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31de6b09fb
* Added fingerprints to GeneralizedSubstruct search * Small change to fire tests * Edits from code review * Updated swig - newobject not required for GeneralizedSubstruct fingerprint methods * GeneralizedSubstruct only supports unique_ptr in SWIG4.1
401 lines
17 KiB
C++
401 lines
17 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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// Tests of the generalized substructure searching code
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//
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#include <catch2/catch_all.hpp>
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#include <tuple>
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#include <utility>
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#include <GraphMol/RDKitBase.h>
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#include <GraphMol/SmilesParse/SmilesParse.h>
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#include <GraphMol/SmilesParse/SmilesWrite.h>
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#include <GraphMol/SmilesParse/SmartsWrite.h>
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#include <GraphMol/GeneralizedSubstruct/XQMol.h>
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#include <GraphMol/TautomerQuery/TautomerQuery.h>
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#include <GraphMol/MolEnumerator/MolEnumerator.h>
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#include <GraphMol/GenericGroups/GenericGroups.h>
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using namespace RDKit;
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using namespace RDKit::GeneralizedSubstruct;
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bool fingerprintsMatch(const ROMol& target, const ExtendedQueryMol& xqm) {
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const auto queryFingerprint = xqm.patternFingerprintQuery();
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const auto targetFingerprint = patternFingerprintTargetMol(target);
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CHECK(queryFingerprint->getNumOnBits() > 0);
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CHECK(targetFingerprint->getNumOnBits() > 0);
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const auto match = AllProbeBitsMatch(*queryFingerprint, *targetFingerprint);
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return match;
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}
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TEST_CASE("molecule basics") {
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auto mol = "Cc1n[nH]c(F)c1"_smarts;
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REQUIRE(mol);
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ExtendedQueryMol xqm = std::make_unique<RWMol>(*mol);
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SECTION("substructure matching and serialization") {
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ExtendedQueryMol xqm2(xqm.toBinary());
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ExtendedQueryMol xqm3(xqm.toJSON(), true);
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for (const auto xq : {&xqm, &xqm2, &xqm3}) {
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CHECK(SubstructMatch(*"CCc1n[nH]c(F)c1"_smiles, *xq).size() == 1);
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CHECK(SubstructMatch(*"CCc1[nH]nc(F)c1"_smiles, *xq).empty());
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CHECK(hasSubstructMatch(*"CCc1n[nH]c(F)c1"_smiles, *xq));
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CHECK(!hasSubstructMatch(*"CCc1[nH]nc(F)c1"_smiles, *xq));
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CHECK(fingerprintsMatch(*"CCc1n[nH]c(F)c1"_smiles, *xq));
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}
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}
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}
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TEST_CASE("enumeration basics") {
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auto mol = "COCC |LN:1:1.3|"_smiles;
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REQUIRE(mol);
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ExtendedQueryMol xqm =
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std::make_unique<MolBundle>(MolEnumerator::enumerate(*mol));
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SECTION("substructure matching and serialization") {
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ExtendedQueryMol xqm2(xqm.toBinary());
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ExtendedQueryMol xqm3(xqm.toJSON(), true);
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for (const auto xq : {&xqm, &xqm2, &xqm3}) {
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CHECK(SubstructMatch(*"COCC"_smiles, *xq).size() == 1);
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CHECK(SubstructMatch(*"COOCC"_smiles, *xq).size() == 1);
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CHECK(SubstructMatch(*"COOOCC"_smiles, *xq).size() == 1);
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CHECK(SubstructMatch(*"COOOOCC"_smiles, *xq).empty());
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CHECK(fingerprintsMatch(*"COCC"_smiles, *xq));
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CHECK(fingerprintsMatch(*"COOCC"_smiles, *xq));
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CHECK(fingerprintsMatch(*"COOOCC"_smiles, *xq));
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}
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}
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}
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TEST_CASE("result counts") {
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auto mol = "COC |LN:1:1.3|"_smiles;
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REQUIRE(mol);
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ExtendedQueryMol xqm =
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std::make_unique<MolBundle>(MolEnumerator::enumerate(*mol));
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SECTION("substructure matching and serialization") {
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ExtendedQueryMol xqm2(xqm.toBinary());
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ExtendedQueryMol xqm3(xqm.toJSON(), true);
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SubstructMatchParameters ps;
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ps.uniquify = false;
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for (const auto xq : {&xqm, &xqm2, &xqm3}) {
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CHECK(SubstructMatch(*"COCC"_smiles, *xq, ps).size() == 2);
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CHECK(SubstructMatch(*"COOCC"_smiles, *xq, ps).size() == 2);
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CHECK(SubstructMatch(*"COOOCC"_smiles, *xq, ps).size() == 2);
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CHECK(SubstructMatch(*"COOOOCC"_smiles, *xq, ps).empty());
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CHECK(fingerprintsMatch(*"COCC"_smiles, *xq));
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CHECK(fingerprintsMatch(*"COOCC"_smiles, *xq));
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CHECK(fingerprintsMatch(*"COOOCC"_smiles, *xq));
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}
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}
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}
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TEST_CASE("tautomer basics") {
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auto mol = "Cc1n[nH]c(F)c1"_smiles;
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REQUIRE(mol);
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ExtendedQueryMol xqm =
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std::unique_ptr<TautomerQuery>(TautomerQuery::fromMol(*mol));
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SECTION("substructure matching and serialization") {
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ExtendedQueryMol xqm2(xqm.toBinary());
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ExtendedQueryMol xqm3(xqm.toJSON(), true);
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for (const auto xq : {&xqm, &xqm2, &xqm3}) {
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CHECK(SubstructMatch(*"CCc1n[nH]c(F)c1"_smiles, *xq).size() == 1);
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CHECK(SubstructMatch(*"CCc1[nH]nc(F)c1"_smiles, *xq).size() == 1);
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CHECK(SubstructMatch(*"CCc1[nH]ncc1"_smiles, *xq).empty());
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CHECK(fingerprintsMatch(*"CCc1n[nH]c(F)c1"_smiles, *xq));
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CHECK(fingerprintsMatch(*"CCc1[nH]nc(F)c1"_smiles, *xq));
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CHECK(!fingerprintsMatch(*"CCc1[nH]ncc1"_smiles, *xq));
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}
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}
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}
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TEST_CASE("tautomer bundle basics") {
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auto mol1 = "Cc1n[nH]c(F)c1"_smiles;
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REQUIRE(mol1);
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auto mol2 = "Cc1n[nH]cc1F"_smiles;
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REQUIRE(mol2);
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std::vector<std::unique_ptr<TautomerQuery>> tbndl;
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tbndl.emplace_back(
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std::unique_ptr<TautomerQuery>(TautomerQuery::fromMol(*mol1)));
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tbndl.emplace_back(
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std::unique_ptr<TautomerQuery>(TautomerQuery::fromMol(*mol2)));
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ExtendedQueryMol xqm =
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std::make_unique<std::vector<std::unique_ptr<TautomerQuery>>>(
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std::move(tbndl));
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SECTION("substructure matching and serialization") {
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ExtendedQueryMol xqm2(xqm.toBinary());
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ExtendedQueryMol xqm3(xqm.toJSON(), true);
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for (const auto xq : {&xqm, &xqm2, &xqm3}) {
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CHECK(SubstructMatch(*"CCc1n[nH]c(F)c1"_smiles, *xq).size() == 1);
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CHECK(SubstructMatch(*"CCc1[nH]nc(F)c1"_smiles, *xq).size() == 1);
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CHECK(SubstructMatch(*"CCc1[nH]ncc1F"_smiles, *xq).size() == 1);
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CHECK(SubstructMatch(*"CCc1n[nH]cc1F"_smiles, *xq).size() == 1);
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CHECK(SubstructMatch(*"CCc1[nH]ncc1"_smiles, *xq).empty());
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CHECK(fingerprintsMatch(*"CCc1n[nH]c(F)c1"_smiles, *xq));
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CHECK(fingerprintsMatch(*"CCc1[nH]nc(F)c1"_smiles, *xq));
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CHECK(fingerprintsMatch(*"CCc1[nH]ncc1F"_smiles, *xq));
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CHECK(fingerprintsMatch(*"CCc1n[nH]cc1F"_smiles, *xq));
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CHECK(!fingerprintsMatch(*"CCc1[nH]ncc1"_smiles, *xq));
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}
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}
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}
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TEST_CASE("createExtendedQueryMol and copy ctors") {
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SECTION("RWMol") {
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auto mol = "COCC"_smiles;
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REQUIRE(mol);
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auto txqm = createExtendedQueryMol(*mol);
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ExtendedQueryMol xqm1(txqm);
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ExtendedQueryMol xqm2(std::make_unique<RWMol>(*mol));
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xqm2 = txqm;
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for (const auto &xqm : {txqm, xqm1, xqm2}) {
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CHECK(std::holds_alternative<ExtendedQueryMol::RWMol_T>(xqm.xqmol));
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CHECK(SubstructMatch(*"COCC"_smiles, xqm).size() == 1);
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CHECK(SubstructMatch(*"COOCC"_smiles, xqm).empty());
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CHECK(fingerprintsMatch(*"COCC"_smiles, xqm));
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CHECK(!fingerprintsMatch(*"COOCC"_smiles, xqm));
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}
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}
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SECTION("MolBundle") {
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auto mol = "COCC |LN:1:1.3|"_smiles;
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REQUIRE(mol);
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auto txqm = createExtendedQueryMol(*mol);
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ExtendedQueryMol xqm1(txqm);
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ExtendedQueryMol xqm2(std::make_unique<RWMol>(*mol));
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xqm2 = txqm;
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for (const auto &xqm : {txqm, xqm1, xqm2}) {
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CHECK(std::holds_alternative<ExtendedQueryMol::MolBundle_T>(xqm.xqmol));
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CHECK(SubstructMatch(*"COCC"_smiles, xqm).size() == 1);
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CHECK(SubstructMatch(*"COOCC"_smiles, xqm).size() == 1);
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CHECK(SubstructMatch(*"COOOCC"_smiles, xqm).size() == 1);
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CHECK(SubstructMatch(*"COOOOCC"_smiles, xqm).empty());
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CHECK(fingerprintsMatch(*"COCC"_smiles, xqm));
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CHECK(fingerprintsMatch(*"COOCC"_smiles, xqm));
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CHECK(fingerprintsMatch(*"COOOCC"_smiles, xqm));
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}
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}
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SECTION("TautomerQuery") {
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auto mol1 = "CC1OC(N)=N1"_smiles;
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REQUIRE(mol1);
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auto txqm = createExtendedQueryMol(*mol1);
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ExtendedQueryMol xqm1(txqm);
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ExtendedQueryMol xqm2(std::make_unique<RWMol>(*mol1));
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xqm2 = txqm;
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for (const auto &xqm : {txqm, xqm1, xqm2}) {
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CHECK(
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std::holds_alternative<ExtendedQueryMol::TautomerQuery_T>(xqm.xqmol));
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CHECK(SubstructMatch(*"CCC1OC(N)=N1"_smiles, xqm).size() == 1);
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CHECK(SubstructMatch(*"CCC1OC(=N)N1"_smiles, *mol1).empty());
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CHECK(SubstructMatch(*"CCC1OC(=N)N1"_smiles, xqm).size() == 1);
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CHECK(SubstructMatch(*"c1[nH]ncc1"_smiles, xqm).empty());
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CHECK(fingerprintsMatch(*"CCC1OC(N)=N1"_smiles, xqm));
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CHECK(fingerprintsMatch(*"CCC1OC(=N)N1"_smiles, xqm));
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CHECK(!fingerprintsMatch(*"c1[nH]ncc1"_smiles, xqm));
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}
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}
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SECTION("TautomerBundle") {
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auto mol1 = "COCC1OC(N)=N1 |LN:1:1.3|"_smiles;
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REQUIRE(mol1);
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auto txqm = createExtendedQueryMol(*mol1);
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ExtendedQueryMol xqm1(txqm);
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ExtendedQueryMol xqm2(std::make_unique<RWMol>(*mol1));
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xqm2 = txqm;
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for (const auto &xqm : {txqm, xqm1, xqm2}) {
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CHECK(std::holds_alternative<ExtendedQueryMol::TautomerBundle_T>(
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xqm.xqmol));
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CHECK(SubstructMatch(*"COCC1(F)OC(N)=N1"_smiles, xqm).size() == 1);
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CHECK(SubstructMatch(*"COOCC1(F)OC(=N)N1"_smiles, xqm).size() == 1);
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CHECK(SubstructMatch(*"COCC1OC(N)=N1"_smiles, xqm).size() == 1);
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CHECK(SubstructMatch(*"COOOOCC1OC(=N)N1"_smiles, xqm).empty());
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CHECK(fingerprintsMatch(*"COCC1(F)OC(N)=N1"_smiles, xqm));
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CHECK(fingerprintsMatch(*"COOCC1(F)OC(=N)N1"_smiles, xqm));
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CHECK(fingerprintsMatch(*"COCC1OC(N)=N1"_smiles, xqm));
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}
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}
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}
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TEST_CASE("test SRUs") {
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SECTION("basics") {
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auto mol = "FCN(CC)-* |Sg:n:2,5:1-2:ht|"_smiles;
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REQUIRE(mol);
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auto xqm = createExtendedQueryMol(*mol);
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CHECK(std::holds_alternative<ExtendedQueryMol::MolBundle_T>(xqm.xqmol));
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// as of v2023.03.1 the SRU enumerator ignores repeat counts, so
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// we won't test limits here.
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CHECK(SubstructMatch(*"FCN(C)CC"_smiles, xqm).size() == 1);
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CHECK(SubstructMatch(*"FCN(O)N(C)CC"_smiles, xqm).size() == 1);
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CHECK(fingerprintsMatch(*"FCN(C)CC"_smiles, xqm));
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CHECK(fingerprintsMatch(*"FCN(O)N(C)CC"_smiles, xqm));
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}
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}
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// there's some redundancy in testing with what's above, but duplicating tests
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// isn't a terrible thing
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TEST_CASE("adjustQueryProperties") {
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bool doEnumeration = true;
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bool doTautomers = true;
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bool adjustQueryProperties = true;
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SECTION("RWMol") {
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auto mol = "COC1CC1"_smiles;
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REQUIRE(mol);
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auto xqm1 = createExtendedQueryMol(*mol, doEnumeration, doTautomers);
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auto xqm2 = createExtendedQueryMol(*mol, doEnumeration, doTautomers,
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adjustQueryProperties);
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MolOps::AdjustQueryParameters aqps =
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MolOps::AdjustQueryParameters::noAdjustments();
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aqps.makeAtomsGeneric = true;
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auto xqm3 = createExtendedQueryMol(*mol, doEnumeration, doTautomers,
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adjustQueryProperties, aqps);
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CHECK(std::holds_alternative<ExtendedQueryMol::RWMol_T>(xqm1.xqmol));
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CHECK(std::holds_alternative<ExtendedQueryMol::RWMol_T>(xqm2.xqmol));
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CHECK(std::holds_alternative<ExtendedQueryMol::RWMol_T>(xqm3.xqmol));
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CHECK(SubstructMatch(*"COC1CC1"_smiles, xqm1).size() == 1);
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CHECK(SubstructMatch(*"COC1CC1"_smiles, xqm2).size() == 1);
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CHECK(SubstructMatch(*"COC1CC1"_smiles, xqm3).size() == 1);
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CHECK(SubstructMatch(*"COC1C(C)C1"_smiles, xqm1).size() == 1);
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CHECK(SubstructMatch(*"COC1C(C)C1"_smiles, xqm2).empty());
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CHECK(SubstructMatch(*"COC1C(C)C1"_smiles, xqm3).size() == 1);
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CHECK(SubstructMatch(*"COC1OC1"_smiles, xqm1).empty());
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CHECK(SubstructMatch(*"COC1OC1"_smiles, xqm2).empty());
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CHECK(SubstructMatch(*"COC1OC1"_smiles, xqm3).size() == 1);
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CHECK(fingerprintsMatch(*"COC1CC1"_smiles, xqm1));
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CHECK(fingerprintsMatch(*"COC1CC1"_smiles, xqm2));
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CHECK(fingerprintsMatch(*"COC1CC1"_smiles, xqm3));
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CHECK(fingerprintsMatch(*"COC1C(C)C1"_smiles, xqm1));
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CHECK(fingerprintsMatch(*"COC1C(C)C1"_smiles, xqm3));
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CHECK(!fingerprintsMatch(*"COC1OC1"_smiles, xqm1));
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CHECK(!fingerprintsMatch(*"COC1OC1"_smiles, xqm2));
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CHECK(fingerprintsMatch(*"COC1OC1"_smiles, xqm3));
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}
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SECTION("MolBundle") {
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auto mol = "COCC |LN:1:1.3|"_smiles;
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REQUIRE(mol);
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auto xqm1 = createExtendedQueryMol(*mol, doEnumeration, doTautomers);
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MolOps::AdjustQueryParameters aqps =
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MolOps::AdjustQueryParameters::noAdjustments();
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aqps.makeBondsGeneric = true;
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auto xqm2 = createExtendedQueryMol(*mol, doEnumeration, doTautomers,
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adjustQueryProperties, aqps);
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CHECK(std::holds_alternative<ExtendedQueryMol::MolBundle_T>(xqm1.xqmol));
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CHECK(std::holds_alternative<ExtendedQueryMol::MolBundle_T>(xqm2.xqmol));
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CHECK(SubstructMatch(*"COC=C"_smiles, xqm1).empty());
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CHECK(SubstructMatch(*"COOC=C"_smiles, xqm1).empty());
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CHECK(SubstructMatch(*"COC=C"_smiles, xqm2).size() == 1);
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CHECK(SubstructMatch(*"COOC=C"_smiles, xqm2).size() == 1);
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CHECK(!fingerprintsMatch(*"COC=C"_smiles, xqm1));
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CHECK(!fingerprintsMatch(*"COOC=C"_smiles, xqm1));
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CHECK(fingerprintsMatch(*"COC=C"_smiles, xqm2));
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CHECK(fingerprintsMatch(*"COOC=C"_smiles, xqm2));
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}
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SECTION("TautomerQuery") {
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auto mol1 = "CC1OC(N)=N1"_smiles;
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REQUIRE(mol1);
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auto xqm1 = createExtendedQueryMol(*mol1, doEnumeration, doTautomers);
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auto xqm2 = createExtendedQueryMol(*mol1, doEnumeration, doTautomers,
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adjustQueryProperties);
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CHECK(
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std::holds_alternative<ExtendedQueryMol::TautomerQuery_T>(xqm1.xqmol));
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CHECK(
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std::holds_alternative<ExtendedQueryMol::TautomerQuery_T>(xqm2.xqmol));
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CHECK(SubstructMatch(*"CC1OC(N)=N1"_smiles, xqm1).size() == 1);
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CHECK(SubstructMatch(*"CC1OC(N)=N1"_smiles, xqm2).size() == 1);
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CHECK(SubstructMatch(*"CC1(F)OC(N)=N1"_smiles, xqm1).size() == 1);
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CHECK(SubstructMatch(*"CC1(F)OC(=N)N1"_smiles, xqm1).size() == 1);
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CHECK(SubstructMatch(*"CC1(F)OC(N)=N1"_smiles, xqm2).empty());
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CHECK(SubstructMatch(*"CC1(F)OC(=N)N1"_smiles, xqm2).empty());
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CHECK(fingerprintsMatch(*"CC1OC(N)=N1"_smiles, xqm1));
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CHECK(fingerprintsMatch(*"CC1OC(N)=N1"_smiles, xqm2));
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CHECK(fingerprintsMatch(*"CC1(F)OC(N)=N1"_smiles, xqm1));
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CHECK(fingerprintsMatch(*"CC1(F)OC(=N)N1"_smiles, xqm1));
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}
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SECTION("TautomerBundle") {
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auto mol1 = "COCC1OC(N)=N1 |LN:1:1.3|"_smiles;
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REQUIRE(mol1);
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auto xqm1 = createExtendedQueryMol(*mol1, doEnumeration, doTautomers);
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auto xqm2 = createExtendedQueryMol(*mol1, doEnumeration, doTautomers,
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adjustQueryProperties);
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CHECK(
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std::holds_alternative<ExtendedQueryMol::TautomerBundle_T>(xqm1.xqmol));
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CHECK(SubstructMatch(*"COCC1OC(N)=N1"_smiles, xqm1).size() == 1);
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CHECK(SubstructMatch(*"COOCC1OC(=N)N1"_smiles, xqm1).size() == 1);
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CHECK(SubstructMatch(*"COCC1OC(N)=N1"_smiles, xqm2).size() == 1);
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CHECK(SubstructMatch(*"COOCC1OC(=N)N1"_smiles, xqm2).size() == 1);
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CHECK(SubstructMatch(*"COCC1(F)OC(N)=N1"_smiles, xqm1).size() == 1);
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CHECK(SubstructMatch(*"COOCC1(F)OC(=N)N1"_smiles, xqm1).size() == 1);
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CHECK(SubstructMatch(*"COCC1(F)OC(N)=N1"_smiles, xqm2).empty());
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CHECK(SubstructMatch(*"COOCC1(F)OC(=N)N1"_smiles, xqm2).empty());
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CHECK(fingerprintsMatch(*"COCC1OC(N)=N1"_smiles, xqm1));
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|
CHECK(fingerprintsMatch(*"COOCC1OC(=N)N1"_smiles, xqm1));
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|
CHECK(fingerprintsMatch(*"COCC1OC(N)=N1"_smiles, xqm2));
|
|
CHECK(fingerprintsMatch(*"COOCC1OC(=N)N1"_smiles, xqm2));
|
|
CHECK(fingerprintsMatch(*"COCC1(F)OC(N)=N1"_smiles, xqm1));
|
|
CHECK(fingerprintsMatch(*"COOCC1(F)OC(=N)N1"_smiles, xqm1));
|
|
}
|
|
}
|
|
|
|
TEST_CASE("controlling which steps are applied") {
|
|
auto mol1 = "COCC1OC(N)=N1 |LN:1:1.3|"_smiles;
|
|
bool doEnumeration = true;
|
|
bool doTautomers = true;
|
|
REQUIRE(mol1);
|
|
{
|
|
auto xqm = createExtendedQueryMol(*mol1, doEnumeration, doTautomers);
|
|
CHECK(
|
|
std::holds_alternative<ExtendedQueryMol::TautomerBundle_T>(xqm.xqmol));
|
|
}
|
|
{
|
|
auto xqm = createExtendedQueryMol(*mol1, doEnumeration, false);
|
|
CHECK(std::holds_alternative<ExtendedQueryMol::MolBundle_T>(xqm.xqmol));
|
|
}
|
|
{
|
|
auto xqm = createExtendedQueryMol(*mol1, false, doTautomers);
|
|
CHECK(std::holds_alternative<ExtendedQueryMol::TautomerQuery_T>(xqm.xqmol));
|
|
}
|
|
{
|
|
auto xqm = createExtendedQueryMol(*mol1, false, false);
|
|
CHECK(std::holds_alternative<ExtendedQueryMol::RWMol_T>(xqm.xqmol));
|
|
}
|
|
}
|
|
|
|
TEST_CASE("interaction with generic groups") {
|
|
// setup a molecule with a generic query:
|
|
auto baseQ = "COC1=NNC(*)=C1 |$;;;;;;AEL_p;$,LN:1:1.3|"_smiles;
|
|
REQUIRE(baseQ);
|
|
auto aqps = MolOps::AdjustQueryParameters::noAdjustments();
|
|
aqps.makeDummiesQueries = true;
|
|
MolOps::adjustQueryProperties(*baseQ, &aqps);
|
|
GenericGroups::setGenericQueriesFromProperties(*baseQ);
|
|
CHECK(baseQ->getAtomWithIdx(6)->hasProp(
|
|
common_properties::_QueryAtomGenericLabel));
|
|
|
|
auto xqm = createExtendedQueryMol(*baseQ);
|
|
CHECK(std::holds_alternative<ExtendedQueryMol::TautomerBundle_T>(xqm.xqmol));
|
|
const auto &tquery = std::get<ExtendedQueryMol::TautomerBundle_T>(xqm.xqmol);
|
|
CHECK(tquery->at(0)->getTautomers()[0]->getAtomWithIdx(7)->hasProp(
|
|
common_properties::_QueryAtomGenericLabel));
|
|
CHECK(tquery->at(0)->getTautomers()[1]->getAtomWithIdx(7)->hasProp(
|
|
common_properties::_QueryAtomGenericLabel));
|
|
SECTION("serialization") {
|
|
ExtendedQueryMol xqm2(xqm.toBinary());
|
|
CHECK(
|
|
std::holds_alternative<ExtendedQueryMol::TautomerBundle_T>(xqm2.xqmol));
|
|
const auto &tquery =
|
|
std::get<ExtendedQueryMol::TautomerBundle_T>(xqm2.xqmol);
|
|
CHECK(tquery->at(0)->getTautomers()[0]->getAtomWithIdx(7)->hasProp(
|
|
common_properties::_QueryAtomGenericLabel));
|
|
CHECK(tquery->at(0)->getTautomers()[1]->getAtomWithIdx(7)->hasProp(
|
|
common_properties::_QueryAtomGenericLabel));
|
|
}
|
|
} |