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https://github.com/rdkit/rdkit.git
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a2767d9f7d
* backup, does not work * working on the C++ side * backup * fix the API * document the new functionality * improve that example * final bit of cleanup * switch to std::function
130 lines
4.2 KiB
C++
130 lines
4.2 KiB
C++
//
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// Copyright (C) 2019 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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#define CATCH_CONFIG_MAIN
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#include "catch.hpp"
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#include <tuple>
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#include <GraphMol/RDKitBase.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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typedef std::tuple<std::string, std::string, size_t> matchCase;
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TEST_CASE("substructure parameters", "[substruct]") {
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SECTION("chirality") {
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auto mol1 = "CCC[C@@H]1CN(CCC)CCN1"_smiles;
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auto mol2 = "CCC[C@H]1CN(CCC)CCN1"_smiles;
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REQUIRE(mol1);
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REQUIRE(mol2);
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SubstructMatchParameters ps;
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// default is to ignore chirality:
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CHECK(SubstructMatch(*mol1, *mol2, ps).size() == 1);
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CHECK(SubstructMatch(*mol1, *mol1, ps).size() == 1);
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ps.useChirality = true;
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CHECK(SubstructMatch(*mol1, *mol2, ps).size() == 0);
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CHECK(SubstructMatch(*mol1, *mol1, ps).size() == 1);
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}
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SECTION("conjugated matching aromaticity 1") {
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auto mol1 = "C1=COC=C1"_smiles;
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REQUIRE(mol1);
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RWMol mol2(*mol1);
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MolOps::Kekulize(mol2);
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SubstructMatchParameters ps;
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CHECK(SubstructMatch(*mol1, mol2, ps).size() == 0);
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CHECK(SubstructMatch(mol2, *mol1, ps).size() == 0);
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ps.aromaticMatchesConjugated = true;
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CHECK(SubstructMatch(*mol1, mol2, ps).size() == 1);
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CHECK(SubstructMatch(mol2, *mol1, ps).size() == 1);
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}
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SECTION("conjugated matching aromaticity 2") {
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auto mol1 = "c1ccccc1"_smiles;
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REQUIRE(mol1);
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RWMol mol2(*mol1);
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MolOps::Kekulize(mol2);
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SubstructMatchParameters ps;
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CHECK(SubstructMatch(*mol1, mol2, ps).size() == 0);
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CHECK(SubstructMatch(mol2, *mol1, ps).size() == 0);
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ps.aromaticMatchesConjugated = true;
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CHECK(SubstructMatch(*mol1, mol2, ps).size() == 1);
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CHECK(SubstructMatch(mol2, *mol1, ps).size() == 1);
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}
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SECTION("conjugated matching aromaticity bulk") {
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std::vector<matchCase> examples;
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examples.push_back(
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std::make_tuple(std::string("c1ccccc1"), std::string("C1CCCCC1"), 0));
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examples.push_back(
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std::make_tuple(std::string("C1CCCCC1"), std::string("c1ccccc1"), 0));
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examples.push_back(std::make_tuple(std::string("O=C1C=CC(=O)C=C1"),
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std::string("c1ccccc1"), 1));
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SubstructMatchParameters ps;
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ps.aromaticMatchesConjugated = true;
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for (const auto &example : examples) {
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// std::cerr << " " << std::get<0>(example) << " - "
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// << std::get<1>(example) << std::endl;
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std::unique_ptr<RWMol> m1(SmilesToMol(std::get<0>(example)));
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REQUIRE(m1);
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std::unique_ptr<RWMol> m2(SmilesToMol(std::get<1>(example)));
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CHECK(SubstructMatch(*m1, *m2, ps).size() == std::get<2>(example));
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}
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}
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SECTION("looping") {
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auto mol1 = "CC(=O)C(=O)C(=O)"_smiles;
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auto mol2 = "C=O"_smiles;
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REQUIRE(mol1);
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REQUIRE(mol2);
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for (auto match : SubstructMatch(*mol1, *mol2)) {
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CHECK(match.size() == 2);
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}
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}
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}
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namespace {
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bool no_match(const ROMol &mol, const std::vector<unsigned int> &ids) {
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return false;
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}
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bool always_match(const ROMol &mol, const std::vector<unsigned int> &ids) {
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return true;
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}
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bool bigger(const ROMol &mol, const std::vector<unsigned int> &ids) {
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return std::accumulate(ids.begin(), ids.end(), 0) > 5;
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}
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} // namespace
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TEST_CASE("providing a final match function", "[substruct]") {
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SECTION("basics") {
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auto mol1 = "CCOC"_smiles;
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auto mol2 = "CCO"_smiles;
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REQUIRE(mol1);
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REQUIRE(mol2);
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SubstructMatchParameters ps;
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CHECK(SubstructMatch(*mol1, *mol2, ps).size() == 1);
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ps.extraFinalCheck = &no_match;
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CHECK(SubstructMatch(*mol1, *mol2, ps).size() == 0);
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ps.extraFinalCheck = &always_match;
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CHECK(SubstructMatch(*mol1, *mol2, ps).size() == 1);
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}
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SECTION("test 2") {
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auto mol1 = "CCOCC"_smiles;
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auto mol2 = "CCO"_smiles;
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REQUIRE(mol1);
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REQUIRE(mol2);
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SubstructMatchParameters ps;
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CHECK(SubstructMatch(*mol1, *mol2, ps).size() == 2);
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ps.extraFinalCheck = &bigger;
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CHECK(SubstructMatch(*mol1, *mol2, ps).size() == 1);
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}
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} |