Class MDLRXNWriter

All Implemented Interfaces:
Closeable, AutoCloseable, IChemObjectIO, IChemObjectWriter

public class MDLRXNWriter extends DefaultChemObjectWriter
Writes a reaction to a MDL rxn or SDF file. Attention: Stoichiometric coefficients have to be natural numbers.
 MDLRXNWriter writer = new MDLRXNWriter(new FileWriter(new File("output.mol")));
 writer.write((Molecule)molecule);
 writer.close();
 
See [Dalby, A. et. al.. Journal of Chemical Information and Computer Sciences. 1992. 32].
Source code:
main
IO options:
NameQuestionDefault
WriteAgentsOutput agents in the RXN filetrue
Belongs to CDK module:
io
Keywords:
file format, MDL RXN file
  • Field Details

  • Constructor Details

    • MDLRXNWriter

      public MDLRXNWriter(Writer out)
      Constructs a new MDLWriter that can write an array of Molecules to a Writer.
      Parameters:
      out - The Writer to write to
    • MDLRXNWriter

      public MDLRXNWriter(OutputStream output)
      Constructs a new MDLWriter that can write an array of Molecules to a given OutputStream.
      Parameters:
      output - The OutputStream to write to
    • MDLRXNWriter

      public MDLRXNWriter()
  • Method Details

    • getFormat

      public IResourceFormat getFormat()
      Description copied from interface: IChemObjectIO
      Returns the IResourceFormat class for this IO class.
    • setWriter

      public void setWriter(Writer out) throws CDKException
      Description copied from interface: IChemObjectWriter
      Sets the Writer from which this ChemObjectWriter should write the contents.
      Throws:
      CDKException
    • setWriter

      public void setWriter(OutputStream output) throws CDKException
      Description copied from interface: IChemObjectWriter
      Sets the OutputStream from which this ChemObjectWriter should write the contents.
      Throws:
      CDKException
    • setRdFields

      public void setRdFields(Map<String,Object> map)
      Here you can set a map which will be used to build rd fields in the file. The entries will be translated to rd fields like this:
      > <key>
      > value
      empty line
      Parameters:
      map - The map to be used, map of String-String pairs
    • close

      public void close() throws IOException
      Flushes the output and closes this object.
      Throws:
      IOException - when the wrapper IO class cannot be closed.
    • accepts

      public boolean accepts(Class<? extends IChemObject> classObject)
      Description copied from interface: IChemObjectIO
      Returns whether the given IChemObject can be read or written.
      Parameters:
      classObject - IChemObject of which is tested if it can be handled.
      Returns:
      true, if the IChemObject can be handled.
    • write

      public void write(IChemObject object) throws CDKException
      Writes a IChemObject to the MDL RXN file formated output. It can only output ChemObjects of type Reaction
      Parameters:
      object - class must be of type Molecule or MoleculeSet.
      Throws:
      CDKException - is thrown if the output does not support the data in the object
      See Also: