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350370abe3
- Switched from dynamic to static allocation for an instance of `MCSParameters` - Switched to using `auto` where possible - Added a few `CHECK_INVARIANT` where appropriate before dereferencing pointers - Moved some inline comments to the previous line to improve readability - Added a early check for `CompleteRingsOnly` in `checkBondRingMatch()` to improve computational efficiency - Removed `RingMatchTableSet` entirely as 1) it is unnecessary since its functionality is already provided by `RingInfo` 2) it abused the `userData` pointer. This allows cleaning up and simplifying the code, particularly the Python wrappers which had a significant amount of added complexity to support it - Removed all the code that was deprecated several releases ago - Reimplemented ringFusionCheck() from scratch to address several bug reports; also switched from std::set to boost::dynamic_bitset for better efficiency - Replaced boost::tie with boost::make_iterator_range - Modernized `for` loops where possible - Removed entirely the QueryRings structure as its functionality is already available in RingInfo - Removed entirely the _DFS() function since the same algorithm can be implemented in a simpler and more efficient way using RingInfo (from 2m28.441s to 2m9.859s for the same task) - Replaced std::vector<bool> with boost::dynamic_bitset - Replaced C-style casts with C++ casts - Replaced some size_t with unsigned int - Refactored checkIfRingsAreClosed() such that checkNoLoneRingAtoms() is not needed anymore - Added a test for slow runtimes with CompleteRingsOnly - Setting Timeout to 0 means no timeout, as it should be - Removed unused `steps` variable from `MaximumCommonSubgraph::growSeeds` - Storing both Atom and Bond pointers and their indices on Seed and MCS data structures is time-consuming and a potential source of incons istencies; storing pointers is sufficient - Promoted `MaximumCommonSubgraph::match` from `private` to `public` - `NewBonds` was declared `mutable`, but `Seed::fillNewBonds()` was incorrectly declared as `non-const`, which caused the need for an ugly (and unnecessary) `const_cast`. I have now removed the `const_cast` and correctly declared functions that alter `NewBonds` as `const`, since `NewBonds` is explicitly `mut able` - Removed some useless random scoping that was peppering the MCS code - Removed a significant amount of duplicate code from the Python wrappers by inheriting from a base `PyMCSWrapper` class - Fixed #6082 - Fixed #5510 - Fixed #5457 - Fixed #5440 - Fixed #5411 - Fixed #3965 - Fixed #6578 Co-authored-by: ptosco <paolo.tosco@novartis.com>
87 lines
2.6 KiB
C++
87 lines
2.6 KiB
C++
//
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// Copyright (C) 2014 Novartis Institutes for BioMedical Research
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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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#pragma once
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#include <vector>
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#include <boost/dynamic_bitset.hpp>
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#include "FMCS.h"
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#include "MatchTable.h"
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namespace RDKit {
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namespace FMCS {
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struct TargetMatch {
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bool Empty{true};
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size_t MatchedAtomSize{0};
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size_t MatchedBondSize{0};
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std::vector<unsigned int> TargetAtomIdx;
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std::vector<unsigned int> TargetBondIdx;
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boost::dynamic_bitset<> VisitedTargetBonds;
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boost::dynamic_bitset<> VisitedTargetAtoms; // for checking rings
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public:
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TargetMatch() {}
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TargetMatch(const TargetMatch& src) { *this = src; }
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TargetMatch& operator=(const TargetMatch& src) {
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Empty = src.Empty;
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if (!Empty) {
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MatchedAtomSize = src.MatchedAtomSize;
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MatchedBondSize = src.MatchedBondSize;
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TargetAtomIdx = src.TargetAtomIdx;
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TargetBondIdx = src.TargetBondIdx;
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VisitedTargetBonds = src.VisitedTargetBonds;
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VisitedTargetAtoms = src.VisitedTargetAtoms;
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}
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return *this;
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}
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bool empty() const { return Empty; }
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void clear() {
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Empty = true;
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TargetAtomIdx.clear();
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TargetBondIdx.clear();
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VisitedTargetBonds.clear();
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VisitedTargetAtoms.clear();
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}
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void init(const Seed& seed, const match_V_t& match, const ROMol& query,
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const Target& target) {
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TargetAtomIdx.clear();
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TargetAtomIdx.resize(query.getNumAtoms(), NotSet);
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TargetBondIdx.clear();
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TargetBondIdx.resize(query.getNumBonds(), NotSet);
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VisitedTargetBonds.resize(target.Molecule->getNumBonds());
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VisitedTargetAtoms.resize(target.Molecule->getNumAtoms());
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VisitedTargetBonds.reset();
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VisitedTargetAtoms.reset();
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MatchedAtomSize = match.size();
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for (const auto& m : match) {
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TargetAtomIdx[seed.MoleculeFragment.Atoms.at(m.first)->getIdx()] =
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m.second;
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VisitedTargetAtoms.set(m.second);
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}
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MatchedBondSize = 0;
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for (const auto bond : seed.MoleculeFragment.Bonds) {
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unsigned int i = bond->getBeginAtomIdx();
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unsigned int j = bond->getEndAtomIdx();
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unsigned int ti = TargetAtomIdx.at(i);
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unsigned int tj = TargetAtomIdx.at(j);
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const auto tb = target.Molecule->getBondBetweenAtoms(ti, tj);
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if (tb) {
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++MatchedBondSize;
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TargetBondIdx[bond->getIdx()] = tb->getIdx(); // add
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VisitedTargetBonds.set(tb->getIdx());
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}
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}
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Empty = false;
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}
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};
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} // namespace FMCS
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} // namespace RDKit
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