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//
// Copyright (C) 2001-2018 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 "AlignMolecules.h"
#include "O3AAlignMolecules.h"
#include <GraphMol/FileParsers/MolSupplier.h>
#include <GraphMol/FileParsers/MolWriters.h>
#include <GraphMol/FileParsers/FileParsers.h>
#include <GraphMol/ROMol.h>
#include <GraphMol/Conformer.h>
#include <GraphMol/Substruct/SubstructMatch.h>
#include <Numerics/Vector.h>
#include <GraphMol/MolPickler.h>
#include <GraphMol/DistGeomHelpers/Embedder.h>
#include <GraphMol/SmilesParse/SmilesParse.h>
#include <GraphMol/ChemTransforms/MolFragmenter.h>
#include <GraphMol/MolTransforms/MolTransforms.h>
#include <ForceField/ForceField.h>
#include <GraphMol/ForceFieldHelpers/UFF/Builder.h>
using namespace RDKit;
void test1MolAlign() {
std::string rdbase = getenv("RDBASE");
std::string fname1 = rdbase + "/Code/GraphMol/MolAlign/test_data/1oir.mol";
ROMol *m1 = MolFileToMol(fname1);
std::string fname2 =
rdbase + "/Code/GraphMol/MolAlign/test_data/1oir_conf.mol";
ROMol *m2 = MolFileToMol(fname2);
double rmsd = MolAlign::alignMol(*m2, *m1);
TEST_ASSERT(RDKit::feq(rmsd, 0.6578) || RDKit::feq(rmsd, 1.0345));
std::string fname3 =
rdbase + "/Code/GraphMol/MolAlign/test_data/1oir_trans.mol";
ROMol *m3 = MolFileToMol(fname3);
const Conformer &conf1 = m2->getConformer(0);
const Conformer &conf2 = m3->getConformer(0);
unsigned int i, nat = m3->getNumAtoms();
for (i = 0; i < nat; i++) {
RDGeom::Point3D pt1 = conf1.getAtomPos(i);
RDGeom::Point3D pt2 = conf2.getAtomPos(i);
TEST_ASSERT(RDKit::feq(pt1.x, pt2.x, 0.001));
TEST_ASSERT(RDKit::feq(pt1.y, pt2.y, 0.001));
TEST_ASSERT(RDKit::feq(pt1.z, pt2.z, 0.001));
}
RDGeom::Transform3D trans;
rmsd = MolAlign::getAlignmentTransform(*m1, *m2, trans);
TEST_ASSERT(RDKit::feq(rmsd, 0.6578) || RDKit::feq(rmsd, 1.0345));
// specify conformations
rmsd = MolAlign::alignMol(*m1, *m2, 0, 0);
TEST_ASSERT(RDKit::feq(rmsd, 0.6578) || RDKit::feq(rmsd, 1.0345));
// provide an atom mapping
delete m1;
delete m2;
delete m3;
}
void test1GetBestRMS() {
std::string rdbase = getenv("RDBASE");
std::string fname =
rdbase + "/Code/GraphMol/MolAlign/test_data/probe_mol.sdf";
SDMolSupplier supplier(fname, true, false);
std::unique_ptr<ROMol> prb(supplier[1]);
std::unique_ptr<ROMol> ref(supplier[2]);
std::unique_ptr<ROMol> prbCopy1(new ROMol(*prb));
std::unique_ptr<ROMol> prbCopy2(new ROMol(*prb));
std::unique_ptr<ROMol> prbCopy3(new ROMol(*prb));
RDGeom::Transform3D bestTrans;
MatchVectType bestMatch;
// alignMol() would return this for the rms: 2.50561
// But the best rms is: 2.43449
double rmsdInPlace = MolAlign::CalcRMS(*prbCopy1, *ref);
TEST_ASSERT(RDKit::feq(rmsdInPlace, 2.6026));
double rmsd = MolAlign::getBestRMS(*prb, *ref);
TEST_ASSERT(RDKit::feq(rmsd, 2.43449));
double rmsdCopy = MolAlign::getBestAlignmentTransform(*prbCopy1, *ref,
bestTrans, bestMatch);
TEST_ASSERT(RDKit::feq(rmsd, rmsdCopy));
TEST_ASSERT(bestMatch.size() == ref->getNumAtoms());
SmilesParserParams params;
params.removeHs = false;
ROMOL_SPTR scaffold(SmilesToMol(
"N1C([H])([H])C([H])([H])C([H])([H])[N+]([H])([H])C([H])([H])C1([H])[H]",
params));
MatchVectType scaffoldMatch;
TEST_ASSERT(SubstructMatch(*ref, *scaffold, scaffoldMatch));
boost::dynamic_bitset<> scaffoldIndices(ref->getNumAtoms());
for (const auto &pair : scaffoldMatch) {
scaffoldIndices.set(pair.second);
}
std::vector<MatchVectType> matches;
TEST_ASSERT(SubstructMatch(*ref, *prb, matches, false));
std::vector<MatchVectType> matchesPruned(matches.size());
std::transform(matches.begin(), matches.end(), matchesPruned.begin(),
[&scaffoldIndices](const auto &match) {
MatchVectType matchPruned;
std::copy_if(match.begin(), match.end(),
std::back_inserter(matchPruned),
[&scaffoldIndices](const auto &pair) {
return scaffoldIndices.test(pair.second);
});
return matchPruned;
});
rmsdInPlace = MolAlign::CalcRMS(*prbCopy2, *ref, -1, -1, matchesPruned);
TEST_ASSERT(RDKit::feq(rmsdInPlace, 2.5672));
rmsd = MolAlign::getBestRMS(*prb, *ref, -1, -1, matchesPruned);
TEST_ASSERT(RDKit::feq(rmsd, 1.14329));
rmsdCopy = MolAlign::getBestAlignmentTransform(
*prbCopy2, *ref, bestTrans, bestMatch, -1, -1, matchesPruned);
TEST_ASSERT(RDKit::feq(rmsd, rmsdCopy));
TEST_ASSERT(bestMatch.size() == scaffoldMatch.size());
RDNumeric::DoubleVector weights(scaffoldIndices.size(), 1.0);
for (unsigned int i = 0; i < scaffoldIndices.size(); ++i) {
if (scaffoldIndices.test(i)) {
weights.setVal(i, 100.0);
}
}
rmsdInPlace =
MolAlign::CalcRMS(*prbCopy3, *ref, -1, -1, matches, 1000, true, &weights);
TEST_ASSERT(RDKit::feq(rmsdInPlace, 17.7959));
rmsd =
MolAlign::getBestRMS(*prb, *ref, -1, -1, matches, 1000, true, &weights);
TEST_ASSERT(RDKit::feq(rmsd, 10.9681));
rmsdCopy = MolAlign::getBestAlignmentTransform(*prbCopy3, *ref, bestTrans,
bestMatch, -1, -1, matches,
1000, true, &weights);
TEST_ASSERT(RDKit::feq(rmsd, rmsdCopy));
TEST_ASSERT(bestMatch.size() == ref->getNumAtoms());
}
void test1MolWithQueryAlign() {
// identical to test1MolAlign except we replace one atom with a QueryAtom
// instead
std::string rdbase = getenv("RDBASE");
std::string fname1 = rdbase + "/Code/GraphMol/MolAlign/test_data/1oir.mol";
auto *m1 = MolFileToMol(fname1);
auto *a1 = new QueryAtom(6);
std::string fname2 =
rdbase + "/Code/GraphMol/MolAlign/test_data/1oir_conf.mol";
auto *m2 = MolFileToMol(fname2);
auto *a2 = new QueryAtom(6);
// we replace the same nitrogen instead with a null
// query 28 and 19 are the "same" atoms
m1->replaceAtom(28, a1);
m2->replaceAtom(19, a2);
double rmsd = MolAlign::alignMol(*m2, *m1);
TEST_ASSERT(RDKit::feq(rmsd, 0.6578) || RDKit::feq(rmsd, 1.0345));
std::string fname3 =
rdbase + "/Code/GraphMol/MolAlign/test_data/1oir_trans.mol";
auto *m3 = MolFileToMol(fname3);
auto *a3 = new QueryAtom(5);
m3->replaceAtom(0, a3);
const Conformer &conf1 = m2->getConformer(0);
const Conformer &conf2 = m3->getConformer(0);
unsigned int i, nat = m3->getNumAtoms();
for (i = 0; i < nat; i++) {
RDGeom::Point3D pt1 = conf1.getAtomPos(i);
RDGeom::Point3D pt2 = conf2.getAtomPos(i);
TEST_ASSERT(RDKit::feq(pt1.x, pt2.x, 0.001));
TEST_ASSERT(RDKit::feq(pt1.y, pt2.y, 0.001));
TEST_ASSERT(RDKit::feq(pt1.z, pt2.z, 0.001));
}
RDGeom::Transform3D trans;
rmsd = MolAlign::getAlignmentTransform(*m1, *m2, trans);
TEST_ASSERT(RDKit::feq(rmsd, 0.6578) || RDKit::feq(rmsd, 1.0345));
// specify conformations
rmsd = MolAlign::alignMol(*m1, *m2, 0, 0);
TEST_ASSERT(RDKit::feq(rmsd, 0.6578) || RDKit::feq(rmsd, 1.0345));
// provide an atom mapping
delete m1;
delete m2;
delete m3;
delete a1;
delete a2;
delete a3;
}
void test2AtomMap() {
std::string rdbase = getenv("RDBASE");
std::string fname1 = rdbase + "/Code/GraphMol/MolAlign/test_data/1oir.mol";
ROMol *m1 = MolFileToMol(fname1);
std::string fname2 =
rdbase + "/Code/GraphMol/MolAlign/test_data/1oir_conf.mol";
ROMol *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));
double rmsd = MolAlign::alignMol(*m2, *m1, 0, 0, &atomMap);
TEST_ASSERT(RDKit::feq(rmsd, 0.8525));
delete m1;
delete m2;
}
void test3Weights() {
std::string rdbase = getenv("RDBASE");
std::string fname1 = rdbase + "/Code/GraphMol/MolAlign/test_data/1oir.mol";
ROMol *m1 = MolFileToMol(fname1);
std::string fname2 =
rdbase + "/Code/GraphMol/MolAlign/test_data/1oir_conf.mol";
ROMol *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));
RDNumeric::DoubleVector wts(6);
wts.setVal(0, 1.0);
wts.setVal(1, 1.0);
wts.setVal(2, 1.0);
wts.setVal(3, 1.0);
wts.setVal(4, 1.0);
wts.setVal(5, 2.0);
double rmsd = MolAlign::alignMol(*m2, *m1, 0, 0, &atomMap, &wts);
TEST_ASSERT(RDKit::feq(rmsd, 0.9513));
delete m1;
delete m2;
}
void testIssue241() {
std::string rdbase = getenv("RDBASE");
std::string fname1 =
rdbase + "/Code/GraphMol/MolAlign/test_data/Issue241.mol";
ROMol *m1 = MolFileToMol(fname1);
std::string res;
MolPickler::pickleMol(*m1, res);
auto *ref = new ROMol(res);
DGeomHelpers::EmbedMolecule(*ref, 30, 239 * 10);
ForceFields::ForceField *ff1 = UFF::constructForceField(*ref);
ff1->initialize();
ff1->minimize(200, 1e-8, 1e-6);
std::string pkl2;
MolPickler::pickleMol(*m1, pkl2);
auto *probe = new ROMol(pkl2);
DGeomHelpers::EmbedMolecule(*probe, 30, 239 * 10);
ForceFields::ForceField *ff2 = UFF::constructForceField(*probe);
ff2->initialize();
ff2->minimize(200, 1e-8, 1e-6);
double rmsd = MolAlign::alignMol(*ref, *probe);
delete ff1;
delete ff2;
delete m1;
delete ref;
delete probe;
TEST_ASSERT(RDKit::feq(rmsd, 0.0));
}
int main() {
std::cout << "***********************************************************\n";
std::cout << "Testing MolAlign\n";
#if 1
std::cout << "\t---------------------------------\n";
std::cout << "\t test1MolAlign \n\n";
test1MolAlign();
std::cout << "\t---------------------------------\n";
std::cout << "\t test1GetBestRMS \n\n";
test1GetBestRMS();
std::cout << "\t---------------------------------\n";
std::cout << "\t test1MolWithQueryAlign \n\n";
test1MolWithQueryAlign();
std::cout << "\t---------------------------------\n";
std::cout << "\t test2AtomMap \n\n";
test2AtomMap();
std::cout << "\t---------------------------------\n";
std::cout << "\t test3Weights \n\n";
test3Weights();
std::cout << "\t---------------------------------\n";
std::cout << "\t testIssue241 \n\n";
testIssue241();
#endif
std::cout << "***********************************************************\n";
}
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