test_class.declarator: builder
test_class.modifier: private static
test_class.original_string: private static IChemObjectBuilder builder;
test_class.type: IChemObjectBuilder
test_class.var_name: builder
test_class.file: storage/ctab/src/test/java/org/openscience/cdk/io/MDLV2000WriterTest.java
test_class.identifier: MDLV2000WriterTest
test_class.superclass: extends ChemObjectIOTest
test_case.body: @Test
      public void writeDimensionField3D() throws Exception {
          IAtomContainer mol  = builder.newAtomContainer();
          IAtom          atom = builder.newAtom();
          atom.setSymbol("C");
          atom.setImplicitHydrogenCount(4);
          atom.setPoint3d(new Point3d(0.5, 0.5, 0.1));
          mol.addAtom(atom);
          StringWriter sw = new StringWriter();
          try (MDLV2000Writer mdlw = new MDLV2000Writer(sw)) {
              mdlw.write(mol);
          }
          assertThat(sw.toString(), containsString("3D"));
      }
test_case.class_method_signature: MDLV2000WriterTest.writeDimensionField3D()
test_case.full_signature: @Test public void writeDimensionField3D()
test_case.identifier: writeDimensionField3D
test_case.invocations: newAtomContainer newAtom setSymbol setImplicitHydrogenCount setPoint3d addAtom write assertThat toString containsString
test_case.modifiers: @Test public
test_case.parameters: ()
test_case.return: void
test_case.signature: void writeDimensionField3D()
focal_class.declarator: OptForceWriteAs2DCoordinates = "ForceWriteAs2DCoordinates"
focal_class.modifier: public static final
focal_class.original_string: public static final String OptForceWriteAs2DCoordinates = "ForceWriteAs2DCoordinates";
focal_class.type: String
focal_class.var_name: OptForceWriteAs2DCoordinates
focal_class.declarator: OptWriteMajorIsotopes        = "WriteMajorIsotopes"
focal_class.modifier: public static final
focal_class.original_string: public static final String OptWriteMajorIsotopes        = "WriteMajorIsotopes";
focal_class.type: String
focal_class.var_name: OptWriteMajorIsotopes
focal_class.declarator: OptWriteAromaticBondTypes    = "WriteAromaticBondTypes"
focal_class.modifier: public static final
focal_class.original_string: public static final String OptWriteAromaticBondTypes    = "WriteAromaticBondTypes";
focal_class.type: String
focal_class.var_name: OptWriteAromaticBondTypes
focal_class.declarator: OptWriteQueryFormatValencies = "WriteQueryFormatValencies"
focal_class.modifier: public static final
focal_class.original_string: public static final String OptWriteQueryFormatValencies = "WriteQueryFormatValencies";
focal_class.type: String
focal_class.var_name: OptWriteQueryFormatValencies
focal_class.declarator: OptWriteDefaultProperties    = "WriteDefaultProperties"
focal_class.modifier: public static final
focal_class.original_string: public static final String OptWriteDefaultProperties    = "WriteDefaultProperties";
focal_class.type: String
focal_class.var_name: OptWriteDefaultProperties
focal_class.declarator: OptProgramName               = "ProgramName"
focal_class.modifier: public static final
focal_class.original_string: public static final String OptProgramName               = "ProgramName";
focal_class.type: String
focal_class.var_name: OptProgramName
focal_class.declarator: logger = LoggingToolFactory.createLoggingTool(MDLV2000Writer.class)
focal_class.modifier: private final static
focal_class.original_string: private final static ILoggingTool logger = LoggingToolFactory.createLoggingTool(MDLV2000Writer.class);
focal_class.type: ILoggingTool
focal_class.var_name: logger
focal_class.declarator: NUMERED_R_GROUP = Pattern.compile("R(\\d+)")
focal_class.modifier: private
focal_class.original_string: private Pattern NUMERED_R_GROUP = Pattern.compile("R(\\d+)");
focal_class.type: Pattern
focal_class.var_name: NUMERED_R_GROUP
focal_class.declarator: NN8   = 8
focal_class.modifier: private static final
focal_class.original_string: private static final int NN8   = 8;
focal_class.type: int
focal_class.var_name: NN8
focal_class.declarator: WIDTH = 3
focal_class.modifier: private static final
focal_class.original_string: private static final int WIDTH = 3;
focal_class.type: int
focal_class.var_name: WIDTH
focal_class.declarator: forceWriteAs2DCoords
focal_class.modifier: private
focal_class.original_string: private BooleanIOSetting forceWriteAs2DCoords;
focal_class.type: BooleanIOSetting
focal_class.var_name: forceWriteAs2DCoords
focal_class.declarator: writeMajorIsotopes
focal_class.modifier: private
focal_class.original_string: private BooleanIOSetting writeMajorIsotopes;
focal_class.type: BooleanIOSetting
focal_class.var_name: writeMajorIsotopes
focal_class.declarator: writeAromaticBondTypes
focal_class.modifier: private
focal_class.original_string: private BooleanIOSetting writeAromaticBondTypes;
focal_class.type: BooleanIOSetting
focal_class.var_name: writeAromaticBondTypes
focal_class.declarator: writeQueryFormatValencies
focal_class.modifier: @Deprecated
      private
focal_class.original_string: @Deprecated
      private BooleanIOSetting writeQueryFormatValencies;
focal_class.type: BooleanIOSetting
focal_class.var_name: writeQueryFormatValencies
focal_class.declarator: writeDefaultProps
focal_class.modifier: private
focal_class.original_string: private BooleanIOSetting writeDefaultProps;
focal_class.type: BooleanIOSetting
focal_class.var_name: writeDefaultProps
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.declarator: writer
focal_class.modifier: private
focal_class.original_string: private BufferedWriter writer;
focal_class.type: BufferedWriter
focal_class.var_name: writer
focal_class.file: storage/ctab/src/main/java/org/openscience/cdk/io/MDLV2000Writer.java
focal_class.identifier: MDLV2000Writer
focal_class.class_method_signature: MDLV2000Writer.MDLV2000Writer(Writer out)
focal_class.full_signature: public  MDLV2000Writer(Writer out)
focal_class.identifier: MDLV2000Writer
focal_class.modifiers: public
focal_class.parameters: (Writer out)
focal_class.signature:  MDLV2000Writer(Writer out)
focal_class.class_method_signature: MDLV2000Writer.MDLV2000Writer(OutputStream output)
focal_class.full_signature: public  MDLV2000Writer(OutputStream output)
focal_class.identifier: MDLV2000Writer
focal_class.modifiers: public
focal_class.parameters: (OutputStream output)
focal_class.signature:  MDLV2000Writer(OutputStream output)
focal_class.class_method_signature: MDLV2000Writer.MDLV2000Writer()
focal_class.full_signature: public  MDLV2000Writer()
focal_class.identifier: MDLV2000Writer
focal_class.modifiers: public
focal_class.parameters: ()
focal_class.signature:  MDLV2000Writer()
focal_class.class_method_signature: MDLV2000Writer.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: MDLV2000Writer.setWriter(Writer out)
focal_class.full_signature: @Override public void setWriter(Writer out)
focal_class.identifier: setWriter
focal_class.modifiers: @Override public
focal_class.parameters: (Writer out)
focal_class.return: void
focal_class.signature: void setWriter(Writer out)
focal_class.class_method_signature: MDLV2000Writer.setWriter(OutputStream output)
focal_class.full_signature: @Override public void setWriter(OutputStream output)
focal_class.identifier: setWriter
focal_class.modifiers: @Override public
focal_class.parameters: (OutputStream output)
focal_class.return: void
focal_class.signature: void setWriter(OutputStream output)
focal_class.class_method_signature: MDLV2000Writer.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: MDLV2000Writer.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: MDLV2000Writer.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: MDLV2000Writer.writeChemFile(IChemFile file)
focal_class.full_signature: private void writeChemFile(IChemFile file)
focal_class.identifier: writeChemFile
focal_class.modifiers: private
focal_class.parameters: (IChemFile file)
focal_class.return: void
focal_class.signature: void writeChemFile(IChemFile file)
focal_class.class_method_signature: MDLV2000Writer.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: MDLV2000Writer.writeMolecule(IAtomContainer container)
focal_class.full_signature: public void writeMolecule(IAtomContainer container)
focal_class.identifier: writeMolecule
focal_class.modifiers: public
focal_class.parameters: (IAtomContainer container)
focal_class.return: void
focal_class.signature: void writeMolecule(IAtomContainer container)
focal_class.class_method_signature: MDLV2000Writer.writeAtomLists(Map<Integer, IAtom> atomLists, BufferedWriter writer)
focal_class.full_signature: private static void writeAtomLists(Map<Integer, IAtom> atomLists, BufferedWriter writer)
focal_class.identifier: writeAtomLists
focal_class.modifiers: private static
focal_class.parameters: (Map<Integer, IAtom> atomLists, BufferedWriter writer)
focal_class.return: void
focal_class.signature: void writeAtomLists(Map<Integer, IAtom> atomLists, BufferedWriter writer)
focal_class.class_method_signature: MDLV2000Writer.isValidAtomListExpression(Expr exp)
focal_class.full_signature: private static boolean isValidAtomListExpression(Expr exp)
focal_class.identifier: isValidAtomListExpression
focal_class.modifiers: private static
focal_class.parameters: (Expr exp)
focal_class.return: boolean
focal_class.signature: boolean isValidAtomListExpression(Expr exp)
focal_class.class_method_signature: MDLV2000Writer.allOrsOfAllowedTypes(Expr expr, Set<Expr.Type> allowedTypes)
focal_class.full_signature: private static boolean allOrsOfAllowedTypes(Expr expr, Set<Expr.Type> allowedTypes)
focal_class.identifier: allOrsOfAllowedTypes
focal_class.modifiers: private static
focal_class.parameters: (Expr expr, Set<Expr.Type> allowedTypes)
focal_class.return: boolean
focal_class.signature: boolean allOrsOfAllowedTypes(Expr expr, Set<Expr.Type> allowedTypes)
focal_class.class_method_signature: MDLV2000Writer.getAtomList(Expr exp)
focal_class.full_signature: private static List<String> getAtomList(Expr exp)
focal_class.identifier: getAtomList
focal_class.modifiers: private static
focal_class.parameters: (Expr exp)
focal_class.return: List<String>
focal_class.signature: List<String> getAtomList(Expr exp)
focal_class.class_method_signature: MDLV2000Writer.getAtomListNumbers(Expr exp)
focal_class.full_signature: private static List<Integer> getAtomListNumbers(Expr exp)
focal_class.identifier: getAtomListNumbers
focal_class.modifiers: private static
focal_class.parameters: (Expr exp)
focal_class.return: List<Integer>
focal_class.signature: List<Integer> getAtomListNumbers(Expr exp)
focal_class.class_method_signature: MDLV2000Writer.getLeafNodes(Expr exr, List<Expr> elist)
focal_class.full_signature: private static void getLeafNodes(Expr exr, List<Expr> elist)
focal_class.identifier: getLeafNodes
focal_class.modifiers: private static
focal_class.parameters: (Expr exr, List<Expr> elist)
focal_class.return: void
focal_class.signature: void getLeafNodes(Expr exr, List<Expr> elist)
focal_class.class_method_signature: MDLV2000Writer.determineCharge(IAtomContainer mol, IAtom atom)
focal_class.full_signature: private int determineCharge(IAtomContainer mol, IAtom atom)
focal_class.identifier: determineCharge
focal_class.modifiers: private
focal_class.parameters: (IAtomContainer mol, IAtom atom)
focal_class.return: int
focal_class.signature: int determineCharge(IAtomContainer mol, IAtom atom)
focal_class.class_method_signature: MDLV2000Writer.determineIsotope(IAtom atom)
focal_class.full_signature: private int determineIsotope(IAtom atom)
focal_class.identifier: determineIsotope
focal_class.modifiers: private
focal_class.parameters: (IAtom atom)
focal_class.return: int
focal_class.signature: int determineIsotope(IAtom atom)
focal_class.class_method_signature: MDLV2000Writer.determineAtomMap(IAtom atom)
focal_class.full_signature: private int determineAtomMap(IAtom atom)
focal_class.identifier: determineAtomMap
focal_class.modifiers: private
focal_class.parameters: (IAtom atom)
focal_class.return: int
focal_class.signature: int determineAtomMap(IAtom atom)
focal_class.class_method_signature: MDLV2000Writer.determineValence(IAtomContainer container, IAtom atom)
focal_class.full_signature: private int determineValence(IAtomContainer container, IAtom atom)
focal_class.identifier: determineValence
focal_class.modifiers: private
focal_class.parameters: (IAtomContainer container, IAtom atom)
focal_class.return: int
focal_class.signature: int determineValence(IAtomContainer container, IAtom atom)
focal_class.class_method_signature: MDLV2000Writer.determineStereoParity(IAtomContainer container,
                                        Map<IAtom, ITetrahedralChirality> atomstereo,
                                        Map<IAtom, Integer> atomindex, IAtom atom)
focal_class.full_signature: private int determineStereoParity(IAtomContainer container,
                                        Map<IAtom, ITetrahedralChirality> atomstereo,
                                        Map<IAtom, Integer> atomindex, IAtom atom)
focal_class.identifier: determineStereoParity
focal_class.modifiers: private
focal_class.parameters: (IAtomContainer container,
                                        Map<IAtom, ITetrahedralChirality> atomstereo,
                                        Map<IAtom, Integer> atomindex, IAtom atom)
focal_class.return: int
focal_class.signature: int determineStereoParity(IAtomContainer container,
                                        Map<IAtom, ITetrahedralChirality> atomstereo,
                                        Map<IAtom, Integer> atomindex, IAtom atom)
focal_class.class_method_signature: MDLV2000Writer.isMajorIsotope(IAtom atom)
focal_class.full_signature: private boolean isMajorIsotope(IAtom atom)
focal_class.identifier: isMajorIsotope
focal_class.modifiers: private
focal_class.parameters: (IAtom atom)
focal_class.return: boolean
focal_class.signature: boolean isMajorIsotope(IAtom atom)
focal_class.class_method_signature: MDLV2000Writer.writeSgroups(IAtomContainer container, BufferedWriter writer, Map<IAtom,Integer> atomidxs)
focal_class.full_signature: private void writeSgroups(IAtomContainer container, BufferedWriter writer, Map<IAtom,Integer> atomidxs)
focal_class.identifier: writeSgroups
focal_class.modifiers: private
focal_class.parameters: (IAtomContainer container, BufferedWriter writer, Map<IAtom,Integer> atomidxs)
focal_class.return: void
focal_class.signature: void writeSgroups(IAtomContainer container, BufferedWriter writer, Map<IAtom,Integer> atomidxs)
focal_class.class_method_signature: MDLV2000Writer.wrap(Collection<T> set, int lim)
focal_class.full_signature: private List<List<T>> wrap(Collection<T> set, int lim)
focal_class.identifier: wrap
focal_class.modifiers: private
focal_class.parameters: (Collection<T> set, int lim)
focal_class.return: List<List<T>>
focal_class.signature: List<List<T>> wrap(Collection<T> set, int lim)
focal_class.class_method_signature: MDLV2000Writer.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: MDLV2000Writer.writeRadicalPattern(Iterator<Map.Entry<Integer, SPIN_MULTIPLICITY>> iterator, int i)
focal_class.full_signature: private void writeRadicalPattern(Iterator<Map.Entry<Integer, SPIN_MULTIPLICITY>> iterator, int i)
focal_class.identifier: writeRadicalPattern
focal_class.modifiers: private
focal_class.parameters: (Iterator<Map.Entry<Integer, SPIN_MULTIPLICITY>> iterator, int i)
focal_class.return: void
focal_class.signature: void writeRadicalPattern(Iterator<Map.Entry<Integer, SPIN_MULTIPLICITY>> iterator, int i)
focal_class.class_method_signature: MDLV2000Writer.formatMDLInt(int x, int n)
focal_class.full_signature: protected static String formatMDLInt(int x, int n)
focal_class.identifier: formatMDLInt
focal_class.modifiers: protected static
focal_class.parameters: (int x, int n)
focal_class.return: String
focal_class.signature: String formatMDLInt(int x, int n)
focal_class.class_method_signature: MDLV2000Writer.formatMDLFloat(float fl)
focal_class.full_signature: protected static String formatMDLFloat(float fl)
focal_class.identifier: formatMDLFloat
focal_class.modifiers: protected static
focal_class.parameters: (float fl)
focal_class.return: String
focal_class.signature: String formatMDLFloat(float fl)
focal_class.class_method_signature: MDLV2000Writer.formatMDLString(String s, int le)
focal_class.full_signature: protected static String formatMDLString(String s, int le)
focal_class.identifier: formatMDLString
focal_class.modifiers: protected static
focal_class.parameters: (String s, int le)
focal_class.return: String
focal_class.signature: String formatMDLString(String s, int le)
focal_class.class_method_signature: MDLV2000Writer.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: MDLV2000Writer.setWriteAromaticBondTypes(boolean val)
focal_class.full_signature: public void setWriteAromaticBondTypes(boolean val)
focal_class.identifier: setWriteAromaticBondTypes
focal_class.modifiers: public
focal_class.parameters: (boolean val)
focal_class.return: void
focal_class.signature: void setWriteAromaticBondTypes(boolean val)
focal_class.class_method_signature: MDLV2000Writer.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 {
          customizeJob();
          try {
              if (object instanceof IChemFile) {
                  writeChemFile((IChemFile) object);
                  return;
              } else if (object instanceof IChemModel) {
                  IChemFile file = object.getBuilder().newInstance(IChemFile.class);
                  IChemSequence sequence = object.getBuilder().newInstance(IChemSequence.class);
                  sequence.addChemModel((IChemModel) object);
                  file.addChemSequence(sequence);
                  writeChemFile((IChemFile) file);
                  return;
              } else if (object instanceof IAtomContainer) {
                  writeMolecule((IAtomContainer) object);
                  return;
              }
          } catch (Exception ex) {
              logger.error(ex.getMessage());
              logger.debug(ex);
              throw new CDKException("Exception while writing MDL file: " + ex.getMessage(), ex);
          }
          throw new CDKException("Only supported is writing of IChemFile, " + "IChemModel, and IAtomContainer objects.");
      }
focal_method.class_method_signature: MDLV2000Writer.write(IChemObject object)
focal_method.full_signature: @Override public void write(IChemObject object)
focal_method.identifier: write
focal_method.invocations: customizeJob writeChemFile newInstance getBuilder newInstance getBuilder addChemModel addChemSequence writeChemFile writeMolecule error getMessage debug getMessage
focal_method.modifiers: @Override public
focal_method.parameters: (IChemObject object)
focal_method.return: void
focal_method.signature: void write(IChemObject object)