ambit2.some

Class DescriptorSOMEShell

java.lang.Object

ambit2.some.DescriptorSOMEShell

All Implemented Interfaces:

IStructureDiagramDepiction<BufferedImage>, IStructureDiagramHighlights, org.openscience.cdk.qsar.IDescriptor, org.openscience.cdk.qsar.IMolecularDescriptor

public class DescriptorSOMEShell
extends Object
implements org.openscience.cdk.qsar.IMolecularDescriptor, IStructureDiagramHighlights

Used by DescriptorSOMEShell
Invokes some.exe from Mopac 7.1 http://www.dddc.ac.cn/adme/myzheng/SOME_1_0.tar.gz.

Author:

Nina Jeliazkova nina@acad.bg Modified 2010-9-4

Field Summary

Fields

Modifier and Type	Field and Description
protected static Logger	logger
protected SOMEShell	some_shell
protected SOMEVisualizer	visualizer

Constructor Summary

Constructors

Constructor and Description
DescriptorSOMEShell()

Method Summary

Modifier and Type	Method and Description
org.openscience.cdk.qsar.DescriptorValue	calculate(org.openscience.cdk.interfaces.IAtomContainer arg0)
protected void	debug(String message)
String[]	getDescriptorNames()
org.openscience.cdk.qsar.result.IDescriptorResult	getDescriptorResultType()
BufferedImage	getImage(org.openscience.cdk.interfaces.IAtomContainer mol)
BufferedImage	getImage(org.openscience.cdk.interfaces.IAtomContainer mol, String ruleID, int width, int height, boolean atomnumbers)
Dimension	getImageSize()
BufferedImage	getLegend(int width, int height)
String[]	getParameterNames()
Object[]	getParameters()
Object	getParameterType(String arg0)
org.openscience.cdk.qsar.DescriptorSpecification	getSpecification()
void	initialise(org.openscience.cdk.interfaces.IChemObjectBuilder arg0)
void	setImageSize(Dimension imageSize)
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

logger

protected static Logger logger

some_shell

protected SOMEShell some_shell

visualizer

protected SOMEVisualizer visualizer

Constructor Detail

DescriptorSOMEShell

public DescriptorSOMEShell()
                    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 arg0)

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)

getImage

public BufferedImage getImage(org.openscience.cdk.interfaces.IAtomContainer mol)
                       throws net.idea.modbcum.i.exceptions.AmbitException

Specified by:

getImage in interface IStructureDiagramDepiction<BufferedImage>

Throws:

net.idea.modbcum.i.exceptions.AmbitException

getImage

public BufferedImage getImage(org.openscience.cdk.interfaces.IAtomContainer mol,
                              String ruleID,
                              int width,
                              int height,
                              boolean atomnumbers)
                       throws net.idea.modbcum.i.exceptions.AmbitException

Specified by:

getImage in interface IStructureDiagramDepiction<BufferedImage>

Throws:

net.idea.modbcum.i.exceptions.AmbitException

getImageSize

public Dimension getImageSize()

Specified by:

getImageSize in interface IStructureDiagramDepiction<BufferedImage>

setImageSize

public void setImageSize(Dimension imageSize)

Specified by:

setImageSize in interface IStructureDiagramDepiction<BufferedImage>

getLegend

public BufferedImage getLegend(int width,
                               int height)
                        throws net.idea.modbcum.i.exceptions.AmbitException

Specified by:

getLegend in interface IStructureDiagramDepiction<BufferedImage>

Throws:

net.idea.modbcum.i.exceptions.AmbitException