void testSFIssue2378119() {
BOOST_LOG(rdErrorLog) << "-------------------------------------" << std::endl;
BOOST_LOG(rdErrorLog) << " Testing SFIssue2378119." << std::endl;
std::string pathName = getenv("RDBASE");
pathName += "/Code/GraphMol/ForceFieldHelpers/MMFF/test_data";
{
RWMol *mol = MolFileToMol(pathName + "/Issue2378119.mol");
TEST_ASSERT(mol);
ForceFields::ForceField *field = MMFF::constructForceField(*mol);
TEST_ASSERT(field);
field->initialize();
double e1 = field->calcEnergy();
TEST_ASSERT(e1 > 0.0 && e1 < 1.0e12);
int needMore = field->minimize(200, 1.0e-6, 1.0e-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 = MMFF::constructForceField(*mol);
TEST_ASSERT(field);
field->initialize();
double e1 = field->calcEnergy();
TEST_ASSERT(e1 == 0.0);
int needMore = field->minimize(200, 1.0e-6, 1.0e-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 =
MMFF::constructForceField(*mol, 100.0, -1, false);
TEST_ASSERT(field);
field->initialize();
double e1 = field->calcEnergy();
TEST_ASSERT(e1 > 0.0 && e1 < 1.0e12);
int needMore = field->minimize(200, 1.0e-6, 1.0e-3);
TEST_ASSERT(!needMore);
double e2 = field->calcEnergy();
TEST_ASSERT(e2 < e1);
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;
}
void runMol(ROMol *mol,int checkEvery=10,bool verbose=true){
ForceFields::ForceField *field;
std::cout << MolToMolBlock(*mol) << "$$$$" << std::endl;
try{
field=UFF::constructForceField(*mol,2.5);
} catch (...) {
field=0;
}
if(field){
field->initialize();
int needMore=1;
int nPasses=0;
while(needMore){
#if 1
needMore = field->minimize(checkEvery);
if(verbose) std::cerr << "\t" << ++nPasses << std::endl;
#else
needMore = field->minimize(1);
std::cout << MolToMolBlock(mol) << "$$$$" << std::endl;
#endif
}
std::cout << MolToMolBlock(*mol) << "$$$$" << std::endl;
delete field;
} else {
std::cerr << "failed";
}
}
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 testIssue242()
{
// 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/MMFF/test_data";
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 = MMFF::constructForceField(*mol);
TEST_ASSERT(field);
field->initialize();
field2 = MMFF::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(200,1.0e-4);
needMore = field2->minimize(200,1.0e-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;
}
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 testCrippenO3AConstraints() {
ROMol *m = SmilesToMol("n1ccc(cc1)-c1ccccc1");
TEST_ASSERT(m);
ROMol *m1 = MolOps::addHs(*m);
delete m;
TEST_ASSERT(m1);
DGeomHelpers::EmbedMolecule(*m1);
MMFF::sanitizeMMFFMol((RWMol &)(*m1));
MMFF::MMFFMolProperties mp(*m1);
TEST_ASSERT(mp.isValid());
ForceFields::ForceField *field = MMFF::constructForceField(*m1, &mp);
field->initialize();
field->minimize();
RWMol *patt = SmartsToMol("nccc-cccc");
MatchVectType matchVect;
TEST_ASSERT(SubstructMatch(*m1, (ROMol &)*patt, matchVect));
unsigned int nIdx = matchVect[0].second;
unsigned int cIdx = matchVect[matchVect.size() - 1].second;
MolTransforms::setDihedralDeg(m1->getConformer(), matchVect[2].second,
matchVect[3].second, matchVect[4].second, matchVect[5].second, 0.0);
ROMol m2(*m1);
MolAlign::randomTransform(m2);
ROMol m3(m2);
unsigned int prbNAtoms = m2.getNumAtoms();
std::vector<double> prbLogpContribs(prbNAtoms);
std::vector<double> prbMRContribs(prbNAtoms);
std::vector<unsigned int> prbAtomTypes(prbNAtoms);
std::vector<std::string> prbAtomTypeLabels(prbNAtoms);
Descriptors::getCrippenAtomContribs(m2, prbLogpContribs,
prbMRContribs, true, &prbAtomTypes, &prbAtomTypeLabels);
MolAlign::O3A *o3a = new MolAlign::O3A(m2, *m1,
&prbLogpContribs, &prbLogpContribs, MolAlign::O3A::CRIPPEN);
TEST_ASSERT(o3a);
o3a->align();
delete o3a;
double d = (m2.getConformer().getAtomPos(cIdx)
- m1->getConformer().getAtomPos(cIdx)).length();
TEST_ASSERT(feq(d, 0.0, 1));
MatchVectType constraintMap;
constraintMap.push_back(std::make_pair(cIdx, nIdx));
o3a = new MolAlign::O3A(m3, *m1, &prbLogpContribs, &prbLogpContribs,
MolAlign::O3A::CRIPPEN, -1, -1, false, 50, 0, &constraintMap);
TEST_ASSERT(o3a);
o3a->align();
delete o3a;
d = (m3.getConformer().getAtomPos(cIdx)
- m1->getConformer().getAtomPos(cIdx)).length();
TEST_ASSERT(feq(d, 7.0, 1.0));
delete m1;
}
int MMFFOptimizeMolecule(ROMol &mol, std::string mmffVariant = "MMFF94",
int maxIters = 200, double nonBondedThresh = 100.0, int confId = -1,
bool ignoreInterfragInteractions = true)
{
int res = -1;
MMFF::MMFFMolProperties mmffMolProperties(mol, mmffVariant);
if (mmffMolProperties.isValid()) {
ForceFields::ForceField *ff = MMFF::constructForceField(mol,
&mmffMolProperties, nonBondedThresh, confId, ignoreInterfragInteractions);
ff->initialize();
res = ff->minimize(maxIters);
delete ff;
}
return res;
}
void testGithub308()
{
BOOST_LOG(rdErrorLog) << "-------------------------------------" << std::endl;
BOOST_LOG(rdErrorLog) << " Testing github 308: crash during MMFF parameterization ." << std::endl;
ROMol *mol = SmilesToMol("FF");
TEST_ASSERT(DGeomHelpers::EmbedMolecule(*mol) >= 0);
int needMore;
ForceFields::ForceField *field = 0;
TEST_ASSERT(mol);
MMFF::MMFFMolProperties mmffMolProperties(*mol);
TEST_ASSERT(mmffMolProperties.isValid());
field = MMFF::constructForceField(*mol);
TEST_ASSERT(field);
field->initialize();
needMore = field->minimize(200, 1.0e-6, 1.0e-3);
TEST_ASSERT(!needMore);
}
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 testMMFFBatch() {
BOOST_LOG(rdErrorLog) << "-------------------------------------" << std::endl;
BOOST_LOG(rdErrorLog)
<< " Testing bulk MMFF (regression to check that things run)."
<< std::endl;
ROMol *mol;
ForceFields::ForceField *field;
std::string pathName = getenv("RDBASE");
pathName += "/Code/GraphMol/ForceFieldHelpers/MMFF/test_data";
SDMolSupplier suppl(pathName + "/bulk.sdf");
int count = 0;
mol = suppl.next();
while (mol && (!(suppl.atEnd()))) {
++count;
std::string origMolBlock = MolToMolBlock(*mol);
BOOST_LOG(rdErrorLog) << "Mol:" << count << std::endl;
try {
field = MMFF::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 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/MMFF/test_data";
mol = MolFileToMol(pathName + "/cyclobutadiene.mol", false);
TEST_ASSERT(mol);
MolOps::sanitizeMol(*mol);
MMFF::MMFFMolProperties *mmffMolProperties =
new MMFF::MMFFMolProperties(*mol);
TEST_ASSERT(mmffMolProperties);
boost::shared_array<boost::uint8_t> nbrMat;
field = new ForceFields::ForceField();
MMFF::Tools::addBonds(*mol, mmffMolProperties, field);
TEST_ASSERT(field->contribs().size() == 8);
nbrMat = MMFF::Tools::buildNeighborMatrix(*mol);
MMFF::Tools::addAngles(*mol, mmffMolProperties, field);
TEST_ASSERT(field->contribs().size() == 20);
MMFF::Tools::addTorsions(*mol, mmffMolProperties, field);
// std::cout << field->contribs().size() << std::endl;
TEST_ASSERT(field->contribs().size() == 36);
MMFF::Tools::addVdW(*mol, 0, mmffMolProperties, field, nbrMat);
delete field;
field = MMFF::constructForceField(*mol);
field->initialize();
needMore = field->minimize(200, 1.0e-6, 1.0e-3);
TEST_ASSERT(!needMore);
delete mol;
delete field;
delete mmffMolProperties;
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 testUFFBuilder2(){
BOOST_LOG(rdErrorLog) << "-------------------------------------" << std::endl;
BOOST_LOG(rdErrorLog) << " Testing UFF builder+minimization." << std::endl;
RWMol *mol;
std::string key;
int needMore;
ForceFields::ForceField *field;
std::string pathName=getenv("RDBASE");
pathName += "/Code/GraphMol/ForceFieldHelpers/UFF/test_data";
mol = MolFileToMol(pathName+"/small1.mol",false);
TEST_ASSERT(mol);
MolOps::sanitizeMol(*mol);
field=UFF::constructForceField(*mol);
TEST_ASSERT(field);
field->initialize();
needMore = field->minimize();
TEST_ASSERT(!needMore);
//std::cout << MolToMolBlock(mol);
delete mol;
delete field;
mol = MolFileToMol(pathName+"/small2.mol",false);
TEST_ASSERT(mol);
MolOps::sanitizeMol(*mol);
field=UFF::constructForceField(*mol);
TEST_ASSERT(field);
field->initialize();
needMore = field->minimize(150);
TEST_ASSERT(!needMore);
//std::cout << MolToMolBlock(mol);
delete mol;
delete field;
mol = MolFileToMol(pathName+"/benzene.mol",false);
TEST_ASSERT(mol);
MolOps::sanitizeMol(*mol);
field=UFF::constructForceField(*mol);
TEST_ASSERT(field);
field->initialize();
needMore = field->minimize();
TEST_ASSERT(!needMore);
//std::cout << MolToMolBlock(mol);
delete mol;
delete field;
mol = MolFileToMol(pathName+"/toluene.mol",false);
TEST_ASSERT(mol);
MolOps::sanitizeMol(*mol);
field=UFF::constructForceField(*mol);
TEST_ASSERT(field);
field->initialize();
needMore = field->minimize();
TEST_ASSERT(!needMore);
//std::cout << MolToMolBlock(mol);
delete mol;
delete field;
mol = MolFileToMol(pathName+"/complex1.mol",false);
TEST_ASSERT(mol);
MolOps::sanitizeMol(*mol);
field=UFF::constructForceField(*mol);
TEST_ASSERT(field);
field->initialize();
needMore = field->minimize();
TEST_ASSERT(!needMore);
//std::cout << MolToMolBlock(mol);
delete mol;
delete field;
BOOST_LOG(rdErrorLog) << " done" << std::endl;
}
void testTorsionAngleM6() {
std::cerr << "-------------------------------------" << std::endl;
std::cerr << " Test CrystalFF torsional term." << std::endl;
ForceFields::ForceField ff;
Point3D p1, p2, p3, p4;
RDGeom::PointPtrVect &ps = ff.positions();
ps.push_back(&p1);
ps.push_back(&p2);
ps.push_back(&p3);
ps.push_back(&p4);
ForceFields::CrystalFF::TorsionAngleContribM6 *contrib;
// ------- ------- ------- ------- ------- ------- -------
// Basic SP3 - SP3
// ------- ------- ------- ------- ------- ------- -------
// [!#1:1][CX4H2:2]!@[CX4H2:3][!#1:4] 1 0.0 1 0.0 1 4.0 1 0.0 1 0.0 1 0.0
std::vector<int> signs(6, 1);
std::vector<double> v(6, 0.0);
v[2] = 4.0;
contrib = new ForceFields::CrystalFF::TorsionAngleContribM6(&ff, 0, 1, 2, 3,
v, signs);
ff.contribs().push_back(ForceFields::ContribPtr(contrib));
p1.x = 0;
p1.y = 1.5;
p1.z = 0;
p2.x = 0.0;
p2.y = 0.0;
p2.z = 0.0;
p3.x = 1.5;
p3.y = 0.0;
p3.z = 0.0;
p4.x = 1.5;
p4.y = 0.0;
p4.z = 1.5;
ff.initialize();
ff.minimize(10, 1e-8, 1e-8);
double cosPhi = ForceFields::MMFF::Utils::calcTorsionCosPhi(
*(RDGeom::Point3D *)ff.positions()[0],
*(RDGeom::Point3D *)ff.positions()[1],
*(RDGeom::Point3D *)ff.positions()[2],
*(RDGeom::Point3D *)ff.positions()[3]);
TEST_ASSERT(RDKit::feq(cosPhi, 0.5, 1e-4));
// ------- ------- ------- ------- ------- ------- -------
// Basic SP2 - SP2
// ------- ------- ------- ------- ------- ------- -------
signs[1] = -1;
v[2] = 0.0;
v[1] = 7.0;
ff.contribs().pop_back();
contrib = new ForceFields::CrystalFF::TorsionAngleContribM6(&ff, 0, 1, 2, 3,
v, signs);
ff.contribs().push_back(ForceFields::ContribPtr(contrib));
p1.x = 0;
p1.y = 1.5;
p1.z = 0.1;
p2.x = 0.0;
p2.y = 0.0;
p2.z = 0.0;
p3.x = 1.5;
p3.y = 0.0;
p3.z = 0.0;
p4.x = 1.5;
p4.y = 0.2;
p4.z = 1.5;
ff.initialize();
ff.minimize(10, 1e-8, 1e-8);
cosPhi = ForceFields::MMFF::Utils::calcTorsionCosPhi(
*(RDGeom::Point3D *)ff.positions()[0],
*(RDGeom::Point3D *)ff.positions()[1],
*(RDGeom::Point3D *)ff.positions()[2],
*(RDGeom::Point3D *)ff.positions()[3]);
TEST_ASSERT(RDKit::feq(cosPhi, 1.0, 1e-4));
}
PyObject *embedBoundsMatrix(python::object boundsMatArg,int maxIters=10,
bool randomizeOnFailure=false,int numZeroFail=2,
python::list weights=python::list(),
int randomSeed=-1){
PyObject *boundsMatObj = boundsMatArg.ptr();
if(!PyArray_Check(boundsMatObj))
throw_value_error("Argument isn't an array");
PyArrayObject *boundsMat=reinterpret_cast<PyArrayObject *>(boundsMatObj);
// get the dimensions of the array
unsigned int nrows = boundsMat->dimensions[0];
unsigned int ncols = boundsMat->dimensions[1];
if(nrows!=ncols)
throw_value_error("The array has to be square");
if(nrows<=0)
throw_value_error("The array has to have a nonzero size");
if (boundsMat->descr->type_num != PyArray_DOUBLE)
throw_value_error("Only double arrays are currently supported");
unsigned int dSize = nrows*nrows;
double *cData = new double[dSize];
double *inData = reinterpret_cast<double *>(boundsMat->data);
memcpy(static_cast<void *>(cData),
static_cast<const void *>(inData),
dSize*sizeof(double));
DistGeom::BoundsMatrix::DATA_SPTR sdata(cData);
DistGeom::BoundsMatrix bm(nrows,sdata);
RDGeom::Point3D *positions=new RDGeom::Point3D[nrows];
std::vector<RDGeom::Point *> posPtrs;
for (unsigned int i = 0; i < nrows; i++) {
posPtrs.push_back(&positions[i]);
}
RDNumeric::DoubleSymmMatrix distMat(nrows, 0.0);
// ---- ---- ---- ---- ---- ---- ---- ---- ----
// start the embedding:
bool gotCoords=false;
for(int iter=0;iter<maxIters && !gotCoords;iter++){
// pick a random distance matrix
DistGeom::pickRandomDistMat(bm,distMat,randomSeed);
// and embed it:
gotCoords=DistGeom::computeInitialCoords(distMat,posPtrs,randomizeOnFailure,
numZeroFail,randomSeed);
// update the seed:
if(randomSeed>=0) randomSeed+=iter*999;
}
if(gotCoords){
std::map<std::pair<int,int>,double> weightMap;
unsigned int nElems=PySequence_Size(weights.ptr());
for(unsigned int entryIdx=0;entryIdx<nElems;entryIdx++){
PyObject *entry=PySequence_GetItem(weights.ptr(),entryIdx);
if(!PySequence_Check(entry) || PySequence_Size(entry)!=3){
throw_value_error("weights argument must be a sequence of 3-sequences");
}
int idx1=PyInt_AsLong(PySequence_GetItem(entry,0));
int idx2=PyInt_AsLong(PySequence_GetItem(entry,1));
double w=PyFloat_AsDouble(PySequence_GetItem(entry,2));
weightMap[std::make_pair(idx1,idx2)]=w;
}
DistGeom::VECT_CHIRALSET csets;
ForceFields::ForceField *field = DistGeom::constructForceField(bm,posPtrs,csets,0.0, 0.0,
&weightMap);
CHECK_INVARIANT(field,"could not build dgeom force field");
field->initialize();
if(field->calcEnergy()>1e-5){
int needMore=1;
while(needMore){
needMore=field->minimize();
}
}
delete field;
} else {
throw_value_error("could not embed matrix");
}
// ---- ---- ---- ---- ---- ---- ---- ---- ----
// construct the results matrix:
npy_intp dims[2];
dims[0] = nrows;
dims[1] = 3;
PyArrayObject *res = (PyArrayObject *)PyArray_SimpleNew(2,dims,NPY_DOUBLE);
double *resData=reinterpret_cast<double *>(res->data);
for(unsigned int i=0;i<nrows;i++){
unsigned int iTab=i*3;
for (unsigned int j = 0; j < 3; ++j) {
resData[iTab + j]=positions[i][j]; //.x;
}
}
delete [] positions;
return PyArray_Return(res);
}
