org.openscience.cdk.graph.rebond

Class RebondTool

java.lang.Object

org.openscience.cdk.graph.rebond.RebondTool

public class RebondTool
extends Object

Provides tools to rebond a molecule from 3D coordinates only. The algorithm uses an efficient algorithm using a Binary Space Partitioning Tree (Bspt). It requires that the atom types are configured such that the covalent bond radii for all atoms are set. The AtomTypeFactory can be used for this.

Author:

Miguel Howard

See Also:

Bspt

Dictionary pointer(s):

rebondFrom3DCoordinates in the Blue Obelisk Chemoinformatics Dictionary [blue-obelisk:rebondFrom3DCoordinates]

Source code:

master

Belongs to CDK module:

standard

Keywords:

rebonding, bond, recalculation

Created on:

2003-05-23

Constructor Summary

Constructors

Constructor and Description
RebondTool(double maxCovalentRadius, double minBondDistance, double bondTolerance)

Method Summary

Modifier and Type	Method and Description
void	rebond(IAtomContainer container) Rebonding using a Binary Space Partition Tree.

Methods inherited from class java.lang.Object

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

Constructor Detail

RebondTool

public RebondTool(double maxCovalentRadius,
                  double minBondDistance,
                  double bondTolerance)

Method Detail

rebond

public void rebond(IAtomContainer container)
            throws CDKException

Rebonding using a Binary Space Partition Tree. Note, that any bonds defined will be deleted first. It assumes the unit of 3D space to be 1 Å.

Throws:

CDKException