org.openscience.cdk.interfaces

Interface IStereoElement

All Superinterfaces:

Cloneable, ICDKObject

All Known Subinterfaces:

IDoubleBondStereochemistry, ITetrahedralChirality

All Known Implementing Classes:

DoubleBondStereochemistry, ExtendedTetrahedral, TetrahedralChirality

public interface IStereoElement
extends ICDKObject

Represents the concept of a stereo element in the molecule. Stereo elements can be that of quadrivalent atoms, cis/trans isomerism around double bonds, but also include axial and helical stereochemistry.

Author:

egonw

Source code:

master

Belongs to CDK module:

interfaces

Keywords:

stereochemistry

Method Summary

Methods

Modifier and Type	Method and Description
boolean	contains(IAtom atom) Does the stereo element contain the provided atom.
IStereoElement	map(Map<IAtom,IAtom> atoms, Map<IBond,IBond> bonds) Map the atoms/bonds in this instance to a new stereo element using the provided atom/bond mapping.

Methods inherited from interface org.openscience.cdk.interfaces.ICDKObject

getBuilder

Method Detail

contains

boolean contains(IAtom atom)

Does the stereo element contain the provided atom.

Parameters:

atom - an atom to test membership

Returns:

whether the atom is present

map

IStereoElement map(Map<IAtom,IAtom> atoms,
                 Map<IBond,IBond> bonds)

Map the atoms/bonds in this instance to a new stereo element using the provided atom/bond mapping. This allows the stereo element to be transferred between a cloned or aligned (i.e. isomorphic) chemical graph. If no mapping is found for a given atom or bond it is replaced with a null reference. However the provided atom and bonds maps must not be null.

Parameters:

atoms - non-null atom mapping, used to convert the original atoms to their mapped counterparts

bonds - non-null bond mapping, used to convert the original bonds to their mapped counterparts

Returns:

a new stereo element in the same configuration but with atoms/bonds replaced with their mapped equivalence.