Class RGroupQueryReader

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

public class RGroupQueryReader extends DefaultChemObjectReader
A reader for Symyx' Rgroup files (RGFiles). An RGfile describes a single molecular query with Rgroups. Each RGfile is a combination of Ctabs defining the root molecule and each member of each Rgroup in the query.

The RGFile format is described in the manual "CTFile Formats" , Chapter 5.

Author:
Mark Rijnbeek
Source code:
main
Belongs to CDK module:
io
Keywords:
Rgroup, R group, R-group
  • Constructor Details

    • RGroupQueryReader

      public RGroupQueryReader()
      Default constructor, input not set.
    • RGroupQueryReader

      public RGroupQueryReader(InputStream in)
      Constructs a new RgroupQueryReader that can read RgroupAtomContainerSet from a given InputStream.
      Parameters:
      in - The InputStream to read from.
    • RGroupQueryReader

      public RGroupQueryReader(Reader in)
      Constructs a new RgroupQueryReader that can read RgroupAtomContainerSet from a given Reader.
      Parameters:
      in - The Reader to read from.
  • Method Details

    • setReader

      public void setReader(Reader input) throws CDKException
      Sets the input Reader.
      Parameters:
      input - Reader object
      Throws:
      CDKException
    • setReader

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

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

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

      public <T extends IChemObject> T read(T object) throws CDKException
      Check input IChemObject and proceed to parse. Accepts/returns IChemObject of type RGroupQuery only.
      Parameters:
      object - class must be of type RGroupQuery
      Returns:
      IChemObject read from file
      Throws:
      CDKException - it is thrown if the type of information is not available from the input