Class MDLReader

All Implemented Interfaces:
Closeable, AutoCloseable, IChemObjectIO, IChemObjectReader, ISimpleChemObjectReader

@Deprecated public class MDLReader extends DefaultChemObjectReader
Deprecated.
This reader is only for molfiles without a version tag, typically the most common molfile now encountered is V2000 and the MDLV2000Reader should be used instead. The V2000 reader can actually read files missing the version tag when in relaxed mode.
Reads a molecule from the original MDL MOL or SDF file [Dalby, A. et. al.. Journal of Chemical Information and Computer Sciences. 1992. 32]. An SD files is read into a IChemSequence of IChemModel's. Each ChemModel will contain one Molecule. If the MDL molfile contains a property block, the MDLV2000Reader should be used.

If all z coordinates are 0.0, then the xy coordinates are taken as 2D, otherwise the coordinates are read as 3D.

The title of the MOL file is read and can be retrieved with:

   molecule.getProperty(CDKConstants.TITLE);
 
Author:
steinbeck, Egon Willighagen
See Also:
Source code:
main
IO options:
NameQuestionDefault
ForceReadAs3DCoordinatesShould coordinates always be read as 3D?false
Belongs to CDK module:
io
Keywords:
file format, MDL molfile, file format, SDF
Created on:
2000-10-02
  • Constructor Details

    • MDLReader

      public MDLReader()
      Deprecated.
    • MDLReader

      public MDLReader(InputStream in)
      Deprecated.
      Constructs a new MDLReader that can read Molecule from a given InputStream.
      Parameters:
      in - The InputStream to read from
    • MDLReader

      public MDLReader(InputStream in, IChemObjectReader.Mode mode)
      Deprecated.
    • MDLReader

      public MDLReader(Reader in)
      Deprecated.
      Constructs a new MDLReader that can read Molecule from a given Reader.
      Parameters:
      in - The Reader to read from
    • MDLReader

      public MDLReader(Reader in, IChemObjectReader.Mode mode)
      Deprecated.
  • Method Details

    • getFormat

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

      public void setReader(Reader input) throws CDKException
      Deprecated.
      Description copied from interface: IChemObjectReader
      Sets the Reader from which this ChemObjectReader should read the contents.
      Throws:
      CDKException
    • setReader

      public void setReader(InputStream input) throws CDKException
      Deprecated.
      Description copied from interface: IChemObjectReader
      Sets the InputStream from which this ChemObjectReader should read the contents.
      Throws:
      CDKException
    • accepts

      public boolean accepts(Class<? extends IChemObject> classObject)
      Deprecated.
      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.
    • read

      public <T extends IChemObject> T read(T object) throws CDKException
      Deprecated.
      Takes an object which subclasses IChemObject, e.g. Molecule, and will read this (from file, database, internet etc). If the specific implementation does not support a specific IChemObject it will throw an Exception.
      Parameters:
      object - The object that subclasses IChemObject
      Returns:
      The IChemObject read
      Throws:
      CDKException
    • close

      public void close() throws IOException
      Deprecated.
      Description copied from interface: IChemObjectIO
      Closes this IChemObjectIO's resources.
      Throws:
      IOException - when the wrapper IO class cannot be closed.
    • customizeJob

      public void customizeJob()
      Deprecated.