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rdkit/Code/ForceField/UFF/testUFFForceField.cpp
Paolo Tosco 4d6f099431 Fixes a bug in TorsionConstraint (#2732) 
* - fixed UFF/MMFF torsion constraints when the dihedral is set to 0.0
- removed some code duplication
- added relevant test and fixed existing ones

* - fix Windows exports

* - added PRECONDITION for RDGeom::Point3D pointers
- removed inline keywords
2019-10-24 16:03:58 +02:00

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// $Id$
//
// Copyright (C) 2004-2008 Greg Landrum and 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 <iostream>
#include <iomanip>
#include <math.h>
#include <RDGeneral/Invariant.h>
#include <RDGeneral/utils.h>
#include <Geometry/point.h>
#include <ForceField/ForceField.h>
#include <ForceField/UFF/Params.h>
#include <ForceField/UFF/BondStretch.h>
#include <ForceField/UFF/AngleBend.h>
#include <ForceField/UFF/Nonbonded.h>
#include <ForceField/UFF/TorsionAngle.h>
#include <ForceField/UFF/DistanceConstraint.h>
#include <ForceField/UFF/AngleConstraint.h>
#include <ForceField/UFF/TorsionConstraint.h>
#include <ForceField/UFF/PositionConstraint.h>
#include <GraphMol/Atom.h>
#include <GraphMol/FileParsers/FileParsers.h>
#include <GraphMol/ForceFieldHelpers/UFF/Builder.h>
#include <GraphMol/MolTransforms/MolTransforms.h>
using namespace RDGeom;
void test1() {
std::cerr << "-------------------------------------" << std::endl;
std::cerr << "Unit tests for force field basics." << std::endl;
ForceFields::ForceField ff;
TEST_ASSERT(ff.dimension() == 3);
Point3D p1(0, 0, 0), p2(1, 0, 0), p3(2, 0, 0), p4(0, 1, 0);
RDGeom::PointPtrVect &ps = ff.positions();
ps.push_back(&p1);
ps.push_back(&p2);
ps.push_back(&p3);
ps.push_back(&p4);
#if 0
Point3D f1,f2,f3,f4;
RDGeom::PointPtrVect &fs=ff.forces();
fs.push_back(&f1);
fs.push_back(&f2);
fs.push_back(&f3);
fs.push_back(&f4);
#endif
TEST_ASSERT(ff.positions().size() == 4);
// TEST_ASSERT(ff.forces().size()==4);
ff.initialize();
TEST_ASSERT(RDKit::feq(ff.distance(0, 1), 1.0));
TEST_ASSERT(RDKit::feq(ff.distance(1, 0), 1.0));
TEST_ASSERT(RDKit::feq(ff.distance(0, 0), 0.0));
TEST_ASSERT(RDKit::feq(ff.distance(0, 2), 2.0));
TEST_ASSERT(RDKit::feq(ff.distance(2, 0), 2.0));
TEST_ASSERT(RDKit::feq(ff.distance(0, 3), 1.0));
TEST_ASSERT(RDKit::feq(ff.distance(3, 0), 1.0));
TEST_ASSERT(RDKit::feq(ff.distance(3, 3), 0.0));
TEST_ASSERT(RDKit::feq(ff.distance(1, 2), 1.0));
TEST_ASSERT(RDKit::feq(ff.distance(2, 1), 1.0));
std::cerr << " done" << std::endl;
}
void testUFF1() {
std::cerr << "-------------------------------------" << std::endl;
std::cerr << "Unit tests for basics of UFF bond-stretch terms." << std::endl;
ForceFields::UFF::AtomicParams p1, p2;
double restLen, forceConstant;
// sp3 carbon:
p1.r1 = .757;
p1.Z1 = 1.912;
p1.GMP_Xi = 5.343;
// sp3 - sp3: checks basics
restLen = ForceFields::UFF::Utils::calcBondRestLength(1.0, &p1, &p1);
TEST_ASSERT(RDKit::feq(restLen, 1.514));
forceConstant =
ForceFields::UFF::Utils::calcBondForceConstant(restLen, &p1, &p1);
TEST_ASSERT(RDKit::feq(forceConstant, 699.5918));
// sp2 carbon:
p2.r1 = .732;
p2.Z1 = 1.912;
p2.GMP_Xi = 5.343;
// sp2 - sp2: checks rBO
restLen = ForceFields::UFF::Utils::calcBondRestLength(2.0, &p2, &p2);
TEST_ASSERT(RDKit::feq(restLen, 1.32883, 1e-5));
forceConstant =
ForceFields::UFF::Utils::calcBondForceConstant(restLen, &p2, &p2);
TEST_ASSERT(RDKit::feq(forceConstant, 1034.69, 1e-2));
// sp3 nitrogen:
p2.r1 = .700;
p2.Z1 = 2.544;
p2.GMP_Xi = 6.899;
// Csp3 - Nsp3: checks rEN
restLen = ForceFields::UFF::Utils::calcBondRestLength(1.0, &p1, &p2);
TEST_ASSERT(RDKit::feq(restLen, 1.451071, 1e-5));
forceConstant =
ForceFields::UFF::Utils::calcBondForceConstant(restLen, &p1, &p2);
TEST_ASSERT(RDKit::feq(forceConstant, 1057.27, 1e-2));
// amide bond: check we can reproduce values from the UFF paper:
// C_R:
p1.r1 = .729;
p1.Z1 = 1.912;
p1.GMP_Xi = 5.343;
// N_R:
p2.r1 = .699;
p2.Z1 = 2.544;
p2.GMP_Xi = 6.899;
restLen = ForceFields::UFF::Utils::calcBondRestLength(
ForceFields::UFF::Params::amideBondOrder, &p1, &p2);
TEST_ASSERT(RDKit::feq(restLen, 1.357, 1e-3)); // NOTE: the paper has 1.366
forceConstant =
ForceFields::UFF::Utils::calcBondForceConstant(restLen, &p1, &p2);
TEST_ASSERT(RDKit::feq(forceConstant, 1293., 1)); // NOTE: the paper has 1293
std::cerr << " done" << std::endl;
}
void testUFF2() {
std::cerr << "-------------------------------------" << std::endl;
std::cerr << "Unit tests for UFF bond-stretch terms." << std::endl;
ForceFields::ForceField ff;
Point3D p1(0, 0, 0), p2(1.514, 0, 0);
RDGeom::PointPtrVect &ps = ff.positions();
ps.push_back(&p1);
ps.push_back(&p2);
ForceFields::UFF::AtomicParams param1;
// sp3 carbon:
param1.r1 = .757;
param1.Z1 = 1.912;
param1.GMP_Xi = 5.343;
// C_3 - C_3, r0=1.514, k01=699.5918
ForceFields::ForceFieldContrib *bs;
bs = new ForceFields::UFF::BondStretchContrib(&ff, 0, 1, 1, &param1, &param1);
ff.contribs().push_back(ForceFields::ContribPtr(bs));
ff.initialize();
double *p, *g;
p = new double[6];
g = new double[6];
for (int i = 0; i < 6; i++) {
p[i] = 0.0;
g[i] = 0.0;
}
double E;
// edge case: zero bond length:
E = bs->getEnergy(p);
TEST_ASSERT(E > 0.0);
bs->getGrad(p, g);
for (int i = 0; i < 6; i++) {
TEST_ASSERT(fabs(g[i]) > 0.0);
}
p[0] = 0;
p[3] = 1.514;
for (int i = 0; i < 6; i++) {
g[i] = 0.0;
}
ff.initialize();
E = bs->getEnergy(p);
TEST_ASSERT(RDKit::feq(E, 0.0));
bs->getGrad(p, g);
for (int i = 0; i < 6; i++) {
TEST_ASSERT(RDKit::feq(g[i], 0.0));
}
(*ff.positions()[1])[0] = 1.814;
p[3] = 1.814;
ff.initialize();
E = bs->getEnergy(p);
TEST_ASSERT(RDKit::feq(E, 31.4816));
bs->getGrad(p, g);
TEST_ASSERT(RDKit::feq(g[0], -209.8775));
TEST_ASSERT(RDKit::feq(g[3], 209.8775));
TEST_ASSERT(RDKit::feq(g[1], 0.0));
TEST_ASSERT(RDKit::feq(g[2], 0.0));
TEST_ASSERT(RDKit::feq(g[4], 0.0));
TEST_ASSERT(RDKit::feq(g[5], 0.0));
// try a different axis:
for (int i = 0; i < 6; i++) {
g[i] = 0.0;
p[i] = 0.0;
}
ff.initialize();
(*ff.positions()[1])[0] = 0.0;
(*ff.positions()[1])[2] = 1.814;
p[5] = 1.814;
E = bs->getEnergy(p);
TEST_ASSERT(RDKit::feq(E, 31.4816));
bs->getGrad(p, g);
TEST_ASSERT(RDKit::feq(g[2], -209.8775));
TEST_ASSERT(RDKit::feq(g[5], 209.8775));
TEST_ASSERT(RDKit::feq(g[0], 0.0));
TEST_ASSERT(RDKit::feq(g[1], 0.0));
TEST_ASSERT(RDKit::feq(g[3], 0.0));
TEST_ASSERT(RDKit::feq(g[4], 0.0));
// try a bit of minimization
RDGeom::Point3D d;
ff.initialize();
(*ff.positions()[1])[2] = 0.0;
(*ff.positions()[1])[0] = 1.814;
ff.minimize(10, 1e-8);
d = *(RDGeom::Point3D *)ff.positions()[0] -
*(RDGeom::Point3D *)ff.positions()[1];
TEST_ASSERT(RDKit::feq(d.length(), 1.514, 1e-3));
// minimize in "3D"
ff.initialize();
(*ff.positions()[1])[2] = 1.1;
(*ff.positions()[1])[1] = 0.9;
(*ff.positions()[1])[0] = 1.00;
ff.minimize(10, 1e-8);
d = *(RDGeom::Point3D *)ff.positions()[0] -
*(RDGeom::Point3D *)ff.positions()[1];
TEST_ASSERT(RDKit::feq(d.length(), 1.514, 1e-3));
delete[] p;
delete[] g;
std::cerr << " done" << std::endl;
}
void testUFF3() {
std::cerr << "-------------------------------------" << std::endl;
std::cerr << "Unit tests for basics of UFF angle terms." << std::endl;
ForceFields::UFF::AtomicParams p1, p2, p3;
double restLen, forceConstant;
// sp3 carbon:
p3.r1 = .757;
p3.Z1 = 1.912;
p3.GMP_Xi = 5.343;
p3.theta0 = 109.47 * M_PI / 180.0;
// sp3 - sp3: checks basics
restLen = ForceFields::UFF::Utils::calcBondRestLength(1.0, &p3, &p3);
TEST_ASSERT(RDKit::feq(restLen, 1.514));
// C_3 - C_3 - C_3
forceConstant = ForceFields::UFF::Utils::calcAngleForceConstant(
p3.theta0, 1, 1, &p3, &p3, &p3);
// TEST_ASSERT(RDKit::feq(forceConstant,699.5918));
// amide bond bend:
// C_R - N_R - C_3
// C_R:
p1.r1 = .729;
p1.Z1 = 1.912;
p1.GMP_Xi = 5.343;
// N_R:
p2.r1 = .699;
p2.Z1 = 2.544;
p2.GMP_Xi = 6.899;
p2.theta0 = 120.0 * M_PI / 180.;
restLen = ForceFields::UFF::Utils::calcBondRestLength(
ForceFields::UFF::Params::amideBondOrder, &p1, &p2);
TEST_ASSERT(RDKit::feq(restLen, 1.357, 1e-3));
restLen = ForceFields::UFF::Utils::calcBondRestLength(1.0, &p2, &p3);
TEST_ASSERT(RDKit::feq(restLen, 1.450, 1e-3));
forceConstant = ForceFields::UFF::Utils::calcAngleForceConstant(
p2.theta0, ForceFields::UFF::Params::amideBondOrder, 1, &p1, &p2, &p3);
TEST_ASSERT(RDKit::feq(forceConstant, 211.0, 1e-1)); // paper has 105.5
std::cerr << " done" << std::endl;
}
void testUFF4() {
std::cerr << "-------------------------------------" << std::endl;
std::cerr << "Unit tests for UFF angle-bend terms." << std::endl;
ForceFields::ForceField ff;
Point3D p1(1.514, 0, 0), p2(0, 0, 0), p3(0.1, 1.5, 0);
RDGeom::PointPtrVect &ps = ff.positions();
ps.push_back(&p1);
ps.push_back(&p2);
ps.push_back(&p3);
ForceFields::UFF::AtomicParams param1;
// sp3 carbon:
param1.r1 = .757;
param1.Z1 = 1.912;
param1.GMP_Xi = 5.343;
// cheat to get the angle to 90 so that testing is easier:
param1.theta0 = 90.0 * M_PI / 180.;
// C_3 - C_3, r0=1.514, k01=699.5918
ForceFields::ForceFieldContrib *contrib;
contrib =
new ForceFields::UFF::BondStretchContrib(&ff, 0, 1, 1, &param1, &param1);
ff.contribs().push_back(ForceFields::ContribPtr(contrib));
contrib =
new ForceFields::UFF::BondStretchContrib(&ff, 1, 2, 1, &param1, &param1);
ff.contribs().push_back(ForceFields::ContribPtr(contrib));
contrib = new ForceFields::UFF::AngleBendContrib(&ff, 0, 1, 2, 1, 1, &param1,
&param1, &param1);
ff.contribs().push_back(ForceFields::ContribPtr(contrib));
RDGeom::Point3D d, v1, v2;
double theta;
#if 1
// ------- ------- ------- ------- ------- ------- -------
// try a bit of minimization
ff.initialize();
ff.minimize(10, 1e-8, 1e-8);
v1 = *(RDGeom::Point3D *)ff.positions()[0] -
*(RDGeom::Point3D *)ff.positions()[1];
v2 = *(RDGeom::Point3D *)ff.positions()[1] -
*(RDGeom::Point3D *)ff.positions()[2];
theta = v1.angleTo(v2);
TEST_ASSERT(RDKit::feq(v1.length(), 1.514, 1e-3));
TEST_ASSERT(RDKit::feq(v2.length(), 1.514, 1e-3));
TEST_ASSERT(RDKit::feq(theta, 90 * M_PI / 180., 1e-4));
// ------- ------- ------- ------- ------- ------- -------
// more complicated atomic coords:
p1.x = 1.3;
p1.y = 0.1;
p1.z = 0.1;
p2.x = -0.1;
p2.y = 0.05;
p2.z = -0.05;
p3.x = 0.1;
p3.y = 1.5;
p3.z = 0.05;
ff.initialize();
ff.minimize(10, 1e-8, 1e-8);
v1 = *(RDGeom::Point3D *)ff.positions()[0] -
*(RDGeom::Point3D *)ff.positions()[1];
v2 = *(RDGeom::Point3D *)ff.positions()[1] -
*(RDGeom::Point3D *)ff.positions()[2];
theta = v1.angleTo(v2);
TEST_ASSERT(RDKit::feq(v1.length(), 1.514, 1e-3));
TEST_ASSERT(RDKit::feq(v2.length(), 1.514, 1e-3));
TEST_ASSERT(RDKit::feq(theta, 90 * M_PI / 180., 1e-4));
// ------- ------- ------- ------- ------- ------- -------
// try for the tetrahedral angle instead of 90:
param1.theta0 = 109.47 * M_PI / 180.;
ff.contribs().pop_back();
contrib = new ForceFields::UFF::AngleBendContrib(&ff, 0, 1, 2, 1, 1, &param1,
&param1, &param1);
ff.contribs().push_back(ForceFields::ContribPtr(contrib));
p1.x = 1.3;
p1.y = 0.1;
p1.z = 0.1;
p2.x = -0.1;
p2.y = 0.05;
p2.z = -0.05;
p3.x = 0.1;
p3.y = 1.5;
p3.z = 0.05;
ff.initialize();
ff.minimize(100, 1e-8, 1e-8);
v1 = *(RDGeom::Point3D *)ff.positions()[0] -
*(RDGeom::Point3D *)ff.positions()[1];
v2 = *(RDGeom::Point3D *)ff.positions()[2] -
*(RDGeom::Point3D *)ff.positions()[1];
theta = v1.angleTo(v2);
TEST_ASSERT(RDKit::feq(v1.length(), 1.514, 1e-3));
TEST_ASSERT(RDKit::feq(v2.length(), 1.514, 1e-3));
TEST_ASSERT(RDKit::feq(theta, param1.theta0, 1e-4));
#endif
// ------- ------- ------- ------- ------- ------- -------
//
// Do a series of "special cases" (i.e. test the functional forms
// for linear, trigonal planar, square planar and octahedral)
//
// ------- ------- ------- ------- ------- ------- -------
// ------- ------- ------- ------- ------- ------- -------
// test a linear molecule:
param1.theta0 = M_PI;
// ff.contribs().pop_back();
// ff.contribs().pop_back();
ff.contribs().pop_back();
contrib = new ForceFields::UFF::AngleBendContrib(&ff, 0, 1, 2, 1, 1, &param1,
&param1, &param1, 2);
ff.contribs().push_back(ForceFields::ContribPtr(contrib));
p1.x = 1.3;
p1.y = 0.1;
p1.z = 0.0;
p2.x = 0.0;
p2.y = 0.0;
p2.z = 0.0;
p3.x = -1.3;
p3.y = 0.1;
p3.z = 0.00;
ff.initialize();
ff.minimize(100, 1e-8, 1e-8);
v1 = *(RDGeom::Point3D *)ff.positions()[0] -
*(RDGeom::Point3D *)ff.positions()[1];
v2 = *(RDGeom::Point3D *)ff.positions()[2] -
*(RDGeom::Point3D *)ff.positions()[1];
theta = v1.angleTo(v2);
TEST_ASSERT(RDKit::feq(v1.length(), 1.514, 1e-3));
TEST_ASSERT(RDKit::feq(v2.length(), 1.514, 1e-3));
std::cerr << "theta = " << theta << "; theta0 = " << param1.theta0
<< std::endl;
TEST_ASSERT(RDKit::feq(theta, param1.theta0, 1e-4));
// ------- ------- ------- ------- ------- ------- -------
// test n=3:
param1.theta0 = 120. * M_PI / 180.0;
// ff.contribs().pop_back();
// ff.contribs().pop_back();
ff.contribs().pop_back();
contrib = new ForceFields::UFF::AngleBendContrib(&ff, 0, 1, 2, 1, 1, &param1,
&param1, &param1, 3);
ff.contribs().push_back(ForceFields::ContribPtr(contrib));
p1.x = 1.3;
p1.y = 0.1;
p1.z = 0.0;
p2.x = 0.0;
p2.y = 0.0;
p2.z = 0.0;
p3.x = -.3;
p3.y = -1.3;
p3.z = 0.00;
ff.initialize();
ff.minimize(100, 1e-8, 1e-8);
v1 = *(RDGeom::Point3D *)ff.positions()[0] -
*(RDGeom::Point3D *)ff.positions()[1];
v2 = *(RDGeom::Point3D *)ff.positions()[2] -
*(RDGeom::Point3D *)ff.positions()[1];
theta = v1.angleTo(v2);
TEST_ASSERT(RDKit::feq(v1.length(), 1.514, 1e-3));
TEST_ASSERT(RDKit::feq(v2.length(), 1.514, 1e-3));
std::cerr << "theta = " << std::fixed << std::setprecision(6) << theta
<< ", param1.theta0 = " << std::fixed << std::setprecision(6)
<< param1.theta0 << std::endl;
TEST_ASSERT(RDKit::feq(theta, param1.theta0, 1e-4));
// ------- ------- ------- ------- ------- ------- -------
// test n=4:
param1.theta0 = M_PI / 2.0;
// ff.contribs().pop_back();
// ff.contribs().pop_back();
ff.contribs().pop_back();
contrib = new ForceFields::UFF::AngleBendContrib(&ff, 0, 1, 2, 1, 1, &param1,
&param1, &param1, 4);
ff.contribs().push_back(ForceFields::ContribPtr(contrib));
p1.x = 1.3;
p1.y = 0.1;
p1.z = 0.0;
p2.x = 0.0;
p2.y = 0.0;
p2.z = 0.0;
p3.x = -.3;
p3.y = -1.3;
p3.z = 0.00;
ff.initialize();
ff.minimize(100, 1e-8, 1e-8);
v1 = *(RDGeom::Point3D *)ff.positions()[0] -
*(RDGeom::Point3D *)ff.positions()[1];
v2 = *(RDGeom::Point3D *)ff.positions()[2] -
*(RDGeom::Point3D *)ff.positions()[1];
theta = v1.angleTo(v2);
TEST_ASSERT(RDKit::feq(v1.length(), 1.514, 1e-3));
TEST_ASSERT(RDKit::feq(v2.length(), 1.514, 1e-3));
TEST_ASSERT(RDKit::feq(theta, param1.theta0, 1e-4));
#if 0
std::cerr << " " << *ff.positions()[0] << std::endl;
std::cerr << " " << *ff.positions()[1] << std::endl;
std::cerr << " " << *ff.positions()[2] << std::endl;
std::cerr << "v1: " << v1 << std::endl;
std::cerr << "v2: " << v2 << std::endl;
std::cerr << "FINAL: " << v1.angleTo(v2) << " " << v1.signedAngleTo(v2) << std::endl;
#endif
std::cerr << " done" << std::endl;
}
void testUFF5() {
std::cerr << "-------------------------------------" << std::endl;
std::cerr << " Test Simple UFF molecule optimizations." << std::endl;
ForceFields::ForceField ff;
Point3D p1, p2, p3, p4, p5, p6;
RDGeom::PointPtrVect &ps = ff.positions();
ps.push_back(&p1);
ps.push_back(&p2);
ps.push_back(&p3);
ps.push_back(&p4);
ps.push_back(&p5);
ps.push_back(&p6);
ForceFields::UFF::AtomicParams param1, param2;
// sp2 carbon:
param1.r1 = .732;
param1.Z1 = 1.912;
param1.GMP_Xi = 5.343;
param1.theta0 = 120. * M_PI / 180.;
// H_1:
param2.r1 = 0.354;
param2.Z1 = 0.712;
param2.GMP_Xi = 4.528;
ForceFields::ForceFieldContrib *contrib;
// build ethylene:
contrib =
new ForceFields::UFF::BondStretchContrib(&ff, 0, 1, 2, &param1, &param1);
ff.contribs().push_back(ForceFields::ContribPtr(contrib));
contrib =
new ForceFields::UFF::BondStretchContrib(&ff, 0, 2, 1, &param1, &param2);
ff.contribs().push_back(ForceFields::ContribPtr(contrib));
contrib =
new ForceFields::UFF::BondStretchContrib(&ff, 0, 3, 1, &param1, &param2);
ff.contribs().push_back(ForceFields::ContribPtr(contrib));
contrib =
new ForceFields::UFF::BondStretchContrib(&ff, 1, 4, 1, &param1, &param2);
ff.contribs().push_back(ForceFields::ContribPtr(contrib));
contrib =
new ForceFields::UFF::BondStretchContrib(&ff, 1, 5, 1, &param1, &param2);
ff.contribs().push_back(ForceFields::ContribPtr(contrib));
contrib = new ForceFields::UFF::AngleBendContrib(&ff, 1, 0, 2, 2, 1, &param1,
&param1, &param2, 3);
ff.contribs().push_back(ForceFields::ContribPtr(contrib));
contrib = new ForceFields::UFF::AngleBendContrib(&ff, 1, 0, 3, 2, 1, &param1,
&param1, &param2, 3);
ff.contribs().push_back(ForceFields::ContribPtr(contrib));
contrib = new ForceFields::UFF::AngleBendContrib(&ff, 2, 0, 3, 1, 1, &param2,
&param1, &param2, 3);
ff.contribs().push_back(ForceFields::ContribPtr(contrib));
contrib = new ForceFields::UFF::AngleBendContrib(&ff, 0, 1, 4, 2, 1, &param1,
&param1, &param2, 3);
ff.contribs().push_back(ForceFields::ContribPtr(contrib));
contrib = new ForceFields::UFF::AngleBendContrib(&ff, 0, 1, 5, 2, 1, &param1,
&param1, &param2, 3);
ff.contribs().push_back(ForceFields::ContribPtr(contrib));
contrib = new ForceFields::UFF::AngleBendContrib(&ff, 4, 1, 5, 1, 1, &param2,
&param1, &param2, 3);
ff.contribs().push_back(ForceFields::ContribPtr(contrib));
// dodge the fact that we're not using torsions yet by putting
// everything in the z=0 plane:
p1.x = -0.58;
p1.y = -0.33;
p1.z = 0.0;
p2.x = 0.58;
p2.y = 0.33;
p2.z = 0.0;
p3.x = -0.61;
p3.y = -1.43;
p3.z = 0.0;
p4.x = -1.54;
p4.y = 0.20;
p4.z = 0.0;
p5.x = 0.61;
p5.y = 1.43;
p5.z = 0.0;
p6.x = 1.54;
p6.y = -0.20;
p6.z = 0.0;
RDGeom::Point3D d, v1, v2;
double theta;
// ------- ------- ------- ------- ------- ------- -------
// try a bit of minimization
ff.initialize();
ff.minimize(10, 1e-8, 1e-8);
double CCDblBondLen =
ForceFields::UFF::Utils::calcBondRestLength(2, &param1, &param1);
double CHBondLen =
ForceFields::UFF::Utils::calcBondRestLength(1, &param1, &param2);
v1 = *(RDGeom::Point3D *)ff.positions()[0] -
*(RDGeom::Point3D *)ff.positions()[1];
v2 = *(RDGeom::Point3D *)ff.positions()[0] -
*(RDGeom::Point3D *)ff.positions()[2];
theta = v1.angleTo(v2);
TEST_ASSERT(RDKit::feq(v1.length(), CCDblBondLen, 1e-3));
TEST_ASSERT(RDKit::feq(v2.length(), CHBondLen, 1e-3));
TEST_ASSERT(RDKit::feq(theta, param1.theta0, 1e-4));
v2 = *(RDGeom::Point3D *)ff.positions()[0] -
*(RDGeom::Point3D *)ff.positions()[3];
theta = v1.angleTo(v2);
TEST_ASSERT(RDKit::feq(v2.length(), CHBondLen, 1e-3));
TEST_ASSERT(RDKit::feq(theta, param1.theta0, 1e-4));
v1 = *(RDGeom::Point3D *)ff.positions()[0] -
*(RDGeom::Point3D *)ff.positions()[2];
theta = v1.angleTo(v2);
TEST_ASSERT(RDKit::feq(theta, param1.theta0, 1e-4));
std::cerr << " done" << std::endl;
}
void testUFF6() {
std::cerr << "-------------------------------------" << std::endl;
std::cerr << "Unit tests for UFF nonbonded terms." << std::endl;
ForceFields::ForceField ff;
Point3D p1(0, 0, 0), p2(0.0, 0, 0);
RDGeom::PointPtrVect &ps = ff.positions();
ps.push_back(&p1);
ps.push_back(&p2);
ForceFields::UFF::AtomicParams param1;
// sp3 carbon:
param1.r1 = .757;
param1.Z1 = 1.912;
param1.GMP_Xi = 5.343;
param1.x1 = 3.851;
param1.D1 = 0.105;
ff.initialize();
ForceFields::ForceFieldContrib *contrib;
contrib = new ForceFields::UFF::vdWContrib(&ff, 0, 1, &param1, &param1);
ff.contribs().push_back(ForceFields::ContribPtr(contrib));
// try a bit of minimization
RDGeom::Point3D d;
ff.initialize();
// edge case: our energy at zero length should be zero:
double E;
E = ff.calcEnergy();
TEST_ASSERT(RDKit::feq(E, 0.0));
(*ff.positions()[0])[0] = 0.0;
(*ff.positions()[1])[0] = 4.0;
ff.minimize(10, 1e-8, 1e-8);
d = *(RDGeom::Point3D *)ff.positions()[0] -
*(RDGeom::Point3D *)ff.positions()[1];
TEST_ASSERT(RDKit::feq(d.length(), 3.851, 1e-3));
// minimize in "3D"
ff.initialize();
(*ff.positions()[0])[0] = 0.0;
(*ff.positions()[0])[1] = 0.0;
(*ff.positions()[0])[2] = 0.0;
(*ff.positions()[1])[2] = 3.1;
(*ff.positions()[1])[1] = 0.9;
(*ff.positions()[1])[0] = 1.00;
ff.minimize(10, 1e-8, 1e-8);
d = *(RDGeom::Point3D *)ff.positions()[0] -
*(RDGeom::Point3D *)ff.positions()[1];
TEST_ASSERT(RDKit::feq(d.length(), 3.851, 1e-3));
std::cerr << " done" << std::endl;
}
void testUFF7() {
std::cerr << "-------------------------------------" << std::endl;
std::cerr << " Test UFF torsional terms." << 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::UFF::AtomicParams param1;
// sp3 carbon:
param1.r1 = .757;
param1.Z1 = 1.912;
param1.GMP_Xi = 5.343;
param1.x1 = 3.851;
param1.D1 = 0.105;
param1.V1 = 2.119;
param1.U1 = 2.0;
RDGeom::Point3D d, v1, v2;
double cosPhi;
ForceFields::ForceFieldContrib *contrib;
// ------- ------- ------- ------- ------- ------- -------
// Basic SP3 - SP3
// ------- ------- ------- ------- ------- ------- -------
contrib = new ForceFields::UFF::TorsionAngleContrib(
&ff, 0, 1, 2, 3, 1, 6, 6, RDKit::Atom::SP3, RDKit::Atom::SP3, &param1,
&param1);
ff.contribs().push_back(ForceFields::ContribPtr(contrib));
#if 1
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);
cosPhi = ForceFields::UFF::Utils::calculateCosTorsion(
*(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
// ------- ------- ------- ------- ------- ------- -------
ff.contribs().pop_back();
contrib = new ForceFields::UFF::TorsionAngleContrib(
&ff, 0, 1, 2, 3, 1, 6, 6, RDKit::Atom::SP2, RDKit::Atom::SP2, &param1,
&param1);
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::UFF::Utils::calculateCosTorsion(
*(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));
// ------- ------- ------- ------- ------- ------- -------
// Basic SP2 - SP3
// ------- ------- ------- ------- ------- ------- -------
ff.contribs().pop_back();
contrib = new ForceFields::UFF::TorsionAngleContrib(
&ff, 0, 1, 2, 3, 1, 6, 6, RDKit::Atom::SP2, RDKit::Atom::SP3, &param1,
&param1);
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(100, 1e-8, 1e-8);
cosPhi = ForceFields::UFF::Utils::calculateCosTorsion(
*(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));
// ------- ------- ------- ------- ------- ------- -------
// special case for group 6 - group 6 bonds:
// ------- ------- ------- ------- ------- ------- -------
ff.contribs().pop_back();
contrib = new ForceFields::UFF::TorsionAngleContrib(
&ff, 0, 1, 2, 3, 1, 8, 8, RDKit::Atom::SP3, RDKit::Atom::SP3, &param1,
&param1);
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(100, 1e-8, 1e-8);
cosPhi = ForceFields::UFF::Utils::calculateCosTorsion(
*(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, 0.0, 1e-4));
// ------- ------- ------- ------- ------- ------- -------
// special case for SP3 group 6 - SP2 other group
// ------- ------- ------- ------- ------- ------- -------
ff.contribs().pop_back();
contrib = new ForceFields::UFF::TorsionAngleContrib(
&ff, 0, 1, 2, 3, 1, 8, 6, RDKit::Atom::SP3, RDKit::Atom::SP2, &param1,
&param1);
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(100, 1e-8, 1e-8);
cosPhi = ForceFields::UFF::Utils::calculateCosTorsion(
*(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, 0.0, 1e-4));
#endif
// ------- ------- ------- ------- ------- ------- -------
// special case for (SP2 -) SP2 - SP3
// ------- ------- ------- ------- ------- ------- -------
ff.contribs().pop_back();
contrib = new ForceFields::UFF::TorsionAngleContrib(
&ff, 0, 1, 2, 3, 1, 6, 6, RDKit::Atom::SP2, RDKit::Atom::SP3, &param1,
&param1, true);
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(100, 1e-8, 1e-8);
cosPhi = ForceFields::UFF::Utils::calculateCosTorsion(
*(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));
std::cerr << " done" << std::endl;
}
void testUFFParams() {
std::cerr << "-------------------------------------" << std::endl;
std::cerr << " Test UFF Parameter objects" << std::endl;
ForceFields::UFF::ParamCollection *params =
ForceFields::UFF::ParamCollection::getParams();
TEST_ASSERT(params);
const ForceFields::UFF::AtomicParams *ptr;
ptr = (*params)("C_3");
TEST_ASSERT(ptr);
TEST_ASSERT(RDKit::feq(ptr->r1, 0.757));
TEST_ASSERT(RDKit::feq(ptr->theta0, 109.47 * M_PI / 180.));
TEST_ASSERT(RDKit::feq(ptr->x1, 3.851));
TEST_ASSERT(RDKit::feq(ptr->D1, 0.105));
TEST_ASSERT(RDKit::feq(ptr->zeta, 12.73));
TEST_ASSERT(RDKit::feq(ptr->Z1, 1.912));
TEST_ASSERT(RDKit::feq(ptr->V1, 2.119));
TEST_ASSERT(RDKit::feq(ptr->GMP_Xi, 5.343));
TEST_ASSERT(RDKit::feq(ptr->GMP_Hardness, 5.063));
TEST_ASSERT(RDKit::feq(ptr->GMP_Radius, 0.759));
ptr = (*params)("N_3");
TEST_ASSERT(ptr);
ptr = (*params)("C_5");
TEST_ASSERT(!ptr);
}
void testUFF8() {
std::cerr << "-------------------------------------" << std::endl;
std::cerr << " Test Simple UFF molecule optimization, part 2." << std::endl;
ForceFields::ForceField ff;
Point3D p1, p2, p3, p4, p5, p6;
RDGeom::PointPtrVect &ps = ff.positions();
ps.push_back(&p1);
ps.push_back(&p2);
ps.push_back(&p3);
ps.push_back(&p4);
ps.push_back(&p5);
ps.push_back(&p6);
ForceFields::UFF::ParamCollection *params =
ForceFields::UFF::ParamCollection::getParams();
const ForceFields::UFF::AtomicParams *param1, *param2;
// C_2 (sp2 carbon):
param1 = (*params)("C_2");
TEST_ASSERT(param1);
// H_:
param2 = (*params)("H_");
TEST_ASSERT(param2);
ForceFields::ForceFieldContrib *contrib;
// build ethylene:
// BONDS:
contrib =
new ForceFields::UFF::BondStretchContrib(&ff, 0, 1, 2, param1, param1);
ff.contribs().push_back(ForceFields::ContribPtr(contrib));
contrib =
new ForceFields::UFF::BondStretchContrib(&ff, 0, 2, 1, param1, param2);
ff.contribs().push_back(ForceFields::ContribPtr(contrib));
contrib =
new ForceFields::UFF::BondStretchContrib(&ff, 0, 3, 1, param1, param2);
ff.contribs().push_back(ForceFields::ContribPtr(contrib));
contrib =
new ForceFields::UFF::BondStretchContrib(&ff, 1, 4, 1, param1, param2);
ff.contribs().push_back(ForceFields::ContribPtr(contrib));
contrib =
new ForceFields::UFF::BondStretchContrib(&ff, 1, 5, 1, param1, param2);
ff.contribs().push_back(ForceFields::ContribPtr(contrib));
// ANGLES:
contrib = new ForceFields::UFF::AngleBendContrib(&ff, 1, 0, 2, 2, 1, param1,
param1, param2, 3);
ff.contribs().push_back(ForceFields::ContribPtr(contrib));
contrib = new ForceFields::UFF::AngleBendContrib(&ff, 1, 0, 3, 2, 1, param1,
param1, param2, 3);
ff.contribs().push_back(ForceFields::ContribPtr(contrib));
contrib = new ForceFields::UFF::AngleBendContrib(&ff, 2, 0, 3, 1, 1, param2,
param1, param2, 3);
ff.contribs().push_back(ForceFields::ContribPtr(contrib));
contrib = new ForceFields::UFF::AngleBendContrib(&ff, 0, 1, 4, 2, 1, param1,
param1, param2, 3);
ff.contribs().push_back(ForceFields::ContribPtr(contrib));
contrib = new ForceFields::UFF::AngleBendContrib(&ff, 0, 1, 5, 2, 1, param1,
param1, param2, 3);
ff.contribs().push_back(ForceFields::ContribPtr(contrib));
contrib = new ForceFields::UFF::AngleBendContrib(&ff, 4, 1, 5, 1, 1, param2,
param1, param2, 3);
ff.contribs().push_back(ForceFields::ContribPtr(contrib));
// DIHEDRALS:
contrib = new ForceFields::UFF::TorsionAngleContrib(
&ff, 2, 0, 1, 4, 2, 6, 6, RDKit::Atom::SP3, RDKit::Atom::SP3, param1,
param1);
ff.contribs().push_back(ForceFields::ContribPtr(contrib));
contrib = new ForceFields::UFF::TorsionAngleContrib(
&ff, 2, 0, 1, 5, 2, 6, 6, RDKit::Atom::SP3, RDKit::Atom::SP3, param1,
param1);
ff.contribs().push_back(ForceFields::ContribPtr(contrib));
contrib = new ForceFields::UFF::TorsionAngleContrib(
&ff, 3, 0, 1, 4, 2, 6, 6, RDKit::Atom::SP3, RDKit::Atom::SP3, param1,
param1);
ff.contribs().push_back(ForceFields::ContribPtr(contrib));
contrib = new ForceFields::UFF::TorsionAngleContrib(
&ff, 3, 0, 1, 5, 2, 6, 6, RDKit::Atom::SP3, RDKit::Atom::SP3, param1,
param1);
ff.contribs().push_back(ForceFields::ContribPtr(contrib));
p1.x = -0.58;
p1.y = -0.33;
p1.z = 0.1;
p2.x = 0.58;
p2.y = 0.33;
p2.z = 0.1;
p3.x = -0.61;
p3.y = -1.43;
p3.z = 0.0;
p4.x = -1.54;
p4.y = 0.20;
p4.z = 0.0;
p5.x = 0.61;
p5.y = 1.43;
p5.z = 0.0;
p6.x = 1.54;
p6.y = -0.20;
p6.z = 0.0;
RDGeom::Point3D d, v1, v2;
double theta;
// ------- ------- ------- ------- ------- ------- -------
// try a bit of minimization
ff.initialize();
ff.minimize(100, 1e-8, 1e-8);
double CCDblBondLen =
ForceFields::UFF::Utils::calcBondRestLength(2, param1, param1);
double CHBondLen =
ForceFields::UFF::Utils::calcBondRestLength(1, param1, param2);
v1 = *(RDGeom::Point3D *)ff.positions()[0] -
*(RDGeom::Point3D *)ff.positions()[1];
v2 = *(RDGeom::Point3D *)ff.positions()[0] -
*(RDGeom::Point3D *)ff.positions()[2];
theta = v1.angleTo(v2);
TEST_ASSERT(RDKit::feq(v1.length(), CCDblBondLen, 1e-3));
TEST_ASSERT(RDKit::feq(v2.length(), CHBondLen, 1e-3));
TEST_ASSERT(RDKit::feq(theta, param1->theta0, 1e-4));
v2 = *(RDGeom::Point3D *)ff.positions()[0] -
*(RDGeom::Point3D *)ff.positions()[3];
theta = v1.angleTo(v2);
TEST_ASSERT(RDKit::feq(v2.length(), CHBondLen, 1e-3));
TEST_ASSERT(RDKit::feq(theta, param1->theta0, 1e-4));
v1 = *(RDGeom::Point3D *)ff.positions()[0] -
*(RDGeom::Point3D *)ff.positions()[2];
theta = v1.angleTo(v2);
TEST_ASSERT(RDKit::feq(theta, param1->theta0, 1e-4));
std::cerr << " done" << std::endl;
}
void testUFFTorsionConflict() {
std::cerr << "-------------------------------------" << std::endl;
std::cerr << " Test UFF Torsion Conflicts." << std::endl;
ForceFields::ForceField ff;
Point3D p1, p2, p3, p4, p5, p6, p7;
RDGeom::PointPtrVect &ps = ff.positions();
ps.push_back(&p1);
ps.push_back(&p2);
ps.push_back(&p3);
ps.push_back(&p4);
ps.push_back(&p5);
ps.push_back(&p6);
ps.push_back(&p7);
ForceFields::UFF::ParamCollection *params =
ForceFields::UFF::ParamCollection::getParams();
const ForceFields::UFF::AtomicParams *param1, *param2, *param3;
// C_2 (sp2 carbon):
param1 = (*params)("C_2");
TEST_ASSERT(param1);
// H_:
param2 = (*params)("H_");
TEST_ASSERT(param2);
// C_3 (sp3 carbon):
param3 = (*params)("C_3");
TEST_ASSERT(param3);
ForceFields::ForceFieldContrib *contrib;
// BONDS:
contrib =
new ForceFields::UFF::BondStretchContrib(&ff, 0, 1, 2, param1, param1);
ff.contribs().push_back(ForceFields::ContribPtr(contrib));
contrib =
new ForceFields::UFF::BondStretchContrib(&ff, 1, 2, 1, param1, param3);
ff.contribs().push_back(ForceFields::ContribPtr(contrib));
contrib =
new ForceFields::UFF::BondStretchContrib(&ff, 1, 3, 1, param1, param2);
ff.contribs().push_back(ForceFields::ContribPtr(contrib));
contrib =
new ForceFields::UFF::BondStretchContrib(&ff, 2, 4, 1, param1, param2);
ff.contribs().push_back(ForceFields::ContribPtr(contrib));
contrib =
new ForceFields::UFF::BondStretchContrib(&ff, 2, 5, 1, param1, param2);
ff.contribs().push_back(ForceFields::ContribPtr(contrib));
contrib =
new ForceFields::UFF::BondStretchContrib(&ff, 2, 6, 1, param1, param2);
ff.contribs().push_back(ForceFields::ContribPtr(contrib));
#if 1
// ANGLES:
contrib = new ForceFields::UFF::AngleBendContrib(&ff, 0, 1, 2, 2.0, 1.0,
param1, param1, param3);
ff.contribs().push_back(ForceFields::ContribPtr(contrib));
contrib = new ForceFields::UFF::AngleBendContrib(&ff, 0, 1, 3, 2.0, 1.0,
param1, param1, param2);
ff.contribs().push_back(ForceFields::ContribPtr(contrib));
contrib = new ForceFields::UFF::AngleBendContrib(&ff, 1, 2, 4, 1.0, 1.0,
param1, param3, param2);
ff.contribs().push_back(ForceFields::ContribPtr(contrib));
contrib = new ForceFields::UFF::AngleBendContrib(&ff, 1, 2, 5, 1.0, 1.0,
param1, param3, param2);
ff.contribs().push_back(ForceFields::ContribPtr(contrib));
contrib = new ForceFields::UFF::AngleBendContrib(&ff, 1, 2, 6, 1.0, 1.0,
param1, param3, param2);
ff.contribs().push_back(ForceFields::ContribPtr(contrib));
contrib = new ForceFields::UFF::AngleBendContrib(&ff, 2, 1, 3, 1.0, 1.0,
param3, param1, param2);
ff.contribs().push_back(ForceFields::ContribPtr(contrib));
#endif
// DIHEDRALS:
contrib = new ForceFields::UFF::TorsionAngleContrib(
&ff, 0, 1, 2, 4, 1.0, 6, 6, RDKit::Atom::SP2, RDKit::Atom::SP3, param1,
param3, true);
ff.contribs().push_back(ForceFields::ContribPtr(contrib));
contrib = new ForceFields::UFF::TorsionAngleContrib(
&ff, 3, 1, 2, 4, 1.0, 6, 6, RDKit::Atom::SP2, RDKit::Atom::SP3, param1,
param3, false);
ff.contribs().push_back(ForceFields::ContribPtr(contrib));
contrib = new ForceFields::UFF::TorsionAngleContrib(
&ff, 0, 1, 2, 5, 1.0, 6, 6, RDKit::Atom::SP2, RDKit::Atom::SP3, param1,
param3, true);
ff.contribs().push_back(ForceFields::ContribPtr(contrib));
contrib = new ForceFields::UFF::TorsionAngleContrib(
&ff, 3, 1, 2, 5, 1.0, 6, 6, RDKit::Atom::SP2, RDKit::Atom::SP3, param1,
param3, false);
ff.contribs().push_back(ForceFields::ContribPtr(contrib));
contrib = new ForceFields::UFF::TorsionAngleContrib(
&ff, 0, 1, 2, 6, 1.0, 6, 6, RDKit::Atom::SP2, RDKit::Atom::SP3, param1,
param3, true);
ff.contribs().push_back(ForceFields::ContribPtr(contrib));
contrib = new ForceFields::UFF::TorsionAngleContrib(
&ff, 3, 1, 2, 6, 1.0, 6, 6, RDKit::Atom::SP2, RDKit::Atom::SP3, param1,
param3, false);
ff.contribs().push_back(ForceFields::ContribPtr(contrib));
p1.x = 0.5411;
p1.y = -0.7741;
p1.z = 0.0902;
p2.x = -0.5622;
p2.y = -0.0368;
p2.z = 0.1202;
p3.x = -0.5101;
p3.y = 1.4485;
p3.z = 0.0816;
p4.x = -1.5285;
p4.y = -0.5341;
p4.z = 0.1892;
p5.x = 0.5097;
p5.y = 1.8065;
p5.z = 0.1988;
p6.x = -1.1436;
p6.y = 1.8781;
p6.z = 0.8983;
p7.x = -0.9145;
p7.y = 1.8185;
p7.z = -0.8983;
RDGeom::Point3D d, v1, v2;
// ------- ------- ------- ------- ------- ------- -------
// try a bit of minimization
ff.initialize();
ff.minimize(100, 1e-8, 1e-8);
#if 1
std::cerr.setf(std::ios_base::fixed, std::ios_base::floatfield);
std::cerr.precision(4);
std::cerr << "C " << *ff.positions()[0] << std::endl;
std::cerr << "C " << *ff.positions()[1] << std::endl;
std::cerr << "C " << *ff.positions()[2] << std::endl;
std::cerr << "H " << *ff.positions()[3] << std::endl;
std::cerr << "H " << *ff.positions()[4] << std::endl;
std::cerr << "O " << *ff.positions()[5] << std::endl;
std::cerr << "F " << *ff.positions()[6] << std::endl;
#endif
std::cerr << " done" << std::endl;
}
void testUFFDistanceConstraints() {
std::cerr << "-------------------------------------" << std::endl;
std::cerr << "Unit tests for UFF distance constraint terms." << std::endl;
ForceFields::ForceField ff;
Point3D p1(0, 0, 0), p2(1.514, 0, 0);
RDGeom::PointPtrVect &ps = ff.positions();
ps.push_back(&p1);
ps.push_back(&p2);
double *p, *g;
p = new double[6];
g = new double[6];
for (int i = 0; i < 6; i++) {
p[i] = 0.0;
g[i] = 0.0;
}
p[0] = 0;
p[3] = 1.40;
ff.initialize();
// C_3 - C_3, r0=1.514, k01=699.5918
ForceFields::ForceFieldContrib *bs;
bs = new ForceFields::UFF::DistanceConstraintContrib(&ff, 0, 1, 1.35, 1.55,
1000.0);
ff.contribs().push_back(ForceFields::ContribPtr(bs));
double E;
E = bs->getEnergy(p);
TEST_ASSERT(RDKit::feq(E, 0.0));
bs->getGrad(p, g);
for (int i = 0; i < 6; i++) {
TEST_ASSERT(RDKit::feq(g[i], 0.0));
}
ff.initialize();
(*ff.positions()[1])[0] = 1.20;
p[3] = 1.20;
E = bs->getEnergy(p);
TEST_ASSERT(RDKit::feq(E, 11.25));
bs->getGrad(p, g);
TEST_ASSERT(RDKit::feq(g[0], 150.0));
TEST_ASSERT(RDKit::feq(g[3], -150.0));
TEST_ASSERT(RDKit::feq(g[1], 0.0));
TEST_ASSERT(RDKit::feq(g[2], 0.0));
TEST_ASSERT(RDKit::feq(g[4], 0.0));
TEST_ASSERT(RDKit::feq(g[5], 0.0));
// try a bit of minimization
RDGeom::Point3D d;
ff.initialize();
(*ff.positions()[1])[2] = 0.0;
(*ff.positions()[1])[0] = 1.20;
ff.minimize(10, 1e-8);
d = *(RDGeom::Point3D *)ff.positions()[0] -
*(RDGeom::Point3D *)ff.positions()[1];
TEST_ASSERT(d.length() >= 1.35)
TEST_ASSERT(d.length() <= 1.55)
ff.initialize();
(*ff.positions()[1])[2] = 0.0;
(*ff.positions()[1])[0] = 1.70;
ff.minimize(10, 1e-8);
d = *(RDGeom::Point3D *)ff.positions()[0] -
*(RDGeom::Point3D *)ff.positions()[1];
TEST_ASSERT(d.length() >= 1.35)
TEST_ASSERT(d.length() <= 1.55)
delete[] p;
delete[] g;
std::cerr << " done" << std::endl;
}
void testUFFAllConstraints() {
std::cerr << "-------------------------------------" << std::endl;
std::cerr << "Unit tests for all UFF constraint terms." << std::endl;
std::string molBlock =
"butane\n"
" RDKit 3D\n"
"butane\n"
" 17 16 0 0 0 0 0 0 0 0999 V2000\n"
" 0.0000 0.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0\n"
" 1.4280 0.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0\n"
" 1.7913 -0.2660 0.9927 H 0 0 0 0 0 0 0 0 0 0 0 0\n"
" 1.9040 1.3004 -0.3485 C 0 0 0 0 0 0 0 0 0 0 0 0\n"
" 1.5407 2.0271 0.3782 H 0 0 0 0 0 0 0 0 0 0 0 0\n"
" 1.5407 1.5664 -1.3411 H 0 0 0 0 0 0 0 0 0 0 0 0\n"
" 3.3320 1.3004 -0.3485 C 0 0 0 0 0 0 0 0 0 0 0 0\n"
" 3.6953 1.5162 -1.3532 H 0 0 0 0 0 0 0 0 0 0 0 0\n"
" 3.8080 0.0192 0.0649 C 0 0 0 0 0 0 0 0 0 0 0 0\n"
" 3.4447 -0.7431 -0.6243 H 0 0 0 0 0 0 0 0 0 0 0 0\n"
" 3.4447 -0.1966 1.0697 H 0 0 0 0 0 0 0 0 0 0 0 0\n"
" 4.8980 0.0192 0.0649 H 0 0 0 0 0 0 0 0 0 0 0 0\n"
" 3.6954 2.0627 0.3408 H 0 0 0 0 0 0 0 0 0 0 0 0\n"
" 1.7913 -0.7267 -0.7267 H 0 0 0 0 0 0 0 0 0 0 0 0\n"
" -0.3633 0.7267 0.7267 H 0 0 0 0 0 0 0 0 0 0 0 0\n"
" -0.3633 -0.9926 0.2660 H 0 0 0 0 0 0 0 0 0 0 0 0\n"
" -0.3633 0.2660 -0.9926 H 0 0 0 0 0 0 0 0 0 0 0 0\n"
" 1 2 1 0 0 0 0\n"
" 1 15 1 0 0 0 0\n"
" 1 16 1 0 0 0 0\n"
" 1 17 1 0 0 0 0\n"
" 2 3 1 0 0 0 0\n"
" 2 4 1 0 0 0 0\n"
" 2 14 1 0 0 0 0\n"
" 4 5 1 0 0 0 0\n"
" 4 6 1 0 0 0 0\n"
" 4 7 1 0 0 0 0\n"
" 7 8 1 0 0 0 0\n"
" 7 9 1 0 0 0 0\n"
" 7 13 1 0 0 0 0\n"
" 9 10 1 0 0 0 0\n"
" 9 11 1 0 0 0 0\n"
" 9 12 1 0 0 0 0\n"
"M END\n";
RDKit::RWMol *mol;
ForceFields::ForceField *field;
// distance constraints
ForceFields::UFF::DistanceConstraintContrib *dc;
mol = RDKit::MolBlockToMol(molBlock, true, false);
TEST_ASSERT(mol);
MolTransforms::setBondLength(mol->getConformer(), 1, 3, 2.0);
field = RDKit::UFF::constructForceField(*mol);
TEST_ASSERT(field);
field->initialize();
dc = new ForceFields::UFF::DistanceConstraintContrib(field, 1, 3, 2.0, 2.0,
1.0e5);
field->contribs().push_back(ForceFields::ContribPtr(dc));
field->minimize();
TEST_ASSERT(RDKit::feq(
MolTransforms::getBondLength(mol->getConformer(), 1, 3), 2.0, 0.1));
delete field;
field = RDKit::UFF::constructForceField(*mol);
field->initialize();
dc = new ForceFields::UFF::DistanceConstraintContrib(field, 1, 3, true, -0.2,
0.2, 1.0e5);
field->contribs().push_back(ForceFields::ContribPtr(dc));
field->minimize();
TEST_ASSERT(MolTransforms::getBondLength(mol->getConformer(), 1, 3) > 1.79);
delete field;
delete mol;
// angle constraints
ForceFields::UFF::AngleConstraintContrib *ac;
mol = RDKit::MolBlockToMol(molBlock, true, false);
TEST_ASSERT(mol);
MolTransforms::setAngleDeg(mol->getConformer(), 1, 3, 6, 90.0);
field = RDKit::UFF::constructForceField(*mol);
TEST_ASSERT(field);
field->initialize();
ac = new ForceFields::UFF::AngleConstraintContrib(field, 1, 3, 6, 90.0, 90.0,
1.0e5);
field->contribs().push_back(ForceFields::ContribPtr(ac));
field->minimize();
TEST_ASSERT(RDKit::feq(
MolTransforms::getAngleDeg(mol->getConformer(), 1, 3, 6), 90.0, 0.5));
delete field;
field = RDKit::UFF::constructForceField(*mol);
field->initialize();
ac = new ForceFields::UFF::AngleConstraintContrib(field, 1, 3, 6, true, -10.0,
10.0, 1.0e5);
field->contribs().push_back(ForceFields::ContribPtr(ac));
field->minimize();
TEST_ASSERT(RDKit::feq(
MolTransforms::getAngleDeg(mol->getConformer(), 1, 3, 6), 100.0, 0.5));
delete field;
MolTransforms::setAngleDeg(mol->getConformer(), 1, 3, 6, 0.0);
field = RDKit::UFF::constructForceField(*mol);
field->initialize();
ac = new ForceFields::UFF::AngleConstraintContrib(field, 1, 3, 6, false,
-10.0, 10.0, 1.0e5);
field->contribs().push_back(ForceFields::ContribPtr(ac));
field->minimize();
TEST_ASSERT(RDKit::feq(
MolTransforms::getAngleDeg(mol->getConformer(), 1, 3, 6), 10.0, 0.5));
delete field;
delete mol;
// torsion constraints
ForceFields::UFF::TorsionConstraintContrib *tc;
mol = RDKit::MolBlockToMol(molBlock, true, false);
TEST_ASSERT(mol);
MolTransforms::setDihedralDeg(mol->getConformer(), 1, 3, 6, 8, 15.0);
field = RDKit::UFF::constructForceField(*mol);
TEST_ASSERT(field);
field->initialize();
tc = new ForceFields::UFF::TorsionConstraintContrib(field, 1, 3, 6, 8, 10.0,
20.0, 1.0e5);
field->contribs().push_back(ForceFields::ContribPtr(tc));
field->minimize();
TEST_ASSERT(
RDKit::feq(MolTransforms::getDihedralDeg(mol->getConformer(), 1, 3, 6, 8),
20.0, 0.5));
delete field;
MolTransforms::setDihedralDeg(mol->getConformer(), 1, 3, 6, 8, -30.0);
field = RDKit::UFF::constructForceField(*mol);
field->initialize();
tc = new ForceFields::UFF::TorsionConstraintContrib(field, 1, 3, 6, 8, true,
-10.0, 8.0, 1.0e5);
field->contribs().push_back(ForceFields::ContribPtr(tc));
field->minimize();
TEST_ASSERT(
RDKit::feq(MolTransforms::getDihedralDeg(mol->getConformer(), 1, 3, 6, 8),
-40.0, 0.5));
delete field;
MolTransforms::setDihedralDeg(mol->getConformer(), 1, 3, 6, 8, -10.0);
field = RDKit::UFF::constructForceField(*mol);
field->initialize();
tc = new ForceFields::UFF::TorsionConstraintContrib(field, 1, 3, 6, 8, false,
-10.0, 8.0, 1.0e6);
field->contribs().push_back(ForceFields::ContribPtr(tc));
field->minimize(500);
TEST_ASSERT(
RDKit::feq(MolTransforms::getDihedralDeg(mol->getConformer(), 1, 3, 6, 8),
-10.0, 0.5));
delete field;
delete mol;
// position constraints
ForceFields::UFF::PositionConstraintContrib *pc;
mol = RDKit::MolBlockToMol(molBlock, true, false);
TEST_ASSERT(mol);
field = RDKit::UFF::constructForceField(*mol);
TEST_ASSERT(field);
field->initialize();
RDGeom::Point3D p = mol->getConformer().getAtomPos(1);
pc = new ForceFields::UFF::PositionConstraintContrib(field, 1, 0.3, 1.0e5);
field->contribs().push_back(ForceFields::ContribPtr(pc));
field->minimize();
RDGeom::Point3D q = mol->getConformer().getAtomPos(1);
TEST_ASSERT((p - q).length() < 0.3);
delete field;
delete mol;
// fixed atoms
mol = RDKit::MolBlockToMol(molBlock, true, false);
TEST_ASSERT(mol);
field = RDKit::UFF::constructForceField(*mol);
TEST_ASSERT(field);
field->initialize();
RDGeom::Point3D fp = mol->getConformer().getAtomPos(1);
field->fixedPoints().push_back(1);
field->minimize();
RDGeom::Point3D fq = mol->getConformer().getAtomPos(1);
TEST_ASSERT((fp - fq).length() < 0.01);
delete field;
delete mol;
std::cerr << " done" << std::endl;
}
void testUFFCopy() {
std::cerr << "-------------------------------------" << std::endl;
std::cerr << "Unit tests for copying UFF ForceFields." << std::endl;
std::string molBlock =
"butane\n"
" RDKit 3D\n"
"butane\n"
" 17 16 0 0 0 0 0 0 0 0999 V2000\n"
" 0.0000 0.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0\n"
" 1.4280 0.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0\n"
" 1.7913 -0.2660 0.9927 H 0 0 0 0 0 0 0 0 0 0 0 0\n"
" 1.9040 1.3004 -0.3485 C 0 0 0 0 0 0 0 0 0 0 0 0\n"
" 1.5407 2.0271 0.3782 H 0 0 0 0 0 0 0 0 0 0 0 0\n"
" 1.5407 1.5664 -1.3411 H 0 0 0 0 0 0 0 0 0 0 0 0\n"
" 3.3320 1.3004 -0.3485 C 0 0 0 0 0 0 0 0 0 0 0 0\n"
" 3.6953 1.5162 -1.3532 H 0 0 0 0 0 0 0 0 0 0 0 0\n"
" 3.8080 0.0192 0.0649 C 0 0 0 0 0 0 0 0 0 0 0 0\n"
" 3.4447 -0.7431 -0.6243 H 0 0 0 0 0 0 0 0 0 0 0 0\n"
" 3.4447 -0.1966 1.0697 H 0 0 0 0 0 0 0 0 0 0 0 0\n"
" 4.8980 0.0192 0.0649 H 0 0 0 0 0 0 0 0 0 0 0 0\n"
" 3.6954 2.0627 0.3408 H 0 0 0 0 0 0 0 0 0 0 0 0\n"
" 1.7913 -0.7267 -0.7267 H 0 0 0 0 0 0 0 0 0 0 0 0\n"
" -0.3633 0.7267 0.7267 H 0 0 0 0 0 0 0 0 0 0 0 0\n"
" -0.3633 -0.9926 0.2660 H 0 0 0 0 0 0 0 0 0 0 0 0\n"
" -0.3633 0.2660 -0.9926 H 0 0 0 0 0 0 0 0 0 0 0 0\n"
" 1 2 1 0 0 0 0\n"
" 1 15 1 0 0 0 0\n"
" 1 16 1 0 0 0 0\n"
" 1 17 1 0 0 0 0\n"
" 2 3 1 0 0 0 0\n"
" 2 4 1 0 0 0 0\n"
" 2 14 1 0 0 0 0\n"
" 4 5 1 0 0 0 0\n"
" 4 6 1 0 0 0 0\n"
" 4 7 1 0 0 0 0\n"
" 7 8 1 0 0 0 0\n"
" 7 9 1 0 0 0 0\n"
" 7 13 1 0 0 0 0\n"
" 9 10 1 0 0 0 0\n"
" 9 11 1 0 0 0 0\n"
" 9 12 1 0 0 0 0\n"
"M END\n";
{
RDKit::RWMol *mol = RDKit::MolBlockToMol(molBlock, true, false);
TEST_ASSERT(mol);
auto *cmol = new RDKit::RWMol(*mol);
TEST_ASSERT(cmol);
ForceFields::ForceField *field = RDKit::UFF::constructForceField(*mol);
TEST_ASSERT(field);
field->initialize();
auto *dc = new ForceFields::UFF::DistanceConstraintContrib(field, 1, 3, 2.0,
2.0, 1.0e5);
field->contribs().push_back(ForceFields::ContribPtr(dc));
field->minimize();
TEST_ASSERT(MolTransforms::getBondLength(mol->getConformer(), 1, 3) > 1.99);
auto *cfield = new ForceFields::ForceField(*field);
cfield->positions().clear();
for (unsigned int i = 0; i < cmol->getNumAtoms(); i++) {
cfield->positions().push_back(&cmol->getConformer().getAtomPos(i));
}
cfield->initialize();
cfield->minimize();
TEST_ASSERT(MolTransforms::getBondLength(cmol->getConformer(), 1, 3) >
1.99);
TEST_ASSERT(RDKit::feq(field->calcEnergy(), cfield->calcEnergy()));
const RDKit::Conformer &conf = mol->getConformer();
const RDKit::Conformer &cconf = cmol->getConformer();
for (unsigned int i = 0; i < mol->getNumAtoms(); i++) {
RDGeom::Point3D p = conf.getAtomPos(i);
RDGeom::Point3D cp = cconf.getAtomPos(i);
TEST_ASSERT(RDKit::feq(p.x, cp.x));
TEST_ASSERT(RDKit::feq(p.y, cp.y));
TEST_ASSERT(RDKit::feq(p.z, cp.z));
}
delete field;
delete cfield;
delete mol;
delete cmol;
}
std::cerr << " done" << std::endl;
}
int main() {
#if 1
test1();
testUFF1();
testUFF2();
testUFF3();
testUFF4();
testUFF5();
testUFF6();
testUFF7();
testUFFParams();
testUFF8();
testUFFTorsionConflict();
#endif
testUFFDistanceConstraints();
testUFFAllConstraints();
testUFFCopy();
}
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