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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>
58 lines
1.7 KiB
C++
58 lines
1.7 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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namespace RDKit {
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namespace FMCS {
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typedef unsigned long long BitSet;
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class Composition2N { // generator of 2^N-1 possible bit combinations
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BitSet Bits, InverseBits;
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BitSet MaxValue, ValueMask; // need for inverse bitset must be 2^N-1
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public:
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Composition2N(BitSet maxValue, BitSet valueMask)
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: Bits(0), InverseBits(0), MaxValue(maxValue), ValueMask(valueMask) {}
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static void compute2N(unsigned int power, BitSet& value) {
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value = 1uLL << power;
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}
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BitSet getBitSet() const {
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return InverseBits; // inverse to generate biggest seed first and then
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// decrease number of external bonds
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}
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bool generateNext() {
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if ((++Bits) <= MaxValue) {
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InverseBits = (~Bits + 1) & ValueMask;
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return true;
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} else {
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return false;
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}
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}
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bool is2Power() const { // one bit is set only
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BitSet bits = getBitSet();
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unsigned int n = 0;
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while (0 == (bits & 1uLL) &&
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++n < sizeof(bits) * 8) { // find lowest bitwise 1
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bits >>= 1u; // shift all zero lower bits
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}
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if (0 != (bits & 1uLL)) {
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bits >>= 1u; // shift first set bit too
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}
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return 0 == bits; // remained bits except lowest 1
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}
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// unused: bool nonZero() {return 0!=getBitSet();}
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bool isSet(unsigned int bit) const {
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return 0 != (getBitSet() & (1uLL << bit));
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}
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};
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} // namespace FMCS
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} // namespace RDKit
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