Package org.openscience.cdk.layout

Class HydrogenPlacer

java.lang.Object

org.openscience.cdk.layout.HydrogenPlacer

public final class HydrogenPlacer
extends Object

This is a wrapper class for some existing methods in AtomPlacer. It helps you to layout 2D and 3D coordinates for hydrogen atoms added to a molecule which already has coordinates for the rest of the atoms.

 IAtomContainer container      = ...;
 HydrogenPlacer hydrogenPlacer = new HydrogenPlacer();
 hydrogenPlacer.placeHydrogens2D(container, 1.5);
 

Author:

Christoph Steinbeck

See Also:

AtomPlacer

Source code:

main

Belongs to CDK module:

sdg

Created on:

2003-08-06

Constructor Summary

Constructors

Constructor	Description
HydrogenPlacer()

Method Summary

Modifier and Type	Method	Description
void	placeHydrogens2D(IAtomContainer container, double bondLength)	Place all hydrogens connected to atoms which have already been laid out.
void	placeHydrogens2D(IAtomContainer container, IAtom atom)	Place hydrogens connected to the given atom using the average bond length in the container.
void	placeHydrogens2D(IAtomContainer container, IAtom atom, double bondLength)	Place hydrogens connected to the provided atom atom using the specified bondLength.

Methods inherited from class java.lang.Object

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

Constructor Detail

HydrogenPlacer

public HydrogenPlacer()

Method Detail

placeHydrogens2D

public void placeHydrogens2D(IAtomContainer container,
                             double bondLength)

Place all hydrogens connected to atoms which have already been laid out.

Parameters:

container - atom container

bondLength - bond length to user

placeHydrogens2D

public void placeHydrogens2D(IAtomContainer container,
                             IAtom atom)

Place hydrogens connected to the given atom using the average bond length in the container.

Parameters:

container - atom container of which atom is a member

atom - the atom of which to place connected hydrogens

Throws:

IllegalArgumentException - if the atom does not have 2d coordinates

See Also:

placeHydrogens2D(org.openscience.cdk.interfaces.IAtomContainer, double)

placeHydrogens2D

public void placeHydrogens2D(IAtomContainer container,
                             IAtom atom,
                             double bondLength)

Place hydrogens connected to the provided atom atom using the specified bondLength.

Parameters:

container - atom container

bondLength - bond length to user

Throws:

IllegalArgumentException - thrown if the atom or container was null or the atom has connected atoms which have not been placed.