Package de.unijena.cheminf.fragment.fingerprint

Interface IFragmentFingerprinter

All Superinterfaces:
org.openscience.cdk.fingerprint.IFingerprinter
All Known Implementing Classes:
FragmentFingerprinter
public interface IFragmentFingerprinter extends org.openscience.cdk.fingerprint.IFingerprinter
Interface for implementing fragment fingerprinters. The interface IFragmentFingerprinter inherits from the CDK interface IFingerprinter and extends it with further methods. IFingerprinter is an interface for the calculation of fingerprints. I.e. classes that implement IFingerprinter can calculate fingerprints for a given IAtomContainer, including a bit and count fingerprint. The extension of the IFingerprinter by further methods now allows the calculation of a fingerprint by the mere comparison of strings. In this context, these strings are to correspond to the unique SMILES of fragments. The extension of the IFingerprinter includes the overloading of the methods that are responsible for the calculation of a count and bit fingerprint. These methods originally expect an IAtomContainer as a parameter. By overloading these methods, the count and bit fingerprints can be calculated without the need for an IAtomContainer, as this calculation is based only on the comparison of strings/unique SMILES of fragments.

  • Method Summary

    Modifier and Type
    Method
    Description
    org.openscience.cdk.fingerprint.IBitFingerprint
    getBitFingerprint(List<String> aListOfUniqueSmiles)
    Method for calculating a bit fingerprint.
    org.openscience.cdk.fingerprint.ICountFingerprint
    getCountFingerprint(List<String> aUniqueSmilesList)
    Method for calculating a count fingerprint.
    org.openscience.cdk.fingerprint.ICountFingerprint
    getCountFingerprint(Map<String,Integer> aUniqueSmilesToFrequencyMap)
    Method for calculating a count fingerprint.

    Methods inherited from interface org.openscience.cdk.fingerprint.IFingerprinter

    getBitFingerprint, getCountFingerprint, getFingerprint, getRawFingerprint, getSize, getVersionDescription

  • Method Details

    • getBitFingerprint

      org.openscience.cdk.fingerprint.IBitFingerprint getBitFingerprint(List<String> aListOfUniqueSmiles)
      Method for calculating a bit fingerprint. This method must be passed a list of unique SMILES/fragments as argument. The fragments can belong to a molecule or represent arbitrary fragments. The method compares this list of fragments with the list of predefined fragments/unique SMILES that was set when the class was initialized. To get the expected fingerprint, unique SMILES should be used. If unique SMILES are not used, the method does not deliver the expected result.
      Parameters:
      aListOfUniqueSmiles - is a list that stores fragments in the form of unique SMILES. To be able to calculate the fingerprint for a molecule, the fragments should belong to one molecule. The fragments are substructures of the molecule.
      Returns:
      the bit fingerprint

    • getCountFingerprint

      org.openscience.cdk.fingerprint.ICountFingerprint getCountFingerprint(Map<String,Integer> aUniqueSmilesToFrequencyMap)
      Method for calculating a count fingerprint. A map must be passed to this method. This map can represent a molecule by its fragments, which are represented by unique SMILES in the key set and their frequencies in the value set. However, this map can also contain arbitrary fragment sets. The method compares the unique SMILES in the key set with the predefined fragments specified when the class is initialized to create the fingerprint. To obtain the expected fingerprint, unique SMILES should be used and the keys in the input map should correspond to the unique SMILES of a molecule. If unique SMILES and molecule fragments are not used, the method will not give the expected result.
      Parameters:
      aUniqueSmilesToFrequencyMap - is a map that maps fragments in the form of unique SMILES to the frequency of unique SMILES. To be able to calculate the fingerprint for a molecule, the fragments must belong to a molecule. The fragments are substructures of the molecule.
      Returns:
      the count fingerprint

    • getCountFingerprint

      org.openscience.cdk.fingerprint.ICountFingerprint getCountFingerprint(List<String> aUniqueSmilesList)
      Method for calculating a count fingerprint. This method must be passed a list of unique SMILES/fragments as argument. The fragments can belong to a molecule or represent arbitrary fragments. The method compares this list of fragments with the list of predefined fragments/unique SMILES that was set when the class was initialized. To get the expected fingerprint, unique SMILES should be used on the one hand and on the other hand the fragments in the input list should correspond to the unique SMILES of a molecule. If unique SMILES and molecule fragments are not used, the method does not deliver the expected result.
      Parameters:
      aUniqueSmilesList - is a list that stores fragments in the form of unique SMILES. If a fragment occurs more than once in the molecule, it is also present more than once in the list. To be able to calculate the fingerprint for a molecule, the fragments should belong to one molecule.
      Returns:
      the count fingerprint