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rdkit/Code/GraphMol/ForceFieldHelpers/UFF/testUFFHelpers.cpp
Nadine Schneider 0132cc72e9 Merge branch 'newCanon' into master3 
Conflicts:
	Code/GraphMol/SmilesParse/test.cpp
2015-04-10 10:25:47 +02:00

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// $Id$
//
// Copyright (C) 2004-2010 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 <RDGeneral/Invariant.h>
#include <RDGeneral/RDLog.h>
#include <RDGeneral/utils.h>
#include <GraphMol/RDKitBase.h>
#include <GraphMol/SmilesParse/SmilesParse.h>
#include <GraphMol/SmilesParse/SmilesWrite.h>
#include <GraphMol/FileParsers/FileParsers.h>
#include <GraphMol/FileParsers/MolSupplier.h>
#include <GraphMol/FileParsers/MolWriters.h>
#include <GraphMol/ForceFieldHelpers/UFF/AtomTyper.h>
#include <GraphMol/ForceFieldHelpers/UFF/Builder.h>
#include <GraphMol/ForceFieldHelpers/UFF/UFF.h>
#include <ForceField/ForceField.h>
#include <GraphMol/DistGeomHelpers/Embedder.h>
#include <boost/math/special_functions/round.hpp>
using namespace RDKit;
#if 1
void testUFFTyper1(){
BOOST_LOG(rdErrorLog) << "-------------------------------------" << std::endl;
BOOST_LOG(rdErrorLog) << " Test UFF atom labels." << std::endl;
ROMol *mol;
std::string key;
mol = SmilesToMol("[SiH3]CC(=O)NC");
TEST_ASSERT(mol);
key = UFF::Tools::getAtomLabel(mol->getAtomWithIdx(0));
TEST_ASSERT(key=="Si3");
key = UFF::Tools::getAtomLabel(mol->getAtomWithIdx(1));
TEST_ASSERT(key=="C_3");
key = UFF::Tools::getAtomLabel(mol->getAtomWithIdx(2));
TEST_ASSERT(key=="C_R");
key = UFF::Tools::getAtomLabel(mol->getAtomWithIdx(3));
TEST_ASSERT(key=="O_R");
key = UFF::Tools::getAtomLabel(mol->getAtomWithIdx(4));
TEST_ASSERT(key=="N_R");
delete mol;
mol = SmilesToMol("CC(=O)C");
TEST_ASSERT(mol);
key = UFF::Tools::getAtomLabel(mol->getAtomWithIdx(0));
TEST_ASSERT(key=="C_3");
key = UFF::Tools::getAtomLabel(mol->getAtomWithIdx(1));
TEST_ASSERT(key=="C_2");
key = UFF::Tools::getAtomLabel(mol->getAtomWithIdx(2));
TEST_ASSERT(key=="O_2");
key = UFF::Tools::getAtomLabel(mol->getAtomWithIdx(3));
TEST_ASSERT(key=="C_3");
delete mol;
mol = SmilesToMol("C(=O)S");
TEST_ASSERT(mol);
key = UFF::Tools::getAtomLabel(mol->getAtomWithIdx(0));
TEST_ASSERT(key=="C_2");
key = UFF::Tools::getAtomLabel(mol->getAtomWithIdx(1));
TEST_ASSERT(key=="O_2");
key = UFF::Tools::getAtomLabel(mol->getAtomWithIdx(2));
TEST_ASSERT(key=="S_3+2");
delete mol;
mol = SmilesToMol("SCS(=O)S(=O)(=O)O");
TEST_ASSERT(mol);
key = UFF::Tools::getAtomLabel(mol->getAtomWithIdx(0));
TEST_ASSERT(key=="S_3+2");
key = UFF::Tools::getAtomLabel(mol->getAtomWithIdx(1));
TEST_ASSERT(key=="C_3");
key = UFF::Tools::getAtomLabel(mol->getAtomWithIdx(2));
TEST_ASSERT(key=="S_3+4");
key = UFF::Tools::getAtomLabel(mol->getAtomWithIdx(4));
TEST_ASSERT(key=="S_3+6");
delete mol;
mol = SmilesToMol("PCP(O)CP(=O)(=O)");
TEST_ASSERT(mol);
key = UFF::Tools::getAtomLabel(mol->getAtomWithIdx(0));
TEST_ASSERT(key=="P_3+3");
key = UFF::Tools::getAtomLabel(mol->getAtomWithIdx(1));
TEST_ASSERT(key=="C_3");
key = UFF::Tools::getAtomLabel(mol->getAtomWithIdx(2));
TEST_ASSERT(key=="P_3+3");
// FIX: I am not 100% convinced that this should be SP2
key = UFF::Tools::getAtomLabel(mol->getAtomWithIdx(5));
TEST_ASSERT(key=="P_3+5");
delete mol;
mol = SmilesToMol("C(F)(Cl)(Br)I");
TEST_ASSERT(mol);
key = UFF::Tools::getAtomLabel(mol->getAtomWithIdx(0));
TEST_ASSERT(key=="C_3");
key = UFF::Tools::getAtomLabel(mol->getAtomWithIdx(1));
TEST_ASSERT(key=="F_");
key = UFF::Tools::getAtomLabel(mol->getAtomWithIdx(2));
TEST_ASSERT(key=="Cl");
key = UFF::Tools::getAtomLabel(mol->getAtomWithIdx(3));
TEST_ASSERT(key=="Br");
key = UFF::Tools::getAtomLabel(mol->getAtomWithIdx(4));
TEST_ASSERT(key=="I_");
delete mol;
mol = SmilesToMol("[Li].[Na].[K].[Rb].[Cs]");
TEST_ASSERT(mol);
key = UFF::Tools::getAtomLabel(mol->getAtomWithIdx(0));
TEST_ASSERT(key=="Li");
key = UFF::Tools::getAtomLabel(mol->getAtomWithIdx(1));
TEST_ASSERT(key=="Na");
key = UFF::Tools::getAtomLabel(mol->getAtomWithIdx(2));
TEST_ASSERT(key=="K_");
key = UFF::Tools::getAtomLabel(mol->getAtomWithIdx(3));
TEST_ASSERT(key=="Rb");
key = UFF::Tools::getAtomLabel(mol->getAtomWithIdx(4));
TEST_ASSERT(key=="Cs");
BOOST_LOG(rdErrorLog) << " done" << std::endl;
}
void testUFFTyper2(){
BOOST_LOG(rdErrorLog) << "-------------------------------------" << std::endl;
BOOST_LOG(rdErrorLog) << " Test UFF atom typer." << std::endl;
ROMol *mol,*mol2;
std::string key;
mol = SmilesToMol("[SiH3]CC(=O)NC");
TEST_ASSERT(mol);
UFF::AtomicParamVect types;
bool foundAll;
boost::tie(types,foundAll)=UFF::getAtomTypes(*mol);
TEST_ASSERT(foundAll);
TEST_ASSERT(types.size()==mol->getNumAtoms());
for(UFF::AtomicParamVect::const_iterator it=types.begin();
it!=types.end();it++){
TEST_ASSERT((*it));
}
mol2 = MolOps::addHs(*mol);
delete mol;
boost::tie(types,foundAll)=UFF::getAtomTypes(*mol2);
TEST_ASSERT(foundAll);
TEST_ASSERT(types.size()==mol2->getNumAtoms());
for(UFF::AtomicParamVect::const_iterator it=types.begin();
it!=types.end();it++){
TEST_ASSERT((*it));
}
// connected with sf.net bug 2094445
mol = SmilesToMol("[SiH2]=C");
TEST_ASSERT(mol);
key = UFF::Tools::getAtomLabel(mol->getAtomWithIdx(0));
TEST_ASSERT(key=="Si3");
key = UFF::Tools::getAtomLabel(mol->getAtomWithIdx(1));
TEST_ASSERT(key=="C_2");
mol = SmilesToMol("[AlH]=C");
TEST_ASSERT(mol);
key = UFF::Tools::getAtomLabel(mol->getAtomWithIdx(0));
TEST_ASSERT(key=="Al3");
key = UFF::Tools::getAtomLabel(mol->getAtomWithIdx(1));
TEST_ASSERT(key=="C_2");
mol = SmilesToMol("[Mg]=C");
TEST_ASSERT(mol);
key = UFF::Tools::getAtomLabel(mol->getAtomWithIdx(0));
TEST_ASSERT(key=="Mg3+2");
key = UFF::Tools::getAtomLabel(mol->getAtomWithIdx(1));
TEST_ASSERT(key=="C_2");
mol = SmilesToMol("[SiH3][Si]([SiH3])=C");
TEST_ASSERT(mol);
key = UFF::Tools::getAtomLabel(mol->getAtomWithIdx(0));
TEST_ASSERT(key=="Si3");
key = UFF::Tools::getAtomLabel(mol->getAtomWithIdx(1));
TEST_ASSERT(key=="Si3");
key = UFF::Tools::getAtomLabel(mol->getAtomWithIdx(2));
TEST_ASSERT(key=="Si3");
key = UFF::Tools::getAtomLabel(mol->getAtomWithIdx(3));
TEST_ASSERT(key=="C_2");
BOOST_LOG(rdErrorLog) << " done" << std::endl;
}
void testUFFBuilder1(){
BOOST_LOG(rdErrorLog) << "-------------------------------------" << std::endl;
BOOST_LOG(rdErrorLog) << " Testing UFF builder tools." << std::endl;
ROMol *mol,*mol2;
std::string key;
UFF::AtomicParamVect types;
bool foundAll;
ForceFields::ForceField *field;
boost::shared_array<boost::uint8_t> nbrMat;
mol = SmilesToMol("CC(O)C");
Conformer *conf = new Conformer(mol->getNumAtoms());
int cid = static_cast<int>(mol->addConformer(conf, true));
TEST_ASSERT(mol);
boost::tie(types,foundAll)=UFF::getAtomTypes(*mol);
TEST_ASSERT(foundAll);
TEST_ASSERT(types.size()==mol->getNumAtoms());
field=new ForceFields::ForceField();
UFF::Tools::addBonds(*mol,types,field);
TEST_ASSERT(field->contribs().size()==3);
nbrMat = UFF::Tools::buildNeighborMatrix(*mol);
TEST_ASSERT(UFF::Tools::getTwoBitCell(nbrMat,0)==UFF::Tools::RELATION_1_X);
TEST_ASSERT(UFF::Tools::getTwoBitCell(nbrMat,1)==UFF::Tools::RELATION_1_2);
TEST_ASSERT(UFF::Tools::getTwoBitCell(nbrMat,2)==UFF::Tools::RELATION_1_3);
TEST_ASSERT(UFF::Tools::getTwoBitCell(nbrMat,3)==UFF::Tools::RELATION_1_3);
UFF::Tools::addAngles(*mol,types,field);
TEST_ASSERT(field->contribs().size()==6);
// there are no non-bonded terms here:
UFF::Tools::addNonbonded(*mol,cid,types,field,nbrMat);
TEST_ASSERT(field->contribs().size()==6);
// and no torsions either, until we add Hs:
UFF::Tools::addTorsions(*mol,types,field);
TEST_ASSERT(field->contribs().size()==6);
delete mol;
delete field;
mol = SmilesToMol("CCOC");
Conformer *conf2 = new Conformer(mol->getNumAtoms());
cid = static_cast<int>(mol->addConformer(conf2, true));
TEST_ASSERT(mol);
boost::tie(types,foundAll)=UFF::getAtomTypes(*mol);
TEST_ASSERT(foundAll);
TEST_ASSERT(types.size()==mol->getNumAtoms());
field=new ForceFields::ForceField();
UFF::Tools::addBonds(*mol,types,field);
TEST_ASSERT(field->contribs().size()==3);
nbrMat = UFF::Tools::buildNeighborMatrix(*mol);
TEST_ASSERT(UFF::Tools::getTwoBitCell(nbrMat,0)==UFF::Tools::RELATION_1_X);
TEST_ASSERT(UFF::Tools::getTwoBitCell(nbrMat,1)==UFF::Tools::RELATION_1_2);
TEST_ASSERT(UFF::Tools::getTwoBitCell(nbrMat,2)==UFF::Tools::RELATION_1_3);
TEST_ASSERT(UFF::Tools::getTwoBitCell(nbrMat,3)==UFF::Tools::RELATION_1_X);
UFF::Tools::addAngles(*mol,types,field);
TEST_ASSERT(field->contribs().size()==5);
UFF::Tools::addNonbonded(*mol,cid,types,field,nbrMat);
TEST_ASSERT(field->contribs().size()==6);
UFF::Tools::addTorsions(*mol,types,field);
TEST_ASSERT(field->contribs().size()==7);
delete mol;
delete field;
mol = SmilesToMol("CO");
Conformer *conf3 = new Conformer(mol->getNumAtoms());
cid = static_cast<int>(mol->addConformer(conf3, true));
TEST_ASSERT(mol);
boost::tie(types,foundAll)=UFF::getAtomTypes(*mol);
TEST_ASSERT(foundAll);
TEST_ASSERT(types.size()==mol->getNumAtoms());
field=new ForceFields::ForceField();
UFF::Tools::addBonds(*mol,types,field);
TEST_ASSERT(field->contribs().size()==1);
nbrMat = UFF::Tools::buildNeighborMatrix(*mol);
TEST_ASSERT(UFF::Tools::getTwoBitCell(nbrMat,0)==UFF::Tools::RELATION_1_X);
TEST_ASSERT(UFF::Tools::getTwoBitCell(nbrMat,1)==UFF::Tools::RELATION_1_2);
UFF::Tools::addAngles(*mol,types,field);
TEST_ASSERT(field->contribs().size()==1);
UFF::Tools::addNonbonded(*mol,cid,types,field,nbrMat);
TEST_ASSERT(field->contribs().size()==1);
UFF::Tools::addTorsions(*mol,types,field);
TEST_ASSERT(field->contribs().size()==1);
mol2 = MolOps::addHs(*mol);
TEST_ASSERT(mol2->getNumAtoms()==6);
delete field;
boost::tie(types,foundAll)=UFF::getAtomTypes(*mol2);
TEST_ASSERT(foundAll);
TEST_ASSERT(types.size()==mol2->getNumAtoms());
field=new ForceFields::ForceField();
UFF::Tools::addBonds(*mol2,types,field);
TEST_ASSERT(field->contribs().size()==5);
nbrMat = UFF::Tools::buildNeighborMatrix(*mol2);
UFF::Tools::addAngles(*mol2,types,field);
TEST_ASSERT(field->contribs().size()==12);
UFF::Tools::addNonbonded(*mol2,cid,types,field,nbrMat);
TEST_ASSERT(field->contribs().size()==15);
UFF::Tools::addTorsions(*mol2,types,field);
TEST_ASSERT(field->contribs().size()==18);
delete mol2;
delete mol;
delete field;
BOOST_LOG(rdErrorLog) << " done" << std::endl;
}
void testUFFBuilder2(){
BOOST_LOG(rdErrorLog) << "-------------------------------------" << std::endl;
BOOST_LOG(rdErrorLog) << " Testing UFF builder+minimization." << std::endl;
std::string pathName=getenv("RDBASE");
pathName += "/Code/GraphMol/ForceFieldHelpers/UFF/test_data";
{
RWMol *mol = MolFileToMol(pathName+"/small1.mol",false);
TEST_ASSERT(mol);
MolOps::sanitizeMol(*mol);
ForceFields::ForceField *field;
field=UFF::constructForceField(*mol);
TEST_ASSERT(field);
field->initialize();
int needMore = field->minimize();
TEST_ASSERT(!needMore);
//std::cout << MolToMolBlock(mol);
delete mol;
delete field;
}
{ // make sure the confId argument works
RWMol *mol = MolFileToMol(pathName+"/small1.mol",false);
TEST_ASSERT(mol);
MolOps::sanitizeMol(*mol);
Conformer *newConf = new Conformer(mol->getConformer());
newConf->setId(111);
mol->addConformer(newConf,false);
RDGeom::Point3D p0=mol->getConformer().getAtomPos(0);
RDGeom::Point3D p1=mol->getConformer().getAtomPos(1);
ForceFields::ForceField *field;
field=UFF::constructForceField(*mol,100,111);
TEST_ASSERT(field);
field->initialize();
int needMore = field->minimize();
TEST_ASSERT(!needMore);
//std::cout << MolToMolBlock(mol);
RDGeom::Point3D np0=mol->getConformer().getAtomPos(0);
RDGeom::Point3D np1=mol->getConformer().getAtomPos(1);
TEST_ASSERT( feq(p0.x, np0.x) );
TEST_ASSERT( feq(p0.y, np0.y) );
TEST_ASSERT( feq(p0.z, np0.z) );
TEST_ASSERT( feq(p1.x, np1.x) );
TEST_ASSERT( feq(p1.y, np1.y) );
TEST_ASSERT( feq(p1.z, np1.z) );
delete mol;
delete field;
}
{
RWMol *mol = MolFileToMol(pathName+"/small2.mol",false);
TEST_ASSERT(mol);
MolOps::sanitizeMol(*mol);
ForceFields::ForceField *field;
field=UFF::constructForceField(*mol);
TEST_ASSERT(field);
field->initialize();
int needMore = field->minimize(150);
TEST_ASSERT(!needMore);
//std::cout << MolToMolBlock(mol);
delete mol;
delete field;
}
{
RWMol *mol = MolFileToMol(pathName+"/benzene.mol",false);
TEST_ASSERT(mol);
MolOps::sanitizeMol(*mol);
ForceFields::ForceField *field;
field=UFF::constructForceField(*mol);
TEST_ASSERT(field);
field->initialize();
int needMore = field->minimize();
TEST_ASSERT(!needMore);
//std::cout << MolToMolBlock(mol);
delete mol;
delete field;
}
{
RWMol *mol = MolFileToMol(pathName+"/toluene.mol",false);
TEST_ASSERT(mol);
MolOps::sanitizeMol(*mol);
ForceFields::ForceField *field;
field=UFF::constructForceField(*mol);
TEST_ASSERT(field);
field->initialize();
int needMore = field->minimize();
TEST_ASSERT(!needMore);
//std::cout << MolToMolBlock(mol);
delete mol;
delete field;
}
{
RWMol *mol = MolFileToMol(pathName+"/complex1.mol",false);
TEST_ASSERT(mol);
MolOps::sanitizeMol(*mol);
ForceFields::ForceField *field;
field=UFF::constructForceField(*mol);
TEST_ASSERT(field);
field->initialize();
int needMore = field->minimize();
TEST_ASSERT(!needMore);
//std::cout << MolToMolBlock(mol);
delete mol;
delete field;
}
{ // test the convenience function
RWMol *mol = MolFileToMol(pathName+"/small1.mol",false);
TEST_ASSERT(mol);
MolOps::sanitizeMol(*mol);
RWMol *mol2 = new RWMol(*mol);
ForceFields::ForceField *field;
field=UFF::constructForceField(*mol);
TEST_ASSERT(field);
field->initialize();
int needMore = field->minimize();
TEST_ASSERT(!needMore);
delete field;
needMore = UFF::UFFOptimizeMolecule(*mol2).first;
TEST_ASSERT(!needMore);
for(unsigned int i=0;i<mol->getNumAtoms();++i){
const RDGeom::Point3D p1=mol->getConformer().getAtomPos(i);
const RDGeom::Point3D p2=mol2->getConformer().getAtomPos(i);
TEST_ASSERT( feq(p1.x, p2.x) );
TEST_ASSERT( feq(p1.y, p2.y) );
TEST_ASSERT( feq(p1.z, p2.z) );
}
delete mol;
delete mol2;
}
{ // test the convenience function for all confs
RWMol *mol = MolFileToMol(pathName+"/complex1.mol",false);
TEST_ASSERT(mol);
MolOps::sanitizeMol(*mol);
RWMol *mol2 = new RWMol(*mol);
Conformer *newConf = new Conformer(mol->getConformer());
newConf->setId(111);
mol->addConformer(newConf,false);
ForceFields::ForceField *field;
field=UFF::constructForceField(*mol,100,111);
TEST_ASSERT(field);
field->initialize();
int needMore = field->minimize();
TEST_ASSERT(!needMore);
delete field;
// the first conf is the same as above,
// but we add a second that's already minimized
newConf = new Conformer(mol->getConformer(111));
newConf->setId(112);
mol2->addConformer(newConf,false);
std::vector<std::pair<int,double> > res;
UFF::UFFOptimizeMoleculeConfs(*mol2,res);
TEST_ASSERT(res.size()==2);
TEST_ASSERT(!res[0].first);
TEST_ASSERT(!res[1].first);
// we expect the energy to go down at least a little bit.
TEST_ASSERT(res[1].second<res[0].second);
for(unsigned int i=0;i<mol->getNumAtoms();++i){
const RDGeom::Point3D p1=mol->getConformer(111).getAtomPos(i);
const RDGeom::Point3D p2=mol2->getConformer(0).getAtomPos(i);
TEST_ASSERT( feq(p1.x, p2.x) );
TEST_ASSERT( feq(p1.y, p2.y) );
TEST_ASSERT( feq(p1.z, p2.z) );
}
delete mol;
delete mol2;
}
BOOST_LOG(rdErrorLog) << " done" << std::endl;
}
void testUFFBatch(){
BOOST_LOG(rdErrorLog) << "-------------------------------------" << std::endl;
BOOST_LOG(rdErrorLog) << " Testing bulk UFF (regression to check that things run)." << std::endl;
ROMol *mol;
std::string key;
ForceFields::ForceField *field;
std::string pathName=getenv("RDBASE");
pathName += "/Code/GraphMol/ForceFieldHelpers/UFF/test_data";
SDMolSupplier suppl(pathName+"/bulk.sdf",false);
int count=0;
mol = suppl.next();
while(mol && !suppl.atEnd() ){
count++;
MolOps::sanitizeMol(*(RWMol *)mol);
std::string origMolBlock = MolToMolBlock(*mol);
BOOST_LOG(rdErrorLog) << "Mol:" << count << std::endl;
try {
field=UFF::constructForceField(*mol);
} catch (...) {
field = 0;
}
if(field){
field->initialize();
int failed=field->minimize(500);
if(failed){
BOOST_LOG(rdErrorLog) << " not converged (code="<<failed<<")" << std::endl;
std::cout << origMolBlock << "$$$$" << std::endl;
std::cout << MolToMolBlock(*mol) << "$$$$" << std::endl;
}
delete field;
}
delete mol;
mol = suppl.next();
}
BOOST_LOG(rdErrorLog) << " done" << std::endl;
}
void testUFFBuilderSpecialCases(){
BOOST_LOG(rdErrorLog) << "-------------------------------------" << std::endl;
BOOST_LOG(rdErrorLog) << " Testing UFF special cases." << std::endl;
RWMol *mol;
std::string key;
int needMore;
RDGeom::Point3D v1,v2;
ForceFields::ForceField *field;
std::string pathName=getenv("RDBASE");
pathName += "/Code/GraphMol/ForceFieldHelpers/UFF/test_data";
// ----------
// Trigonal bipyramid
// ----------
mol = MolFileToMol(pathName+"/tbp.mol",false);
TEST_ASSERT(mol);
MolOps::sanitizeMol(*mol);
const Conformer &conf = mol->getConformer();
field=UFF::constructForceField(*mol);
TEST_ASSERT(field);
field->initialize();
needMore = field->minimize(200,1e-8,1e-4);
TEST_ASSERT(!needMore);
v1 = conf.getAtomPos(0).directionVector(conf.getAtomPos(1));
v2 = conf.getAtomPos(0).directionVector(conf.getAtomPos(2));
TEST_ASSERT(feq(v1.dotProduct(v2),-1.0,1e-3));
v2 = conf.getAtomPos(0).directionVector(conf.getAtomPos(3));
TEST_ASSERT(feq(v1.dotProduct(v2),0.0,1e-3));
v2 = conf.getAtomPos(0).directionVector(conf.getAtomPos(4));
TEST_ASSERT(feq(v1.dotProduct(v2),0.0,1e-3));
v2 = conf.getAtomPos(0).directionVector(conf.getAtomPos(5));
TEST_ASSERT(feq(v1.dotProduct(v2),0.0,1e-3));
v1 = conf.getAtomPos(0).directionVector(conf.getAtomPos(2));
v2 = conf.getAtomPos(0).directionVector(conf.getAtomPos(3));
TEST_ASSERT(feq(v1.dotProduct(v2),0.0,1e-3));
v2 = conf.getAtomPos(0).directionVector(conf.getAtomPos(4));
TEST_ASSERT(feq(v1.dotProduct(v2),0.0,1e-3));
v2 = conf.getAtomPos(0).directionVector(conf.getAtomPos(5));
TEST_ASSERT(feq(v1.dotProduct(v2),0.0,1e-3));
v1 = conf.getAtomPos(0).directionVector(conf.getAtomPos(3));
v2 = conf.getAtomPos(0).directionVector(conf.getAtomPos(4));
TEST_ASSERT(feq(v1.dotProduct(v2),-0.5,1e-3));
v2 = conf.getAtomPos(0).directionVector(conf.getAtomPos(5));
TEST_ASSERT(feq(v1.dotProduct(v2),-0.5,1e-3));
v1 = conf.getAtomPos(0).directionVector(conf.getAtomPos(4));
v2 = conf.getAtomPos(0).directionVector(conf.getAtomPos(5));
TEST_ASSERT(feq(v1.dotProduct(v2),-0.5,1e-3));
delete mol;
delete field;
BOOST_LOG(rdErrorLog) << " done" << std::endl;
}
void testIssue239(){
BOOST_LOG(rdErrorLog) << "-------------------------------------" << std::endl;
BOOST_LOG(rdErrorLog) << " Testing Issue239." << std::endl;
RWMol *mol;
int needMore;
ForceFields::ForceField *field;
double e1,e2;
std::string pathName=getenv("RDBASE");
pathName += "/Code/GraphMol/ForceFieldHelpers/UFF/test_data";
mol = MolFileToMol(pathName+"/Issue239.mol",false);
TEST_ASSERT(mol);
MolOps::sanitizeMol(*mol);
field=UFF::constructForceField(*mol);
TEST_ASSERT(field);
field->initialize();
needMore = field->minimize(200,1e-6,1e-3);
e1 = field->calcEnergy();
needMore = field->minimize(200,1e-6,1e-3);
e2 = field->calcEnergy();
TEST_ASSERT(feq(e2,e1,0.1));
delete mol;
delete field;
BOOST_LOG(rdErrorLog) << " done" << std::endl;
}
#endif
void testIssue242(){
#if 0
// FIX: Changes to the forcefield (connected to Issue 408) have
// made it so that this particular problem no longer manifests
// in this molecule/embedding. A new test case is needed.
BOOST_LOG(rdErrorLog) << "-------------------------------------" << std::endl;
BOOST_LOG(rdErrorLog) << " Testing Issue242." << std::endl;
RWMol *mol,*mol2;
int needMore;
ForceFields::ForceField *field=0,*field2=0;
std::string mb1,mb2;
double e1,e2;
std::string pathName=getenv("RDBASE");
pathName += "/Code/GraphMol/ForceFieldHelpers/UFF/test_data";
mol = MolFileToMol(pathName+"/Issue242.mol");
TEST_ASSERT(mol);
mol2 = MolFileToMol(pathName+"/Issue242.mol");
TEST_ASSERT(mol2);
TEST_ASSERT(DGeomHelpers::EmbedMolecule(*mol2,30,2300)>=0);
mb1 = MolToMolBlock(*mol);
mb2 = MolToMolBlock(*mol2);
//BOOST_LOG(rdInfoLog) << "\nMol1\n" << mb1 << std::endl;
//BOOST_LOG(rdInfoLog) << "\nMol2\n" << mb2 << std::endl;
field=UFF::constructForceField(*mol);
TEST_ASSERT(field);
field->initialize();
field2=UFF::constructForceField(*mol2);
TEST_ASSERT(field2);
field2->initialize();
e1 = field->calcEnergy();
e2 = field2->calcEnergy();
BOOST_LOG(rdInfoLog) << "E1: " << e1 << std::endl;
BOOST_LOG(rdInfoLog) << "E2: " << e2 << std::endl;
//TEST_ASSERT(feq(e2,e1,0.1));
needMore = field->minimize(600,1e-4);
TEST_ASSERT(!needMore)
needMore = field2->minimize(600,1e-4);
TEST_ASSERT(!needMore)
e1 = field->calcEnergy();
e2 = field2->calcEnergy();
BOOST_LOG(rdInfoLog) << "E1: " << e1 << std::endl;
BOOST_LOG(rdInfoLog) << "E2: " << e2 << std::endl;
TEST_ASSERT(feq(e2,e1,1.0));
needMore = field->minimize(600,1e-4);
TEST_ASSERT(!needMore)
needMore = field2->minimize(600,1e-4);
TEST_ASSERT(!needMore)
e1 = field->calcEnergy();
e2 = field2->calcEnergy();
BOOST_LOG(rdInfoLog) << "rE1: " << e1 << std::endl;
BOOST_LOG(rdInfoLog) << "rE2: " << e2 << std::endl;
TEST_ASSERT(feq(e2,e1,1.0));
delete mol;
delete mol2;
delete field;
delete field2;
mol = MolFileToMol(pathName+"/Issue242-2.mol");
TEST_ASSERT(mol);
mol2 = MolFileToMol(pathName+"/Issue242-2.mol");
TEST_ASSERT(mol2);
TEST_ASSERT(DGeomHelpers::EmbedMolecule(*mol2,30,2370)>=0);
mb1 = MolToMolBlock(*mol);
mb2 = MolToMolBlock(*mol2);
//std::cout << mb1 << "------\n";
//std::cout << mb2 << "------\n";
field=UFF::constructForceField(*mol);
TEST_ASSERT(field);
field->initialize();
field2=UFF::constructForceField(*mol2);
TEST_ASSERT(field2);
field2->initialize();
e1 = field->calcEnergy();
e2 = field2->calcEnergy();
BOOST_LOG(rdInfoLog) << "E1: " << e1 << std::endl;
BOOST_LOG(rdInfoLog) << "E2: " << e2 << std::endl;
//TEST_ASSERT(feq(e2,e1,0.1));
needMore = field->minimize(200,1e-4);
needMore = field2->minimize(200,1e-4);
e1 = field->calcEnergy();
e2 = field2->calcEnergy();
BOOST_LOG(rdInfoLog) << "E1: " << e1 << std::endl;
BOOST_LOG(rdInfoLog) << "E2: " << e2 << std::endl;
TEST_ASSERT(feq(e2,e1,0.1));
delete mol;
delete mol2;
delete field;
delete field2;
BOOST_LOG(rdErrorLog) << " done" << std::endl;
#endif
}
void testSFIssue1653802(){
BOOST_LOG(rdErrorLog) << "-------------------------------------" << std::endl;
BOOST_LOG(rdErrorLog) << " Testing SFIssue1653802." << std::endl;
RWMol *mol;
int needMore;
ForceFields::ForceField *field;
std::string pathName=getenv("RDBASE");
pathName += "/Code/GraphMol/ForceFieldHelpers/UFF/test_data";
mol = MolFileToMol(pathName+"/cyclobutadiene.mol",false);
TEST_ASSERT(mol);
MolOps::sanitizeMol(*mol);
UFF::AtomicParamVect types;
bool foundAll;
boost::shared_array<boost::uint8_t> nbrMat;
boost::tie(types,foundAll)=UFF::getAtomTypes(*mol);
TEST_ASSERT(foundAll);
TEST_ASSERT(types.size()==mol->getNumAtoms());
field=new ForceFields::ForceField();
UFF::Tools::addBonds(*mol,types,field);
TEST_ASSERT(field->contribs().size()==8);
nbrMat = UFF::Tools::buildNeighborMatrix(*mol);
UFF::Tools::addAngles(*mol,types,field);
TEST_ASSERT(field->contribs().size()==20);
UFF::Tools::addTorsions(*mol,types,field);
//std::cout << field->contribs().size() << std::endl;
TEST_ASSERT(field->contribs().size()==36);
UFF::Tools::addNonbonded(*mol,0,types,field,nbrMat);
delete field;
field = UFF::constructForceField(*mol);
field->initialize();
needMore = field->minimize(200,1e-6,1e-3);
TEST_ASSERT(!needMore);
delete mol;
delete field;
BOOST_LOG(rdErrorLog) << " done" << std::endl;
}
void testSFIssue2378119(){
BOOST_LOG(rdErrorLog) << "-------------------------------------" << std::endl;
BOOST_LOG(rdErrorLog) << " Testing SFIssue2378119." << std::endl;
std::string pathName=getenv("RDBASE");
pathName += "/Code/GraphMol/ForceFieldHelpers/UFF/test_data";
{
RWMol *mol = MolFileToMol(pathName+"/Issue2378119.mol");
TEST_ASSERT(mol);
ForceFields::ForceField *field=UFF::constructForceField(*mol);
TEST_ASSERT(field);
field->initialize();
double e1 = field->calcEnergy();
TEST_ASSERT(e1>0.0 && e1<1e12);
int needMore = field->minimize(200,1e-6,1e-3);
TEST_ASSERT(!needMore);
double e2 = field->calcEnergy();
TEST_ASSERT(e2<e1);
delete mol;
delete field;
}
{
RWMol *mol = MolFileToMol(pathName+"/Issue2378119.2.mol");
TEST_ASSERT(mol);
ForceFields::ForceField *field=UFF::constructForceField(*mol);
TEST_ASSERT(field);
field->initialize();
double e1 = field->calcEnergy();
TEST_ASSERT(e1==0.0);
int needMore = field->minimize(200,1e-6,1e-3);
TEST_ASSERT(!needMore);
double e2 = field->calcEnergy();
TEST_ASSERT(e2==e1);
delete mol;
delete field;
}
{
RWMol *mol = MolFileToMol(pathName+"/Issue2378119.2.mol");
TEST_ASSERT(mol);
ForceFields::ForceField *field=UFF::constructForceField(*mol,100.0,-1,false);
TEST_ASSERT(field);
field->initialize();
double e1 = field->calcEnergy();
TEST_ASSERT(e1>0.0 && e1<1e12);
int needMore = field->minimize(200,1e-6,1e-3);
TEST_ASSERT(!needMore);
double e2 = field->calcEnergy();
TEST_ASSERT(e2<e1);
delete mol;
delete field;
}
BOOST_LOG(rdErrorLog) << " done" << std::endl;
}
void testMissingParams(){
BOOST_LOG(rdErrorLog) << "-------------------------------------" << std::endl;
BOOST_LOG(rdErrorLog) << " Testing handling missing parameters." << std::endl;
{
UFF::AtomicParamVect types;
bool foundAll;
ROMol *mol = SmilesToMol("[Cu](C)(C)(C)(C)C");
TEST_ASSERT(mol);
ROMol *mol2 = MolOps::addHs(*mol);
delete mol;
TEST_ASSERT(DGeomHelpers::EmbedMolecule(*mol2)>=0);
boost::tie(types,foundAll)=UFF::getAtomTypes(*mol2);
TEST_ASSERT(!foundAll);
TEST_ASSERT(types.size()==mol2->getNumAtoms());
TEST_ASSERT(!types[0]);
// make sure we can optimize anyway:
ForceFields::ForceField *field=UFF::constructForceField(*mol2,types);
TEST_ASSERT(field);
field->initialize();
double e1=field->calcEnergy();
int needMore = field->minimize();
TEST_ASSERT(needMore);
double e2 = field->calcEnergy();
TEST_ASSERT(e2<e1);
//std::cerr<<" DE: "<<e1<<" -> "<<e2<<std::endl;
delete mol2;
delete field;
}
BOOST_LOG(rdErrorLog) << " done" << std::endl;
}
void testSFIssue3009337(){
BOOST_LOG(rdErrorLog) << "-------------------------------------" << std::endl;
BOOST_LOG(rdErrorLog) << " Testing SFIssue3009337." << std::endl;
std::string pathName=getenv("RDBASE");
pathName += "/Code/GraphMol/ForceFieldHelpers/UFF/test_data";
{
RWMol *mol = MolFileToMol(pathName+"/Issue3009337.mol",true,false);
TEST_ASSERT(mol);
ForceFields::ForceField *field=UFF::constructForceField(*mol);
TEST_ASSERT(field);
field->initialize();
double e1 = field->calcEnergy();
TEST_ASSERT(e1>0.0 && e1<1e12);
int needMore = field->minimize(200,1e-6,1e-3);
TEST_ASSERT(!needMore);
double e2 = field->calcEnergy();
TEST_ASSERT(e2<e1);
delete mol;
delete field;
}
{
RWMol *mol = MolFileToMol(pathName+"/Issue3009337.2.mol",true,false);
TEST_ASSERT(mol);
ForceFields::ForceField *field=UFF::constructForceField(*mol);
TEST_ASSERT(field);
field->initialize();
double e1 = field->calcEnergy();
TEST_ASSERT(e1>0.0 && e1<1e12);
int needMore = field->minimize(200,1e-6,1e-3);
TEST_ASSERT(!needMore);
double e2 = field->calcEnergy();
TEST_ASSERT(e2<e1);
delete mol;
delete field;
}
BOOST_LOG(rdErrorLog) << " done" << std::endl;
}
void testGitHubIssue62() {
BOOST_LOG(rdErrorLog) << "-------------------------------------" << std::endl;
BOOST_LOG(rdErrorLog) << " Testing GitHubIssue62." << std::endl;
std::string pathName=getenv("RDBASE");
pathName += "/Code/GraphMol/ForceFieldHelpers/UFF/test_data";
{
double energyValues[] =
{ 38.687, 174.698, 337.986, 115.248,
2.482, 1.918, 10.165, 98.469, 39.078,
267.236, 15.747, 202.121, 205.539,
20.044, 218.986, 79.627 };
SmilesMolSupplier smiSupplier(pathName + "/Issue62.smi");
SDWriter *sdfWriter = new SDWriter(pathName + "/Issue62.sdf");
for (unsigned int i = 0; i < smiSupplier.length(); ++i) {
ROMol *mol = MolOps::addHs(*(smiSupplier[i]));
TEST_ASSERT(mol);
std::string molName = "";
if (mol->hasProp(common_properties::_Name)) {
mol->getProp(common_properties::_Name, molName);
}
DGeomHelpers::EmbedMolecule(*mol);
ForceFields::ForceField *field = UFF::constructForceField(*mol);
TEST_ASSERT(field);
field->initialize();
int needMore = field->minimize(200, 1.e-6, 1.e-3);
TEST_ASSERT(!needMore);
sdfWriter->write(*mol);
double e = field->calcEnergy();
BOOST_LOG(rdErrorLog) << molName << " " << e << std::endl;
TEST_ASSERT(fabs(e - energyValues[i]) < 1.);
}
sdfWriter->close();
BOOST_LOG(rdErrorLog) << " done" << std::endl;
}
}
void testUFFParamGetters()
{
BOOST_LOG(rdErrorLog) << "-------------------------------------" << std::endl;
BOOST_LOG(rdErrorLog) << " Test UFF force-field parameter getters." << std::endl;
{
ROMol *mol = SmilesToMol("c1ccccc1CCNN");
TEST_ASSERT(mol);
ROMol *molH = MolOps::addHs(*mol);
TEST_ASSERT(molH);
ForceFields::UFF::UFFBond uffBondStretchParams;
TEST_ASSERT(UFF::getUFFBondStretchParams(*molH, 6, 7, uffBondStretchParams));
TEST_ASSERT(((int)boost::math::round(uffBondStretchParams.kb * 1000) == 699592)
&& ((int)boost::math::round(uffBondStretchParams.r0 * 1000) == 1514));
TEST_ASSERT(!UFF::getUFFBondStretchParams(*molH, 0, 7, uffBondStretchParams));
ForceFields::UFF::UFFAngle uffAngleBendParams;
TEST_ASSERT(UFF::getUFFAngleBendParams(*molH, 6, 7, 8, uffAngleBendParams));
TEST_ASSERT(((int)boost::math::round(uffAngleBendParams.ka * 1000) == 143325)
&& ((int)boost::math::round(uffAngleBendParams.theta0 * 1000) == 109470));
TEST_ASSERT(!UFF::getUFFAngleBendParams(*molH, 0, 7, 8, uffAngleBendParams));
ForceFields::UFF::UFFTor uffTorsionParams;
TEST_ASSERT(UFF::getUFFTorsionParams(*molH, 6, 7, 8, 9, uffTorsionParams));
TEST_ASSERT(((int)boost::math::round(uffTorsionParams.V * 1000) == 976));
TEST_ASSERT(!UFF::getUFFTorsionParams(*molH, 0, 7, 8, 9, uffTorsionParams));
ForceFields::UFF::UFFInv uffInversionParams;
TEST_ASSERT(UFF::getUFFInversionParams(*molH, 6, 5, 4, 0, uffInversionParams));
TEST_ASSERT(((int)boost::math::round(uffInversionParams.K * 1000) == 2000));
TEST_ASSERT(!UFF::getUFFInversionParams(*molH, 6, 5, 4, 1, uffInversionParams));
ForceFields::UFF::UFFVdW uffVdWParams;
TEST_ASSERT(UFF::getUFFVdWParams(*molH, 0, 9, uffVdWParams));
TEST_ASSERT(((int)boost::math::round(uffVdWParams.x_ij * 1000) == 3754)
&& ((int)boost::math::round(uffVdWParams.D_ij * 1000) == 85));
}
}
#ifdef RDK_TEST_MULTITHREADED
namespace {
void runblock_uff(const std::vector<ROMol *> &mols,const std::vector<double> &energies,
unsigned int count,unsigned int idx){
for(unsigned int rep=0;rep<1000;++rep){
for(unsigned int i=0;i<mols.size();++i){
if(i%count != idx) continue;
ROMol *mol = mols[i];
ForceFields::ForceField *field = 0;
if(!(rep%100)){
BOOST_LOG(rdErrorLog) << "Rep: "<<rep<<" Mol:" << i << std::endl;
}
try {
field = UFF::constructForceField(*mol);
} catch (...) {
field = 0;
}
TEST_ASSERT(field);
field->initialize();
int failed = field->minimize(500);
TEST_ASSERT(!failed);
double eng=field->calcEnergy();
TEST_ASSERT(feq(eng,energies[i]));
delete field;
}
}
}
}
#include <boost/thread.hpp>
void testUFFMultiThread(){
BOOST_LOG(rdErrorLog) << "-------------------------------------" << std::endl;
BOOST_LOG(rdErrorLog) << " Test UFF multithreading" << std::endl;
ForceFields::ForceField *field;
std::string pathName = getenv("RDBASE");
pathName += "/Code/GraphMol/ForceFieldHelpers/UFF/test_data";
SDMolSupplier suppl(pathName + "/bulk.sdf");
std::vector<ROMol *> mols;
while(!suppl.atEnd()&&mols.size()<100){
ROMol *mol=0;
try{
mol=suppl.next();
} catch(...){
continue;
}
if(!mol) continue;
mols.push_back(mol);
}
std::cerr<<"generating reference data"<<std::endl;
std::vector<double> energies(mols.size(),0.0);
for(unsigned int i=0;i<mols.size();++i){
ROMol mol(*mols[i]);
ForceFields::ForceField *field = 0;
try {
field = UFF::constructForceField(mol);
} catch (...) {
field = 0;
}
TEST_ASSERT(field);
field->initialize();
int failed = field->minimize(500);
TEST_ASSERT(!failed);
energies[i]=field->calcEnergy();
delete field;
}
boost::thread_group tg;
std::cerr<<"processing"<<std::endl;
unsigned int count=4;
for(unsigned int i=0;i<count;++i){
std::cerr<<" launch :"<<i<<std::endl;std::cerr.flush();
tg.add_thread(new boost::thread(runblock_uff,mols,energies,count,i));
}
tg.join_all();
BOOST_FOREACH(ROMol *mol,mols){
delete mol;
}
BOOST_LOG(rdErrorLog) << " done" << std::endl;
}
void testUFFMultiThread2(){
BOOST_LOG(rdErrorLog) << "-------------------------------------" << std::endl;
BOOST_LOG(rdErrorLog) << " Test UFF multithreading2" << std::endl;
std::string pathName = getenv("RDBASE");
pathName += "/Code/GraphMol/ForceFieldHelpers/UFF/test_data";
SDMolSupplier suppl(pathName + "/bulk.sdf");
ROMol *m=suppl[4];
TEST_ASSERT(m);
ROMol *om = new ROMol(*m);
for(unsigned int i=0;i<1000;++i){
m->addConformer(new Conformer(m->getConformer()),true);
}
std::vector<std::pair<int,double> > res;
UFF::UFFOptimizeMolecule(*om);
UFF::UFFOptimizeMoleculeConfs(*m,res,4);
for(unsigned int i=1;i<res.size();++i){
TEST_ASSERT(!res[i].first);
TEST_ASSERT(feq(res[i].second,res[0].second,.00001));
}
for(unsigned int i=0;i<m->getNumAtoms();++i){
RDGeom::Point3D p0=om->getConformer().getAtomPos(i);
RDGeom::Point3D np0=m->getConformer().getAtomPos(i);
TEST_ASSERT( feq(p0.x, np0.x) );
TEST_ASSERT( feq(p0.y, np0.y) );
TEST_ASSERT( feq(p0.z, np0.z) );
np0=m->getConformer(11).getAtomPos(i); // pick some random other conformer
TEST_ASSERT( feq(p0.x, np0.x) );
TEST_ASSERT( feq(p0.y, np0.y) );
TEST_ASSERT( feq(p0.z, np0.z) );
}
delete m;
delete om;
BOOST_LOG(rdErrorLog) << " done" << std::endl;
}
#endif
//-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*
//
//-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*
int main(){
RDLog::InitLogs();
#if 1
testUFFTyper1();
testUFFTyper2();
testUFFBuilder1();
testUFFBuilder2();
testUFFBatch();
testUFFBuilderSpecialCases();
testIssue239();
testIssue242();
testSFIssue1653802();
testSFIssue2378119();
testUFFParamGetters();
testMissingParams();
testSFIssue3009337();
#ifdef RDK_TEST_MULTITHREADED
testUFFMultiThread();
testUFFMultiThread2();
#endif
#endif
testGitHubIssue62();
}
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