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529 lines
14 KiB
C++
529 lines
14 KiB
C++
//
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// Copyright (C) 2020 Greg Landrum
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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 <RDGeneral/test.h>
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#include "catch.hpp"
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#include <GraphMol/RDKitBase.h>
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#include <GraphMol/FileParsers/FileParsers.h>
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#include <GraphMol/SmilesParse/SmilesWrite.h>
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#include <GraphMol/SmilesParse/SmilesParse.h>
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#include <GraphMol/SmilesParse/SmartsWrite.h>
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#include "MolEnumerator.h"
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using namespace RDKit;
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TEST_CASE("PositionVariation", "[MolEnumerator]") {
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auto mol1 = R"CTAB(
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Mrv2007 06232015292D
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0 0 0 0 0 999 V3000
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M V30 BEGIN CTAB
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M V30 COUNTS 9 8 0 0 0
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M V30 BEGIN ATOM
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M V30 1 C -1.7083 2.415 0 0
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M V30 2 C -3.042 1.645 0 0
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M V30 3 C -3.042 0.105 0 0
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M V30 4 N -1.7083 -0.665 0 0
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M V30 5 C -0.3747 0.105 0 0
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M V30 6 C -0.3747 1.645 0 0
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M V30 7 * -0.8192 1.3883 0 0
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M V30 8 O -0.8192 3.6983 0 0
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M V30 9 C 0.5145 4.4683 0 0
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M V30 END ATOM
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M V30 BEGIN BOND
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M V30 1 1 1 2
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M V30 2 2 2 3
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M V30 3 1 3 4
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M V30 4 2 4 5
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M V30 5 1 5 6
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M V30 6 2 1 6
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M V30 7 1 7 8 ENDPTS=(3 1 5 6) ATTACH=ANY
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M V30 8 1 8 9
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M V30 END BOND
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M V30 END CTAB
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M END)CTAB"_ctab;
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REQUIRE(mol1);
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auto mol2 = R"CTAB(
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Mrv2007 06242006032D
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0 0 0 0 0 999 V3000
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M V30 BEGIN CTAB
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M V30 COUNTS 10 8 0 0 0
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M V30 BEGIN ATOM
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M V30 1 C -1.7083 2.415 0 0
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M V30 2 C -3.042 1.645 0 0
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M V30 3 C -3.042 0.105 0 0
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M V30 4 N -1.7083 -0.665 0 0
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M V30 5 C -0.3747 0.105 0 0
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M V30 6 C -0.3747 1.645 0 0
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M V30 7 * -3.042 0.875 0 0
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M V30 8 F -5.0434 0.875 0 0
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M V30 9 * -1.0415 2.03 0 0
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M V30 10 Cl -1.0415 4.34 0 0
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M V30 END ATOM
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M V30 BEGIN BOND
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M V30 1 1 1 2
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M V30 2 2 2 3
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M V30 3 1 3 4
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M V30 4 2 4 5
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M V30 5 1 5 6
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M V30 6 2 1 6
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M V30 7 1 7 8 ENDPTS=(2 2 3) ATTACH=ANY
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M V30 8 1 9 10 ENDPTS=(2 1 6) ATTACH=ANY
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M V30 END BOND
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M V30 END CTAB
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M END
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)CTAB"_ctab;
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REQUIRE(mol2);
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SECTION("PositionVariationOp unit tests 1") {
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MolEnumerator::PositionVariationOp op(*mol1);
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auto vcnts = op.getVariationCounts();
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REQUIRE(vcnts.size() == 1);
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CHECK(vcnts[0] == 3);
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{
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std::vector<size_t> elems{1};
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std::unique_ptr<ROMol> newmol(op(elems));
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CHECK(MolToSmiles(*newmol) == "COc1ccccn1");
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}
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{
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std::vector<size_t> elems{2};
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std::unique_ptr<ROMol> newmol(op(elems));
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CHECK(MolToSmiles(*newmol) == "COc1cccnc1");
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}
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}
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SECTION("PositionVariationOp unit tests 2") {
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MolEnumerator::PositionVariationOp op(*mol2);
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auto vcnts = op.getVariationCounts();
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REQUIRE(vcnts.size() == 2);
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CHECK(vcnts[0] == 2);
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CHECK(vcnts[1] == 2);
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{
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std::vector<size_t> elems{1, 0};
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std::unique_ptr<ROMol> newmol(op(elems));
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CHECK(MolToSmiles(*newmol) == "Fc1cc(Cl)ccn1");
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}
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{
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std::vector<size_t> elems{0, 1};
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std::unique_ptr<ROMol> newmol(op(elems));
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CHECK(MolToSmiles(*newmol) == "Fc1cncc(Cl)c1");
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}
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}
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SECTION("PositionVariationOp unit tests 3") {
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MolEnumerator::PositionVariationOp op;
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op.initFromMol(*mol1);
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auto vcnts = op.getVariationCounts();
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REQUIRE(vcnts.size() == 1);
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CHECK(vcnts[0] == 3);
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}
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SECTION("enumeration basics 1") {
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MolEnumerator::MolEnumeratorParams ps;
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ps.dp_operation = std::shared_ptr<MolEnumerator::MolEnumeratorOp>(
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new MolEnumerator::PositionVariationOp());
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auto bundle = MolEnumerator::enumerate(*mol1, ps);
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CHECK(bundle.size() == 3);
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CHECK(bundle.getMols()[0]->getAtomWithIdx(0)->getDegree() == 3);
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CHECK(bundle.getMols()[0]->getAtomWithIdx(0)->getImplicitValence() == 0);
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std::vector<std::string> tsmis = {"COc1ccncc1", "COc1ccccn1", "COc1cccnc1"};
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std::vector<std::string> smis;
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for (const auto &molp : bundle.getMols()) {
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smis.push_back(MolToSmiles(*molp));
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}
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CHECK(smis == tsmis);
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}
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SECTION("enumeration basics 2") {
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MolEnumerator::MolEnumeratorParams ps;
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ps.dp_operation = std::shared_ptr<MolEnumerator::MolEnumeratorOp>(
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new MolEnumerator::PositionVariationOp());
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auto bundle = MolEnumerator::enumerate(*mol2, ps);
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CHECK(bundle.size() == 4);
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std::vector<std::string> tsmis = {"Fc1cnccc1Cl", "Fc1cncc(Cl)c1",
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"Fc1cc(Cl)ccn1", "Fc1ccc(Cl)cn1"};
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std::vector<std::string> smis;
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for (const auto &molp : bundle.getMols()) {
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smis.push_back(MolToSmiles(*molp));
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}
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CHECK(smis == tsmis);
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}
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}
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TEST_CASE("LINKNODE", "[MolEnumerator]") {
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auto mol1 = R"CTAB(one linknode
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Mrv2007 06222005102D
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0 0 0 0 0 999 V3000
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M V30 BEGIN CTAB
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M V30 COUNTS 6 6 0 0 0
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M V30 BEGIN ATOM
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M V30 1 C 8.25 12.1847 0 0
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M V30 2 C 6.9164 12.9547 0 0
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M V30 3 C 6.9164 14.4947 0 0
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M V30 4 C 9.5836 14.4947 0 0
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M V30 5 C 9.5836 12.9547 0 0
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M V30 6 O 8.25 10.6447 0 0
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M V30 END ATOM
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M V30 BEGIN BOND
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M V30 1 1 1 2
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M V30 2 1 2 3
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M V30 3 1 4 5
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M V30 4 1 1 5
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M V30 5 1 3 4
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M V30 6 1 1 6
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M V30 END BOND
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M V30 LINKNODE 1 4 2 1 2 1 5
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M V30 END CTAB
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M END)CTAB"_ctab;
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REQUIRE(mol1);
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SECTION("LinkNode unit tests 1") {
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MolEnumerator::LinkNodeOp op;
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op.initFromMol(*mol1);
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auto vcnts = op.getVariationCounts();
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REQUIRE(vcnts.size() == 1);
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CHECK(vcnts[0] == 4);
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{
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std::vector<size_t> elems{0};
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std::unique_ptr<ROMol> newmol(op(elems));
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CHECK(MolToSmiles(*newmol) == "OC1CCCC1");
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}
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{
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std::vector<size_t> elems{2};
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std::unique_ptr<ROMol> newmol(op(elems));
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CHECK(MolToSmiles(*newmol) == "OC1CCCCC(O)C1O");
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}
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}
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SECTION("LinkNode unit tests 2") {
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auto mol2 = R"CTAB(two linknodes
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Mrv2014 07072016412D
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0 0 0 0 0 999 V3000
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M V30 BEGIN CTAB
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M V30 COUNTS 7 7 0 0 0
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M V30 BEGIN ATOM
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M V30 1 C 8.25 12.1847 0 0
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M V30 2 C 6.9164 12.9547 0 0
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M V30 3 C 7.2366 14.4611 0 0
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M V30 4 C 8.7681 14.622 0 0
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M V30 5 C 9.3945 13.2151 0 0
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M V30 6 O 8.25 10.6447 0 0
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M V30 7 F 9.5382 15.9557 0 0
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M V30 END ATOM
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M V30 BEGIN BOND
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M V30 1 1 1 2
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M V30 2 1 2 3
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M V30 3 1 4 5
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M V30 4 1 1 5
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M V30 5 1 3 4
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M V30 6 1 1 6
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M V30 7 1 4 7
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M V30 END BOND
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M V30 LINKNODE 1 3 2 1 2 1 5
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M V30 LINKNODE 1 4 2 4 3 4 5
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M V30 END CTAB
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M END)CTAB"_ctab;
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REQUIRE(mol2);
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MolEnumerator::LinkNodeOp op;
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op.initFromMol(*mol2);
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auto vcnts = op.getVariationCounts();
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REQUIRE(vcnts.size() == 2);
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CHECK(vcnts[0] == 3);
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CHECK(vcnts[1] == 4);
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{
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std::vector<size_t> elems{0, 0};
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std::unique_ptr<ROMol> newmol(op(elems));
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CHECK(MolToSmiles(*newmol) == "OC1CCC(F)C1");
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}
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{
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std::vector<size_t> elems{2, 0};
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std::unique_ptr<ROMol> newmol(op(elems));
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CHECK(MolToSmiles(*newmol) == "OC1CCC(F)CC(O)C1O");
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}
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{
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std::vector<size_t> elems{1, 2};
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std::unique_ptr<ROMol> newmol(op(elems));
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CHECK(MolToSmiles(*newmol) == "OC1CCC(F)C(F)C(F)CC1O");
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}
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}
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SECTION("LinkNode unit tests 3") {
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auto mol = R"CTAB(neighboring linknodes
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Mrv2014 07082008052D
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0 0 0 0 0 999 V3000
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M V30 BEGIN CTAB
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M V30 COUNTS 9 9 0 0 0
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M V30 BEGIN ATOM
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M V30 1 C 8.25 12.1847 0 0
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M V30 2 C 6.9164 12.9547 0 0
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M V30 3 C 7.2366 14.4611 0 0
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M V30 4 C 8.7681 14.622 0 0
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M V30 5 C 9.3945 13.2151 0 0
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M V30 6 O 8.25 10.6447 0 0
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M V30 7 F 9.5382 15.9557 0 0
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M V30 8 C 9.5837 9.8747 0 0
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M V30 9 C 10.9008 12.8949 0 0
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M V30 END ATOM
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M V30 BEGIN BOND
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M V30 1 1 1 2
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M V30 2 1 2 3
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M V30 3 1 4 5
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M V30 4 1 1 5
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M V30 5 1 3 4
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M V30 6 1 1 6
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M V30 7 1 4 7
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M V30 8 1 6 8
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M V30 9 1 5 9
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M V30 END BOND
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M V30 LINKNODE 1 3 2 1 2 1 5
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M V30 LINKNODE 1 2 2 5 1 5 4
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M V30 END CTAB
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M END
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)CTAB"_ctab;
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REQUIRE(mol);
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MolEnumerator::LinkNodeOp op;
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op.initFromMol(*mol);
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auto vcnts = op.getVariationCounts();
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REQUIRE(vcnts.size() == 2);
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CHECK(vcnts[0] == 3);
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CHECK(vcnts[1] == 2);
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{
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std::vector<size_t> elems{0, 0};
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std::unique_ptr<ROMol> newmol(op(elems));
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CHECK(MolToSmiles(*newmol) == "COC1CCC(F)C1C");
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}
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{
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std::vector<size_t> elems{1, 0};
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std::unique_ptr<ROMol> newmol(op(elems));
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CHECK(MolToSmiles(*newmol) == "COC1CCC(F)C(C)C1OC");
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}
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{
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std::vector<size_t> elems{1, 1};
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std::unique_ptr<ROMol> newmol(op(elems));
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CHECK(MolToSmiles(*newmol) == "COC1CCC(F)C(C)C(C)C1OC");
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}
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}
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SECTION("LinkNode unit tests: isotopes") {
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auto mol = R"CTAB(isotopes and linknodes
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Mrv2014 07082008362D
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0 0 0 0 0 999 V3000
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M V30 BEGIN CTAB
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M V30 COUNTS 4 4 0 0 0
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M V30 BEGIN ATOM
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M V30 1 C 0.5 19.6392 0 0 MASS=14
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M V30 2 C -0.27 18.3054 0 0 MASS=15
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M V30 3 C 1.27 18.3054 0 0 MASS=13
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M V30 4 O 2.6037 17.5354 0 0 MASS=12
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M V30 END ATOM
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M V30 BEGIN BOND
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M V30 1 1 1 2
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M V30 2 1 3 1
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M V30 3 1 2 3
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M V30 4 1 3 4
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M V30 END BOND
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M V30 LINKNODE 1 3 2 3 1 3 2
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M V30 END CTAB
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M END
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)CTAB"_ctab;
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REQUIRE(mol);
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MolEnumerator::LinkNodeOp op;
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op.initFromMol(*mol);
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auto vcnts = op.getVariationCounts();
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REQUIRE(vcnts.size() == 1);
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CHECK(vcnts[0] == 3);
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{
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std::vector<size_t> elems{1};
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std::unique_ptr<ROMol> newmol(op(elems));
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CHECK(MolToSmiles(*newmol) == "[12OH][13CH]1[14CH2][15CH2][13CH]1[12OH]");
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}
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}
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SECTION("LinkNode unit tests: no linknodes") {
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auto mol = R"CTAB(no linknodes
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Mrv2007 06222005102D
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0 0 0 0 0 999 V3000
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M V30 BEGIN CTAB
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M V30 COUNTS 6 6 0 0 0
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M V30 BEGIN ATOM
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M V30 1 C 8.25 12.1847 0 0
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M V30 2 C 6.9164 12.9547 0 0
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M V30 3 C 6.9164 14.4947 0 0
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M V30 4 C 9.5836 14.4947 0 0
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M V30 5 C 9.5836 12.9547 0 0
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M V30 6 O 8.25 10.6447 0 0
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M V30 END ATOM
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M V30 BEGIN BOND
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M V30 1 1 1 2
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M V30 2 1 2 3
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M V30 3 1 4 5
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M V30 4 1 1 5
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M V30 5 1 3 4
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M V30 6 1 1 6
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M V30 END BOND
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M V30 END CTAB
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M END)CTAB"_ctab;
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REQUIRE(mol);
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MolEnumerator::LinkNodeOp op;
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op.initFromMol(*mol);
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auto vcnts = op.getVariationCounts();
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REQUIRE(vcnts.size() == 0);
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}
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SECTION("enumeration basics 1") {
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MolEnumerator::MolEnumeratorParams ps;
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ps.dp_operation = std::shared_ptr<MolEnumerator::MolEnumeratorOp>(
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new MolEnumerator::LinkNodeOp());
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auto bundle = MolEnumerator::enumerate(*mol1, ps);
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std::vector<std::string> tsmis = {"OC1CCCC1", "OC1CCCCC1O",
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"OC1CCCCC(O)C1O", "OC1CCCCC(O)C(O)C1O"};
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CHECK(bundle.size() == tsmis.size());
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std::vector<std::string> smis;
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for (const auto &molp : bundle.getMols()) {
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smis.push_back(MolToSmiles(*molp));
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}
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CHECK(smis == tsmis);
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}
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SECTION("enumeration basics 2") {
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auto mol = R"CTAB(no linknodes
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Mrv2007 06222005102D
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0 0 0 0 0 999 V3000
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M V30 BEGIN CTAB
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M V30 COUNTS 6 6 0 0 0
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M V30 BEGIN ATOM
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M V30 1 C 8.25 12.1847 0 0
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M V30 2 C 6.9164 12.9547 0 0
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M V30 3 C 6.9164 14.4947 0 0
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M V30 4 C 9.5836 14.4947 0 0
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M V30 5 C 9.5836 12.9547 0 0
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M V30 6 O 8.25 10.6447 0 0
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M V30 END ATOM
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M V30 BEGIN BOND
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M V30 1 1 1 2
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M V30 2 1 2 3
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M V30 3 1 4 5
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M V30 4 1 1 5
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M V30 5 1 3 4
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M V30 6 1 1 6
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M V30 END BOND
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M V30 END CTAB
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M END)CTAB"_ctab;
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REQUIRE(mol);
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MolEnumerator::MolEnumeratorParams ps;
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ps.dp_operation = std::shared_ptr<MolEnumerator::MolEnumeratorOp>(
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new MolEnumerator::LinkNodeOp());
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auto bundle = MolEnumerator::enumerate(*mol, ps);
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CHECK(bundle.size() == 0);
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}
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}
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TEST_CASE("multiple enumeration points", "[MolEnumerator]") {
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auto mol1 = R"CTAB(
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Mrv2014 12212013392D
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0 0 0 0 0 999 V3000
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M V30 BEGIN CTAB
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M V30 COUNTS 12 12 0 0 0
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M V30 BEGIN ATOM
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M V30 1 C -6 4.7484 0 0
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M V30 2 C -7.3337 3.9784 0 0
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M V30 3 N -7.3337 2.4383 0 0
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M V30 4 C -6 1.6683 0 0
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M V30 5 C -4.6663 2.4383 0 0
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M V30 6 C -4.6663 3.9784 0 0
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M V30 7 C -5.8773 0.0617 0 0
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M V30 8 C -3.2136 0.2013 0 0
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M V30 9 C -4.5052 -0.6374 0 0
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M V30 10 O -4.4246 -2.1753 0 0
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M V30 11 * -6 4.235 0 0
|
|
M V30 12 C -4.845 6.2355 0 0
|
|
M V30 END ATOM
|
|
M V30 BEGIN BOND
|
|
M V30 1 1 1 2
|
|
M V30 2 2 2 3
|
|
M V30 3 1 3 4
|
|
M V30 4 2 4 5
|
|
M V30 5 1 5 6
|
|
M V30 6 2 1 6
|
|
M V30 7 1 8 9
|
|
M V30 8 1 7 9
|
|
M V30 9 1 5 8
|
|
M V30 10 1 7 4
|
|
M V30 11 1 9 10
|
|
M V30 12 1 11 12 ENDPTS=(3 1 2 6) ATTACH=ANY
|
|
M V30 END BOND
|
|
M V30 LINKNODE 1 3 2 9 7 9 8
|
|
M V30 END CTAB
|
|
M END
|
|
)CTAB"_ctab;
|
|
REQUIRE(mol1);
|
|
std::vector<std::string> tsmis = {
|
|
"Cc1cnc2c(c1)CC(O)C2", "Cc1cnc2c(c1)CC(O)C(O)C2",
|
|
"Cc1cnc2c(c1)CC(O)C(O)C(O)C2", "Cc1ccc2c(n1)CC(O)C2",
|
|
"Cc1ccc2c(n1)CC(O)C(O)C2", "Cc1ccc2c(n1)CC(O)C(O)C(O)C2",
|
|
"Cc1ccnc2c1CC(O)C2", "Cc1ccnc2c1CC(O)C(O)C2",
|
|
"Cc1ccnc2c1CC(O)C(O)C(O)C2"};
|
|
SECTION("test1") {
|
|
std::vector<MolEnumerator::MolEnumeratorParams> paramsList;
|
|
MolEnumerator::MolEnumeratorParams posVariationParams;
|
|
posVariationParams.dp_operation =
|
|
std::shared_ptr<MolEnumerator::MolEnumeratorOp>(
|
|
new MolEnumerator::PositionVariationOp());
|
|
paramsList.push_back(posVariationParams);
|
|
MolEnumerator::MolEnumeratorParams linkParams;
|
|
linkParams.dp_operation = std::shared_ptr<MolEnumerator::MolEnumeratorOp>(
|
|
new MolEnumerator::LinkNodeOp());
|
|
paramsList.push_back(linkParams);
|
|
auto bundle = MolEnumerator::enumerate(*mol1, paramsList);
|
|
CHECK(bundle.size() == tsmis.size());
|
|
for (const auto &molp : bundle.getMols()) {
|
|
auto smi = MolToSmiles(*molp);
|
|
// std::cerr << smi << std::endl;
|
|
CHECK(std::find(tsmis.begin(), tsmis.end(), smi) != tsmis.end());
|
|
}
|
|
}
|
|
SECTION("test2") {
|
|
auto bundle = MolEnumerator::enumerate(*mol1);
|
|
CHECK(bundle.size() == tsmis.size());
|
|
for (const auto &molp : bundle.getMols()) {
|
|
auto smi = MolToSmiles(*molp);
|
|
CHECK(std::find(tsmis.begin(), tsmis.end(), smi) != tsmis.end());
|
|
}
|
|
}
|
|
SECTION("edges1") {
|
|
std::vector<MolEnumerator::MolEnumeratorParams> paramsList;
|
|
auto bundle = MolEnumerator::enumerate(*mol1, paramsList);
|
|
CHECK(bundle.size() == 0);
|
|
}
|
|
SECTION("edges2") {
|
|
std::vector<MolEnumerator::MolEnumeratorParams> paramsList;
|
|
MolEnumerator::MolEnumeratorParams posVariationParams;
|
|
posVariationParams.dp_operation =
|
|
std::shared_ptr<MolEnumerator::MolEnumeratorOp>(
|
|
new MolEnumerator::PositionVariationOp());
|
|
paramsList.push_back(posVariationParams);
|
|
MolEnumerator::MolEnumeratorParams linkParams;
|
|
linkParams.dp_operation = std::shared_ptr<MolEnumerator::MolEnumeratorOp>(
|
|
new MolEnumerator::LinkNodeOp());
|
|
paramsList.push_back(linkParams);
|
|
auto mol = "c1ccccc1"_smiles;
|
|
auto bundle = MolEnumerator::enumerate(*mol, paramsList);
|
|
CHECK(bundle.size() == 0);
|
|
}
|
|
} |