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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>
45 lines
1.3 KiB
C++
45 lines
1.3 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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// graph topology in terms of indices in source molecule
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#include <RDGeneral/export.h>
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#pragma once
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#include <RDGeneral/BoostStartInclude.h>
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#include <boost/graph/adjacency_list.hpp>
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#include <RDGeneral/BoostEndInclude.h>
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namespace RDKit {
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namespace FMCS {
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typedef unsigned int AtomIdx_t;
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typedef unsigned int BondIdx_t;
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typedef boost::adjacency_list<boost::vecS, boost::vecS, boost::undirectedS,
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AtomIdx_t, BondIdx_t>
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Graph_t;
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class RDKIT_FMCS_EXPORT Graph : public Graph_t {
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public:
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typedef edge_iterator EDGE_ITER;
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typedef std::pair<EDGE_ITER, EDGE_ITER> BOND_ITER_PAIR;
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void addAtom(unsigned int atom) {
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Graph::vertex_descriptor which = boost::add_vertex(*this);
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(*this)[which] = atom;
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}
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void addBond(unsigned int bond, unsigned int beginAtom,
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unsigned int endAtom) {
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bool res;
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Graph_t::edge_descriptor which;
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boost::tie(which, res) = boost::add_edge(beginAtom, endAtom, *this);
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(*this)[which] = bond;
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}
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};
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} // namespace FMCS
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} // namespace RDKit
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