ambit2.core.processors.structure

Class AbstractPropertyGenerator<P>

java.lang.Object

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

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

All Implemented Interfaces:

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

Direct Known Subclasses:

AtomEnvironmentGenerator, AtomEnvironmentMatrixGenerator, BitSetGenerator, SMARTSPropertiesGenerator

public abstract class AbstractPropertyGenerator<P>
extends net.idea.modbcum.p.DefaultAmbitProcessor<IStructureRecord,IStructureRecord>

Transforms IStructureRecord into IAtomContainer , calculates some property and assigns it to IStructureRecord

Author:

nina

See Also:

Serialized Form

Field Summary

Fields

Modifier and Type	Field and Description
protected MoleculeReader	reader

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

enabled, logger, propertyChangeSupport

Constructor Summary

Constructors

Constructor and Description
AbstractPropertyGenerator()

Method Summary

Modifier and Type	Method and Description
void	close()
protected abstract P	generateProperty(org.openscience.cdk.interfaces.IAtomContainer atomContainer)
protected org.openscience.cdk.interfaces.IAtomContainer	getAtomContainer(IStructureRecord target)
protected abstract Property	getProperty()
protected abstract Property	getTimeProperty()
void	open()
IStructureRecord	process(IStructureRecord target)

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

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

Methods inherited from class java.lang.Object

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

Field Detail

reader

protected MoleculeReader reader

Constructor Detail

AbstractPropertyGenerator

public AbstractPropertyGenerator()

Method Detail

process

public IStructureRecord process(IStructureRecord target)
                         throws net.idea.modbcum.i.exceptions.AmbitException

Throws:

net.idea.modbcum.i.exceptions.AmbitException

getProperty

protected abstract Property getProperty()

getTimeProperty

protected abstract Property getTimeProperty()

generateProperty

protected abstract P generateProperty(org.openscience.cdk.interfaces.IAtomContainer atomContainer)
                               throws net.idea.modbcum.i.exceptions.AmbitException

Throws:

net.idea.modbcum.i.exceptions.AmbitException

getAtomContainer

protected org.openscience.cdk.interfaces.IAtomContainer getAtomContainer(IStructureRecord target)
                                                                  throws net.idea.modbcum.i.exceptions.AmbitException

Throws:

net.idea.modbcum.i.exceptions.AmbitException

open

public void open()
          throws Exception

Specified by:

open in interface net.idea.modbcum.i.processors.IProcessor<IStructureRecord,IStructureRecord>

Overrides:

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

Throws:

Exception

close

public void close()
           throws Exception

Specified by:

close in interface net.idea.modbcum.i.processors.IProcessor<IStructureRecord,IStructureRecord>

Overrides:

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

Throws:

Exception