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//
// Copyright (C) 2017-2022 Novartis Institutes for BioMedical Research and
// other RDKit contributors
//
// @@ 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.
//
#ifndef RGROUP_DECOMP_DATA
#define RGROUP_DECOMP_DATA
#include "RGroupCore.h"
#include "RGroupScore.h"
#include "RGroupFingerprintScore.h"
#include <vector>
#include <map>
namespace RDKit {
extern const std::string _rgroupInputDummy;
struct RGroupDecompData {
// matches[mol_idx] == vector of potential matches
std::map<int, RCore> cores;
std::map<std::string, int> newCores; // new "cores" found along the way
int newCoreLabel = EMPTY_CORE_LABEL;
// this caches the size of the previous matches vector
// such that the size of the current chunk can be inferred
size_t previousMatchSize = 0;
// the default for Greedy/GreedyChunks is keeping only the best
// permutation after each call to process()
bool prunePermutations = true;
RGroupDecompositionParameters params;
std::vector<std::vector<RGroupMatch>> matches;
std::set<int> labels;
std::vector<size_t> permutation;
unsigned int pruneLength = 0U;
FingerprintVarianceScoreData prunedFingerprintVarianceScoreData;
std::map<int, std::vector<int>> userLabels;
std::vector<int> processedRlabels;
std::map<int, int> finalRlabelMapping;
mutable RGroupScorer rGroupScorer;
RGroupDecompData(const RWMol &inputCore,
RGroupDecompositionParameters inputParams);
RGroupDecompData(const std::vector<ROMOL_SPTR> &inputCores,
RGroupDecompositionParameters inputParams);
void addCore(const ROMol &inputCore);
void prepareCores();
void setRlabel(Atom *atom, int rlabel);
int getRlabel(Atom *atom) const;
double scoreFromPrunedData(const std::vector<size_t> &permutation,
bool reset = true);
void prune();
// Return the RGroups with the current "best" permutation
// of matches.
std::vector<RGroupMatch> GetCurrentBestPermutation() const;
class UsedLabels {
public:
std::set<int> labels_used;
bool add(int rlabel);
int next();
};
void addCoreUserLabels(const RWMol &core, std::set<int> &userLabels);
void addAtoms(RWMol &mol,
const std::vector<std::pair<Atom *, Atom *>> &atomsToAdd);
bool replaceHydrogenCoreDummy(const RGroupMatch &match, RWMol &core,
const Atom &atom, const int currentLabel,
const int rLabel);
void relabelCore(RWMol &core, std::map<int, int> &mappings,
UsedLabels &used_labels, const std::set<int> &indexLabels,
const std::map<int, std::vector<int>> &extraAtomRLabels,
const RGroupMatch *const match = nullptr);
void relabelRGroup(RGroupData &rgroup, const std::map<int, int> &mappings);
// relabel the core and sidechains using the specified user labels
// if matches exist for non labelled atoms, these are added as well
void relabel();
double score(const std::vector<size_t> &permutation,
FingerprintVarianceScoreData *fingerprintVarianceScoreData =
nullptr) const;
RGroupDecompositionProcessResult process(bool pruneMatches,
bool finalize = false);
private:
void addInputCore(const ROMol &inputCore);
};
} // namespace RDKit
#endif
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