ambit2.mopac

Class DescriptorMopacShell

java.lang.Object

ambit2.mopac.DescriptorMopacShell

All Implemented Interfaces:

org.openscience.cdk.qsar.IDescriptor, org.openscience.cdk.qsar.IMolecularDescriptor

Direct Known Subclasses:

MopacOriginalStructure

public class DescriptorMopacShell
extends Object
implements org.openscience.cdk.qsar.IMolecularDescriptor

Used by DescriptorMopacShell
Invokes mopac.exe from Mopac 7.1 http://openmopac.net/Downloads/Downloads.html.
Doesn't work for molecules with number of heavy atoms > 60, number of all atoms > 120.

Author:

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

Field Summary

Fields

Modifier and Type	Field and Description
static String	EHOMO
static String	ELUMO
protected String	force_field
protected AbstractMopacShell	mopac_shell
protected String[]	params

Constructor Summary

Constructors

Constructor and Description
DescriptorMopacShell()

Method Summary

Modifier and Type	Method and Description
org.openscience.cdk.qsar.DescriptorValue	calculate(org.openscience.cdk.interfaces.IAtomContainer mol)
protected void	debug(String message)
String[]	getDescriptorNames()
org.openscience.cdk.qsar.result.IDescriptorResult	getDescriptorResultType()
String[]	getParameterNames()
Object[]	getParameters()
Object	getParameterType(String arg0)
org.openscience.cdk.qsar.DescriptorSpecification	getSpecification()
void	initialise(org.openscience.cdk.interfaces.IChemObjectBuilder arg0)
boolean	isErrorIfDisconnected()
void	setErrorIfDisconnected(boolean errorIfDisconnected)
void	setParameters(Object[] arg0)
String	toString()

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, wait, wait, wait

Field Detail

params

protected String[] params

EHOMO

public static final String EHOMO

See Also:

Constant Field Values

ELUMO

public static final String ELUMO

See Also:

Constant Field Values

force_field

protected String force_field

mopac_shell

protected AbstractMopacShell mopac_shell

Constructor Detail

DescriptorMopacShell

public DescriptorMopacShell()
                     throws ShellException

Throws:

ShellException

Method Detail

initialise

public void initialise(org.openscience.cdk.interfaces.IChemObjectBuilder arg0)

Specified by:

initialise in interface org.openscience.cdk.qsar.IDescriptor

toString

public String toString()

Overrides:

toString in class Object

getParameterNames

public String[] getParameterNames()

Specified by:

getParameterNames in interface org.openscience.cdk.qsar.IDescriptor

getParameters

public Object[] getParameters()

Specified by:

getParameters in interface org.openscience.cdk.qsar.IDescriptor

getParameterType

public Object getParameterType(String arg0)

Specified by:

getParameterType in interface org.openscience.cdk.qsar.IDescriptor

getSpecification

public org.openscience.cdk.qsar.DescriptorSpecification getSpecification()

Specified by:

getSpecification in interface org.openscience.cdk.qsar.IDescriptor

setParameters

public void setParameters(Object[] arg0)
                   throws org.openscience.cdk.exception.CDKException

Specified by:

setParameters in interface org.openscience.cdk.qsar.IDescriptor

Throws:

org.openscience.cdk.exception.CDKException

calculate

public org.openscience.cdk.qsar.DescriptorValue calculate(org.openscience.cdk.interfaces.IAtomContainer mol)

Specified by:

calculate in interface org.openscience.cdk.qsar.IMolecularDescriptor

getDescriptorNames

public String[] getDescriptorNames()

Specified by:

getDescriptorNames in interface org.openscience.cdk.qsar.IDescriptor

getDescriptorResultType

public org.openscience.cdk.qsar.result.IDescriptorResult getDescriptorResultType()

Specified by:

getDescriptorResultType in interface org.openscience.cdk.qsar.IMolecularDescriptor

debug

protected void debug(String message)

isErrorIfDisconnected

public boolean isErrorIfDisconnected()

setErrorIfDisconnected

public void setErrorIfDisconnected(boolean errorIfDisconnected)