Package chemaxon.descriptors

Class ECFPGenerator

java.lang.Object
chemaxon.descriptors.MDGenerator
chemaxon.descriptors.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 Details

    • ECFPGenerator

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

  • Method Details

    • 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