Package org.openscience.cdk.io

Class GamessReader

java.lang.Object
org.openscience.cdk.io.ChemObjectIO
org.openscience.cdk.io.DefaultChemObjectReader
org.openscience.cdk.io.GamessReader
All Implemented Interfaces:
Closeable, AutoCloseable, IChemObjectIO, IChemObjectReader, ISimpleChemObjectReader
public class GamessReader extends DefaultChemObjectReader
A reader for GAMESS log file.

Expected behaviour:
The "GamessReader" object is able to read GAMESS output log file format.

Limitations:
This reader was developed from a small set of example log files, and therefore, is not guaranteed to properly read all GAMESS output. If you have problems, please contact the author of this code, not the developers of GAMESS.

Implementation
Available feature(s):

  • Molecular coordinates: Each set of coordinates is added to the ChemFile in the order they are found.
Unavailable feature(s):
  • Energies: They are associated with the previously read set of coordinates.
  • Normal coordinates of vibrations: They are associated with the previously read set of coordinates.

References:
GAMESS is a quantum chemistry program by Gordon research group atIowa State University.

Author:
Bradley A. Smith
Source code:
main
Belongs to CDK module:
extra
Keywords:
Gamess, file format, output, log file

  • Field Details

    • BOHR_UNIT

      public static final boolean BOHR_UNIT
      Boolean constant used to specify that the coordinates are given in Bohr units.
      See Also:

    • BOHR_TO_ANGSTROM

      public static final double BOHR_TO_ANGSTROM
      Double constant that contains the conversion factor from Bohr unit to Ångstrom unit.
      See Also:

    • ANGSTROM_UNIT

      public static final boolean ANGSTROM_UNIT
      Boolean constant used to specify that the coordinates are given in Ångstrom units.
      See Also:

    • UNEXPECTED_END_OF_INPUT

      public static final String UNEXPECTED_END_OF_INPUT
      See Also:

  • Constructor Details

    • GamessReader

      public GamessReader(Reader inputReader)
      Constructs a new "GamessReader" object given a "Reader" object as input.

      The "Reader" object may be an instantiable object from the "Reader" hierarchy.
      For more detail about the "Reader" objects that are really accepted by this "GamessReader" see accepts(IChemObject) method documentation.

      Parameters:
      inputReader - The "Reader" object given as input parameter.
      See Also:

    • GamessReader

      public GamessReader(InputStream input)

    • GamessReader

      public GamessReader()

  • 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> 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.

    • read

      public <T extends IChemObject> T read(T object) throws CDKException
      Description copied from interface: ISimpleChemObjectReader
      Reads an IChemObject of type "object" from input. The constructor of the actual implementation may take a Reader as input to get a very flexible reader that can read from string, files, etc.
      Parameters:
      object - the type of object to return
      Returns:
      returns an object of that contains the content (or part) of the input content
      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.