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4140f95a79
* restore "oops, exponential is a pain" code snippet in the RGD algorithm * - added MAX_PERMUTATIONS constant - added comments about what the restored snippet does - removed unused permutationProduct variable * changes in response to review --------- Co-authored-by: ptosco <paolo.tosco@novartis.com>
114 lines
3.5 KiB
C++
114 lines
3.5 KiB
C++
//
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// Copyright (C) 2017-2022 Novartis Institutes for BioMedical Research and
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// other RDKit contributors
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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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#ifndef RGROUP_DECOMP_DATA
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#define RGROUP_DECOMP_DATA
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#include "RGroupCore.h"
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#include "RGroupScore.h"
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#include "RGroupFingerprintScore.h"
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#include <vector>
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#include <map>
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namespace RDKit {
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extern const std::string _rgroupInputDummy;
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struct RGroupDecompData {
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// matches[mol_idx] == vector of potential matches
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std::map<int, RCore> cores;
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std::map<std::string, int> newCores; // new "cores" found along the way
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int newCoreLabel = EMPTY_CORE_LABEL;
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// this caches the size of the previous matches vector
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// such that the size of the current chunk can be inferred
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size_t previousMatchSize = 0;
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// the default for Greedy/GreedyChunks is keeping only the best
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// permutation after each call to process()
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bool prunePermutations = true;
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RGroupDecompositionParameters params;
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std::vector<std::vector<RGroupMatch>> matches;
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std::set<int> labels;
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std::vector<size_t> permutation;
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unsigned int pruneLength = 0U;
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FingerprintVarianceScoreData prunedFingerprintVarianceScoreData;
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std::map<int, std::vector<int>> userLabels;
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std::vector<int> processedRlabels;
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std::map<int, int> finalRlabelMapping;
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mutable RGroupScorer rGroupScorer;
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RGroupDecompData(const RWMol &inputCore,
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RGroupDecompositionParameters inputParams);
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RGroupDecompData(const std::vector<ROMOL_SPTR> &inputCores,
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RGroupDecompositionParameters inputParams);
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void addCore(const ROMol &inputCore);
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void prepareCores();
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void setRlabel(Atom *atom, int rlabel);
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int getRlabel(Atom *atom) const;
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double scoreFromPrunedData(const std::vector<size_t> &permutation,
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bool reset = true);
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void prune();
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// Return the RGroups with the current "best" permutation
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// of matches.
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std::vector<RGroupMatch> GetCurrentBestPermutation() const;
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class UsedLabels {
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public:
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std::set<int> labels_used;
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bool add(int rlabel);
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int next();
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};
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void addCoreUserLabels(const RWMol &core, std::set<int> &userLabels);
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void addAtoms(RWMol &mol,
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const std::vector<std::pair<Atom *, Atom *>> &atomsToAdd);
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bool replaceHydrogenCoreDummy(const RGroupMatch &match, RWMol &core,
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const Atom &atom, const int currentLabel,
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const int rLabel);
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void relabelCore(RWMol &core, std::map<int, int> &mappings,
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UsedLabels &used_labels, const std::set<int> &indexLabels,
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const std::map<int, std::vector<int>> &extraAtomRLabels,
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const RGroupMatch *const match = nullptr);
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void relabelRGroup(RGroupData &rgroup, const std::map<int, int> &mappings);
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// relabel the core and sidechains using the specified user labels
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// if matches exist for non labelled atoms, these are added as well
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void relabel();
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double score(const std::vector<size_t> &permutation,
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FingerprintVarianceScoreData *fingerprintVarianceScoreData =
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nullptr) const;
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RGroupDecompositionProcessResult process(bool pruneMatches,
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bool finalize = false);
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private:
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void addInputCore(const ROMol &inputCore);
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};
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} // namespace RDKit
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#endif
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