Package org.openscience.cdk.fingerprint

Class HybridizationFingerprinter

  • All Implemented Interfaces:
    IFingerprinter
    public class HybridizationFingerprinter
extends Fingerprinter
implements IFingerprinter
    Generates a fingerprint for a given IAtomContainer. Fingerprints are one-dimensional bit arrays, where bits are set according to a the occurrence of a particular structural feature (See for example the Daylight inc. theory manual for more information). Fingerprints allow for a fast screening step to exclude candidates for a substructure search in a database. They are also a means for determining the similarity of chemical structures.

    A fingerprint is generated for an AtomContainer with this code:

       Molecule molecule = new Molecule();
   IFingerprinter fingerprinter =
     new HybridizationFingerprinter();
   BitSet fingerprint = fingerprinter.getFingerprint(molecule);
   fingerprint.size(); // returns 1024 by default
   fingerprint.length(); // returns the highest set bit

    The FingerPrinter assumes that hydrogens are explicitly given! Furthermore, if pseudo atoms or atoms with malformed symbols are present, their atomic number is taken as one more than the last element currently supported in PeriodicTable.

    Unlike the Fingerprinter, this fingerprinter does not take into account aromaticity. Instead, it takes into account SP2 IAtomType.Hybridization.

    Source code:
    main
    Belongs to CDK module:
    standard
    Keywords:
    fingerprint, similarity

    • Constructor Detail

      • HybridizationFingerprinter

        public HybridizationFingerprinter()
        Creates a fingerprint generator of length DEFAULT_SIZE and with a search depth of DEFAULT_SEARCH_DEPTH.

      • HybridizationFingerprinter

        public HybridizationFingerprinter​(int size)

      • HybridizationFingerprinter

        public HybridizationFingerprinter​(int size,
                                  int searchDepth)
        Constructs a fingerprint generator that creates fingerprints of the given size, using a generation algorithm with the given search depth.
        Parameters:
        size - The desired size of the fingerprint
        searchDepth - The desired depth of search

    • Method Detail

      • getBondSymbol

        protected String getBondSymbol​(IBond bond)
        Gets the bond Symbol attribute of the Fingerprinter class.
        Overrides:
        getBondSymbol in class Fingerprinter
        Parameters:
        bond - Description of the Parameter
        Returns:
        The bondSymbol value