Package org.openscience.cdk.fragment

Class FragmentUtils

java.lang.Object

org.openscience.cdk.fragment.FragmentUtils

public class FragmentUtils
extends Object

Helper methods for fragmentation algorithms. Most of these methods are specific to the fragmentation algorithms in this package and so are protected. In general, these methods will not be used by the rest of the API or by other users of the library.

Author:

Rajarshi Guha

Belongs to CDK module:

fragment

Constructor Summary

Constructors

Constructor	Description
FragmentUtils()

Method Summary

Modifier and Type	Method	Description
protected static IAtomContainer	makeAtomContainer(IAtom atom, List<IBond> parts, IAtom excludedAtom)
protected static List<IAtomContainer>	splitMolecule(IAtomContainer atomContainer, IBond bond)	Non destructively split a molecule into two parts at the specified bond.
protected static List<IBond>	traverse(IAtomContainer atomContainer, IAtom atom, List<IBond> bondList)

Methods inherited from class java.lang.Object

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

Constructor Detail

FragmentUtils

public FragmentUtils()

Method Detail

splitMolecule

protected static List<IAtomContainer> splitMolecule(IAtomContainer atomContainer,
                                                    IBond bond)

Non destructively split a molecule into two parts at the specified bond. Note that if a ring bond is specified, the resultant list will contain teh opened ring twice.

Parameters:

atomContainer - The molecule to split

bond - The bond to split at

Returns:

A list containing the two parts of the molecule

makeAtomContainer

protected static IAtomContainer makeAtomContainer(IAtom atom,
                                                  List<IBond> parts,
                                                  IAtom excludedAtom)

traverse

protected static List<IBond> traverse(IAtomContainer atomContainer,
                                      IAtom atom,
                                      List<IBond> bondList)