Class CFGenerator


  • @PublicAPI
    public class CFGenerator
    extends MDGenerator
    The CFGenerator class generates topological fingerprints of molecular graphs.

    Basic concepts
    A binary string (series of 0 and 1) is constructed based on local connectivity atoms and atom types. The length of the series is a predefined constant parameter. Two further parameters influence the fingerprints gerenerated: number of bonds, which determines the number size of local neighborhood of atoms takes into account by providing an upper limit for the length of path starting from each atom; and the number of bits to be set in the fingerprint for each property identified.

    Typical usage
    For the sake of optimal memory usage one instance of this class can generate fingerprints for a series of molecular graphs by the consecutive call to the generate() method.
    In most cases the generator is not intended to be used directly. When molecules are taken from files or databases the corresponding MolecularDescriptors can be generated by the appropriate MDReader object. Alternatively, MolecularDescriptor.generate( final Molecule ) is the simplest way to obtain a descriptor corresponding to a molecular structure.

    Example of the direct use of the class within an application:
          CFGenerator gen = new CFGenerator();
          ChemicalFingerprint fp = new ChemicalFingerprint( new CFParameters() );
          Molecule mol = getFirstMoleculeFromSomewhere();
          while ( mol != null ) {
              gen.generate( mol, fp );
              doSomethingWith( fp );
              mol = getNextMoleculeFromSomewhere();
          }
     
    Since:
    JChem 2.0
    • Constructor Detail

      • CFGenerator

        public CFGenerator()
        Creates a new instance of CFGenerator which can be used to generate chemical fingerprints for an arbitrary number of molecules.
        Since:
        JChem 5.8
      • CFGenerator

        @Deprecated
        public CFGenerator​(int length)
        Deprecated.
        since 5.4
        Creates a new instance of CFGenerator which can be used to generate chemical fingerprints for an arbitrary number of molecules.
        Parameters:
        length - length of the chemical fingerprint in bits
        Since:
        JChem 2.2
    • Method Detail

      • generate

        public String[] generate​(Molecule m,
                                 MolecularDescriptor d)
                          throws MDGeneratorException
        Generates the chemical fingerprint for the given molecule. New instance of the ChemicalFingerprint object is not allocated, the MolecularDescriptor provided as a method parameter is updated (and it has to be allocated and initialized by the client of this class).
        Specified by:
        generate in class MDGenerator
        Parameters:
        m - molecule for which the fingerprint is created
        d - the chemical fingerprint generated
        Returns:
        names of tags (properties) set (added) during fingerprint generation, it is always null in the case of ChemicalFingerprint
        Throws:
        MDGeneratorException - in the case of any failures to generate the descriptor
      • generate

        public String[] generate​(Molecule m,
                                 int[] aidxs,
                                 MolecularDescriptor d)
                          throws MDGeneratorException
        Generates the partial chemical fingerprint for the given molecule. New instance of the ChemicalFingerprint object is not allocated, the MolecularDescriptor provided as a method parameter is updated (and it has to be allocated and initialized by the client of this class).

        Partial fingerprint is fingerprint for paths containing the given atoms. The algorithm performs the full path enumeration over the molecule, but only sets bits in the resulting fingerprint for paths containing the given atoms.

        Parameters:
        m - molecule for which the fingerprint is created
        aidxs - atom indexes that define the partial fingerprint generation
        d - the chemical fingerprint generated
        Returns:
        names of tags (properties) set (added) during fingerprint generation, it is always null in the case of ChemicalFingerprint
        Throws:
        MDGeneratorException
      • calcFreqCount

        protected int calcFreqCount​(MolecularDescriptor d)
        Updates statistics gathered on fingerprints generated and get the number of non-zero cells.
        Overrides:
        calcFreqCount in class MDGenerator
        Parameters:
        d - newly generated MolecularDescriptor
        Returns:
        brightness of the fingerprint
        Since:
        JChem 2.1