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80381c61fd
* C++ implementation of equivalent atoms via SMARTS. * Python wrapper. * Tidy. * Check for too many classes. * Better handling of spaces in split. * Pass string by reference. Doh. * Add ignoreBondOrders option.
96 lines
3.5 KiB
C++
96 lines
3.5 KiB
C++
//
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// Copyright (C) David Cosgrove 2023
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//
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// @@ All Rights Reserved @@
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// This file is part of the RDKit.
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// The contents are covered by the terms of the BSD license
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// which is included in the file license.txt, found at the root
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// of the RDKit source tree.
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//
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#include <RDGeneral/export.h>
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#ifndef RDKIT_RASCAL_DETAILS_H
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#define RDKIT_RASCAL_DETAILS_H
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#include <map>
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#include <GraphMol/RascalMCES/RascalOptions.h>
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#include <GraphMol/RascalMCES/RascalResult.h>
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namespace RDKit {
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class ROMol;
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namespace RascalMCES {
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struct RascalClusterOptions;
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namespace details {
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struct ClusNode {
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std::shared_ptr<RascalResult> d_res;
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double d_sim;
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unsigned int d_mol1Num, d_mol2Num;
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};
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RDKIT_RASCALMCES_EXPORT double tier1Sim(
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const RDKit::ROMol &mol1, const RDKit::ROMol &mol2,
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std::map<int, std::vector<std::pair<int, int>>> °Seqs1,
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std::map<int, std::vector<std::pair<int, int>>> °Seqs2);
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RDKIT_RASCALMCES_EXPORT double tier2Sim(
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const ROMol &mol1, const ROMol &mol2,
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const std::map<int, std::vector<std::pair<int, int>>> °Seqs1,
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const std::map<int, std::vector<std::pair<int, int>>> °Seqs2,
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const std::vector<unsigned int> &bondLabels1,
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const std::vector<unsigned int> &bondLabels2);
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RDKIT_RASCALMCES_EXPORT void getBondLabels(
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const RDKit::ROMol &mol1, const RDKit::ROMol &mol2,
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const RascalOptions &opts, std::vector<unsigned int> &bondLabels1,
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std::vector<unsigned int> &bondLabels2);
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std::vector<std::vector<ClusNode>> buildProximityGraph(
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const std::vector<std::shared_ptr<ROMol>> &mols,
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const RascalClusterOptions &clusOpts);
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RDKIT_RASCALMCES_EXPORT bool resultCompare(const RascalResult &res1,
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const RascalResult &res2);
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RDKIT_RASCALMCES_EXPORT void extractClique(
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const std::vector<unsigned int> &clique,
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const std::vector<std::pair<int, int>> &vtxPairs, bool swapped,
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std::vector<std::pair<int, int>> &bondMatches);
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// do some simple cleaning of the SMARTS, to make it more user-friendly.
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RDKIT_RASCALMCES_EXPORT void cleanSmarts(std::string &smarts,
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const std::string &equivalentAtoms);
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// Primarily for debugging, these write out the corresponding bonds/atoms
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// in Python list format, for ease of cut/paste into a highlighted image
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// creation.
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RDKIT_RASCALMCES_EXPORT void printBondMatches(const RascalResult &res,
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std::ostream &os);
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RDKIT_RASCALMCES_EXPORT void printAtomMatches(const RascalResult &res,
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std::ostream &os);
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// This prints out the scores in the order they are used in resultCompare.
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RDKIT_RASCALMCES_EXPORT void printScores(const RascalResult &res,
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std::ostream &os);
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// Calculate the Johnson similarity between the two molecules using the given
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// bondMatches. It's the fraction of the 2 molecules that are in common,
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// somewhat akin to the tanimoto - the square of the number of atoms plus
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// number of bonds in the MCES divided by the product of the sums of the number
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// of atoms and bonds in the 2 molecules.
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// It has nothing to do with lying UK politicians.
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RDKIT_RASCALMCES_EXPORT double johnsonSimilarity(
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const std::vector<std::pair<int, int>> &bondMatches,
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const std::vector<std::pair<int, int>> &atomMatches,
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const RDKit::ROMol &mol1, const RDKit::ROMol &mol2);
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} // namespace details
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} // namespace RascalMCES
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} // namespace RDKit
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#endif // RDKIT_RASCAL_MCES_H
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