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21225e63b3
* move testSubstructMatch to catch2 * modernization * modernization * switch to catch2 * modernize * convert to catch2 * update * move to catch * please be quiet * move to catch2 * changes in response to review --------- Co-authored-by: = <=>
104 lines
3.5 KiB
C++
104 lines
3.5 KiB
C++
//
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// Copyright (C) 2005-2026 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 <Geometry/UniformGrid3D.h>
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#include "ShapeEncoder.h"
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#include "ShapeUtils.h"
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#include <GraphMol/RDKitBase.h>
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#include <GraphMol/FileParsers/FileParsers.h>
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#include <GraphMol/SmilesParse/SmilesParse.h>
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#include <Geometry/GridUtils.h>
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#include <GraphMol/MolAlign/AlignMolecules.h>
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#include <GraphMol/MolTransforms/MolTransforms.h>
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#include <GraphMol/Substruct/SubstructMatch.h>
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using namespace RDKit;
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TEST_CASE("Encode", "[shapehelpers]") {
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RDGeom::UniformGrid3D grd(30.0, 16.0, 10.0);
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std::string rdbase = getenv("RDBASE");
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std::string fname1 =
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rdbase + "/Code/GraphMol/ShapeHelpers/test_data/1oir.mol";
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auto m = v2::FileParsers::MolFromMolFile(fname1);
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REQUIRE(m);
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MolTransforms::canonicalizeMol(*m);
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MolShapes::EncodeShape(*m, grd, 0);
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CHECK(grd.getOccupancyVect()->getTotalVal() == 7405);
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}
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TEST_CASE("Compare", "[shapehelpers]") {
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std::string rdbase = getenv("RDBASE");
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std::string fname1 =
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rdbase + "/Code/GraphMol/ShapeHelpers/test_data/1oir.mol";
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auto m = v2::FileParsers::MolFromMolFile(fname1);
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REQUIRE(m);
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MolTransforms::canonicalizeMol(*m);
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auto mdup = v2::FileParsers::MolFromMolFile(fname1);
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REQUIRE(mdup);
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MolTransforms::canonicalizeMol(*mdup);
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double dist = MolShapes::tanimotoDistance(*m, *mdup);
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CHECK_THAT(dist, Catch::Matchers::WithinAbs(0.0, 1e-8));
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dist = MolShapes::tverskyIndex(*m, *mdup, 1.0, 1.0);
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CHECK_THAT(dist, Catch::Matchers::WithinAbs(1.0, 1e-8));
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m = v2::FileParsers::MolFromMolFile(fname1);
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REQUIRE(m);
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std::string fname2 =
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rdbase + "/Code/GraphMol/ShapeHelpers/test_data/1oir_conf.mol";
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auto m2 = v2::FileParsers::MolFromMolFile(fname2);
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REQUIRE(m2);
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double rmsd = MolAlign::alignMol(*m, *m2);
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CHECK(rmsd >= 0.0);
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dist = MolShapes::tanimotoDistance(*m, *m2);
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CHECK_THAT(dist, Catch::Matchers::WithinAbs(0.31, 0.01));
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dist = MolShapes::tverskyIndex(*m, *m2, 1.0, 1.0);
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CHECK_THAT(dist, Catch::Matchers::WithinAbs(0.68, 0.01));
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m2 = v2::FileParsers::MolFromMolFile(fname2);
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MatchVectType atomMap;
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atomMap.push_back(std::pair<int, int>(18, 27));
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atomMap.push_back(std::pair<int, int>(13, 23));
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atomMap.push_back(std::pair<int, int>(21, 14));
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atomMap.push_back(std::pair<int, int>(24, 7));
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atomMap.push_back(std::pair<int, int>(9, 19));
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atomMap.push_back(std::pair<int, int>(16, 30));
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rmsd = MolAlign::alignMol(*m2, *m, 0, 0, &atomMap);
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dist = MolShapes::tanimotoDistance(*m, *m2);
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CHECK_THAT(dist, Catch::Matchers::WithinAbs(0.3561, 0.01));
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}
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TEST_CASE("GitHub #4364", "[shapehelpers]") {
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std::string rdbase = getenv("RDBASE");
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std::string fname1 =
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rdbase + "/Code/GraphMol/ShapeHelpers/test_data/1oir.mol";
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auto m = v2::FileParsers::MolFromMolFile(fname1);
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REQUIRE(m);
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MolTransforms::canonicalizeMol(*m);
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std::string fname2 =
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rdbase + "/Code/GraphMol/ShapeHelpers/test_data/1oir_conf.mol";
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auto m2 = v2::FileParsers::MolFromMolFile(fname2);
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REQUIRE(m2);
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MolTransforms::canonicalizeMol(*m2);
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int cid1 = -1, cid2 = -1;
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auto dist = MolShapes::tanimotoDistance(*m, *m2, cid1, cid2);
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CHECK_THAT(dist, Catch::Matchers::WithinAbs(0.31, 0.01));
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double gridSpacing = 1.0;
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auto dist2 = MolShapes::tanimotoDistance(*m, *m2, cid1, cid2, gridSpacing);
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CHECK(fabs(dist2 - dist) > 0.001);
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}
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