org.helm.chemtoolkit.chemaxon

Class ChemMolecule

java.lang.Object

org.helm.chemtoolkit.AbstractMolecule

org.helm.chemtoolkit.chemaxon.ChemMolecule

All Implemented Interfaces:

org.helm.chemtoolkit.IChemObjectBase

public class ChemMolecule
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 and Description
ChemMolecule(chemaxon.struc.Molecule molecule)
ChemMolecule(chemaxon.struc.Molecule molecule, org.helm.chemtoolkit.AttachmentList attachments)

Method Summary

Methods

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

ChemMolecule

public ChemMolecule(chemaxon.struc.Molecule molecule)

ChemMolecule

public ChemMolecule(chemaxon.struc.Molecule molecule,
            org.helm.chemtoolkit.AttachmentList attachments)

Method Detail

getMolecule

public chemaxon.struc.Molecule getMolecule()

Specified by:

getMolecule in class org.helm.chemtoolkit.AbstractMolecule

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 node)

Specified by:

addIBase in class org.helm.chemtoolkit.AbstractMolecule

dearomatize

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

Specified by:

dearomatize in class org.helm.chemtoolkit.AbstractMolecule

Throws:

org.helm.chemtoolkit.CTKException

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

getIBondArray

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

Specified by:

getIBondArray in class org.helm.chemtoolkit.AbstractMolecule

cloneMolecule

public org.helm.chemtoolkit.AbstractMolecule cloneMolecule()

Specified by:

cloneMolecule in class org.helm.chemtoolkit.AbstractMolecule

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

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

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 node)

Specified by:

removeIBase in class org.helm.chemtoolkit.AbstractMolecule