ambit2.core.processors

Class StructureNormalizer

java.lang.Object

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

ambit2.core.processors.StructureNormalizer

All Implemented Interfaces:

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

public class StructureNormalizer
extends net.idea.modbcum.p.DefaultAmbitProcessor<IStructureRecord,IStructureRecord>

See Also:

Serialized Form

Field Summary

Fields

Modifier and Type	Field and Description
protected boolean	build2D
protected Structure2DBuilder	builder
protected DXParser	dxParser
protected InchiPropertyKey	inchiKey
protected InchiProcessor	inchiProcessor
protected MoleculeReader	molReader
protected SmilesKey	smilesKey
protected StructureTypeProcessor	strucType

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

enabled, logger, propertyChangeSupport

Constructor Summary

Constructors

Constructor and Description
StructureNormalizer()

Method Summary

Modifier and Type	Method and Description
protected org.openscience.cdk.interfaces.IAtomContainer	build2d(org.openscience.cdk.interfaces.IAtomContainer molecule, IStructureRecord.STRUC_TYPE structype)
boolean	isBuild2D()
IStructureRecord	process(IStructureRecord structure)
void	setBuild2D(boolean build2d)

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

addPropertyChangeListener, addPropertyChangeListener, close, getID, isEnabled, open, removePropertyChangeListener, removePropertyChangeListener, setEnabled, toString

Methods inherited from class java.lang.Object

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

Field Detail

molReader

protected transient MoleculeReader molReader

smilesKey

protected transient SmilesKey smilesKey

inchiKey

protected transient InchiPropertyKey inchiKey

strucType

protected transient StructureTypeProcessor strucType

inchiProcessor

protected transient InchiProcessor inchiProcessor

builder

protected transient Structure2DBuilder builder

dxParser

protected DXParser dxParser

build2D

protected boolean build2D

Constructor Detail

StructureNormalizer

public StructureNormalizer()

Method Detail

process

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

Throws:

net.idea.modbcum.i.exceptions.AmbitException

isBuild2D

public boolean isBuild2D()

setBuild2D

public void setBuild2D(boolean build2d)

build2d

protected org.openscience.cdk.interfaces.IAtomContainer build2d(org.openscience.cdk.interfaces.IAtomContainer molecule,
                                                                IStructureRecord.STRUC_TYPE structype)
                                                         throws net.idea.modbcum.i.exceptions.AmbitException

Throws:

net.idea.modbcum.i.exceptions.AmbitException