org.openscience.cdk.signature

Class MoleculeSignature

java.lang.Object

signature.AbstractGraphSignature

org.openscience.cdk.signature.MoleculeSignature

public class MoleculeSignature
extends signature.AbstractGraphSignature

A molecule signature is a way to produce AtomSignatures and to get the canonical [Faulon, J. L., Collins, M. J., and Carr, R. D., The Signature Molecular Descriptor. 4. Canonizing Molecules Using Extended Valence Sequences, Journal of Chemical Information and Computer Sciences, 2004, 44:427-436] signature string for a molecule. There are several possible uses for a molecule signature.

Firstly, a signature with a height greater than the diameter of a molecule can be used to reconstruct the molecule. In this sense, the signature string is like a SMILES [Weininger, David, SMILES, a Chemical Language and Information System. 1. Introduction to Methodology and Encoding Rules, Journal of Chemical Information and Computer Sciences, 1988, 28:31-36, Weininger, David and Weininger, Arthur and Weininger, Joseph L., SMILES 2. Algorithm for Generation of Unique SMILES Notation, Journal of Chemical Information and Computer Sciences, 1989, 29:97-101] string. It is more verbose, but it will work for all molecules.

Secondly, the set of signatures for a molecule partition the atoms into equivalence classes (or 'orbits' - see the Orbit class). This is similar to partitioning atoms by Morgan number [Morgan, H.L., The Generation of a Unique Machine Description for Chemical Structures - A Technique Developed at Chemical Abstracts Service., J.Chem.Doc., 1965, 5:107-113] except that it works for 3-regular graphs like fullerenes.

Thirdly, signatures can be calculated at different heights to give descriptions of the connectivity around atoms. 'Height' is the same as the idea of a 'sphere' in HOSE codes, and signatures are also path descriptors in this sense.

So, for example, to get the canonical signature for a molecule:

 IAtomContainer diamantane = MoleculeFactory.makeBenzene();
 MoleculeSignature moleculeSignature = new MoleculeSignature(diamantane);
 String canonicalSignature = moleculeSignature.toCanonicalString();
 

to get the orbits of this molecule:

 List<Orbit> orbits = moleculeSignature.calculateOrbits();
 

and to get the height-2 signature string of just atom 5:

 String hSignatureForAtom5 = moleculeSignature.signatureStringForVertex(5, 2);
 

it is also possible to get AtomSignatures using the signatureForVertex method - which is just a convenience method equivalent to calling the constructor of an AtomSignature class.

Author:

maclean

Source code:

master

Belongs to CDK module:

signature

Constructor Summary

Constructors

Constructor and Description
MoleculeSignature(IAtomContainer molecule) Creates a signature that represents this molecule.
MoleculeSignature(IAtomContainer molecule, int height) Creates a signature with a maximum height of height for molecule molecule.

Method Summary

Methods

Modifier and Type	Method and Description
List<Orbit>	calculateOrbits() Calculates the orbits of the atoms of the molecule.
static IAtomContainer	fromSignatureString(String signatureString, IChemObjectBuilder coBuilder) Builder for molecules (rather, for atom containers) from signature strings.
protected int	getVertexCount()
signature.AbstractVertexSignature	signatureForVertex(int vertexIndex)
String	signatureStringForVertex(int vertexIndex)
String	signatureStringForVertex(int vertexIndex, int height)
String	toCanonicalSignatureString(int height) Make a canonical signature string of a given height.

Methods inherited from class signature.AbstractGraphSignature

getCanonicalLabels, getGraphSignature, getHeight, getMaximalSignature, getMinimalSignature, getSortedSignatures, getSymmetryClasses, getSymmetryClasses, getVertexSignatures, getVertexSignatureStrings, isCanonicallyLabelled, reconstructCanonicalEdgeString, reconstructCanonicalGraph, toCanonicalString, toFullString

Methods inherited from class java.lang.Object

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

Constructor Detail

MoleculeSignature

public MoleculeSignature(IAtomContainer molecule)

Creates a signature that represents this molecule.

Parameters:

molecule - the molecule to convert to a signature

MoleculeSignature

public MoleculeSignature(IAtomContainer molecule,
                 int height)

Creates a signature with a maximum height of height for molecule molecule.

Parameters:

molecule - the molecule to convert to a signature

height - the maximum height of the signature

Method Detail

getVertexCount

protected int getVertexCount()

Specified by:

getVertexCount in class signature.AbstractGraphSignature

signatureStringForVertex

public String signatureStringForVertex(int vertexIndex)

Specified by:

signatureStringForVertex in class signature.AbstractGraphSignature

signatureStringForVertex

public String signatureStringForVertex(int vertexIndex,
                              int height)

Specified by:

signatureStringForVertex in class signature.AbstractGraphSignature

signatureForVertex

public signature.AbstractVertexSignature signatureForVertex(int vertexIndex)

Specified by:

signatureForVertex in class signature.AbstractGraphSignature

calculateOrbits

public List<Orbit> calculateOrbits()

Calculates the orbits of the atoms of the molecule.

Returns:

a list of orbits

fromSignatureString

public static IAtomContainer fromSignatureString(String signatureString,
                                 IChemObjectBuilder coBuilder)

Builder for molecules (rather, for atom containers) from signature strings.

Parameters:

signatureString - the signature string to use

coBuilder - IChemObjectBuilder to build the returned atom container from

Returns:

an atom container

toCanonicalSignatureString

public String toCanonicalSignatureString(int height)

Make a canonical signature string of a given height.

Parameters:

height - the maximum height to make signatures

Returns:

the canonical signature string