CDKAtom (helm2-chemistrytoolkit-cdk 1.3.3 API)

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 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	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

All Methods Instance Methods Concrete Methods
Modifier and Type	Method	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