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// $Id$
//
// Copyright (C) 2015 Sereina Riniker
//
// @@ 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 <RDGeneral/utils.h>
#include <Geometry/point.h>
#include <GraphMol/RDKitBase.h>
#include <GraphMol/SmilesParse/SmilesParse.h>
#include <ForceField/MMFF/Params.h>
#include <ForceField/MMFF/TorsionAngle.h>
#include <GraphMol/ForceFieldHelpers/CrystalFF/TorsionAngleM6.h>
#include <GraphMol/ForceFieldHelpers/CrystalFF/TorsionPreferences.h>
#include <GraphMol/MolOps.h>
#include <GraphMol/MolTransforms/MolTransforms.h>
#include <ForceField/ForceField.h>
#include <iostream>
#include <string>
#include <math.h>
using namespace RDGeom;
using namespace RDKit;
void testTorsionAngleM6() {
std::cerr << "-------------------------------------" << std::endl;
std::cerr << " Test CrystalFF torsional term." << std::endl;
ForceFields::ForceField ff;
Point3D p1, p2, p3, p4;
RDGeom::PointPtrVect &ps = ff.positions();
ps.push_back(&p1);
ps.push_back(&p2);
ps.push_back(&p3);
ps.push_back(&p4);
ForceFields::CrystalFF::TorsionAngleContribM6 *contrib;
// ------- ------- ------- ------- ------- ------- -------
// Basic SP3 - SP3
// ------- ------- ------- ------- ------- ------- -------
// [!#1:1][CX4H2:2]!@[CX4H2:3][!#1:4] 1 0.0 1 0.0 1 4.0 1 0.0 1 0.0 1 0.0
std::vector<int> signs(6, 1);
std::vector<double> v(6, 0.0);
v[2] = 4.0;
contrib = new ForceFields::CrystalFF::TorsionAngleContribM6(&ff, 0, 1, 2, 3,
v, signs);
ff.contribs().push_back(ForceFields::ContribPtr(contrib));
p1.x = 0;
p1.y = 1.5;
p1.z = 0;
p2.x = 0.0;
p2.y = 0.0;
p2.z = 0.0;
p3.x = 1.5;
p3.y = 0.0;
p3.z = 0.0;
p4.x = 1.5;
p4.y = 0.0;
p4.z = 1.5;
ff.initialize();
ff.minimize(10, 1e-8, 1e-8);
double cosPhi = ForceFields::MMFF::Utils::calcTorsionCosPhi(
*(RDGeom::Point3D *)ff.positions()[0],
*(RDGeom::Point3D *)ff.positions()[1],
*(RDGeom::Point3D *)ff.positions()[2],
*(RDGeom::Point3D *)ff.positions()[3]);
TEST_ASSERT(RDKit::feq(cosPhi, 0.5, 1e-4));
// ------- ------- ------- ------- ------- ------- -------
// Basic SP2 - SP2
// ------- ------- ------- ------- ------- ------- -------
signs[1] = -1;
v[2] = 0.0;
v[1] = 7.0;
ff.contribs().pop_back();
contrib = new ForceFields::CrystalFF::TorsionAngleContribM6(&ff, 0, 1, 2, 3,
v, signs);
ff.contribs().push_back(ForceFields::ContribPtr(contrib));
p1.x = 0;
p1.y = 1.5;
p1.z = 0.1;
p2.x = 0.0;
p2.y = 0.0;
p2.z = 0.0;
p3.x = 1.5;
p3.y = 0.0;
p3.z = 0.0;
p4.x = 1.5;
p4.y = 0.2;
p4.z = 1.5;
ff.initialize();
ff.minimize(10, 1e-8, 1e-8);
cosPhi = ForceFields::MMFF::Utils::calcTorsionCosPhi(
*(RDGeom::Point3D *)ff.positions()[0],
*(RDGeom::Point3D *)ff.positions()[1],
*(RDGeom::Point3D *)ff.positions()[2],
*(RDGeom::Point3D *)ff.positions()[3]);
TEST_ASSERT(RDKit::feq(cosPhi, 1.0, 1e-4));
}
void testTorsionPrefs() {
ROMol *mol;
mol = SmilesToMol("CCCC");
TEST_ASSERT(mol);
std::vector<std::vector<int> > expTorsionAtoms;
std::vector<std::pair<std::vector<int>, std::vector<double> > >
expTorsionAngles;
std::vector<std::vector<int> > improperAtoms;
ForceFields::CrystalFF::getExperimentalTorsions(
*mol, expTorsionAtoms, expTorsionAngles, improperAtoms, true, false,
1, false);
TEST_ASSERT(expTorsionAtoms.size() == 1);
TEST_ASSERT(expTorsionAngles.size() == 1);
TEST_ASSERT(expTorsionAtoms[0][0] == 0);
TEST_ASSERT(expTorsionAtoms[0][3] == 3);
TEST_ASSERT(expTorsionAngles[0].first.size() == 6);
TEST_ASSERT(expTorsionAngles[0].second.size() == 6);
delete mol;
mol = SmilesToMol("CCCCC");
TEST_ASSERT(mol);
ForceFields::CrystalFF::getExperimentalTorsions(
*mol, expTorsionAtoms, expTorsionAngles, improperAtoms, true, false,
1, false);
TEST_ASSERT(expTorsionAtoms.size() == 2);
TEST_ASSERT(expTorsionAngles.size() == 2);
}
int main() {
testTorsionAngleM6();
testTorsionPrefs();
return 0;
}
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