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https://github.com/rdkit/rdkit.git
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972b31e239
* switch the Query infrastructure to use std::function * add releasenotes mention * refactor makeAtomInRingOfSizeQuery() to use lambdas and support range queries * add 'k' atom query to SMARTS * changes in response to review
105 lines
3.7 KiB
C++
105 lines
3.7 KiB
C++
//
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// Copyright (C) 2023 Greg Landrum and other RDKit contributors
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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 <GraphMol/RDKitBase.h>
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#include <GraphMol/QueryOps.h>
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#include <GraphMol/SmilesParse/SmilesParse.h>
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using namespace RDKit;
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TEST_CASE(
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"github #6106: Dummy atoms should not be considered to be metals for M and MH queries") {
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const auto m = "C*[Fe]"_smiles;
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REQUIRE(m);
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SECTION("M") {
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std::unique_ptr<ATOM_OR_QUERY> q(makeMAtomQuery());
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REQUIRE(q);
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CHECK(!q->Match(m->getAtomWithIdx(0)));
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CHECK(!q->Match(m->getAtomWithIdx(1)));
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CHECK(q->Match(m->getAtomWithIdx(2)));
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}
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SECTION("MH") {
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std::unique_ptr<ATOM_OR_QUERY> q(makeMHAtomQuery());
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REQUIRE(q);
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CHECK(!q->Match(m->getAtomWithIdx(0)));
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CHECK(!q->Match(m->getAtomWithIdx(1)));
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CHECK(q->Match(m->getAtomWithIdx(2)));
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}
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}
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TEST_CASE("range queries for atom ring membership") {
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auto m = "C1C2C1CC2C"_smiles;
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REQUIRE(m);
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SECTION("as range queries") {
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{
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std::unique_ptr<ATOM_RANGE_QUERY> q(makeAtomInRingOfSizeQuery(3, 4));
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REQUIRE(q);
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CHECK(q->Match(m->getAtomWithIdx(0)));
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CHECK(q->Match(m->getAtomWithIdx(1)));
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CHECK(q->Match(m->getAtomWithIdx(3)));
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CHECK(!q->Match(m->getAtomWithIdx(5)));
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}
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{
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std::unique_ptr<ATOM_RANGE_QUERY> q(makeAtomInRingOfSizeQuery(4, 6));
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REQUIRE(q);
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CHECK(!q->Match(m->getAtomWithIdx(0)));
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CHECK(q->Match(m->getAtomWithIdx(1)));
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CHECK(q->Match(m->getAtomWithIdx(3)));
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CHECK(!q->Match(m->getAtomWithIdx(5)));
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}
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{
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// this is how we use the queries in the SMARTS parser
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std::unique_ptr<ATOM_LESSEQUAL_QUERY> q(
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makeAtomSimpleQuery<ATOM_LESSEQUAL_QUERY>(3, [](Atom const *at) {
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return queryAtomIsInRingOfSize(at, 3, -1);
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}));
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REQUIRE(q);
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CHECK(q->Match(m->getAtomWithIdx(0)));
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CHECK(q->Match(m->getAtomWithIdx(1)));
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CHECK(q->Match(m->getAtomWithIdx(3)));
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CHECK(!q->Match(m->getAtomWithIdx(5)));
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}
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{ // this is how we use the queries in the SMARTS parser
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std::unique_ptr<ATOM_GREATEREQUAL_QUERY> q(
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makeAtomSimpleQuery<ATOM_GREATEREQUAL_QUERY>(3, [](Atom const *at) {
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return queryAtomIsInRingOfSize(at, -1, 3);
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}));
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REQUIRE(q);
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CHECK(q->Match(m->getAtomWithIdx(0)));
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CHECK(q->Match(m->getAtomWithIdx(1)));
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CHECK(!q->Match(m->getAtomWithIdx(3)));
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CHECK(!q->Match(m->getAtomWithIdx(5)));
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}
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}
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SECTION("query function") {
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CHECK(queryAtomIsInRingOfSize(m->getAtomWithIdx(0), 3, -1) == 3);
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CHECK(queryAtomIsInRingOfSize(m->getAtomWithIdx(1), 3, -1) == 3);
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CHECK(queryAtomIsInRingOfSize(m->getAtomWithIdx(3), 3, -1) == 4);
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CHECK(queryAtomIsInRingOfSize(m->getAtomWithIdx(5), 3, -1) == -1);
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CHECK(queryAtomIsInRingOfSize(m->getAtomWithIdx(0), -1, 3) == 3);
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CHECK(queryAtomIsInRingOfSize(m->getAtomWithIdx(1), -1, 3) == 3);
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CHECK(queryAtomIsInRingOfSize(m->getAtomWithIdx(3), -1, 3) ==
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std::numeric_limits<int>::max());
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CHECK(queryAtomIsInRingOfSize(m->getAtomWithIdx(5), -1, 3) ==
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std::numeric_limits<int>::max());
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CHECK(queryAtomIsInRingOfSize(m->getAtomWithIdx(0), 3, 4) == 3);
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CHECK(queryAtomIsInRingOfSize(m->getAtomWithIdx(1), 3, 4) == 3);
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CHECK(queryAtomIsInRingOfSize(m->getAtomWithIdx(3), 3, 4) == 4);
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CHECK(queryAtomIsInRingOfSize(m->getAtomWithIdx(5), 3, 4) == -1);
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CHECK(queryAtomIsInRingOfSize(m->getAtomWithIdx(3), 0, 4) == 4);
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CHECK(queryAtomIsInRingOfSize(m->getAtomWithIdx(5), 0, 4) == -1);
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}
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} |