ambit2.mopac

Class Mopac7Writer

java.lang.Object

org.openscience.cdk.io.ChemObjectIO

org.openscience.cdk.io.DefaultChemObjectWriter

ambit2.mopac.Mopac7Writer

All Implemented Interfaces:

Closeable, AutoCloseable, org.openscience.cdk.io.IChemObjectIO, org.openscience.cdk.io.IChemObjectWriter

public class Mopac7Writer
extends org.openscience.cdk.io.DefaultChemObjectWriter

Prepares input file for running MOPAC by AbstractMopacShell
Optimization is switched on if there are no coordinates. If only 2D coordinates are supplied, then an initial structure is generated by ShellMengine

Author:

Nina Jeliazkova nina@acad.bg Modified 2008-12-13

Field Summary

Fields

Modifier and Type	Field and Description
protected String	blank
protected String[]	default_mopac_commands
protected String	mopac_commands
protected NumberFormat	nf
protected int	optimize

Constructor Summary

Constructors

Constructor and Description
Mopac7Writer(OutputStream out)
Mopac7Writer(Writer out)

Method Summary

Modifier and Type	Method and Description
boolean	accepts(Class classObject)
void	close()
void	generate2d(org.openscience.cdk.interfaces.IAtomContainer a)
org.openscience.cdk.io.formats.IResourceFormat	getFormat()
String	getMopacCommands()
String	getTitle()
int	isOptimize()
void	setMopacCommands(String commands)
void	setOptimize(int optimize)
void	setWriter(OutputStream writer)
void	setWriter(Writer writer)
String	toString()
void	write(org.openscience.cdk.interfaces.IChemObject arg0)
protected void	writeAtom(org.openscience.cdk.interfaces.IAtom atom, double x, double y, double z, int optimize)

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

default_mopac_commands

protected String[] default_mopac_commands

mopac_commands

protected String mopac_commands

blank

protected String blank

optimize

protected int optimize

nf

protected NumberFormat nf

Constructor Detail

Mopac7Writer

public Mopac7Writer(OutputStream out)
             throws Exception

Throws:

Exception

Mopac7Writer

public Mopac7Writer(Writer out)
             throws Exception

Throws:

Exception

Method Detail

generate2d

public void generate2d(org.openscience.cdk.interfaces.IAtomContainer a)
                throws org.openscience.cdk.exception.CDKException

Throws:

org.openscience.cdk.exception.CDKException

write

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

Throws:

org.openscience.cdk.exception.CDKException

writeAtom

protected void writeAtom(org.openscience.cdk.interfaces.IAtom atom,
                         double x,
                         double y,
                         double z,
                         int optimize)
                  throws IOException

Throws:

IOException

close

public void close()
           throws IOException

Throws:

IOException

isOptimize

public int isOptimize()

Returns:

true if to perform optimization of the structure

setOptimize

public void setOptimize(int optimize)

Parameters:

optimize - true if to perform optimization of the structure

toString

public String toString()

Overrides:

toString in class Object

accepts

public boolean accepts(Class classObject)

getFormat

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

setWriter

public void setWriter(OutputStream writer)
               throws org.openscience.cdk.exception.CDKException

Throws:

org.openscience.cdk.exception.CDKException

setWriter

public void setWriter(Writer writer)
               throws org.openscience.cdk.exception.CDKException

Throws:

org.openscience.cdk.exception.CDKException

getTitle

public String getTitle()

getMopacCommands

public String getMopacCommands()

setMopacCommands

public void setMopacCommands(String commands)