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https://github.com/rdkit/rdkit.git
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abfddf2a79
* Add many new c++ catch2 performance benchmarks. * inline splitmix64 from boost, splitmix64 is not always available in boost. fun fact, this version is ~twice as fast * reduce intensity of memory pressure test, target 200MB usage. * new bench compound; accept suggestion from code review * bench MolToCXSmiles * Update Code/Bench/stereo.cpp * impl first part of the suggestions from code reveiw * impl second part of the suggestions from code reveiw
110 lines
2.9 KiB
C++
110 lines
2.9 KiB
C++
#include <catch2/catch_all.hpp>
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#include <string>
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#include <vector>
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#include <istream>
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#include <filesystem>
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#include "bench_common.hpp"
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#include <GraphMol/ROMol.h>
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#include <GraphMol/SmilesParse/SmilesParse.h>
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#include <GraphMol/Substruct/SubstructMatch.h>
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using namespace RDKit;
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namespace bench_substruct_match {
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std::filesystem::path relative_to_rdbase(
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const std::filesystem::path &relative) {
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char *rdbase = std::getenv("RDBASE");
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if (!rdbase) {
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throw std::runtime_error("RDBASE environment variable not set");
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}
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std::filesystem::path path(rdbase);
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path /= relative;
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return path;
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}
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std::vector<std::string> parse_smarts_examples(std::istream &in) {
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std::vector<std::string> examples;
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std::string line;
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while (std::getline(in, line)) {
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if (line.starts_with("#") || line.starts_with(" ") || line.empty()) {
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continue;
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}
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std::istringstream ss(line);
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std::string smarts;
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std::getline(ss, smarts, ' ');
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examples.push_back(line);
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}
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return examples;
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}
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std::vector<std::string> load_smarts_examples(std::filesystem::path &path) {
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std::ifstream file(path);
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return parse_smarts_examples(file);
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}
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std::vector<ROMol> load_smarts_queries(const std::filesystem::path &relative) {
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auto path = relative_to_rdbase(relative);
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auto examples = load_smarts_examples(path);
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std::vector<ROMol> queries;
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for (const auto &example : examples) {
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auto query = v2::SmilesParse::MolFromSmarts(example);
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REQUIRE(query);
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queries.push_back(std::move(*query));
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}
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return queries;
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}
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} // namespace bench_substruct_match
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TEST_CASE("ROMol::GetSubstructMatch", "[substruct_match]") {
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auto samples = bench_common::load_samples();
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auto query = v2::SmilesParse::MolFromSmarts(
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"[#6,#7]1:[#6,#7]:[#6](:[#6,#7]:[#6,#7]:[#6]:1-[#17,#35,#53,#9])-[#5](-[#8])-[#8]");
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BENCHMARK("ROMol::GetSubstructMatch") {
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auto total = 0;
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for (auto &mol : samples) {
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auto matches = SubstructMatch(mol, *query);
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total += matches.size();
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}
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return total;
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};
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}
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TEST_CASE("ROMol::GetSubstructMatch RLewis", "[substruct_match]") {
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auto mols = bench_common::load_samples();
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auto queries = bench_substruct_match::load_smarts_queries(
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"Data/SmartsLib/RLewis_smarts.txt");
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BENCHMARK("ROMol::GetSubstructMatch RLewis") {
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auto total = 0;
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for (const auto &mol : mols) {
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for (const auto &query : queries) {
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auto matches = SubstructMatch(mol, query);
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total += matches.size();
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}
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}
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return total;
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};
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}
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TEST_CASE("ROMol::GetSubstructMatch patty", "[substruct_match]") {
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auto mols = bench_common::load_samples();
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auto queries = bench_substruct_match::load_smarts_queries(
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"Data/SmartsLib/patty_rules.txt");
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BENCHMARK("ROMol::GetSubstructMatch patty") {
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auto total = 0;
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for (const auto &mol : mols) {
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for (const auto &query : queries) {
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auto matches = SubstructMatch(mol, query);
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total += matches.size();
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}
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}
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return total;
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};
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}
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