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// $Id$
//
// Copyright (C) 2003-2006 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/Invariant.h>
#include <RDGeneral/utils.h>
#include <Geometry/Transform3D.h>
#include <iostream>
#include <GraphMol/RDKitBase.h>
#include <GraphMol/SmilesParse/SmilesParse.h>
#include <GraphMol/FileParsers/FileParsers.h>
#include <Geometry/point.h>
#include "MolTransforms.h"
using namespace RDKit;
using namespace MolTransforms;
bool comparePts(const RDGeom::Point3D &pt1, const RDGeom::Point3D &pt2,
double tol = 1.0e-4) {
RDGeom::Point3D tpt = pt1;
tpt -= pt2;
return (tpt.length() < tol);
}
void test1Canonicalization() {
ROMol *mol = SmilesToMol("C", 0, 1);
Conformer *conf = new Conformer(1);
conf->setAtomPos(0, RDGeom::Point3D(4.0, 5.0, 6.0));
int cid = mol->addConformer(conf, true);
CHECK_INVARIANT(cid >= 0, "")
RDGeom::Point3D pt = computeCentroid(*conf);
CHECK_INVARIANT(comparePts(pt, RDGeom::Point3D(4.0, 5.0, 6.0)), "");
RDGeom::Transform3D *trans = computeCanonicalTransform(*conf);
transformConformer(*conf, *trans);
CHECK_INVARIANT(
comparePts(conf->getAtomPos(0), RDGeom::Point3D(0.0, 0.0, 0.0)), "");
conf->setAtomPos(0, RDGeom::Point3D(4.0, 5.0, 6.0));
canonicalizeConformer(*conf);
CHECK_INVARIANT(
comparePts(conf->getAtomPos(0), RDGeom::Point3D(0.0, 0.0, 0.0)), "");
delete mol;
// delete conf;
delete trans;
// lets try two points now
mol = SmilesToMol("CC", 0, 1);
conf = new Conformer(2);
conf->setAtomPos(0, RDGeom::Point3D(0.0, 0.0, 0.0));
conf->setAtomPos(1, RDGeom::Point3D(1.5, 0.0, 0.0));
cid = mol->addConformer(conf, true);
trans = computeCanonicalTransform(*conf);
canonicalizeConformer(*conf);
CHECK_INVARIANT(
comparePts(conf->getAtomPos(0), RDGeom::Point3D(-0.75, 0.0, 0.0)), "");
CHECK_INVARIANT(
comparePts(conf->getAtomPos(1), RDGeom::Point3D(0.75, 0.0, 0.0)), "");
conf->setAtomPos(0, RDGeom::Point3D(0.0, 0.0, 0.0));
conf->setAtomPos(1, RDGeom::Point3D(0.0, 1.5, 0.0));
trans = computeCanonicalTransform(*conf);
canonicalizeConformer(*conf);
CHECK_INVARIANT(
comparePts(conf->getAtomPos(0), RDGeom::Point3D(-0.75, 0.0, 0.0)), "");
CHECK_INVARIANT(
comparePts(conf->getAtomPos(1), RDGeom::Point3D(0.75, 0.0, 0.0)), "");
delete mol;
delete trans;
mol = SmilesToMol("CC", 0, 1);
conf = new Conformer(2);
conf->setAtomPos(0, RDGeom::Point3D(0.0, 0.0, 0.0));
conf->setAtomPos(1, RDGeom::Point3D(1.5, 0.0, 0.0));
cid = mol->addConformer(conf, true);
trans = computeCanonicalTransform(*conf);
transformConformer(*conf, *trans);
canonicalizeConformer(*conf);
CHECK_INVARIANT(
comparePts(conf->getAtomPos(0), RDGeom::Point3D(-0.75, 0.0, 0.0)), "");
CHECK_INVARIANT(
comparePts(conf->getAtomPos(1), RDGeom::Point3D(0.75, 0.0, 0.0)), "");
delete mol;
delete trans;
mol = SmilesToMol("C1CC1", 0, 1);
conf = new Conformer(3);
conf->setAtomPos(0, RDGeom::Point3D(0.58, -0.66, -0.08));
conf->setAtomPos(1, RDGeom::Point3D(-0.88, -0.18, -0.04));
conf->setAtomPos(2, RDGeom::Point3D(.26, 0.82, 0.14));
cid = mol->addConformer(conf, true);
// trans = computeCanonicalTransform(*conf);
// transformConformer(*conf, *trans);
canonicalizeConformer(*conf);
CHECK_INVARIANT(
comparePts(conf->getAtomPos(0), RDGeom::Point3D(-0.6418, 0.6158, 0.0)),
"");
CHECK_INVARIANT(
comparePts(conf->getAtomPos(1), RDGeom::Point3D(-0.2029, -0.8602, 0.0)),
"");
CHECK_INVARIANT(
comparePts(conf->getAtomPos(2), RDGeom::Point3D(0.8447, 0.2445, 0.0)),
"");
MolToMolFile(*mol, "junk.mol", 0);
// CHECK_INVARIANT(comparePts(conf->getAtomPos(0), RDGeom::Point3D(-0.75, 0.0,
// 0.0)), "");
// CHECK_INVARIANT(comparePts(conf->getAtomPos(1), RDGeom::Point3D(0.75, 0.0,
// 0.0)), "");
delete mol;
std::string rdbase = getenv("RDBASE");
std::string fname1 =
rdbase + "/Code/GraphMol/MolTransforms/test_data/1oir.mol";
mol = MolFileToMol(fname1);
std::string fname2 =
rdbase + "/Code/GraphMol/MolTransforms/test_data/1oir_canon.mol";
ROMol *mol2 = MolFileToMol(fname2);
Conformer &conf1 = mol->getConformer(0);
canonicalizeConformer(conf1);
Conformer &conf2 = mol2->getConformer();
unsigned int i, nats = mol->getNumAtoms();
for (i = 0; i < nats; ++i) {
CHECK_INVARIANT(comparePts(conf1.getAtomPos(i), conf2.getAtomPos(i)), "");
}
delete mol;
delete mol2;
}
void test1() {
std::cout << " ----------> Test1 " << std::endl;
std::cout << " Finished <---------- " << std::endl;
}
void testGetSetBondLength() {
std::string rdbase = getenv("RDBASE");
std::string fName =
rdbase +
"/Code/GraphMol/MolTransforms/test_data/3-cyclohexylpyridine.mol";
RWMol *m = MolFileToMol(fName, true, false);
TEST_ASSERT(m);
Conformer &conf = m->getConformer();
double dist = getBondLength(conf, 0, 19);
TEST_ASSERT(RDKit::feq(dist, 1.36));
setBondLength(conf, 0, 19, 2.5);
dist = getBondLength(conf, 0, 19);
TEST_ASSERT(RDKit::feq(dist, 2.5));
setBondLength(conf, 19, 0, 3.0);
dist = getBondLength(conf, 0, 19);
TEST_ASSERT(RDKit::feq(dist, 3.0));
}
void testGetSetAngle() {
std::string rdbase = getenv("RDBASE");
std::string fName =
rdbase +
"/Code/GraphMol/MolTransforms/test_data/3-cyclohexylpyridine.mol";
RWMol *m = MolFileToMol(fName, true, false);
TEST_ASSERT(m);
Conformer &conf = m->getConformer();
double angle = getAngleDeg(conf, 0, 19, 21);
TEST_ASSERT(RDKit::feq(RDKit::round(angle * 10) / 10, 109.7));
setAngleDeg(conf, 0, 19, 21, 125.0);
angle = getAngleDeg(conf, 0, 19, 21);
TEST_ASSERT(RDKit::feq(angle, 125.0));
setAngleRad(conf, 21, 19, 0, M_PI / 2.);
angle = getAngleRad(conf, 0, 19, 21);
TEST_ASSERT(RDKit::feq(angle, M_PI / 2.));
angle = getAngleDeg(conf, 0, 19, 21);
TEST_ASSERT(RDKit::feq(angle, 90.0));
}
void testGetSetDihedral() {
std::string rdbase = getenv("RDBASE");
std::string fName =
rdbase +
"/Code/GraphMol/MolTransforms/test_data/3-cyclohexylpyridine.mol";
RWMol *m = MolFileToMol(fName, true, false);
TEST_ASSERT(m);
Conformer &conf = m->getConformer();
double dihedral = getDihedralDeg(conf, 0, 19, 21, 24);
TEST_ASSERT(RDKit::feq(RDKit::round(dihedral * 100) / 100, 176.05));
setDihedralDeg(conf, 8, 0, 19, 21, 65.0);
dihedral = getDihedralDeg(conf, 8, 0, 19, 21);
TEST_ASSERT(RDKit::feq(dihedral, 65.0));
setDihedralDeg(conf, 8, 0, 19, 21, -130.0);
dihedral = getDihedralDeg(conf, 8, 0, 19, 21);
TEST_ASSERT(RDKit::feq(dihedral, -130.0));
setDihedralRad(conf, 21, 19, 0, 8, -2. / 3. * M_PI);
dihedral = getDihedralRad(conf, 8, 0, 19, 21);
TEST_ASSERT(RDKit::feq(dihedral, -2. / 3. * M_PI));
dihedral = getDihedralDeg(conf, 8, 0, 19, 21);
TEST_ASSERT(RDKit::feq(dihedral, -120.0));
}
int main() {
// test1();
std::cout << "***********************************************************\n";
std::cout << "Testing MolTransforms\n";
std::cout << "\t---------------------------------\n";
std::cout << "\t test1Canonicalization \n\n";
test1Canonicalization();
std::cout << "\t---------------------------------\n";
std::cout << "\t testGetSetBondLength \n\n";
testGetSetBondLength();
std::cout << "\t---------------------------------\n";
std::cout << "\t testGetSetAngle \n\n";
testGetSetAngle();
std::cout << "\t---------------------------------\n";
std::cout << "\t testGetSetDihedral \n\n";
testGetSetDihedral();
std::cout << "***********************************************************\n";
return (0);
}
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