org.openscience.cdk.io

Class Mopac7Reader

java.lang.Object

org.openscience.cdk.io.ChemObjectIO

org.openscience.cdk.io.DefaultChemObjectReader

org.openscience.cdk.io.Mopac7Reader

All Implemented Interfaces:

Closeable, AutoCloseable, IChemObjectIO, IChemObjectReader, ISimpleChemObjectReader

public class Mopac7Reader
extends DefaultChemObjectReader

Reads MOPAC output, extracts several electronic parameters and assigns them as a molecule properties.

Parameters: "NO. OF FILLED LEVELS", "TOTAL ENERGY","FINAL HEAT OF FORMATION", "IONIZATION POTENTIAL", "ELECTRONIC ENERGY","CORE-CORE REPULSION","MOLECULAR WEIGHT".

Doesn't update structure coordinates ! (TODO fix)

Author:

Nina Jeliazkova <nina@acad.bg>

Source code:

master

Belongs to CDK module:

io

Nested Class Summary

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

IChemObjectReader.Mode

Field Summary

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

errorHandler, mode

Constructor Summary

Constructors

Constructor and Description
Mopac7Reader() Constructs a new Mopac7reader that can read a molecule.
Mopac7Reader(InputStream input) Constructs a new Mopac7reader that can read a molecule from a given InputStream.
Mopac7Reader(Reader input) Constructs a new Mopac7reader that can read a molecule from a given Reader.

Method Summary

Methods

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 input) 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

Constructor Detail

Mopac7Reader

public Mopac7Reader(Reader input)

Constructs a new Mopac7reader that can read a molecule from a given Reader.

Parameters:

input - The Reader to read from

Mopac7Reader

public Mopac7Reader(InputStream input)

Constructs a new Mopac7reader that can read a molecule from a given InputStream.

Parameters:

input - The InputStream to read from

Mopac7Reader

public Mopac7Reader()

Constructs a new Mopac7reader that can read a molecule. The reader to read from has yet to be set.

Method Detail

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

setReader

public void setReader(Reader input)
               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

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.

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.

getFormat

public IResourceFormat getFormat()

Description copied from interface: IChemObjectIO

Returns the IResourceFormat class for this IO class.