mirror of
https://github.com/rdkit/rdkit.git
synced 2026-06-04 21:54:27 +08:00
125 lines
3.9 KiB
C++
125 lines
3.9 KiB
C++
//
|
|
// Copyright (C) 2005-2021 Greg Landrum and other RDKit contributors
|
|
//
|
|
// @@ 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/FileParsers/FileParsers.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);
|
|
delete m;
|
|
|
|
CHECK_INVARIANT(grd.getOccupancyVect()->getTotalVal() == 7405, "");
|
|
}
|
|
|
|
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, 0.31, 0.01), "");
|
|
dist = MolShapes::tverskyIndex(*m, *m2, 1.0, 1.0);
|
|
CHECK_INVARIANT(RDKit::feq(dist, 0.68, 0.01), "");
|
|
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, 0.3593), "");
|
|
delete m;
|
|
delete m2;
|
|
}
|
|
|
|
void testGithub4364() {
|
|
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";
|
|
std::unique_ptr<RWMol> m(MolFileToMol(fname1));
|
|
MolTransforms::canonicalizeMol(*m);
|
|
|
|
std::string fname2 =
|
|
rdbase + "/Code/GraphMol/ShapeHelpers/test_data/1oir_conf.mol";
|
|
std::unique_ptr<RWMol> m2(MolFileToMol(fname2));
|
|
MolTransforms::canonicalizeMol(*m2);
|
|
int cid1 = -1, cid2 = -1;
|
|
auto dist = MolShapes::tanimotoDistance(*m, *m2, cid1, cid2);
|
|
TEST_ASSERT(RDKit::feq(dist, 0.31, 0.01));
|
|
double gridSpacing = 1.0;
|
|
auto dist2 = MolShapes::tanimotoDistance(*m, *m2, cid1, cid2, gridSpacing);
|
|
TEST_ASSERT(fabs(dist - dist2) > 0.001);
|
|
}
|
|
|
|
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();
|
|
#endif
|
|
std::cout << "\t---------------------------------\n";
|
|
std::cout << "\t testGithub4364 \n\n";
|
|
testGithub4364();
|
|
std::cout << "***********************************************************\n";
|
|
return 0;
|
|
}
|