ambit2.descriptors.processors

Class AtomEnvironmentMatrixGenerator

java.lang.Object

net.idea.modbcum.p.DefaultAmbitProcessor<IStructureRecord,IStructureRecord>

ambit2.core.processors.structure.AbstractPropertyGenerator<HashIntDescriptorResult>

ambit2.descriptors.processors.AtomEnvironmentMatrixGenerator

All Implemented Interfaces:

Serializable, net.idea.modbcum.i.processors.IProcessor<IStructureRecord,IStructureRecord>

public class AtomEnvironmentMatrixGenerator
extends AbstractPropertyGenerator<HashIntDescriptorResult>

A processor to generate atom environments. Uses ambit2.data.descriptors.AtomEnvironmentMatrixr for actual generation. The result is contained in HashIntDescriptorResult and is assigned as a molecule property with a name AmbitCONSTANTS.AtomEnvironment.
Used by ambit2.database.writers.AtomEnvironmentMatrixWriter

See Also:

Serialized Form

Field Summary

Fields

Modifier and Type	Field and Description
protected FPTable	fpmode
protected org.openscience.cdk.tools.CDKHydrogenAdder	hAdder
protected AtomEnvironentMatrix	matrix

Fields inherited from class ambit2.core.processors.structure.AbstractPropertyGenerator

reader

Fields inherited from class net.idea.modbcum.p.DefaultAmbitProcessor

enabled, logger, propertyChangeSupport

Constructor Summary

Constructors

Constructor and Description
AtomEnvironmentMatrixGenerator()
AtomEnvironmentMatrixGenerator(int maxLevels)

Method Summary

Modifier and Type	Method and Description
HashIntDescriptorResult	generateProperty(org.openscience.cdk.interfaces.IAtomContainer atomContainer)
Integer	getMaxLevels()
Property	getProperty()
protected Property	getTimeProperty()
void	setMaxLevels(Integer maxLevels)
String	toString()

Methods inherited from class ambit2.core.processors.structure.AbstractPropertyGenerator

close, getAtomContainer, open, process

Methods inherited from class net.idea.modbcum.p.DefaultAmbitProcessor

addPropertyChangeListener, addPropertyChangeListener, getID, isEnabled, removePropertyChangeListener, removePropertyChangeListener, setEnabled

Methods inherited from class java.lang.Object

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

Field Detail

hAdder

protected org.openscience.cdk.tools.CDKHydrogenAdder hAdder

matrix

protected AtomEnvironentMatrix matrix

fpmode

protected FPTable fpmode

Constructor Detail

AtomEnvironmentMatrixGenerator

public AtomEnvironmentMatrixGenerator()
                               throws Exception

Throws:

Exception

AtomEnvironmentMatrixGenerator

public AtomEnvironmentMatrixGenerator(int maxLevels)
                               throws Exception

Throws:

Exception

Method Detail

generateProperty

public HashIntDescriptorResult generateProperty(org.openscience.cdk.interfaces.IAtomContainer atomContainer)
                                         throws net.idea.modbcum.i.exceptions.AmbitException

Specified by:

generateProperty in class AbstractPropertyGenerator<HashIntDescriptorResult>

Throws:

net.idea.modbcum.i.exceptions.AmbitException

toString

public String toString()

Overrides:

toString in class net.idea.modbcum.p.DefaultAmbitProcessor<IStructureRecord,IStructureRecord>

getMaxLevels

public Integer getMaxLevels()

setMaxLevels

public void setMaxLevels(Integer maxLevels)

getProperty

public Property getProperty()

Specified by:

getProperty in class AbstractPropertyGenerator<HashIntDescriptorResult>

getTimeProperty

protected Property getTimeProperty()

Specified by:

getTimeProperty in class AbstractPropertyGenerator<HashIntDescriptorResult>