Package org.openscience.cdk.graph.rebond
Class RebondTool
- java.lang.Object
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- org.openscience.cdk.graph.rebond.RebondTool
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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
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Constructor Summary
Constructors Constructor Description RebondTool(double maxCovalentRadius, double minBondDistance, double bondTolerance)
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Method Summary
All Methods Instance Methods Concrete Methods Modifier and Type Method Description void
rebond(IAtomContainer container)
Rebonding using a Binary Space Partition Tree.
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Method Detail
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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
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