org.helm.chemtoolkit

Class AbstractMolecule

java.lang.Object

org.helm.chemtoolkit.AbstractMolecule

All Implemented Interfaces:

IChemObjectBase

public abstract class AbstractMolecule
extends Object
implements IChemObjectBase

Author:

chistyakov

Nested Class Summary

Nested Classes

Modifier and Type	Class and Description
static class	AbstractMolecule.Flag

Field Summary

Fields

Modifier and Type	Field and Description
protected List<IAtomBase>	atoms
protected AttachmentList	attachments

Constructor Summary

Constructors

Modifier	Constructor and Description
protected	AbstractMolecule()

Method Summary

Methods

Modifier and Type	Method and Description
abstract void	addIBase(IChemObjectBase object)
abstract void	changeAtomLabel(int index, int toIndex)
void	clearFlags()
abstract AbstractMolecule	cloneMolecule()
abstract void	dearomatize()
abstract void	generateCoordinates(int dem)
AttachmentList	getAttachments()
List<IAtomBase>	getIAtomArray()
abstract List<IBondBase>	getIBondArray()
static int	getIdFromLabel(String label)
abstract Object	getMolecule()
IAtomBase	getRGroupAtom(int groupId, boolean rgatom)
Map<String,IAtomBase>	getRgroups()
abstract boolean	isSingleStereo(IAtomBase atom) check a given atom connections
void	removeAttachment(IAtomBase toRemove) removes a given attachment from molecule
abstract void	removeIBase(IChemObjectBase object)
abstract void	removeINode(IAtomBase node)
void	setAttachments(AttachmentList attachments)

Methods inherited from class java.lang.Object

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

Field Detail

attachments

protected AttachmentList attachments

atoms

protected List<IAtomBase> atoms

Constructor Detail

AbstractMolecule

protected AbstractMolecule()

Method Detail

getAttachments

public AttachmentList getAttachments()

setAttachments

public void setAttachments(AttachmentList attachments)

getRgroups

public Map<String,IAtomBase> getRgroups()
                                 throws CTKException

Throws:

CTKException

getIdFromLabel

public static int getIdFromLabel(String label)

getRGroupAtom

public IAtomBase getRGroupAtom(int groupId,
                      boolean rgatom)
                        throws CTKException

Throws:

CTKException

clearFlags

public void clearFlags()

getMolecule

public abstract Object getMolecule()

dearomatize

public abstract void dearomatize()
                          throws CTKException

Throws:

CTKException

generateCoordinates

public abstract void generateCoordinates(int dem)
                                  throws CTKException

Throws:

CTKException

removeINode

public abstract void removeINode(IAtomBase node)
                          throws CTKException

Throws:

CTKException

addIBase

public abstract void addIBase(IChemObjectBase object)

removeIBase

public abstract void removeIBase(IChemObjectBase object)

getIBondArray

public abstract List<IBondBase> getIBondArray()

cloneMolecule

public abstract AbstractMolecule cloneMolecule()
                                        throws CTKException

Throws:

CTKException

changeAtomLabel

public abstract void changeAtomLabel(int index,
                   int toIndex)
                              throws CTKException

Throws:

CTKException

isSingleStereo

public abstract boolean isSingleStereo(IAtomBase atom)
                                throws CTKException

check a given atom connections

Parameters:

atom - to check

Returns:

true if a atom has a single stereo connection

Throws:

CTKException

removeAttachment

public void removeAttachment(IAtomBase toRemove)
                      throws CTKException

removes a given attachment from molecule

Parameters:

toRemove - a atom to be removed

Throws:

CTKException

getIAtomArray

public List<IAtomBase> getIAtomArray()