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b558de22c6
* split MolAlign lib into two pieces * further dependency cleanup * release notes update * add a missing dependency to the new library
253 lines
7.8 KiB
C++
253 lines
7.8 KiB
C++
//
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// Copyright (C) 2001-2018 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 "AlignMolecules.h"
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#include "O3AAlignMolecules.h"
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#include <GraphMol/FileParsers/MolSupplier.h>
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#include <GraphMol/FileParsers/MolWriters.h>
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#include <GraphMol/FileParsers/FileParsers.h>
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#include <GraphMol/ROMol.h>
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#include <GraphMol/Conformer.h>
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#include <GraphMol/Substruct/SubstructMatch.h>
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#include <Numerics/Vector.h>
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#include <GraphMol/MolPickler.h>
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#include <GraphMol/DistGeomHelpers/Embedder.h>
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#include <GraphMol/SmilesParse/SmilesParse.h>
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#include <GraphMol/MolTransforms/MolTransforms.h>
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#include <ForceField/ForceField.h>
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#include <GraphMol/ForceFieldHelpers/UFF/Builder.h>
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using namespace RDKit;
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void test1MolAlign() {
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std::string rdbase = getenv("RDBASE");
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std::string fname1 = rdbase + "/Code/GraphMol/MolAlign/test_data/1oir.mol";
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ROMol *m1 = MolFileToMol(fname1);
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std::string fname2 =
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rdbase + "/Code/GraphMol/MolAlign/test_data/1oir_conf.mol";
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ROMol *m2 = MolFileToMol(fname2);
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double rmsd = MolAlign::alignMol(*m2, *m1);
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TEST_ASSERT(RDKit::feq(rmsd, 0.6578) || RDKit::feq(rmsd, 1.0345));
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std::string fname3 =
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rdbase + "/Code/GraphMol/MolAlign/test_data/1oir_trans.mol";
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ROMol *m3 = MolFileToMol(fname3);
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const Conformer &conf1 = m2->getConformer(0);
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const Conformer &conf2 = m3->getConformer(0);
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unsigned int i, nat = m3->getNumAtoms();
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for (i = 0; i < nat; i++) {
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RDGeom::Point3D pt1 = conf1.getAtomPos(i);
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RDGeom::Point3D pt2 = conf2.getAtomPos(i);
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TEST_ASSERT(RDKit::feq(pt1.x, pt2.x, 0.001));
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TEST_ASSERT(RDKit::feq(pt1.y, pt2.y, 0.001));
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TEST_ASSERT(RDKit::feq(pt1.z, pt2.z, 0.001));
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}
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RDGeom::Transform3D trans;
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rmsd = MolAlign::getAlignmentTransform(*m1, *m2, trans);
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TEST_ASSERT(RDKit::feq(rmsd, 0.6578) || RDKit::feq(rmsd, 1.0345));
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// specify conformations
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rmsd = MolAlign::alignMol(*m1, *m2, 0, 0);
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TEST_ASSERT(RDKit::feq(rmsd, 0.6578) || RDKit::feq(rmsd, 1.0345));
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// provide an atom mapping
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delete m1;
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delete m2;
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delete m3;
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}
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void test1GetBestRMS() {
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std::string rdbase = getenv("RDBASE");
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std::string fname =
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rdbase + "/Code/GraphMol/MolAlign/test_data/probe_mol.sdf";
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SDMolSupplier supplier(fname, true, false);
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ROMol *m1 = supplier[1];
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ROMol *m2 = supplier[2];
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// alignMol() would return this for the rms: 2.50561
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// But the best rms is: 2.43449
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double rmsd = MolAlign::getBestRMS(*m1, *m2);
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TEST_ASSERT(RDKit::feq(rmsd, 2.43449));
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delete m1;
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delete m2;
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}
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void test1MolWithQueryAlign() {
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// identical to test1MolAlign except we replace one atom with a QueryAtom
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// instead
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std::string rdbase = getenv("RDBASE");
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std::string fname1 = rdbase + "/Code/GraphMol/MolAlign/test_data/1oir.mol";
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auto *m1 = MolFileToMol(fname1);
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auto *a1 = new QueryAtom(6);
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std::string fname2 =
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rdbase + "/Code/GraphMol/MolAlign/test_data/1oir_conf.mol";
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auto *m2 = MolFileToMol(fname2);
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auto *a2 = new QueryAtom(6);
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// we replace the same nitrogen instead with a null
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// query 28 and 19 are the "same" atoms
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m1->replaceAtom(28, a1);
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m2->replaceAtom(19, a2);
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double rmsd = MolAlign::alignMol(*m2, *m1);
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TEST_ASSERT(RDKit::feq(rmsd, 0.6578) || RDKit::feq(rmsd, 1.0345));
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std::string fname3 =
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rdbase + "/Code/GraphMol/MolAlign/test_data/1oir_trans.mol";
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auto *m3 = MolFileToMol(fname3);
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auto *a3 = new QueryAtom(5);
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m3->replaceAtom(0, a3);
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const Conformer &conf1 = m2->getConformer(0);
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const Conformer &conf2 = m3->getConformer(0);
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unsigned int i, nat = m3->getNumAtoms();
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for (i = 0; i < nat; i++) {
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RDGeom::Point3D pt1 = conf1.getAtomPos(i);
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RDGeom::Point3D pt2 = conf2.getAtomPos(i);
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TEST_ASSERT(RDKit::feq(pt1.x, pt2.x, 0.001));
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TEST_ASSERT(RDKit::feq(pt1.y, pt2.y, 0.001));
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TEST_ASSERT(RDKit::feq(pt1.z, pt2.z, 0.001));
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}
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RDGeom::Transform3D trans;
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rmsd = MolAlign::getAlignmentTransform(*m1, *m2, trans);
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TEST_ASSERT(RDKit::feq(rmsd, 0.6578) || RDKit::feq(rmsd, 1.0345));
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// specify conformations
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rmsd = MolAlign::alignMol(*m1, *m2, 0, 0);
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TEST_ASSERT(RDKit::feq(rmsd, 0.6578) || RDKit::feq(rmsd, 1.0345));
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// provide an atom mapping
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delete m1;
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delete m2;
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delete m3;
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delete a1;
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delete a2;
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delete a3;
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}
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void test2AtomMap() {
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std::string rdbase = getenv("RDBASE");
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std::string fname1 = rdbase + "/Code/GraphMol/MolAlign/test_data/1oir.mol";
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ROMol *m1 = MolFileToMol(fname1);
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std::string fname2 =
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rdbase + "/Code/GraphMol/MolAlign/test_data/1oir_conf.mol";
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ROMol *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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double rmsd = MolAlign::alignMol(*m2, *m1, 0, 0, &atomMap);
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TEST_ASSERT(RDKit::feq(rmsd, 0.8525));
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delete m1;
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delete m2;
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}
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void test3Weights() {
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std::string rdbase = getenv("RDBASE");
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std::string fname1 = rdbase + "/Code/GraphMol/MolAlign/test_data/1oir.mol";
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ROMol *m1 = MolFileToMol(fname1);
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std::string fname2 =
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rdbase + "/Code/GraphMol/MolAlign/test_data/1oir_conf.mol";
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ROMol *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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RDNumeric::DoubleVector wts(6);
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wts.setVal(0, 1.0);
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wts.setVal(1, 1.0);
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wts.setVal(2, 1.0);
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wts.setVal(3, 1.0);
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wts.setVal(4, 1.0);
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wts.setVal(5, 2.0);
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double rmsd = MolAlign::alignMol(*m2, *m1, 0, 0, &atomMap, &wts);
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TEST_ASSERT(RDKit::feq(rmsd, 0.9513));
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delete m1;
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delete m2;
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}
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void testIssue241() {
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std::string rdbase = getenv("RDBASE");
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std::string fname1 =
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rdbase + "/Code/GraphMol/MolAlign/test_data/Issue241.mol";
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ROMol *m1 = MolFileToMol(fname1);
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std::string res;
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MolPickler::pickleMol(*m1, res);
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auto *ref = new ROMol(res);
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DGeomHelpers::EmbedMolecule(*ref, 30, 239 * 10);
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ForceFields::ForceField *ff1 = UFF::constructForceField(*ref);
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ff1->initialize();
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ff1->minimize(200, 1e-8, 1e-6);
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std::string pkl2;
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MolPickler::pickleMol(*m1, pkl2);
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auto *probe = new ROMol(pkl2);
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DGeomHelpers::EmbedMolecule(*probe, 30, 239 * 10);
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ForceFields::ForceField *ff2 = UFF::constructForceField(*probe);
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ff2->initialize();
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ff2->minimize(200, 1e-8, 1e-6);
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double rmsd = MolAlign::alignMol(*ref, *probe);
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delete ff1;
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delete ff2;
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delete m1;
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delete ref;
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delete probe;
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TEST_ASSERT(RDKit::feq(rmsd, 0.0));
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}
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int main() {
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std::cout << "***********************************************************\n";
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std::cout << "Testing MolAlign\n";
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#if 1
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std::cout << "\t---------------------------------\n";
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std::cout << "\t test1MolAlign \n\n";
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test1MolAlign();
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std::cout << "\t---------------------------------\n";
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std::cout << "\t test1GetBestRMS \n\n";
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test1GetBestRMS();
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std::cout << "\t---------------------------------\n";
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std::cout << "\t test1MolWithQueryAlign \n\n";
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test1MolWithQueryAlign();
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std::cout << "\t---------------------------------\n";
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std::cout << "\t test2AtomMap \n\n";
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test2AtomMap();
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std::cout << "\t---------------------------------\n";
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std::cout << "\t test3Weights \n\n";
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test3Weights();
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std::cout << "\t---------------------------------\n";
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std::cout << "\t testIssue241 \n\n";
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testIssue241();
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#endif
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std::cout << "***********************************************************\n";
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}
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