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//
// Copyright (C) 2025 David Cosgrove
//
// @@ 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.
//
#include <chrono>
#include <random>
#include <vector>
#include <GraphMol/MolOps.h>
#include <GraphMol/SmilesParse/SmilesParse.h>
#include <GraphMol/SmilesParse/SmilesWrite.h>
#include <GraphMol/Substruct/SubstructMatch.h>
#include <catch2/catch_all.hpp>
#include <GraphMol/RascalMCES/RascalMCES.h>
#include <GraphMol/RascalMCES/RascalOptions.h>
#include <GraphMol/RascalMCES/RascalResult.h>
#include <GraphMol/RascalMCES/RascalDetails.h>
using namespace RDKit;
using namespace RDKit::RascalMCES;
using namespace RDKit::RascalMCES::details;
void check_smarts_ok(const RDKit::ROMol &mol1, const RDKit::ROMol &mol2,
const RascalResult &res) {
auto qmol = v2::SmilesParse::MolFromSmarts(res.getSmarts());
REQUIRE(qmol);
RDKit::MatchVectType dont_care;
CHECK(RDKit::SubstructMatch(mol1, *qmol, dont_care));
CHECK(RDKit::SubstructMatch(mol2, *qmol, dont_care));
}
TEST_CASE("benchmarks") {
// As well as timings, this also tests that the same result is produced from
// random ordering of the input molecules i.e. the results aren't input order
// dependent.
std::vector<std::tuple<std::string, std::string, std::string, double, int,
unsigned int, int>>
tests = {{"juglone", "Oc1cccc2C(=O)C=CC(=O)c12",
"O1C(=O)C=Cc2cc(OC)c(O)cc12", 0.5, 100, 8, 10},
{"methadone", "c1ccccc1C(C(=O)CC)(c1ccccc1)CC(C)N(C)C",
"c1ccccc1C1(CCN(C)CC1)C(=O)OCC", 0.6, 100, 16, 20},
{"symmetrical",
"c1c(OC)c(OC)c(OC)cc1C(=O)OCCCOC(=O)c1cc(OC)c(OC)c(OC)c1",
"c1c(OC)c(OC)c(OC)cc1C(=O)OCCOC(=O)c1cc(OC)c(OC)c(OC)c1", 0.7,
100, 32, 50},
{"testosterone", "CC12CCC3C(C1CCC2O)CCC4=CC(=O)CCC34C",
"CC12CCC3C(C1CCC2O)CCC4=C3C=CC(=C4)O", 0.6, 100, 16, 50}};
std::vector<double> timings;
std::random_device rd;
std::mt19937 g(rd());
// It's convenient if the same test is run each time.
g.seed(1);
RascalOptions opts;
for (const auto &test : tests) {
auto m1 = std::unique_ptr<ROMol>(RDKit::SmilesToMol(std::get<1>(test)));
auto m2 = std::unique_ptr<ROMol>(RDKit::SmilesToMol(std::get<2>(test)));
opts.similarityThreshold = std::get<3>(test);
std::vector<unsigned int> atom1Inds(m1->getNumAtoms(), 0);
std::iota(atom1Inds.begin(), atom1Inds.end(), 0);
std::vector<unsigned int> atom2Inds(m2->getNumAtoms(), 0);
std::iota(atom2Inds.begin(), atom2Inds.end(), 0);
auto t1 = std::chrono::high_resolution_clock::now();
for (int i = 0; i < std::get<4>(test); ++i) {
std::shuffle(atom1Inds.begin(), atom1Inds.end(), g);
std::unique_ptr<ROMol> randmol1(MolOps::renumberAtoms(*m1, atom1Inds));
std::shuffle(atom2Inds.begin(), atom2Inds.end(), g);
std::unique_ptr<ROMol> randmol2(MolOps::renumberAtoms(*m2, atom2Inds));
auto res = rascalMCES(*randmol1, *randmol2, opts);
REQUIRE(res.size() == 1);
REQUIRE(std::get<5>(test) == res.front().getBondMatches().size());
check_smarts_ok(*randmol1, *randmol2, res.front());
}
auto t2 = std::chrono::high_resolution_clock::now();
timings.push_back(
std::chrono::duration_cast<std::chrono::milliseconds>(t2 - t1).count() /
std::get<4>(test));
}
// Make sure we haven't slowed it down a lot.
// for (size_t i = 0; i < tests.size(); ++i) {
// std::cout << "TIMING : " << std::get<0>(tests[i]) << " took " <<
// timings[i]
// << " milliseconds on average of " << std::get<4>(tests[i])
// << " runs\n";
// }
for (size_t i = 0; i < tests.size(); ++i) {
auto ref_time = std::get<6>(tests[i]);
#ifndef NDEBUG // allow more time for debug builds
ref_time *= 5;
#endif
REQUIRE(timings[i] < ref_time);
}
}
TEST_CASE("timeout") {
auto m1 =
"O[C@@H]1CC[C@H](C[C@H]1OC)C[C@@H](C)[C@@H]4CC(=O)[C@H](C)/C=C(\\C)[C@@H](O)[C@@H](OC)C(=O)[C@H](C)C[C@H](C)\\C=C\\C=C\\C=C(/C)[C@@H](OC)C[C@@H]2CC[C@@H](C)[C@@](O)(O2)C(=O)C(=O)N3CCCC[C@H]3C(=O)O4"_smiles;
REQUIRE(m1);
auto m2 =
"CCC1C=C(CC(CC(C2C(CC(C(O2)(C(=O)C(=O)N3CCCCC3C(=O)OC(C(C(CC1=O)O)C)C(=CC4CCC(C(C4)OC)O)C)O)C)OC)OC)C)C"_smiles;
REQUIRE(m2);
{
RascalOptions opts;
opts.timeout = 10;
opts.maxBondMatchPairs = 2000;
auto res = rascalMCES(*m1, *m2, opts);
REQUIRE(res.size() == 1);
REQUIRE(res.front().getBondMatches().size() >= 39);
check_smarts_ok(*m1, *m2, res.front());
}
{
RascalOptions opts;
opts.timeout = 70;
opts.maxBondMatchPairs = 2000;
auto res = rascalMCES(*m1, *m2, opts);
REQUIRE(res.size() == 1);
REQUIRE(res.front().getBondMatches().size() >= 44);
check_smarts_ok(*m1, *m2, res.front());
}
{
RascalOptions opts;
opts.timeout = 120;
opts.maxBondMatchPairs = 2000;
auto res = rascalMCES(*m1, *m2, opts);
REQUIRE(res.size() == 1);
REQUIRE(res.front().getBondMatches().size() >= 44);
check_smarts_ok(*m1, *m2, res.front());
}
}
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