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a75018fe38
* disable builds of the StructChecker code by default * operator"" _smarts() doesn't need to catch sanitization errors * remove unused function * turn back on some tests that shouldn't have been disabled * Remove unused code from SMARTS parser and simplify a bit SmilesParseOps::AddFragToMol is now used only from the SMARTS parser, so we can simplify the API * Removes obsolete special case code for SMARTS This was relevant when organic atoms in SMARTS queries were stored as two-part queries. * improve SMARTS testing make sure we can generate SMARTS from all the examples and then parse that again. * Fixes #2814 * Fixes #2815 * some additional smarts tests to improve coverage * test copy ctor and getPos * remove obsolete test_list files * include tests for the morgan invariant generators * more cleanups and coverage improvements * remove files that were mistakenly added
102 lines
3.1 KiB
C++
102 lines
3.1 KiB
C++
//
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// Copyright (C) 2005-2019 Rational Discovery LLC
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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 <RDGeneral/test.h>
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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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void test1Encode() {
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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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ROMol *m = MolFileToMol(fname1);
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MolTransforms::canonicalizeMol(*m);
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MolShapes::EncodeShape(*m, grd, 0);
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delete m;
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CHECK_INVARIANT(grd.getOccupancyVect()->getTotalVal() == 7405, "");
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}
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void test2Compare() {
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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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ROMol *m = MolFileToMol(fname1);
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MolTransforms::canonicalizeMol(*m);
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ROMol *mdup = MolFileToMol(fname1);
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MolTransforms::canonicalizeMol(*mdup);
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double dist = MolShapes::tanimotoDistance(*m, *mdup);
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CHECK_INVARIANT(dist == 0.0, "");
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dist = MolShapes::tverskyIndex(*m, *mdup, 1.0, 1.0);
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CHECK_INVARIANT(dist == 1.0, "");
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delete m;
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delete mdup;
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m = MolFileToMol(fname1);
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std::string fname2 =
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rdbase + "/Code/GraphMol/ShapeHelpers/test_data/1oir_conf.mol";
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ROMol *m2 = MolFileToMol(fname2);
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double rmsd = MolAlign::alignMol(*m, *m2);
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CHECK_INVARIANT(rmsd >= 0.0, "");
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dist = MolShapes::tanimotoDistance(*m, *m2);
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CHECK_INVARIANT(RDKit::feq(dist, 0.31, 0.01), "");
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dist = MolShapes::tverskyIndex(*m, *m2, 1.0, 1.0);
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CHECK_INVARIANT(RDKit::feq(dist, 0.68, 0.01), "");
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delete m2;
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m2 = MolFileToMol(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_INVARIANT(RDKit::feq(dist, 0.3593), "");
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delete m;
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delete m2;
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}
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int main() {
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#if 1
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std::cout << "***********************************************************\n";
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std::cout << "Testing ShapeHelpers\n";
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std::cout << "\t---------------------------------\n";
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std::cout << "\t test1Encode \n\n";
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test1Encode();
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std::cout << "\t---------------------------------\n";
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std::cout << "\t test2Compare \n\n";
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test2Compare();
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std::cout << "***********************************************************\n";
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#endif
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return 0;
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}
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