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// $Id$
//
// Copyright (C) 2005-2006 Rational Discovery LLC
//
// @@ All Rights Reserved @@
// This file is part of the RDKit.
// The contents are covered by the terms of the BSD license
// which is included in the file license.txt, found at the root
// of the RDKit source tree.
//
#include <RDGeneral/test.h>
#include <Geometry/UniformGrid3D.h>
#include "ShapeEncoder.h"
#include "ShapeUtils.h"
#include <GraphMol/RDKitBase.h>
//#include <GraphMol/DistGeomHelpers/Embedder.h>
#include <GraphMol/FileParsers/FileParsers.h>
//#include <GraphMol/ForceFieldHelpers/UFF/Builder.h>
//#include <ForceField/ForceField.h>
#include <GraphMol/SmilesParse/SmilesParse.h>
#include <Geometry/GridUtils.h>
#include <GraphMol/MolAlign/AlignMolecules.h>
#include <GraphMol/MolTransforms/MolTransforms.h>
#include <GraphMol/Substruct/SubstructMatch.h>
using namespace RDKit;
void test1Encode() {
RDGeom::UniformGrid3D grd(30.0, 16.0, 10.0);
std::string rdbase = getenv("RDBASE");
std::string fname1 =
rdbase + "/Code/GraphMol/ShapeHelpers/test_data/1oir.mol";
ROMol *m = MolFileToMol(fname1);
MolTransforms::canonicalizeMol(*m);
MolShapes::EncodeShape(*m, grd, 0);
// RDGeom::writeGridToFile(grd, "junk.grd");
// MolToMolFile(m, "junk.mol", 0);
CHECK_INVARIANT(grd.getOccupancyVect()->getTotalVal() == 9250, "");
}
void test2Compare() {
RDGeom::UniformGrid3D grd(30.0, 16.0, 10.0);
std::string rdbase = getenv("RDBASE");
std::string fname1 =
rdbase + "/Code/GraphMol/ShapeHelpers/test_data/1oir.mol";
ROMol *m = MolFileToMol(fname1);
MolTransforms::canonicalizeMol(*m);
ROMol *mdup = MolFileToMol(fname1);
MolTransforms::canonicalizeMol(*mdup);
double dist = MolShapes::tanimotoDistance(*m, *mdup);
CHECK_INVARIANT(dist == 0.0, "");
dist = MolShapes::tverskyIndex(*m, *mdup, 1.0, 1.0);
CHECK_INVARIANT(dist == 1.0, "");
delete m;
delete mdup;
m = MolFileToMol(fname1);
std::string fname2 =
rdbase + "/Code/GraphMol/ShapeHelpers/test_data/1oir_conf.mol";
ROMol *m2 = MolFileToMol(fname2);
double rmsd = MolAlign::alignMol(*m, *m2);
CHECK_INVARIANT(rmsd >= 0.0, "");
dist = MolShapes::tanimotoDistance(*m, *m2);
CHECK_INVARIANT(RDKit::feq(dist, 0.2813), "");
dist = MolShapes::tverskyIndex(*m, *m2, 1.0, 1.0);
CHECK_INVARIANT(RDKit::feq(dist, 0.7187), "");
delete m2;
m2 = MolFileToMol(fname2);
MatchVectType atomMap;
atomMap.push_back(std::pair<int, int>(18, 27));
atomMap.push_back(std::pair<int, int>(13, 23));
atomMap.push_back(std::pair<int, int>(21, 14));
atomMap.push_back(std::pair<int, int>(24, 7));
atomMap.push_back(std::pair<int, int>(9, 19));
atomMap.push_back(std::pair<int, int>(16, 30));
rmsd = MolAlign::alignMol(*m2, *m, 0, 0, &atomMap);
dist = MolShapes::tanimotoDistance(*m, *m2);
CHECK_INVARIANT(RDKit::feq(dist, 0.3244), "");
delete m;
delete m2;
}
void test3Methane() {
std::string rdbase = getenv("RDBASE");
std::string fname =
rdbase + "/Code/GraphMol/ShapeHelpers/test_data/methane.mol";
ROMol *m = MolFileToMol(fname);
RDGeom::Point3D dims, offSet;
MolShapes::computeConfDimsAndOffset(m->getConformer(), dims, offSet, nullptr,
3.0);
std::cout << dims << " " << offSet << "\n";
RDGeom::UniformGrid3D grd(6.5, 6.5, 6.5);
// dims.x, dims.y, dims.z, 0.5, DiscreteValueVect::TWOBITVALUE, &offSet);
MolShapes::EncodeShape(*m, grd, 0);
RDGeom::writeGridToFile(grd, "methane.grd");
}
int main() {
#if 1
std::cout << "***********************************************************\n";
std::cout << "Testing ShapeHelpers\n";
std::cout << "\t---------------------------------\n";
std::cout << "\t test1Encode \n\n";
test1Encode();
std::cout << "\t---------------------------------\n";
std::cout << "\t test2Compare \n\n";
test2Compare();
std::cout << "***********************************************************\n";
#endif
// test3Methane();
return 0;
}
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