ambit2.mopac

Class Mopac7Reader

java.lang.Object

org.openscience.cdk.io.ChemObjectIO

org.openscience.cdk.io.DefaultChemObjectReader

ambit2.mopac.Mopac7Reader

All Implemented Interfaces:

Closeable, AutoCloseable, org.openscience.cdk.io.IChemObjectIO, org.openscience.cdk.io.IChemObjectReader, org.openscience.cdk.io.ISimpleChemObjectReader

public class Mopac7Reader
extends org.openscience.cdk.io.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)
Used in AbstractMopacShell

Author:

Nina Jeliazkova nina@acad.bg Modified 2006-4-8

Nested Class Summary

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

org.openscience.cdk.io.IChemObjectReader.Mode

Field Summary

Fields

Modifier and Type	Field and Description
protected static String	eigenvalues
protected static String	filledLevels
protected static org.openscience.cdk.tools.LoggingTool	logger
static String[]	parameters
static String[]	units

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

errorHandler, mode

Constructor Summary

Constructors

Constructor and Description
Mopac7Reader(InputStream input)
Mopac7Reader(Reader in) Contructs a new Mopac7reader that can read Molecule from a given Reader.

Method Summary

Modifier and Type	Method and Description
boolean	accepts(Class classObject)
protected void	calcHomoLumo(org.openscience.cdk.interfaces.IAtomContainer mol)
void	close()
org.openscience.cdk.io.formats.IResourceFormat	getFormat()
org.openscience.cdk.interfaces.IChemObject	read(org.openscience.cdk.interfaces.IChemObject arg0)
void	setReader(InputStream arg0)
void	setReader(Reader arg0)
String	toString()

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, wait, wait, wait

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

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

Field Detail

logger

protected static org.openscience.cdk.tools.LoggingTool logger

parameters

public static String[] parameters

units

public static String[] units

eigenvalues

protected static String eigenvalues

filledLevels

protected static String filledLevels

Constructor Detail

Mopac7Reader

public Mopac7Reader(Reader in)

Contructs a new Mopac7reader that can read Molecule from a given Reader.

Parameters:

in - The Reader to read from

Mopac7Reader

public Mopac7Reader(InputStream input)

Method Detail

read

public org.openscience.cdk.interfaces.IChemObject read(org.openscience.cdk.interfaces.IChemObject arg0)
                                                throws org.openscience.cdk.exception.CDKException

Throws:

org.openscience.cdk.exception.CDKException

calcHomoLumo

protected void calcHomoLumo(org.openscience.cdk.interfaces.IAtomContainer mol)

setReader

public void setReader(Reader arg0)
               throws org.openscience.cdk.exception.CDKException

Throws:

org.openscience.cdk.exception.CDKException

setReader

public void setReader(InputStream arg0)
               throws org.openscience.cdk.exception.CDKException

Throws:

org.openscience.cdk.exception.CDKException

close

public void close()
           throws IOException

Throws:

IOException

toString

public String toString()

Overrides:

toString in class Object

accepts

public boolean accepts(Class classObject)

getFormat

public org.openscience.cdk.io.formats.IResourceFormat getFormat()