Package org.openscience.cdk.isomorphism

Class AtomMappingTools

java.lang.Object

org.openscience.cdk.isomorphism.AtomMappingTools

public class AtomMappingTools
extends Object

Source code:

main

Belongs to CDK module:

standard

Constructor Summary

Constructors

Constructor	Description
AtomMappingTools()

Method Summary

Modifier and Type	Method	Description
static Map<Integer,Integer>	mapAtomsOfAlignedStructures(IAtomContainer firstAtomContainer, IAtomContainer secondAtomContainer, Map<Integer,Integer> mappedAtoms)	Returns a Map with the AtomNumbers, the first number corresponds to the first (or the largest AtomContainer) atomContainer.

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Constructor Details

AtomMappingTools

public AtomMappingTools()

Method Details

mapAtomsOfAlignedStructures

public static Map<Integer,Integer> mapAtomsOfAlignedStructures(IAtomContainer firstAtomContainer,
 IAtomContainer secondAtomContainer,
 Map<Integer,Integer> mappedAtoms)
                                                        throws CDKException

Returns a Map with the AtomNumbers, the first number corresponds to the first (or the largest AtomContainer) atomContainer. Only for similar and aligned molecules with coordinates!

Parameters:

firstAtomContainer - the (largest) first aligned AtomContainer which is the reference

secondAtomContainer - the second aligned AtomContainer

Returns:

a Map of the mapped atoms

Throws:

CDKException - if there is an error in the UniversalIsomorphismTester