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https://github.com/rdkit/rdkit.git
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865175104b
in the MolTransforms namespace:
* getBondLength(conf, iAtomId, jAtomId)
(only in this case, atoms need not be covalently bonded)
* setBondLength(conf, iAtomId, jAtomId, value)
* getAngleRad(conf, iAtomId, jAtomId, kAtomId)
* setAngleRad(conf, iAtomId, jAtomId, kAtomId, value)
* getAngleDeg(conf, iAtomId, jAtomId, kAtomId)
* setAngleDeg(conf, iAtomId, jAtomId, kAtomId, value)
* getDihedralRad(conf, iAtomId, jAtomId, kAtomId, lAtomId)
* setDihedralRad(conf, iAtomId, jAtomId, kAtomId, lAtomId, value)
* getDihedralDeg(conf, iAtomId, jAtomId, kAtomId, lAtomId)
* setDihedralDeg(conf, iAtomId, jAtomId, kAtomId, lAtomId, value)
- added the corresponding Python wrappers in rdMolTransforms
(same prototype as C++; as usual all Python methods
have an uppercase initial)
- added relevant C++/Python tests
205 lines
7.4 KiB
C++
205 lines
7.4 KiB
C++
// $Id$
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//
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// Copyright (C) 2003-2006 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/Invariant.h>
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#include <RDGeneral/utils.h>
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#include <Geometry/Transform3D.h>
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#include <iostream>
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#include <GraphMol/RDKitBase.h>
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#include <GraphMol/SmilesParse/SmilesParse.h>
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#include <GraphMol/FileParsers/FileParsers.h>
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#include <Geometry/point.h>
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#include "MolTransforms.h"
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using namespace RDKit;
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using namespace MolTransforms;
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bool comparePts(const RDGeom::Point3D &pt1, const RDGeom::Point3D &pt2, double tol=1.0e-4) {
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RDGeom::Point3D tpt = pt1;
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tpt -= pt2;
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return (tpt.length() < tol);
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}
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void test1Canonicalization() {
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ROMol *mol = SmilesToMol("C", 0, 1);
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Conformer *conf = new Conformer(1);
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conf->setAtomPos(0, RDGeom::Point3D(4.0, 5.0, 6.0));
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int cid = mol->addConformer(conf, true);
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RDGeom::Point3D pt = computeCentroid(*conf);
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CHECK_INVARIANT(comparePts(pt, RDGeom::Point3D(4.0, 5.0, 6.0)), "");
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RDGeom::Transform3D *trans = computeCanonicalTransform(*conf);
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transformConformer(*conf, *trans);
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CHECK_INVARIANT(comparePts(conf->getAtomPos(0), RDGeom::Point3D(0.0, 0.0, 0.0)), "");
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conf->setAtomPos(0, RDGeom::Point3D(4.0, 5.0, 6.0));
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canonicalizeConformer(*conf);
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CHECK_INVARIANT(comparePts(conf->getAtomPos(0), RDGeom::Point3D(0.0, 0.0, 0.0)), "");
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delete mol;
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//delete conf;
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delete trans;
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// lets try two points now
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mol = SmilesToMol("CC", 0, 1);
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conf = new Conformer(2);
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conf->setAtomPos(0, RDGeom::Point3D(0.0, 0.0, 0.0));
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conf->setAtomPos(1, RDGeom::Point3D(1.5, 0.0, 0.0));
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cid = mol->addConformer(conf, true);
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trans = computeCanonicalTransform(*conf);
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canonicalizeConformer(*conf);
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CHECK_INVARIANT(comparePts(conf->getAtomPos(0), RDGeom::Point3D(-0.75, 0.0, 0.0)), "");
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CHECK_INVARIANT(comparePts(conf->getAtomPos(1), RDGeom::Point3D(0.75, 0.0, 0.0)), "");
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conf->setAtomPos(0, RDGeom::Point3D(0.0, 0.0, 0.0));
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conf->setAtomPos(1, RDGeom::Point3D(0.0, 1.5, 0.0));
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trans = computeCanonicalTransform(*conf);
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canonicalizeConformer(*conf);
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CHECK_INVARIANT(comparePts(conf->getAtomPos(0), RDGeom::Point3D(-0.75, 0.0, 0.0)), "");
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CHECK_INVARIANT(comparePts(conf->getAtomPos(1), RDGeom::Point3D(0.75, 0.0, 0.0)), "");
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delete mol;
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delete trans;
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mol = SmilesToMol("CC", 0, 1);
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conf = new Conformer(2);
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conf->setAtomPos(0, RDGeom::Point3D(0.0, 0.0, 0.0));
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conf->setAtomPos(1, RDGeom::Point3D(1.5, 0.0, 0.0));
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cid = mol->addConformer(conf, true);
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trans = computeCanonicalTransform(*conf);
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transformConformer(*conf, *trans);
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canonicalizeConformer(*conf);
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CHECK_INVARIANT(comparePts(conf->getAtomPos(0), RDGeom::Point3D(-0.75, 0.0, 0.0)), "");
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CHECK_INVARIANT(comparePts(conf->getAtomPos(1), RDGeom::Point3D(0.75, 0.0, 0.0)), "");
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delete mol;
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delete trans;
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mol = SmilesToMol("C1CC1", 0, 1);
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conf = new Conformer(3);
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conf->setAtomPos(0, RDGeom::Point3D(0.58, -0.66, -0.08));
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conf->setAtomPos(1, RDGeom::Point3D(-0.88, -0.18, -0.04));
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conf->setAtomPos(2, RDGeom::Point3D(.26, 0.82, 0.14));
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cid = mol->addConformer(conf, true);
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//trans = computeCanonicalTransform(*conf);
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//transformConformer(*conf, *trans);
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canonicalizeConformer(*conf);
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CHECK_INVARIANT(comparePts(conf->getAtomPos(0), RDGeom::Point3D(-0.6418, 0.6158, 0.0)), "");
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CHECK_INVARIANT(comparePts(conf->getAtomPos(1), RDGeom::Point3D(-0.2029, -0.8602, 0.0)), "");
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CHECK_INVARIANT(comparePts(conf->getAtomPos(2), RDGeom::Point3D(0.8447, 0.2445, 0.0)), "");
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MolToMolFile(*mol, "junk.mol", 0);
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//CHECK_INVARIANT(comparePts(conf->getAtomPos(0), RDGeom::Point3D(-0.75, 0.0, 0.0)), "");
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//CHECK_INVARIANT(comparePts(conf->getAtomPos(1), RDGeom::Point3D(0.75, 0.0, 0.0)), "");
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delete mol;
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std::string rdbase = getenv("RDBASE");
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std::string fname1 = rdbase + "/Code/GraphMol/MolTransforms/test_data/1oir.mol";
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mol = MolFileToMol(fname1);
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std::string fname2 = rdbase + "/Code/GraphMol/MolTransforms/test_data/1oir_canon.mol";
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ROMol *mol2 = MolFileToMol(fname2);
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Conformer &conf1 = mol->getConformer(0);
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canonicalizeConformer(conf1);
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Conformer &conf2 = mol2->getConformer();
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unsigned int i, nats = mol->getNumAtoms();
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for (i = 0; i < nats; ++i) {
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CHECK_INVARIANT(comparePts(conf1.getAtomPos(i), conf2.getAtomPos(i)), "");
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}
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delete mol;
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delete mol2;
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}
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void test1(){
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std::cout << " ----------> Test1 "<< std::endl;
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std::cout << " Finished <---------- "<< std::endl;
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}
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void testGetSetBondLength() {
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std::string rdbase = getenv("RDBASE");
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std::string fName = rdbase + "/Code/GraphMol/MolTransforms/test_data/3-cyclohexylpyridine.mol";
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RWMol *m = MolFileToMol(fName, true, false);
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TEST_ASSERT(m);
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Conformer &conf = m->getConformer();
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double dist = getBondLength(conf, 0, 19);
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TEST_ASSERT(RDKit::feq(dist, 1.36));
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setBondLength(conf, 0, 19, 2.5);
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dist = getBondLength(conf, 0, 19);
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TEST_ASSERT(RDKit::feq(dist, 2.5));
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setBondLength(conf, 19, 0, 3.0);
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dist = getBondLength(conf, 0, 19);
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TEST_ASSERT(RDKit::feq(dist, 3.0));
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}
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void testGetSetAngle() {
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std::string rdbase = getenv("RDBASE");
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std::string fName = rdbase + "/Code/GraphMol/MolTransforms/test_data/3-cyclohexylpyridine.mol";
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RWMol *m = MolFileToMol(fName, true, false);
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TEST_ASSERT(m);
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Conformer &conf = m->getConformer();
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double angle = getAngleDeg(conf, 0, 19, 21);
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TEST_ASSERT(RDKit::feq(RDKit::round(angle * 10) / 10, 109.7));
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setAngleDeg(conf, 0, 19, 21, 125.0);
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angle = getAngleDeg(conf, 0, 19, 21);
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TEST_ASSERT(RDKit::feq(angle, 125.0));
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setAngleRad(conf, 21, 19, 0, M_PI / 2.);
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angle = getAngleRad(conf, 0, 19, 21);
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TEST_ASSERT(RDKit::feq(angle, M_PI / 2.));
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angle = getAngleDeg(conf, 0, 19, 21);
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TEST_ASSERT(RDKit::feq(angle, 90.0));
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}
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void testGetSetDihedral() {
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std::string rdbase = getenv("RDBASE");
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std::string fName = rdbase + "/Code/GraphMol/MolTransforms/test_data/3-cyclohexylpyridine.mol";
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RWMol *m = MolFileToMol(fName, true, false);
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TEST_ASSERT(m);
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Conformer &conf = m->getConformer();
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double dihedral = getDihedralDeg(conf, 0, 19, 21, 24);
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TEST_ASSERT(RDKit::feq(RDKit::round(dihedral * 100) / 100, 176.05));
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setDihedralDeg(conf, 8, 0, 19, 21, 65.0);
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dihedral = getDihedralDeg(conf, 8, 0, 19, 21);
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TEST_ASSERT(RDKit::feq(dihedral, 65.0));
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setDihedralDeg(conf, 8, 0, 19, 21, -130.0);
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dihedral = getDihedralDeg(conf, 8, 0, 19, 21);
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TEST_ASSERT(RDKit::feq(dihedral, -130.0));
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setDihedralRad(conf, 21, 19, 0, 8, -2. / 3. * M_PI);
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dihedral = getDihedralRad(conf, 8, 0, 19, 21);
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TEST_ASSERT(RDKit::feq(dihedral, -2. / 3. * M_PI));
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dihedral = getDihedralDeg(conf, 8, 0, 19, 21);
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TEST_ASSERT(RDKit::feq(dihedral, -120.0));
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}
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int main() {
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//test1();
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std::cout << "***********************************************************\n";
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std::cout << "Testing MolTransforms\n";
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std::cout << "\t---------------------------------\n";
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std::cout << "\t test1Canonicalization \n\n";
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test1Canonicalization();
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std::cout << "\t---------------------------------\n";
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std::cout << "\t testGetSetBondLength \n\n";
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testGetSetBondLength();
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std::cout << "\t---------------------------------\n";
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std::cout << "\t testGetSetAngle \n\n";
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testGetSetAngle();
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std::cout << "\t---------------------------------\n";
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std::cout << "\t testGetSetDihedral \n\n";
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testGetSetDihedral();
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std::cout << "***********************************************************\n";
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return(0);
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}
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