org.openscience.cdk.graph.rebond
Class RebondTool

java.lang.Object
  org.openscience.cdk.graph.rebond.RebondTool

@TestClass(value="org.openscience.cdk.graph.rebond.RebondToolTest")
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

Keywords:

rebonding, bond, recalculation

Created on:

2003-05-23

Belongs to CDK module:

standard

Dictionary pointer(s):

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

Source code:

HEAD

Constructor Summary

RebondTool(double maxCovalentRadius, double minBondDistance, double bondTolerance)

Method Summary

void	rebond(IAtomContainer container) Rebonding using a Binary Space Partition Tree.

Methods inherited from class java.lang.Object

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

Constructor Detail

RebondTool

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

Method Detail

rebond

@TestMethod(value="testRebond_IAtomContainer")
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 Âle;ngstrom.

Throws:

CDKException