Class ECFPGenerator

  • All Implemented Interfaces:
    chemaxon.license.Licensable

    @PublicAPI
    public class ECFPGenerator
    extends MDGenerator
    implements chemaxon.license.Licensable
    The ECFPGenerator class generates ECFP fingerprints of molecular graphs.

    Basic concepts
    A binary string (series of 0 and 1) is constructed based on the local neighborhoods of the atoms. The length of the series is a predefined constant parameter. One further parameter specifies the diameter of the neighborhood considered for each atom.

    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:

        ECFPGenerator gen = new ECFPGenerator();
        ECFP fp = new ECFP(new ECFPParameters());
        Molecule mol = getFirstMoleculeFromSomewhere();
        while (mol != null) {
            gen.generate(mol, fp);
            doSomethingWith(fp);
            mol = getNextMoleculeFromSomewhere();
        }
     

    Since:
    JChem 5.4
    • Constructor Detail

      • ECFPGenerator

        public ECFPGenerator()
        Creates a new instance of ECFPGenerator, which can be used to generate ECFP fingerprints for an arbitrary number of molecules.
    • Method Detail

      • isLicensed

        public boolean isLicensed()
        Returns information about the licensing of the product.
        Specified by:
        isLicensed in interface chemaxon.license.Licensable
        Returns:
        true if the product is correctly licensed
      • setLicenseEnvironment

        public void setLicenseEnvironment​(String env)
        Sets the license environment.
        Specified by:
        setLicenseEnvironment in interface chemaxon.license.Licensable
      • generate

        public String[] generate​(Molecule mol,
                                 MolecularDescriptor descr)
                          throws MDGeneratorException
        Generates the ECFP fingerprint for the given molecule. New instance of the ECFP object is not allocated, the ECFP 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:
        mol - molecule for which the fingerprint is created
        descr - the ECFP fingerprint object
        Returns:
        names of tags (properties) set (added) during fingerprint generation, it is always null in the case of ECFP
        Throws:
        MDGeneratorException - in the case of any failures to generate the descriptor
      • 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 ECFP
        Returns:
        brightness of the fingerprint