Package org.openscience.cdk.io
Class Gaussian03Reader
- java.lang.Object
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- org.openscience.cdk.io.ChemObjectIO
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- org.openscience.cdk.io.DefaultChemObjectReader
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- org.openscience.cdk.io.Gaussian03Reader
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- All Implemented Interfaces:
Closeable
,AutoCloseable
,IChemObjectIO
,IChemObjectReader
,ISimpleChemObjectReader
public class Gaussian03Reader extends DefaultChemObjectReader
A reader for Gaussian03 output. Gaussian 03 is a quantum chemistry program by Gaussian, Inc. (http://www.gaussian.com/).Molecular coordinates, energies, and normal coordinates of vibrations are read. Each set of coordinates is added to the ChemFile in the order they are found. Energies and vibrations are associated with the previously read set of coordinates.
This reader was developed from a small set of example output files, and therefore, is not guaranteed to properly read all Gaussian03 output. If you have problems, please contact the author of this code, not the developers of Gaussian03.
This code was adaptated by Jonathan from Gaussian98Reader written by Bradley, and ported to CDK by Egon.
- Author:
- Jonathan C. Rienstra-Kiracofe <jrienst@emory.edu>, Bradley A. Smith <yeldar@home.com>, Egon Willighagen
- Source code:
- main
- Belongs to CDK module:
- io
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Nested Class Summary
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Nested classes/interfaces inherited from interface org.openscience.cdk.io.IChemObjectReader
IChemObjectReader.Mode
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Field Summary
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Fields inherited from class org.openscience.cdk.io.DefaultChemObjectReader
errorHandler, mode
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Constructor Summary
Constructors Constructor Description Gaussian03Reader()
Gaussian03Reader(InputStream input)
Gaussian03Reader(Reader reader)
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Method Summary
All Methods Instance Methods Concrete Methods Modifier and Type Method Description boolean
accepts(Class<? extends IChemObject> classObject)
Returns whether the givenIChemObject
can be read or written.void
close()
Closes this IChemObjectIO's resources.IResourceFormat
getFormat()
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
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
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Methods inherited from class org.openscience.cdk.io.ChemObjectIO
addChemObjectIOListener, addSetting, addSettings, fireIOSettingQuestion, getIOSettings, getListeners, getSetting, getSetting, getSettings, hasSetting, removeChemObjectIOListener
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Methods inherited from class java.lang.Object
clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
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Methods inherited from interface org.openscience.cdk.io.IChemObjectIO
addChemObjectIOListener, addSetting, addSettings, getIOSettings, getListeners, getSetting, getSetting, getSettings, hasSetting, removeChemObjectIOListener
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Constructor Detail
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Gaussian03Reader
public Gaussian03Reader(Reader reader)
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Gaussian03Reader
public Gaussian03Reader(InputStream input)
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Gaussian03Reader
public Gaussian03Reader()
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Method Detail
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getFormat
public IResourceFormat getFormat()
Description copied from interface:IChemObjectIO
Returns theIResourceFormat
class for this IO class.
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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
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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
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accepts
public boolean accepts(Class<? extends IChemObject> classObject)
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
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
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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.
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