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
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.
- 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
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Nested Class Summary
Nested classes/interfaces inherited from interface org.openscience.cdk.io.IChemObjectReader
IChemObjectReader.Mode
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Field Summary
FieldsModifier and TypeFieldDescriptionstatic final boolean
Boolean constant used to specify that the coordinates are given in Ångstrom units.static final double
Double constant that contains the conversion factor from Bohr unit to Ångstrom unit.static final boolean
Boolean constant used to specify that the coordinates are given in Bohr units.static final String
Fields inherited from class org.openscience.cdk.io.DefaultChemObjectReader
errorHandler, mode
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Constructor Summary
ConstructorsConstructorDescriptionGamessReader
(InputStream input) GamessReader
(Reader inputReader) Constructs a new "GamessReader" object given a "Reader" object as input. -
Method Summary
Modifier and TypeMethodDescriptionboolean
accepts
(Class<? extends IChemObject> classObject) Returns whether the givenIChemObject
can be read or written.void
close()
Closes this IChemObjectIO's resources.Returns theIResourceFormat
class for this IO class.<T extends IChemObject>
Tread
(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
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
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Field Details
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BOHR_UNIT
public static final boolean BOHR_UNITBoolean constant used to specify that the coordinates are given in Bohr units.- See Also:
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BOHR_TO_ANGSTROM
public static final double BOHR_TO_ANGSTROMDouble constant that contains the conversion factor from Bohr unit to Ångstrom unit.- See Also:
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ANGSTROM_UNIT
public static final boolean ANGSTROM_UNITBoolean constant used to specify that the coordinates are given in Ångstrom units.- See Also:
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UNEXPECTED_END_OF_INPUT
- See Also:
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Constructor Details
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GamessReader
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" seeaccepts(IChemObject)
method documentation.- Parameters:
inputReader
- The "Reader" object given as input parameter.- See Also:
-
GamessReader
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GamessReader
public GamessReader()
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Method Details
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getFormat
Description copied from interface:IChemObjectIO
Returns theIResourceFormat
class for this IO class. -
setReader
Description copied from interface:IChemObjectReader
Sets the Reader from which this ChemObjectReader should read the contents.- Throws:
CDKException
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setReader
Description copied from interface:IChemObjectReader
Sets the InputStream from which this ChemObjectReader should read the contents.- Throws:
CDKException
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accepts
Description copied from interface:IChemObjectIO
Returns whether the givenIChemObject
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.
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read
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
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close
Description copied from interface:IChemObjectIO
Closes this IChemObjectIO's resources.- Throws:
IOException
- when the wrapper IO class cannot be closed.
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