Class AbstractFingerprinter

java.lang.Object
org.openscience.cdk.fingerprint.AbstractFingerprinter
All Implemented Interfaces:
IFingerprinter
Direct Known Subclasses:
AtomPairs2DFingerprinter, CircularFingerprinter, EStateFingerprinter, Fingerprinter, LingoFingerprinter, MACCSFingerprinter, PubchemFingerprinter, ShortestPathFingerprinter, SignatureFingerprinter, SubstructureFingerprinter

public abstract class AbstractFingerprinter extends Object implements IFingerprinter
  • Constructor Details

    • AbstractFingerprinter

      public AbstractFingerprinter()
  • Method Details

    • getParameters

      protected List<Map.Entry<String,String>> getParameters()
      Base classes should override this method to report the parameters they are configured with.
      Returns:
      The key=value pairs of configured parameters
    • getVersionDescription

      public final String getVersionDescription()
      Description copied from interface: IFingerprinter
      Generate a fingerprint type version description in chemfp's FPS format. We report the library version rather than an individual version per fingerprint, although this is awkward as many fingerprint's don't/won't change between releases and we can not keep compatibility we guarantee we document how the fingerprint was encoded.
      Examples:
       #type=CDK-Fingerprinter/2.0 searchDepth=7 pathLimit=2000 hashPseudoAtoms=true
       #type=CDK-CircularFingerprint/2.0 classType=ECFP4
       
      Specified by:
      getVersionDescription in interface IFingerprinter
      Returns:
      version description.
    • getFingerprint

      public BitSet getFingerprint(IAtomContainer mol) throws CDKException
      Generate a binary fingerprint as a bit. This method will usually delegate to IFingerprinter.getBitFingerprint(IAtomContainer) and invoke IBitFingerprint.asBitSet(), it is included for backwards compatibility.
      Specified by:
      getFingerprint in interface IFingerprinter
      Parameters:
      mol - molecule
      Returns:
      BitSet
      Throws:
      CDKException - problem generating fingerprint