Package org.openscience.cdk.io

Class 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 Detail

      • BOHR_UNIT

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

      • 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:
        Constant Field Values

      • ANGSTROM_UNIT

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

    • Constructor Detail

      • 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:
        accepts(Class), Reader

      • GamessReader

        public GamessReader​(InputStream input)

      • GamessReader

        public GamessReader()

    • Method Detail

      • 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.