Class CIFReader

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

public class CIFReader extends DefaultChemObjectReader
This is not a reader for the CIF and mmCIF crystallographic formats. It is able, however, to extract some content from such files. It's very ad hoc, not written using any dictionary. So please complain if something is not working. In addition, the things it does read are considered experimental.

The CIF example on the IUCR website has been tested, as well as Crambin (1CRN) in the PDB database.

Author:
E.L. Willighagen
Source code:
main
Belongs to CDK module:
io
Keywords:
file format, CIF, file format, mmCIF
Created on:
2003-10-12
  • Constructor Details

    • CIFReader

      public CIFReader(Reader input)
      Create an CIF like file reader.
      Parameters:
      input - source of CIF data
    • CIFReader

      public CIFReader(InputStream input)
    • CIFReader

      public CIFReader()
  • Method Details

    • getFormat

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

      public void setReader(Reader reader) throws CDKException
      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
      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> testClass)
      Description copied from interface: IChemObjectIO
      Returns whether the given IChemObject can be read or written.
      Parameters:
      testClass - 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
      Read a ChemFile from input.
      Parameters:
      object - the type of object to return
      Returns:
      the content in a ChemFile object
      Throws:
      CDKException - it is thrown if the type of information is not available from the input
    • 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.