Interface IFingerprinter

All Known Implementing Classes:
AbstractFingerprinter, AtomPairs2DFingerprinter, CircularFingerprinter, EStateFingerprinter, ExtendedFingerprinter, Fingerprinter, GraphOnlyFingerprinter, HybridizationFingerprinter, KlekotaRothFingerprinter, LingoFingerprinter, MACCSFingerprinter, PubchemFingerprinter, ShortestPathFingerprinter, SignatureFingerprinter, SubstructureFingerprinter

public interface IFingerprinter
Interface for fingerprint calculators.
Author:
egonw
Source code:
main
Belongs to CDK module:
core
Keywords:
fingerprint
  • Method Details

    • getVersionDescription

      String getVersionDescription()
      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
       
      Returns:
      version description.
    • getFingerprint

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

      IBitFingerprint getBitFingerprint(IAtomContainer container) throws CDKException
      Returns the bit fingerprint for the given IAtomContainer.
      Parameters:
      container - IAtomContainer for which the fingerprint should be calculated.
      Returns:
      the bit fingerprint
      Throws:
      CDKException - may be thrown if there is an error during aromaticity detection or (for key based fingerprints) if there is a SMARTS parsing error
      UnsupportedOperationException - if the Fingerprinter can not produce bit fingerprints
    • getCountFingerprint

      ICountFingerprint getCountFingerprint(IAtomContainer container) throws CDKException
      Returns the count fingerprint for the given IAtomContainer.
      Parameters:
      container - IAtomContainer for which the fingerprint should be calculated.
      Returns:
      the count fingerprint
      Throws:
      CDKException - if there is an error during aromaticity detection or (for key based fingerprints) if there is a SMARTS parsing error.
      UnsupportedOperationException - if the Fingerprinter can not produce count fingerprints
    • getRawFingerprint

      Map<String,Integer> getRawFingerprint(IAtomContainer container) throws CDKException
      Returns the raw representation of the fingerprint for the given IAtomContainer. The raw representation contains counts as well as the key strings.
      Parameters:
      container - IAtomContainer for which the fingerprint should be calculated.
      Returns:
      the raw fingerprint
      Throws:
      CDKException
    • getSize

      int getSize()
      Returns the size (or length) of the fingerprint.
      Returns:
      the size of the fingerprint