.full_signature: private static int nullAsZero(Integer x)
focal_class.identifier: nullAsZero
focal_class.modifiers: private static
focal_class.parameters: (Integer x)
focal_class.return: int
focal_class.signature: int nullAsZero(Integer x)
focal_class.class_method_signature: MDLV3000Writer.findIdx(Map<T, Integer> idxs, T obj)
focal_class.full_signature: private static Integer findIdx(Map<T, Integer> idxs, T obj)
focal_class.identifier: findIdx
focal_class.modifiers: private static
focal_class.parameters: (Map<T, Integer> idxs, T obj)
focal_class.return: Integer
focal_class.signature: Integer findIdx(Map<T, Integer> idxs, T obj)
focal_class.class_method_signature: MDLV3000Writer.getProgName()
focal_class.full_signature: private String getProgName()
focal_class.identifier: getProgName
focal_class.modifiers: private
focal_class.parameters: ()
focal_class.return: String
focal_class.signature: String getProgName()
focal_class.class_method_signature: MDLV3000Writer.writeHeader(IAtomContainer mol)
focal_class.full_signature: private void writeHeader(IAtomContainer mol)
focal_class.identifier: writeHeader
focal_class.modifiers: private
focal_class.parameters: (IAtomContainer mol)
focal_class.return: void
focal_class.signature: void writeHeader(IAtomContainer mol)
focal_class.class_method_signature: MDLV3000Writer.getLocalParity(Map<IChemObject, Integer> idxs, ITetrahedralChirality stereo)
focal_class.full_signature: private static Stereo getLocalParity(Map<IChemObject, Integer> idxs, ITetrahedralChirality stereo)
focal_class.identifier: getLocalParity
focal_class.modifiers: private static
focal_class.parameters: (Map<IChemObject, Integer> idxs, ITetrahedralChirality stereo)
focal_class.return: Stereo
focal_class.signature: Stereo getLocalParity(Map<IChemObject, Integer> idxs, ITetrahedralChirality stereo)
focal_class.class_method_signature: MDLV3000Writer.writeAtomBlock(IAtomContainer mol, IAtom[] atoms, Map<IChemObject, Integer> idxs,
                                  Map<IAtom, ITetrahedralChirality> atomToStereo)
focal_class.full_signature: private void writeAtomBlock(IAtomContainer mol, IAtom[] atoms, Map<IChemObject, Integer> idxs,
                                  Map<IAtom, ITetrahedralChirality> atomToStereo)
focal_class.identifier: writeAtomBlock
focal_class.modifiers: private
focal_class.parameters: (IAtomContainer mol, IAtom[] atoms, Map<IChemObject, Integer> idxs,
                                  Map<IAtom, ITetrahedralChirality> atomToStereo)
focal_class.return: void
focal_class.signature: void writeAtomBlock(IAtomContainer mol, IAtom[] atoms, Map<IChemObject, Integer> idxs,
                                  Map<IAtom, ITetrahedralChirality> atomToStereo)
focal_class.class_method_signature: MDLV3000Writer.getSymbol(IAtom atom, int elem)
focal_class.full_signature: private String getSymbol(IAtom atom, int elem)
focal_class.identifier: getSymbol
focal_class.modifiers: private
focal_class.parameters: (IAtom atom, int elem)
focal_class.return: String
focal_class.signature: String getSymbol(IAtom atom, int elem)
focal_class.class_method_signature: MDLV3000Writer.writeBondBlock(IAtomContainer mol,
                                  Map<IChemObject, Integer> idxs)
focal_class.full_signature: private void writeBondBlock(IAtomContainer mol,
                                  Map<IChemObject, Integer> idxs)
focal_class.identifier: writeBondBlock
focal_class.modifiers: private
focal_class.parameters: (IAtomContainer mol,
                                  Map<IChemObject, Integer> idxs)
focal_class.return: void
focal_class.signature: void writeBondBlock(IAtomContainer mol,
                                  Map<IChemObject, Integer> idxs)
focal_class.class_method_signature: MDLV3000Writer.pushHydrogensToBack(IAtomContainer mol, Map<IChemObject, Integer> atomToIdx)
focal_class.full_signature: private IAtom[] pushHydrogensToBack(IAtomContainer mol, Map<IChemObject, Integer> atomToIdx)
focal_class.identifier: pushHydrogensToBack
focal_class.modifiers: private
focal_class.parameters: (IAtomContainer mol, Map<IChemObject, Integer> atomToIdx)
focal_class.return: IAtom[]
focal_class.signature: IAtom[] pushHydrogensToBack(IAtomContainer mol, Map<IChemObject, Integer> atomToIdx)
focal_class.class_method_signature: MDLV3000Writer.getSgroups(IAtomContainer mol)
focal_class.full_signature: private List<Sgroup> getSgroups(IAtomContainer mol)
focal_class.identifier: getSgroups
focal_class.modifiers: private
focal_class.parameters: (IAtomContainer mol)
focal_class.return: List<Sgroup>
focal_class.signature: List<Sgroup> getSgroups(IAtomContainer mol)
focal_class.class_method_signature: MDLV3000Writer.getNumberOfDimensions(IAtomContainer mol)
focal_class.full_signature: private int getNumberOfDimensions(IAtomContainer mol)
focal_class.identifier: getNumberOfDimensions
focal_class.modifiers: private
focal_class.parameters: (IAtomContainer mol)
focal_class.return: int
focal_class.signature: int getNumberOfDimensions(IAtomContainer mol)
focal_class.class_method_signature: MDLV3000Writer.writeSgroupBlock(List<Sgroup> sgroups, Map<IChemObject, Integer> idxs)
focal_class.full_signature: private void writeSgroupBlock(List<Sgroup> sgroups, Map<IChemObject, Integer> idxs)
focal_class.identifier: writeSgroupBlock
focal_class.modifiers: private
focal_class.parameters: (List<Sgroup> sgroups, Map<IChemObject, Integer> idxs)
focal_class.return: void
focal_class.signature: void writeSgroupBlock(List<Sgroup> sgroups, Map<IChemObject, Integer> idxs)
focal_class.class_method_signature: MDLV3000Writer.writeMol(IAtomContainer mol)
focal_class.full_signature: private void writeMol(IAtomContainer mol)
focal_class.identifier: writeMol
focal_class.modifiers: private
focal_class.parameters: (IAtomContainer mol)
focal_class.return: void
focal_class.signature: void writeMol(IAtomContainer mol)
focal_class.class_method_signature: MDLV3000Writer.write(IChemObject object)
focal_class.full_signature: @Override public void write(IChemObject object)
focal_class.identifier: write
focal_class.modifiers: @Override public
focal_class.parameters: (IChemObject object)
focal_class.return: void
focal_class.signature: void write(IChemObject object)
focal_class.class_method_signature: MDLV3000Writer.setWriter(Writer writer)
focal_class.full_signature: @Override public void setWriter(Writer writer)
focal_class.identifier: setWriter
focal_class.modifiers: @Override public
focal_class.parameters: (Writer writer)
focal_class.return: void
focal_class.signature: void setWriter(Writer writer)
focal_class.class_method_signature: MDLV3000Writer.setWriter(OutputStream writer)
focal_class.full_signature: @Override public void setWriter(OutputStream writer)
focal_class.identifier: setWriter
focal_class.modifiers: @Override public
focal_class.parameters: (OutputStream writer)
focal_class.return: void
focal_class.signature: void setWriter(OutputStream writer)
focal_class.class_method_signature: MDLV3000Writer.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: MDLV3000Writer.accepts(Class<? extends IChemObject> c)
focal_class.full_signature: @Override public boolean accepts(Class<? extends IChemObject> c)
focal_class.identifier: accepts
focal_class.modifiers: @Override public
focal_class.parameters: (Class<? extends IChemObject> c)
focal_class.return: boolean
focal_class.signature: boolean accepts(Class<? extends IChemObject> c)
focal_class.class_method_signature: MDLV3000Writer.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: MDLV3000Writer.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: MDLV3000Writer.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.superclass: extends DefaultChemObjectWriter
focal_method.body: @Override
      public void write(IChemObject object) throws CDKException {
          try {
              if (IAtomContainer.class.isInstance(object))
                  writeMol((IAtomContainer) object);
              else
                  throw new CDKException("Unsupported ChemObject " + object.getClass());
          } catch (IOException ex) {
              throw new CDKException("Could not write V3000 format", ex);
          }
      }
focal_method.class_method_signature: MDLV3000Writer.write(IChemObject object)
focal_method.full_signature: @Override public void write(IChemObject object)
focal_method.identifier: write
focal_method.invocations: isInstance writeMol getClass
focal_method.modifiers: @Override public
focal_method.parameters: (IChemObject object)
focal_method.return: void
focal_method.signature: void write(IChemObject object)