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:
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 Details

    • RebondTool

      public RebondTool(double maxCovalentRadius, double minBondDistance, double bondTolerance)
  • Method Details

    • 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