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/*
* MIT License
*
* Copyright (c) 2023 Betuel Sevindik, Felix Baensch, Jonas Schaub, Christoph Steinbeck, and Achim Zielesny
*
* Permission is hereby granted, free of charge, to any person obtaining a copy
* of this software and associated documentation files (the "Software"), to deal
* in the Software without restriction, including without limitation the rights
* to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
* copies of the Software, and to permit persons to whom the Software is
* furnished to do so, subject to the following conditions:
*
* The above copyright notice and this permission notice shall be included in all
* copies or substantial portions of the Software.
*
* THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
* IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
* FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
* AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
* LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
* OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
* SOFTWARE.
*/
package de.unijena.cheminf.fragment.fingerprint;
import org.openscience.cdk.fingerprint.IBitFingerprint;
import org.openscience.cdk.fingerprint.ICountFingerprint;
import org.openscience.cdk.fingerprint.IFingerprinter;
import java.util.List;
import java.util.Map;
/**
* 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.
*
*
* @author Betuel Sevindik
* @version 1.0.0.0
*/
public interface IFragmentFingerprinter extends IFingerprinter {
//
/**
* 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.
*
* @param 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.
* @return the bit fingerprint
*/
IBitFingerprint getBitFingerprint(List aListOfUniqueSmiles);
//
/**
* 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.
*
* @param 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.
* @return the count fingerprint
*/
ICountFingerprint getCountFingerprint(Map aUniqueSmilesToFrequencyMap);
//
/**
* 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.
*
* @param 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.
* @return the count fingerprint
*/
ICountFingerprint getCountFingerprint(List aUniqueSmilesList);
//
}
