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testForceField.cpp
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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 <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 <GraphMol/Atom.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,1.462929,1e-5));
forceConstant=ForceFields::UFF::Utils::calcBondForceConstant(restLen,&p1,&p2);
TEST_ASSERT(RDKit::feq(forceConstant,1031.77,1e-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,1.368,1e-3)); // NOTE: the paper has 1.366
forceConstant=ForceFields::UFF::Utils::calcBondForceConstant(restLen,&p1,&p2);
TEST_ASSERT(RDKit::feq(forceConstant,1260.,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,¶m1,¶m1);
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,1.368,1e-3));
restLen=ForceFields::UFF::Utils::calcBondRestLength(1.0,&p2,&p3);
TEST_ASSERT(RDKit::feq(restLen,1.462,1e-3));
forceConstant=ForceFields::UFF::Utils::calcAngleForceConstant(p2.theta0,ForceFields::UFF::Params::amideBondOrder,1,
&p1,&p2,&p3);
TEST_ASSERT(RDKit::feq(forceConstant,123.5,1e-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,¶m1,¶m1);
ff.contribs().push_back(ForceFields::ContribPtr(contrib));
contrib = new ForceFields::UFF::BondStretchContrib(&ff,1,2,1,¶m1,¶m1);
ff.contribs().push_back(ForceFields::ContribPtr(contrib));
contrib = new ForceFields::UFF::AngleBendContrib(&ff,0,1,2,1,1,¶m1,¶m1,¶m1);
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,¶m1,¶m1,¶m1);
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,¶m1,¶m1,¶m1,2);
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));
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,¶m1,¶m1,¶m1,3);
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));
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,¶m1,¶m1,¶m1,4);
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,¶m1,¶m1);
ff.contribs().push_back(ForceFields::ContribPtr(contrib));
contrib = new ForceFields::UFF::BondStretchContrib(&ff,0,2,1,¶m1,¶m2);
ff.contribs().push_back(ForceFields::ContribPtr(contrib));
contrib = new ForceFields::UFF::BondStretchContrib(&ff,0,3,1,¶m1,¶m2);
ff.contribs().push_back(ForceFields::ContribPtr(contrib));
contrib = new ForceFields::UFF::BondStretchContrib(&ff,1,4,1,¶m1,¶m2);
ff.contribs().push_back(ForceFields::ContribPtr(contrib));
contrib = new ForceFields::UFF::BondStretchContrib(&ff,1,5,1,¶m1,¶m2);
ff.contribs().push_back(ForceFields::ContribPtr(contrib));
contrib = new ForceFields::UFF::AngleBendContrib(&ff,1,0,2,2,1,¶m1,¶m1,¶m2,3);
ff.contribs().push_back(ForceFields::ContribPtr(contrib));
contrib = new ForceFields::UFF::AngleBendContrib(&ff,1,0,3,2,1,¶m1,¶m1,¶m2,3);
ff.contribs().push_back(ForceFields::ContribPtr(contrib));
contrib = new ForceFields::UFF::AngleBendContrib(&ff,2,0,3,1,1,¶m2,¶m1,¶m2,3);
ff.contribs().push_back(ForceFields::ContribPtr(contrib));
contrib = new ForceFields::UFF::AngleBendContrib(&ff,0,1,4,2,1,¶m1,¶m1,¶m2,3);
ff.contribs().push_back(ForceFields::ContribPtr(contrib));
contrib = new ForceFields::UFF::AngleBendContrib(&ff,0,1,5,2,1,¶m1,¶m1,¶m2,3);
ff.contribs().push_back(ForceFields::ContribPtr(contrib));
contrib = new ForceFields::UFF::AngleBendContrib(&ff,4,1,5,1,1,¶m2,¶m1,¶m2,3);
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,¶m1,¶m1);
double CHBondLen=ForceFields::UFF::Utils::calcBondRestLength(1,¶m1,¶m2);
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,¶m1,¶m1);
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,param2;
// 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;
// H_1:
param2.r1 = 0.354;
param2.Z1 = 0.712;
param2.GMP_Xi = 4.528;
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,
¶m1,¶m1);
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,
¶m1,¶m1);
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,
¶m1,¶m1);
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,
¶m1,¶m1);
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,
¶m1,¶m1);
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,
¶m1,¶m1,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));