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:

master

Belongs to CDK module:

extra

Keywords:

Gamess, file format, output, log file

Nested Class Summary

Nested classes/interfaces inherited from interface org.openscience.cdk.io.IChemObjectReader

IChemObjectReader.Mode

Field Summary

Fields

Modifier and Type	Field and Description
static boolean	ANGSTROM_UNIT Boolean constant used to specify that the coordinates are given in Ångstrom units.
static double	BOHR_TO_ANGSTROM Double constant that contains the conversion factor from Bohr unit to Ångstrom unit.
static boolean	BOHR_UNIT Boolean constant used to specify that the coordinates are given in Bohr units.

Fields inherited from class org.openscience.cdk.io.DefaultChemObjectReader

errorHandler, mode

Constructor Summary

Constructors

Constructor and Description
GamessReader()
GamessReader(InputStream input)
GamessReader(Reader inputReader) Constructs a new "GamessReader" object given a "Reader" object as input.

Method Summary

Modifier and Type	Method and Description
boolean	accepts(Class<? extends IChemObject> classObject) Returns whether the given IChemObject can be read or written.
void	close() Closes this IChemObjectIO's resources.
IResourceFormat	getFormat() Returns the IResourceFormat class for this IO class.
<T extends IChemObject> T	read(T object) Reads an IChemObject of type "object" from input.
void	setReader(InputStream input) Sets the InputStream from which this ChemObjectReader should read the contents.
void	setReader(Reader reader) Sets the Reader from which this ChemObjectReader should read the contents.

Methods inherited from class org.openscience.cdk.io.DefaultChemObjectReader

fireFrameRead, handleError, handleError, handleError, handleError, setErrorHandler, setReaderMode

Methods inherited from class org.openscience.cdk.io.ChemObjectIO

addChemObjectIOListener, addSetting, addSettings, fireIOSettingQuestion, getIOSettings, getListeners, getSetting, getSetting, getSettings, hasSetting, removeChemObjectIOListener

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Methods inherited from interface org.openscience.cdk.io.IChemObjectIO

addChemObjectIOListener, addSetting, addSettings, getIOSettings, getListeners, getSetting, getSetting, getSettings, hasSetting, removeChemObjectIOListener

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

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.