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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_DETAILS_H
#define RDKIT_RASCAL_DETAILS_H
#include <map>
#include <GraphMol/RascalMCES/RascalOptions.h>
#include <GraphMol/RascalMCES/RascalResult.h>
namespace RDKit {
class ROMol;
namespace RascalMCES {
struct RascalClusterOptions;
namespace details {
struct ClusNode {
std::shared_ptr<RascalResult> d_res;
double d_sim;
unsigned int d_mol1Num, d_mol2Num;
};
RDKIT_RASCALMCES_EXPORT double tier1Sim(
const RDKit::ROMol &mol1, const RDKit::ROMol &mol2,
std::map<int, std::vector<std::pair<int, int>>> °Seqs1,
std::map<int, std::vector<std::pair<int, int>>> °Seqs2);
RDKIT_RASCALMCES_EXPORT double tier2Sim(
const ROMol &mol1, const ROMol &mol2,
const std::map<int, std::vector<std::pair<int, int>>> °Seqs1,
const std::map<int, std::vector<std::pair<int, int>>> °Seqs2,
const std::vector<unsigned int> &bondLabels1,
const std::vector<unsigned int> &bondLabels2);
RDKIT_RASCALMCES_EXPORT void getBondLabels(
const RDKit::ROMol &mol1, const RDKit::ROMol &mol2,
const RascalOptions &opts, std::vector<unsigned int> &bondLabels1,
std::vector<unsigned int> &bondLabels2);
std::vector<std::vector<ClusNode>> buildProximityGraph(
const std::vector<std::shared_ptr<ROMol>> &mols,
const RascalClusterOptions &clusOpts);
RDKIT_RASCALMCES_EXPORT bool resultCompare(const RascalResult &res1,
const RascalResult &res2);
RDKIT_RASCALMCES_EXPORT void extractClique(
const std::vector<unsigned int> &clique,
const std::vector<std::pair<int, int>> &vtxPairs, bool swapped,
std::vector<std::pair<int, int>> &bondMatches);
// do some simple cleaning of the SMARTS, to make it more user-friendly.
RDKIT_RASCALMCES_EXPORT void cleanSmarts(std::string &smarts,
const std::string &equivalentAtoms);
// Primarily for debugging, these write out the corresponding bonds/atoms
// in Python list format, for ease of cut/paste into a highlighted image
// creation.
RDKIT_RASCALMCES_EXPORT void printBondMatches(const RascalResult &res,
std::ostream &os);
RDKIT_RASCALMCES_EXPORT void printAtomMatches(const RascalResult &res,
std::ostream &os);
// This prints out the scores in the order they are used in resultCompare.
RDKIT_RASCALMCES_EXPORT void printScores(const RascalResult &res,
std::ostream &os);
// Calculate the Johnson similarity between the two molecules using the given
// bondMatches. It's the fraction of the 2 molecules that are in common,
// somewhat akin to the tanimoto - the square of the number of atoms plus
// number of bonds in the MCES divided by the product of the sums of the number
// of atoms and bonds in the 2 molecules.
// It has nothing to do with lying UK politicians.
RDKIT_RASCALMCES_EXPORT double johnsonSimilarity(
const std::vector<std::pair<int, int>> &bondMatches,
const std::vector<std::pair<int, int>> &atomMatches,
const RDKit::ROMol &mol1, const RDKit::ROMol &mol2);
} // namespace details
} // namespace RascalMCES
} // namespace RDKit
#endif // RDKIT_RASCAL_MCES_H
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