Package 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.. Journal of Chemical Information and Computer Sciences. 2004. 44] 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. Journal of Chemical Information and Computer Sciences. 1988. 28, Weininger, David et. al.. Journal of Chemical Information and Computer Sciences. 1989. 29] 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.. J.Chem.Doc.. 1965. 5] 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:
main
Belongs to CDK module:
signature

  • Constructor Details

    • 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 Details

    • 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