Package org.openscience.cdk.graph.rebond
Class RebondTool
java.lang.Object
org.openscience.cdk.graph.rebond.RebondTool
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
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Constructor Summary
ConstructorsConstructorDescriptionRebondTool
(double maxCovalentRadius, double minBondDistance, double bondTolerance) -
Method Summary
Modifier and TypeMethodDescriptionvoid
rebond
(IAtomContainer container) Rebonding using a Binary Space Partition Tree.
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Constructor Details
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RebondTool
public RebondTool(double maxCovalentRadius, double minBondDistance, double bondTolerance)
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Method Details
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rebond
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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