org.openscience.cdk.graph.rebond
Class RebondTool

java.lang.Object
  extended by 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