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* run clang-format-18 across Code/*.cpp and Code/*.h * run clang-format-18 across External
119 lines
4.0 KiB
C++
119 lines
4.0 KiB
C++
//
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// Copyright (C) 2020-2021 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_CORE
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#define RGROUP_CORE
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#include <GraphMol/SmilesParse/SmartsWrite.h>
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#include "../RDKitBase.h"
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#include "RGroupUtils.h"
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#include "GraphMol/Substruct/SubstructMatch.h"
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// #define VERBOSE 1
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namespace RDKit {
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class TautomerQuery;
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//! RCore is the core common to a series of molecules
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struct RCore {
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boost::shared_ptr<RWMol> core;
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// core with terminal user R groups stripped for matching
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boost::shared_ptr<RWMol> matchingMol;
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boost::shared_ptr<RWMol> labelledCore;
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// Bitset: indices corresponding to atoms bearing user-defined labels are 1
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boost::dynamic_bitset<> core_atoms_with_user_labels;
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// Number of user labelled rgroups in the core
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size_t numberUserRGroups = 0;
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RCore() {}
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RCore(const RWMol &c) : core(new RWMol(c)) { init(); }
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void init();
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inline bool isCoreAtomUserLabelled(int idx) const {
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return core_atoms_with_user_labels.test(idx);
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}
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void countUserRGroups() {
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numberUserRGroups = core_atoms_with_user_labels.count();
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}
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// Find all the core atoms that have user
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// label and set their indices to 1 into core_atoms_with_user_labels
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void findIndicesWithRLabel();
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// Return a copy of core where dummy atoms are replaced by
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// the respective matching atom in mol, while other atoms have
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// their aromatic flag and formal charge copied from
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// the respective matching atom in mol
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ROMOL_SPTR replaceCoreAtomsWithMolMatches(const ROMol &mol,
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const MatchVectType &match) const;
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// Final core returned to user, created by extracting core from target
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// molecule
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RWMOL_SPTR extractCoreFromMolMatch(
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const ROMol &mol, const MatchVectType &match,
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const RGroupDecompositionParameters ¶ms) const;
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std::vector<MatchVectType> matchTerminalUserRGroups(
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const RWMol &target, MatchVectType match,
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const SubstructMatchParameters &sssParams) const;
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std::shared_ptr<TautomerQuery> getMatchingTautomerQuery();
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inline bool isTerminalRGroupWithUserLabel(const int idx) const {
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return terminalRGroupAtomToNeighbor.find(idx) !=
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terminalRGroupAtomToNeighbor.end();
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}
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/*
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* For when onlyMatchAtRGroups = true. Checks the query core can satisfy all
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* attachment points. Including when two user defined attachment points can
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* match the same target atom.
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*/
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[[deprecated("please use checkAllBondsToRGroupPresent")]]
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bool checkAllBondsToAttachmentPointPresent(
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const ROMol &mol, const int attachmentIdx,
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const MatchVectType &mapping) const;
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/*
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* For when onlyMatchAtRGroups = true. Checks the query core can satisfy all
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* attachment points. Including when two user defined attachment points can
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* match the same target atom.
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*/
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bool checkAllBondsToRGroupPresent(
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const ROMol &mol, const int attachmentIdx,
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const std::vector<std::vector<int>> &targetToCoreIndices) const;
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private:
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// The set of atom indices in the core for terminal R groups with atom indices
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// with or without user labels
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std::set<int> terminalRGroupAtoms;
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// An atom index map of terminal R groups to their heavy atom neighbor
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std::map<int, int> terminalRGroupAtomToNeighbor;
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// TautomerQuery for matching
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bool checkedForTautomerQuery = false;
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std::shared_ptr<TautomerQuery> matchingTautomerQuery = nullptr;
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void replaceCoreAtom(RWMol &mol, Atom &atom, const Atom &other) const;
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// Convert a matching molecule index to a core index
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int matchingIndexToCoreIndex(int matchingIndex) const;
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// Build the matching molecule (core minus user R groups)
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void buildMatchingMol();
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// Add attachment points to unlabelled R Groups
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void addDummyAtomsToUnlabelledCoreAtoms();
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};
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} // namespace RDKit
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#endif
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