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