ambit2.descriptors.processors

Class AtomEnvironmentGenerator

java.lang.Object

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

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

ambit2.descriptors.processors.AtomEnvironmentGenerator

All Implemented Interfaces:

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

public class AtomEnvironmentGenerator
extends AbstractPropertyGenerator<AtomEnvironmentList>

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

Author:

Nina Jeliazkova nina@acad.bg, Patrik Rydberg Modified Jan 3, 2012

See Also:

Serialized Form

Field Summary

Fields

Modifier and Type	Field and Description
protected AtomEnvironmentDescriptor	aeDescriptor
protected Object[]	aeParams
protected boolean	createSubLevels
protected FPTable	fpmode
protected org.openscience.cdk.tools.CDKHydrogenAdder	hAdder
protected Integer	maxLevels
protected boolean	noDuplicates
protected boolean	useHydrogens

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
AtomEnvironmentGenerator()

Method Summary

Modifier and Type	Method and Description
protected AtomEnvironmentDescriptor	createAtomEnvironmentDescriptor()
AtomEnvironmentList	generateProperty(org.openscience.cdk.interfaces.IAtomContainer atomContainer)
Integer	getMaxLevels()
Property	getProperty()
protected Property	getTimeProperty()
boolean	isCreateSubLevels()
boolean	isNoDuplicates()
boolean	isUseHydrogens()
void	setCreateSubLevels(boolean createSubLevels)
void	setMaxLevels(Integer maxLevels)
void	setNoDuplicates(boolean noDuplicates)
void	setUseHydrogens(boolean useHydrogens)
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

aeDescriptor

protected AtomEnvironmentDescriptor aeDescriptor

aeParams

protected Object[] aeParams

useHydrogens

protected boolean useHydrogens

maxLevels

protected Integer maxLevels

createSubLevels

protected boolean createSubLevels

noDuplicates

protected boolean noDuplicates

fpmode

protected FPTable fpmode

Constructor Detail

AtomEnvironmentGenerator

public AtomEnvironmentGenerator()

Method Detail

createAtomEnvironmentDescriptor

protected AtomEnvironmentDescriptor createAtomEnvironmentDescriptor()

generateProperty

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

Specified by:

generateProperty in class AbstractPropertyGenerator<AtomEnvironmentList>

Throws:

net.idea.modbcum.i.exceptions.AmbitException

toString

public String toString()

Overrides:

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

isUseHydrogens

public boolean isUseHydrogens()

setUseHydrogens

public void setUseHydrogens(boolean useHydrogens)

getMaxLevels

public Integer getMaxLevels()

setMaxLevels

public void setMaxLevels(Integer maxLevels)

isNoDuplicates

public boolean isNoDuplicates()

setNoDuplicates

public void setNoDuplicates(boolean noDuplicates)

isCreateSubLevels

public boolean isCreateSubLevels()

setCreateSubLevels

public void setCreateSubLevels(boolean createSubLevels)

getProperty

public Property getProperty()

Specified by:

getProperty in class AbstractPropertyGenerator<AtomEnvironmentList>

getTimeProperty

protected Property getTimeProperty()

Specified by:

getTimeProperty in class AbstractPropertyGenerator<AtomEnvironmentList>