RebondTool (cdk 2.10 API)

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:
main

Belongs to CDK module:
standard

Keywords:

rebonding, bond, recalculation

Created on:

2003-05-23

- Constructor Summary
  
  Constructors
  Constructor Description
  
  RebondTool(double maxCovalentRadius, double minBondDistance, double bondTolerance)
- Method Summary
  
  All Methods Instance Methods Concrete Methods
  Modifier and Type Method 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