org.helm.chemtoolkit.cdk

Class CDKAtom

java.lang.Object

org.helm.chemtoolkit.IAtomBase

org.helm.chemtoolkit.cdk.CDKAtom

All Implemented Interfaces:

org.helm.chemtoolkit.IChemObjectBase

public class CDKAtom
extends org.helm.chemtoolkit.IAtomBase

Author:

chistyakov

Field Summary

Fields

Modifier and Type	Field and Description
protected org.openscience.cdk.interfaces.IAtom	atom
protected List<CDKBond>	bonds
protected int	boundCount
protected int	rGroup

Fields inherited from class org.helm.chemtoolkit.IAtomBase

flag

Constructor Summary

Constructors

Constructor and Description
CDKAtom(org.openscience.cdk.interfaces.IAtom atom)
CDKAtom(org.openscience.cdk.interfaces.IAtom atom, int rGroup)
CDKAtom(org.openscience.cdk.interfaces.IAtom atom, int rGroup, List<org.openscience.cdk.interfaces.IBond> bonds)

Method Summary

Methods

Modifier and Type	Method and Description
boolean	compare(Object obj)
int	getIAtno()
org.helm.chemtoolkit.IBondBase	getIBond(int arg0)
int	getIBondCount()
org.openscience.cdk.interfaces.IAtom	getMolAtom()
int	getRgroup()
void	setRgroup(int rGroup)

Methods inherited from class org.helm.chemtoolkit.IAtomBase

getFlag, setFlag

Methods inherited from class java.lang.Object

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

Field Detail

atom

protected org.openscience.cdk.interfaces.IAtom atom

rGroup

protected int rGroup

bonds

protected List<CDKBond> bonds

boundCount

protected int boundCount

Constructor Detail

CDKAtom

public CDKAtom(org.openscience.cdk.interfaces.IAtom atom)

Parameters:

atom - given atom

CDKAtom

public CDKAtom(org.openscience.cdk.interfaces.IAtom atom,
       int rGroup)

CDKAtom

public CDKAtom(org.openscience.cdk.interfaces.IAtom atom,
       int rGroup,
       List<org.openscience.cdk.interfaces.IBond> bonds)

Parameters:

atom - given atom

rGroup - given rgroup

bonds - list of bonds

Method Detail

getMolAtom

public org.openscience.cdk.interfaces.IAtom getMolAtom()

Specified by:

getMolAtom in class org.helm.chemtoolkit.IAtomBase

getIBondCount

public int getIBondCount()

Specified by:

getIBondCount in class org.helm.chemtoolkit.IAtomBase

getIBond

public org.helm.chemtoolkit.IBondBase getIBond(int arg0)
                                        throws org.helm.chemtoolkit.CTKException

Specified by:

getIBond in class org.helm.chemtoolkit.IAtomBase

Throws:

org.helm.chemtoolkit.CTKException

getRgroup

public int getRgroup()

Specified by:

getRgroup in class org.helm.chemtoolkit.IAtomBase

getIAtno

public int getIAtno()

Specified by:

getIAtno in class org.helm.chemtoolkit.IAtomBase

compare

public boolean compare(Object obj)

Specified by:

compare in class org.helm.chemtoolkit.IAtomBase

setRgroup

public void setRgroup(int rGroup)
               throws org.helm.chemtoolkit.CTKException

Specified by:

setRgroup in class org.helm.chemtoolkit.IAtomBase

Throws:

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