ambit2.descriptors

Class FunctionalGroupDescriptor

java.lang.Object

ambit2.descriptors.FunctionalGroupDescriptor

All Implemented Interfaces:

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

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

Functional groups (by SMARTS)

Author:

nina

Field Summary

Fields

Modifier and Type	Field and Description
protected List<FunctionalGroup>	groups
protected HydrogenAdderProcessor	hp
protected static Logger	logger
protected String[]	names
String[]	paramNames
protected boolean	verbose

Constructor Summary

Constructors

Constructor and Description
FunctionalGroupDescriptor()

Method Summary

Modifier and Type	Method and Description
org.openscience.cdk.qsar.DescriptorValue	calculate(org.openscience.cdk.interfaces.IAtomContainer atomcontainer)
String[]	getDescriptorNames()
org.openscience.cdk.qsar.result.IDescriptorResult	getDescriptorResultType()
String[]	getParameterNames()
Object[]	getParameters()
Object	getParameterType(String name)
org.openscience.cdk.qsar.DescriptorSpecification	getSpecification()
void	initialise(org.openscience.cdk.interfaces.IChemObjectBuilder arg0)
boolean	isVerbose()
protected void	setGroups(List<FunctionalGroup> groups)
void	setParameters(Object[] params) 3 parameters : Smarts,name,hint; first two are mandatory.
void	setVerbose(boolean verbose)
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

paramNames

public final String[] paramNames

groups

protected List<FunctionalGroup> groups

names

protected String[] names

hp

protected HydrogenAdderProcessor hp

verbose

protected boolean verbose

Constructor Detail

FunctionalGroupDescriptor

public FunctionalGroupDescriptor()

Method Detail

isVerbose

public boolean isVerbose()

initialise

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

Specified by:

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

setVerbose

public void setVerbose(boolean verbose)

setGroups

protected void setGroups(List<FunctionalGroup> groups)

getDescriptorNames

public String[] getDescriptorNames()

Specified by:

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

calculate

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

Specified by:

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

getParameterNames

public String[] getParameterNames()

Specified by:

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

getParameterType

public Object getParameterType(String name)

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[] params)
                   throws org.openscience.cdk.exception.CDKException

3 parameters : Smarts,name,hint; first two are mandatory.

Specified by:

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

Throws:

org.openscience.cdk.exception.CDKException

getParameters

public Object[] getParameters()

Specified by:

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

toString

public String toString()

Overrides:

toString in class Object

getDescriptorResultType

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

Specified by:

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