Package org.helm.chemtoolkit.cdk

Class CDKMolecule

java.lang.Object

org.helm.chemtoolkit.AbstractMolecule

org.helm.chemtoolkit.cdk.CDKMolecule

All Implemented Interfaces:

org.helm.chemtoolkit.IChemObjectBase

public class CDKMolecule
extends org.helm.chemtoolkit.AbstractMolecule

Author:

chistyakov

Nested Class Summary

Nested classes/interfaces inherited from class org.helm.chemtoolkit.AbstractMolecule

org.helm.chemtoolkit.AbstractMolecule.Flag

Field Summary

Fields inherited from class org.helm.chemtoolkit.AbstractMolecule

atoms, attachments

Constructor Summary

Constructors

Constructor	Description
CDKMolecule(org.openscience.cdk.interfaces.IAtomContainer molecule)
CDKMolecule(org.openscience.cdk.interfaces.IAtomContainer molecule, org.helm.chemtoolkit.AttachmentList attachments)

Method Summary

Modifier and Type	Method	Description
void	addIBase(org.helm.chemtoolkit.IChemObjectBase object)
void	changeAtomLabel(int index, int toIndex)
org.helm.chemtoolkit.AbstractMolecule	cloneMolecule()
void	dearomatize()
void	generateCoordinates(int dem)
List<org.helm.chemtoolkit.IBondBase>	getIBondArray()
org.openscience.cdk.interfaces.IAtomContainer	getMolecule()
Map<String,org.helm.chemtoolkit.IAtomBase>	getRgroups()
boolean	isSingleStereo(org.helm.chemtoolkit.IAtomBase atom)
void	removeIBase(org.helm.chemtoolkit.IChemObjectBase object)
void	removeINode(org.helm.chemtoolkit.IAtomBase node)

Methods inherited from class org.helm.chemtoolkit.AbstractMolecule

clearFlags, getAttachments, getIAtomArray, getIdFromLabel, getRGroupAtom, removeAttachment, setAttachments

Methods inherited from class java.lang.Object

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

Constructor Detail

CDKMolecule

public CDKMolecule(org.openscience.cdk.interfaces.IAtomContainer molecule)

CDKMolecule

public CDKMolecule(org.openscience.cdk.interfaces.IAtomContainer molecule,
                   org.helm.chemtoolkit.AttachmentList attachments)

Method Detail

getRgroups

public Map<String,org.helm.chemtoolkit.IAtomBase> getRgroups()
                                                            throws org.helm.chemtoolkit.CTKException

Overrides:

getRgroups in class org.helm.chemtoolkit.AbstractMolecule

Throws:

org.helm.chemtoolkit.CTKException

dearomatize

public void dearomatize()
                 throws org.helm.chemtoolkit.CTKException

Specified by:

dearomatize in class org.helm.chemtoolkit.AbstractMolecule

Throws:

org.helm.chemtoolkit.CTKException

removeINode

public void removeINode(org.helm.chemtoolkit.IAtomBase node)
                 throws org.helm.chemtoolkit.CTKException

Specified by:

removeINode in class org.helm.chemtoolkit.AbstractMolecule

Throws:

org.helm.chemtoolkit.CTKException

addIBase

public void addIBase(org.helm.chemtoolkit.IChemObjectBase object)

Specified by:

addIBase in class org.helm.chemtoolkit.AbstractMolecule

getIBondArray

public List<org.helm.chemtoolkit.IBondBase> getIBondArray()

Specified by:

getIBondArray in class org.helm.chemtoolkit.AbstractMolecule

cloneMolecule

public org.helm.chemtoolkit.AbstractMolecule cloneMolecule()
                                                    throws org.helm.chemtoolkit.CTKException

Specified by:

cloneMolecule in class org.helm.chemtoolkit.AbstractMolecule

Throws:

org.helm.chemtoolkit.CTKException

generateCoordinates

public void generateCoordinates(int dem)
                         throws org.helm.chemtoolkit.CTKException

Specified by:

generateCoordinates in class org.helm.chemtoolkit.AbstractMolecule

Throws:

org.helm.chemtoolkit.CTKException - general ChemToolKit exception passed to HELMToolKit

getMolecule

public org.openscience.cdk.interfaces.IAtomContainer getMolecule()

Specified by:

getMolecule in class org.helm.chemtoolkit.AbstractMolecule

Returns:

IAtomContainer

changeAtomLabel

public void changeAtomLabel(int index,
                            int toIndex)
                     throws org.helm.chemtoolkit.CTKException

Specified by:

changeAtomLabel in class org.helm.chemtoolkit.AbstractMolecule

Throws:

org.helm.chemtoolkit.CTKException - general ChemToolKit exception passed to HELMToolKit

isSingleStereo

public boolean isSingleStereo(org.helm.chemtoolkit.IAtomBase atom)
                       throws org.helm.chemtoolkit.CTKException

Specified by:

isSingleStereo in class org.helm.chemtoolkit.AbstractMolecule

Throws:

org.helm.chemtoolkit.CTKException

removeIBase

public void removeIBase(org.helm.chemtoolkit.IChemObjectBase object)

Specified by:

removeIBase in class org.helm.chemtoolkit.AbstractMolecule