org.openscience.cdk.geometry.cip

Class CIPTool

java.lang.Object

org.openscience.cdk.geometry.cip.CIPTool

public class CIPTool
extends Object

Tool to help determine the R,S and stereochemistry definitions of a subset of the CIP rules [Cahn, R.S. and Ingold, C. and Prelog, V., Specification of Molecular Chirality, Angew. Chem. Int. Ed., 1966, 5:385-415]. The used set up sub rules are specified in the CIPLigandRule class.

Basic use starts from a ITetrahedralChirality and therefore assumes atoms with four neighbours:

 IAtom[] ligandAtoms =
   mol.getConnectedAtomsList(centralAtom).toArray(new IAtom[4]);
 ITetrahedralChirality tetraStereo = new TetrahedralChirality(
   centralAtom, ligandAtoms, Stereo.ANTI_CLOCKWISE
 );
 CIP_CHIRALITY cipChirality = CIPTool.getCIPChirality(mol, tetraStereo);
 

The IBond.Stereo value can be reconstructed from 3D coordinates with the StereoTool.

Source code:

master

Belongs to CDK module:

cip

Nested Class Summary

Nested Classes

Modifier and Type	Class and Description
static class	CIPTool.CIP_CHIRALITY Enumeration with the two tetrahedral chiralities defined by the CIP schema.

Field Summary

Fields

Modifier and Type	Field and Description
static int	HYDROGEN IAtom index to indicate an implicit hydrogen, not present in the chemical graph.

Constructor Summary

Constructors

Constructor and Description
CIPTool()

Method Summary

Methods

Modifier and Type	Method and Description
static boolean	checkIfAllLigandsAreDifferent(ILigand[] ligands) Checks if each next ILigand is different from the previous one according to the CIPLigandRule.
static org.openscience.cdk.geometry.cip.LigancyFourChirality	defineLigancyFourChirality(IAtomContainer container, int chiralAtom, int ligand1, int ligand2, int ligand3, int ligand4, ITetrahedralChirality.Stereo stereo) Creates a ligancy for chirality around a single chiral atom, where the involved atoms are identified by there index in the IAtomContainer.
static ILigand	defineLigand(IAtomContainer container, VisitedAtoms visitedAtoms, int chiralAtom, int ligandAtom) Creates a ligand attached to a single chiral atom, where the involved atoms are identified by there index in the IAtomContainer.
static CIPTool.CIP_CHIRALITY	getCIPChirality(IAtomContainer container, IDoubleBondStereochemistry stereoCenter)
static CIPTool.CIP_CHIRALITY	getCIPChirality(IAtomContainer container, ITetrahedralChirality stereoCenter) Returns the R or S chirality according to the CIP rules, based on the given chirality information.
static CIPTool.CIP_CHIRALITY	getCIPChirality(org.openscience.cdk.geometry.cip.LigancyFourChirality stereoCenter) Returns the R or S chirality according to the CIP rules, based on the given chirality information.
static ILigand[]	getLigandLigands(ILigand ligand) Returns a CIP-expanded array of side chains of a ligand.
static void	label(IAtomContainer container) Convenience method for labelling all stereo elements.
static ILigand[]	order(ILigand[] ligands) Reorders the ILigand objects in the array according to the CIP rules.

Methods inherited from class java.lang.Object

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

Field Detail

HYDROGEN

public static final int HYDROGEN

IAtom index to indicate an implicit hydrogen, not present in the chemical graph.

See Also:

Constant Field Values

Constructor Detail

CIPTool

public CIPTool()

Method Detail

getCIPChirality

public static CIPTool.CIP_CHIRALITY getCIPChirality(org.openscience.cdk.geometry.cip.LigancyFourChirality stereoCenter)

Returns the R or S chirality according to the CIP rules, based on the given chirality information.

Parameters:

stereoCenter - Chiral center for which the CIP chirality is to be determined as LigancyFourChirality object.

Returns:

A CIPTool.CIP_CHIRALITY value.

label

public static void label(IAtomContainer container)

Convenience method for labelling all stereo elements. The CIPTool.CIP_CHIRALITY is determined for each element and stored as as String on the CDKConstants.CIP_DESCRIPTOR property key. Atoms/bonds that are not stereocenters have no label assigned and the property will be null.

Parameters:

container - structure to label

getCIPChirality

public static CIPTool.CIP_CHIRALITY getCIPChirality(IAtomContainer container,
                                    ITetrahedralChirality stereoCenter)

Returns the R or S chirality according to the CIP rules, based on the given chirality information.

Parameters:

container - IAtomContainer to which the stereoCenter belongs.

stereoCenter - Chiral center for which the CIP chirality is to be determined as ITetrahedralChirality object.

Returns:

A CIPTool.CIP_CHIRALITY value.

getCIPChirality

public static CIPTool.CIP_CHIRALITY getCIPChirality(IAtomContainer container,
                                    IDoubleBondStereochemistry stereoCenter)

checkIfAllLigandsAreDifferent

public static boolean checkIfAllLigandsAreDifferent(ILigand[] ligands)

Checks if each next ILigand is different from the previous one according to the CIPLigandRule. It assumes that the input is sorted based on that rule.

Parameters:

ligands - array of ILigand to check

Returns:

true, if all ligands are different

order

public static ILigand[] order(ILigand[] ligands)

Reorders the ILigand objects in the array according to the CIP rules.

Parameters:

ligands - Array of ILigands to be reordered.

Returns:

Reordered array of ILigands.

defineLigancyFourChirality

public static org.openscience.cdk.geometry.cip.LigancyFourChirality defineLigancyFourChirality(IAtomContainer container,
                                                                               int chiralAtom,
                                                                               int ligand1,
                                                                               int ligand2,
                                                                               int ligand3,
                                                                               int ligand4,
                                                                               ITetrahedralChirality.Stereo stereo)

Creates a ligancy for chirality around a single chiral atom, where the involved atoms are identified by there index in the IAtomContainer. For the four ligand atoms, HYDROGEN can be passed as index, which will indicate the presence of an implicit hydrogen, not explicitly present in the chemical graph of the given container.

Parameters:

container - IAtomContainer for which the returned ILigands are defined

chiralAtom - int pointing to the IAtom index of the chiral atom

ligand1 - int pointing to the IAtom index of the first ILigand

ligand2 - int pointing to the IAtom index of the second ILigand

ligand3 - int pointing to the IAtom index of the third ILigand

ligand4 - int pointing to the IAtom index of the fourth ILigand

stereo - ITetrahedralChirality.Stereo for the chirality

Returns:

the created LigancyFourChirality

defineLigand

public static ILigand defineLigand(IAtomContainer container,
                   VisitedAtoms visitedAtoms,
                   int chiralAtom,
                   int ligandAtom)

Creates a ligand attached to a single chiral atom, where the involved atoms are identified by there index in the IAtomContainer. For ligand atom, HYDROGEN can be passed as index, which will indicate the presence of an implicit hydrogen, not explicitly present in the chemical graph of the given container.

Parameters:

container - IAtomContainer for which the returned ILigands are defined

visitedAtoms - a list of atoms already visited in the analysis

chiralAtom - an integer pointing to the IAtom index of the chiral atom

ligandAtom - an integer pointing to the IAtom index of the ILigand

Returns:

the created ILigand

getLigandLigands

public static ILigand[] getLigandLigands(ILigand ligand)

Returns a CIP-expanded array of side chains of a ligand. If the ligand atom is only connected to the chiral atom, the method will return an empty list. The expansion involves the CIP rules, so that a double bonded oxygen will be represented twice in the list.

Parameters:

ligand - the ILigand for which to return the ILigands

Returns:

a ILigand array with the side chains of the ligand atom