ambit2.core.processors.structure

Class MoleculeReader

java.lang.Object

net.idea.modbcum.p.DefaultAmbitProcessor<IStructureRecord,org.openscience.cdk.interfaces.IAtomContainer>

ambit2.core.processors.structure.MoleculeReader

All Implemented Interfaces:

Serializable, net.idea.modbcum.i.processors.IProcessor<IStructureRecord,org.openscience.cdk.interfaces.IAtomContainer>

public class MoleculeReader
extends net.idea.modbcum.p.DefaultAmbitProcessor<IStructureRecord,org.openscience.cdk.interfaces.IAtomContainer>

See Also:

Serialized Form

Field Summary

Fields

Modifier and Type	Field and Description
protected boolean	atomtypingonsmiles
protected CASProcessor	casTransformer
protected org.openscience.cdk.tools.CDKHydrogenAdder	hadder
protected org.openscience.cdk.inchi.InChIGeneratorFactory	inchiFactory
protected boolean	removeCDKTitle
protected org.openscience.cdk.smiles.SmilesParser	smiParser

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

enabled, logger, propertyChangeSupport

Constructor Summary

Constructors

Constructor and Description
MoleculeReader()
MoleculeReader(boolean atomtypingonsmiles, boolean removeCDKTitle)

Method Summary

Modifier and Type	Method and Description
protected org.openscience.cdk.interfaces.IAtomContainer	handleFormat(IStructureRecord.MOL_TYPE format, IStructureRecord target)
boolean	isAtomtypingonsmiles()
boolean	isRemoveCDKTitle()
org.openscience.cdk.interfaces.IAtomContainer	process(IStructureRecord target)
void	setAtomtypingonsmiles(boolean atomtypingonsmiles)
void	setRemoveCDKTitle(boolean removeCDKTitle)

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

inchiFactory

protected org.openscience.cdk.inchi.InChIGeneratorFactory inchiFactory

casTransformer

protected CASProcessor casTransformer

smiParser

protected org.openscience.cdk.smiles.SmilesParser smiParser

hadder

protected org.openscience.cdk.tools.CDKHydrogenAdder hadder

atomtypingonsmiles

protected boolean atomtypingonsmiles

removeCDKTitle

protected boolean removeCDKTitle

Constructor Detail

MoleculeReader

public MoleculeReader()

MoleculeReader

public MoleculeReader(boolean atomtypingonsmiles,
                      boolean removeCDKTitle)

Method Detail

isRemoveCDKTitle

public boolean isRemoveCDKTitle()

setRemoveCDKTitle

public void setRemoveCDKTitle(boolean removeCDKTitle)

isAtomtypingonsmiles

public boolean isAtomtypingonsmiles()

setAtomtypingonsmiles

public void setAtomtypingonsmiles(boolean atomtypingonsmiles)

process

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

Throws:

net.idea.modbcum.i.exceptions.AmbitException

handleFormat

protected org.openscience.cdk.interfaces.IAtomContainer handleFormat(IStructureRecord.MOL_TYPE format,
                                                                     IStructureRecord target)
                                                              throws net.idea.modbcum.i.exceptions.AmbitException

Throws:

net.idea.modbcum.i.exceptions.AmbitException