org.openscience.cdk.geometry.cip

Class Ligand

java.lang.Object

org.openscience.cdk.geometry.cip.Ligand

All Implemented Interfaces:

ILigand

Direct Known Subclasses:

ImplicitHydrogenLigand

public class Ligand
extends Object
implements ILigand

Concept of a ligand in CIP terms, reflecting a side chain of a central atom that can have precedence over another.

Source code:

master

Belongs to CDK module:

cip

Constructor Summary

Constructors

Constructor and Description
Ligand(IAtomContainer container, VisitedAtoms visitedAtoms, IAtom centralAtom, IAtom ligandAtom)

Method Summary

Modifier and Type	Method and Description
IAtomContainer	getAtomContainer() IAtomContainer of which this ligand is part.
IAtom	getCentralAtom() The central IAtom to which this ligand is connected via one IBond.
IAtom	getLigandAtom() IAtom of the ligand that is connected to the chiral IAtom via one IBond.
VisitedAtoms	getVisitedAtoms() Returns a list of visitedAtoms.
boolean	isVisited(IAtom atom) Returns a true if the atom has been visited before.

Methods inherited from class java.lang.Object

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

Constructor Detail

Ligand

public Ligand(IAtomContainer container,
              VisitedAtoms visitedAtoms,
              IAtom centralAtom,
              IAtom ligandAtom)

Method Detail

getAtomContainer

public IAtomContainer getAtomContainer()

IAtomContainer of which this ligand is part.

Specified by:

getAtomContainer in interface ILigand

Returns:

the IAtomContainer

getCentralAtom

public IAtom getCentralAtom()

The central IAtom to which this ligand is connected via one IBond.

Specified by:

getCentralAtom in interface ILigand

Returns:

the central atom

getLigandAtom

public IAtom getLigandAtom()

IAtom of the ligand that is connected to the chiral IAtom via one IBond.

Specified by:

getLigandAtom in interface ILigand

Returns:

the ligand atom

getVisitedAtoms

public VisitedAtoms getVisitedAtoms()

Returns a list of visitedAtoms.

Specified by:

getVisitedAtoms in interface ILigand

Returns:

a VisitedAtoms list with visited atoms

isVisited

public boolean isVisited(IAtom atom)

Returns a true if the atom has been visited before.

Specified by:

isVisited in interface ILigand

Parameters:

atom - the atom to be analyzed

Returns:

true if the IAtom is the chiral atom, or part of the ligand