Class 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 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