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* Create a function to extract some specified atoms from a ROMol as a new ROMol by creating new graph (#8742) This adds a new api, `RDKit::MolOps::ExtractMolFragment`, to allow efficient extractions of mol fragments from large mols. Compared to the approach where we delete "unwanted" atoms/bonds from the input mol, this api is faster for small mols (about 2x faster) and at least 3x faster for big mols (was 10x faster for "CCC"*1000). * clang-format * review comments * cleanup * Consolidate copying subsets of molecules * Readd missing tests * Update comment to restart build * Remove missing test * Remove debugging comment, fix warnings * Fix warnings on gcc11 * Add docs * Make vector<bool> dynamic_bitset<> * Update copyright * Add swig wrappers * Use new designated constructor API * Fix windows builds * Change enum values from unsigned int to integer * Fix unsigned int variable * Update Code/GraphMol/Wrap/test_subset.py Co-authored-by: Greg Landrum <greg.landrum@gmail.com> * Update Code/GraphMol/Subset.cpp Co-authored-by: Greg Landrum <greg.landrum@gmail.com> * Update Code/JavaWrappers/gmwrapper/src-test/org/RDKit/ChemTransformsTests.java Co-authored-by: Greg Landrum <greg.landrum@gmail.com> * Reponse to review * Fix documentation * Remove comments * Remove unnecessary comments * Fix one liners * Change assertion to be clearer (and not one-liners) * Run clang-format --------- Co-authored-by: Your Name <you@example.com> Co-authored-by: Hussein Faara <hussein.faara@schrodinger.com> Co-authored-by: Brian Kelley <bkelley@glysade.com> Co-authored-by: Greg Landrum <greg.landrum@gmail.com>
61 lines
1.7 KiB
C++
61 lines
1.7 KiB
C++
//
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// Copyright (C) 2023 Greg Landrum
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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 <catch2/catch_all.hpp>
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#include <RDGeneral/test.h>
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#include <GraphMol/RDKitBase.h>
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#include <GraphMol/SmilesParse/SmilesParse.h>
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#include <GraphMol/Subgraphs/Subgraphs.h>
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#include <GraphMol/Subgraphs/SubgraphUtils.h>
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#include <algorithm>
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using namespace RDKit;
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TEST_CASE("shortestPathsOnly") {
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SECTION("basics, findAllPathsOfLengthN") {
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auto m = "CC1CCC1"_smiles;
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REQUIRE(m);
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bool useBonds = true;
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bool useHs = false;
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int rootedAt = -1;
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bool onlyShortestPaths = true;
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auto ps = findAllPathsOfLengthN(*m, 4);
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CHECK(ps.size() == 3);
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ps = findAllPathsOfLengthN(*m, 4, useBonds, useHs, rootedAt,
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onlyShortestPaths);
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CHECK(ps.empty());
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ps = findAllPathsOfLengthN(*m, 3);
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CHECK(ps.size() == 6);
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std::cerr << "---------" << std::endl;
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ps = findAllPathsOfLengthN(*m, 3, useBonds, useHs, rootedAt,
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onlyShortestPaths);
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CHECK(ps.size() == 2);
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}
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SECTION("basics, findAllPathsOfLengthsMtoN") {
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auto m = "CC1CCC1"_smiles;
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REQUIRE(m);
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bool useBonds = true;
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bool useHs = false;
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int rootedAt = -1;
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bool onlyShortestPaths = true;
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auto ps = findAllPathsOfLengthsMtoN(*m, 3, 4);
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CHECK(ps.size() == 2);
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CHECK(ps[3].size() == 6);
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CHECK(ps[4].size() == 3);
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ps = findAllPathsOfLengthsMtoN(*m, 3, 4, useBonds, useHs, rootedAt,
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onlyShortestPaths);
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CHECK(ps.size() == 1);
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CHECK(ps[3].size() == 2);
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}
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}
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