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//
// Copyright (C) David Cosgrove 2023
//
// @@ All Rights Reserved @@
// This file is part of the RDKit.
// The contents are covered by the terms of the BSD license
// which is included in the file license.txt, found at the root
// of the RDKit source tree.
//
#include <RDGeneral/export.h>
#ifndef RDKIT_RASCAL_MCES_H
#define RDKIT_RASCAL_MCES_H
#include <vector>
#include <GraphMol/RascalMCES/RascalClusterOptions.h>
#include <GraphMol/RascalMCES/RascalOptions.h>
#include <GraphMol/RascalMCES/RascalResult.h>
namespace RDKit {
class ROMol;
namespace RascalMCES {
// Find one or more MCESs between the two molecules. The MCES is the
// Maximum Common Edge Substructure, and is the largest set of bonds
// common to the 2 molecules.
/*!
*
* @param mol1 : first molecule
* @param mol2 : second molecule for MCES determination.
* @param opts : (optional) set of options controlling the MCES determination
* @return : vector of RascalResult objects.
*/
RDKIT_RASCALMCES_EXPORT std::vector<RascalResult> rascalMCES(
const ROMol &mol1, const ROMol &mol2,
const RascalOptions &opts = RascalOptions());
// Cluster the molecules using the Johnson similarity from rascalMCES
// and the algorithm of
// 'A Line Graph Algorithm for Clustering Chemical Structures Based
// on Common Substructural Cores', JW Raymond, PW Willett.
// https://match.pmf.kg.ac.rs/electronic_versions/Match48/match48_197-207.pdf
// https://eprints.whiterose.ac.uk/77598/
// This is a fuzzy clustering algorithm, so a molecule may appear in more than
// one cluster. The final cluster is all the molecules that didn't fit into
// another cluster (the singletons).
/*!
*
* @param mols : molecules to cluster
* @param clusOpts : (optional) cluster options
* @return clusters as vector of vectors of unsigned ints - indices into the
* input mols vector
*/
RDKIT_RASCALMCES_EXPORT std::vector<std::vector<unsigned int>> rascalCluster(
const std::vector<std::shared_ptr<ROMol>> &mols,
const RascalClusterOptions &clusOpts = RascalClusterOptions());
// Cluster the molecules using the Johnson similarity from rascalMCES and
// the Butina algorithm. Butina JCICS 39 747-750 (1999).
/*!
*
* @param mols : molecules to cluster
* @param clusOpts : (optional) cluster options
* @return clusters as vector of vectors of unsigned ints - indices into the
* input mols vector
*/
RDKIT_RASCALMCES_EXPORT std::vector<std::vector<unsigned int>>
rascalButinaCluster(
const std::vector<std::shared_ptr<ROMol>> &mols,
const RascalClusterOptions &clusOpts = RascalClusterOptions());
} // namespace RascalMCES
} // namespace RDKit
#endif // RDKIT_RASCAL_MCES_H
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