void testGithub224() {
BOOST_LOG(rdErrorLog) << "-------------------------------------" << std::endl;
BOOST_LOG(rdErrorLog)
<< " Testing github 224: crash during MMFF parameterization ."
<< std::endl;
{
ROMol *mol = SmilesToMol("[1*]C");
TEST_ASSERT(mol);
MMFF::MMFFMolProperties *mmffMolProperties =
new MMFF::MMFFMolProperties(*mol);
TEST_ASSERT(mmffMolProperties);
TEST_ASSERT(!mmffMolProperties->isValid());
delete mol;
delete mmffMolProperties;
}
{
ROMol *mol = SmilesToMol("[1*]c1ccc(S(=O)(=O)Nc2ccc([2*])cc2)cc1");
TEST_ASSERT(mol);
MMFF::MMFFMolProperties *mmffMolProperties =
new MMFF::MMFFMolProperties(*mol);
TEST_ASSERT(mmffMolProperties);
TEST_ASSERT(!mmffMolProperties->isValid());
delete mol;
delete mmffMolProperties;
}
BOOST_LOG(rdErrorLog) << " done" << std::endl;
}
ForceFields::PyMMFFMolProperties *GetMMFFMolProperties
(ROMol &mol, std::string mmffVariant = "MMFF94",
unsigned int mmffVerbosity = MMFF::MMFF_VERBOSITY_NONE)
{
MMFF::MMFFMolProperties *mmffMolProperties =
new MMFF::MMFFMolProperties(mol, mmffVariant, mmffVerbosity);
ForceFields::PyMMFFMolProperties *pyMP = NULL;
if (mmffMolProperties && mmffMolProperties->isValid()) {
pyMP = new ForceFields::PyMMFFMolProperties(mmffMolProperties);
}
return pyMP;
}
void testGithub162()
{
BOOST_LOG(rdErrorLog) << "-------------------------------------" << std::endl;
BOOST_LOG(rdErrorLog) << " Testing github 162: Incorrect SMILES after MMFF parameterization ." << std::endl;
{
ROMol *mol = SmilesToMol("C1=CNC=C1");
TEST_ASSERT(mol);
TEST_ASSERT(mol->getAtomWithIdx(2)->getNumExplicitHs()==1);
MMFF::MMFFMolProperties *mmffMolProperties = new MMFF::MMFFMolProperties(*mol);
TEST_ASSERT(mmffMolProperties);
TEST_ASSERT(mmffMolProperties->isValid());
TEST_ASSERT(mol->getAtomWithIdx(2)->getNumExplicitHs()==1);
delete mol;
delete mmffMolProperties;
}
BOOST_LOG(rdErrorLog) << " done" << std::endl;
}
python::tuple getMMFFO3AForConfs(
ROMol &prbMol, ROMol &refMol, int numThreads, python::object prbProps,
python::object refProps, int refCid = -1, bool reflect = false,
unsigned int maxIters = 50, unsigned int options = 0,
python::list constraintMap = python::list(),
python::list constraintWeights = python::list()) {
MatchVectType *cMap =
(python::len(constraintMap) ? _translateAtomMap(constraintMap) : NULL);
RDNumeric::DoubleVector *cWts = NULL;
if (cMap) {
cWts = _translateWeights(constraintWeights);
if (cWts) {
if ((*cMap).size() != (*cWts).size()) {
throw_value_error(
"The number of weights should match the number of constraints");
}
}
for (unsigned int i = 0; i < (*cMap).size(); ++i) {
if (((*cMap)[i].first < 0) ||
((*cMap)[i].first >= rdcast<int>(prbMol.getNumAtoms())) ||
((*cMap)[i].second < 0) ||
((*cMap)[i].second >= rdcast<int>(refMol.getNumAtoms()))) {
throw_value_error("Constrained atom idx out of range");
}
if ((prbMol[(*cMap)[i].first]->getAtomicNum() == 1) ||
(refMol[(*cMap)[i].second]->getAtomicNum() == 1)) {
throw_value_error("Constrained atoms must be heavy atoms");
}
}
}
ForceFields::PyMMFFMolProperties *prbPyMMFFMolProperties = NULL;
MMFF::MMFFMolProperties *prbMolProps = NULL;
ForceFields::PyMMFFMolProperties *refPyMMFFMolProperties = NULL;
MMFF::MMFFMolProperties *refMolProps = NULL;
if (prbProps != python::object()) {
prbPyMMFFMolProperties =
python::extract<ForceFields::PyMMFFMolProperties *>(prbProps);
prbMolProps = prbPyMMFFMolProperties->mmffMolProperties.get();
} else {
prbMolProps = new MMFF::MMFFMolProperties(prbMol);
if (!prbMolProps->isValid()) {
throw_value_error("missing MMFF94 parameters for probe molecule");
}
}
if (refProps != python::object()) {
refPyMMFFMolProperties =
python::extract<ForceFields::PyMMFFMolProperties *>(refProps);
refMolProps = refPyMMFFMolProperties->mmffMolProperties.get();
} else {
refMolProps = new MMFF::MMFFMolProperties(refMol);
if (!refMolProps->isValid()) {
throw_value_error("missing MMFF94 parameters for reference molecule");
}
}
std::vector<boost::shared_ptr<O3A> > res;
{
NOGIL gil;
getO3AForProbeConfs(prbMol, refMol, prbMolProps, refMolProps, res,
numThreads, MolAlign::O3A::MMFF94, refCid, reflect,
maxIters, options, cMap, cWts);
}
python::list pyres;
for (unsigned int i = 0; i < res.size(); ++i) {
pyres.append(new PyO3A(res[i]));
}
if (!prbPyMMFFMolProperties) delete prbMolProps;
if (!refPyMMFFMolProperties) delete refMolProps;
if (cMap) {
delete cMap;
}
if (cWts) {
delete cWts;
}
return python::tuple(pyres);
}
void testMMFFParamGetters() {
BOOST_LOG(rdErrorLog) << "-------------------------------------" << std::endl;
BOOST_LOG(rdErrorLog) << " Test MMFF force-field parameter getters."
<< std::endl;
{
ROMol *mol = SmilesToMol("c1ccccc1CCNN");
TEST_ASSERT(mol);
ROMol *molH = MolOps::addHs(*mol);
TEST_ASSERT(molH);
MMFF::MMFFMolProperties *mmffMolProperties =
new MMFF::MMFFMolProperties(*molH);
TEST_ASSERT(mmffMolProperties);
TEST_ASSERT(mmffMolProperties->isValid());
unsigned int bondType;
ForceFields::MMFF::MMFFBond mmffBondStretchParams[2];
TEST_ASSERT(mmffMolProperties->getMMFFBondStretchParams(
*molH, 6, 7, bondType, mmffBondStretchParams[0]));
TEST_ASSERT(
(bondType == 0) &&
((int)boost::math::round(mmffBondStretchParams[0].r0 * 1000) == 1508) &&
((int)boost::math::round(mmffBondStretchParams[0].kb * 1000) == 4258));
TEST_ASSERT(!(mmffMolProperties->getMMFFBondStretchParams(
*molH, 0, 7, bondType, mmffBondStretchParams[0])));
unsigned int angleType;
ForceFields::MMFF::MMFFAngle mmffAngleBendParams;
TEST_ASSERT(mmffMolProperties->getMMFFAngleBendParams(
*molH, 6, 7, 8, angleType, mmffAngleBendParams));
TEST_ASSERT(
(angleType == 0) &&
((int)boost::math::round(mmffAngleBendParams.theta0 * 1000) ==
108290) &&
((int)boost::math::round(mmffAngleBendParams.ka * 1000) == 777));
TEST_ASSERT(!(mmffMolProperties->getMMFFAngleBendParams(
*molH, 0, 7, 8, angleType, mmffAngleBendParams)));
unsigned int stretchBendType;
ForceFields::MMFF::MMFFStbn mmffStretchBendParams;
TEST_ASSERT(mmffMolProperties->getMMFFStretchBendParams(
*molH, 6, 7, 8, stretchBendType, mmffStretchBendParams,
mmffBondStretchParams, mmffAngleBendParams));
TEST_ASSERT(
(stretchBendType == 0) &&
((int)boost::math::round(mmffStretchBendParams.kbaIJK * 1000) == 136) &&
((int)boost::math::round(mmffStretchBendParams.kbaKJI * 1000) == 282) &&
((int)boost::math::round(mmffAngleBendParams.theta0 * 1000) ==
108290) &&
((int)boost::math::round(mmffAngleBendParams.ka * 1000) == 777) &&
((int)boost::math::round(mmffBondStretchParams[0].r0 * 1000) == 1508) &&
((int)boost::math::round(mmffBondStretchParams[0].kb * 1000) == 4258) &&
((int)boost::math::round(mmffBondStretchParams[1].r0 * 1000) == 1451) &&
((int)boost::math::round(mmffBondStretchParams[1].kb * 1000) == 5084));
TEST_ASSERT(!(mmffMolProperties->getMMFFStretchBendParams(
*molH, 0, 7, 8, stretchBendType, mmffStretchBendParams,
mmffBondStretchParams, mmffAngleBendParams)));
unsigned int torType;
ForceFields::MMFF::MMFFTor mmffTorsionParams;
TEST_ASSERT(mmffMolProperties->getMMFFTorsionParams(
*molH, 6, 7, 8, 9, torType, mmffTorsionParams));
TEST_ASSERT(
(torType == 0) &&
((int)boost::math::round(mmffTorsionParams.V1 * 1000) == 0) &&
((int)boost::math::round(mmffTorsionParams.V2 * 1000) == -300) &&
((int)boost::math::round(mmffTorsionParams.V3 * 1000) == 500));
TEST_ASSERT(!(mmffMolProperties->getMMFFTorsionParams(
*molH, 0, 7, 8, 9, torType, mmffTorsionParams)));
ForceFields::MMFF::MMFFOop mmffOopBendParams;
TEST_ASSERT(mmffMolProperties->getMMFFOopBendParams(*molH, 6, 5, 4, 0,
mmffOopBendParams));
TEST_ASSERT(((int)boost::math::round(mmffOopBendParams.koop * 1000) == 40));
TEST_ASSERT(!(mmffMolProperties->getMMFFOopBendParams(*molH, 6, 5, 4, 1,
mmffOopBendParams)));
ForceFields::MMFF::MMFFVdWRijstarEps mmffVdWParams;
RWMol *patt = SmartsToMol("NN[H]");
MatchVectType matchVect;
TEST_ASSERT(SubstructMatch(*molH, (ROMol &)*patt, matchVect));
unsigned int nIdx = matchVect[0].second;
unsigned int hIdx = matchVect[2].second;
TEST_ASSERT(mmffMolProperties->getMMFFVdWParams(nIdx, hIdx, mmffVdWParams));
TEST_ASSERT(
((int)boost::math::round(mmffVdWParams.R_ij_starUnscaled * 1000) ==
3321) &&
((int)boost::math::round(mmffVdWParams.epsilonUnscaled * 1000) == 34) &&
((int)boost::math::round(mmffVdWParams.R_ij_star * 1000) == 2657) &&
((int)boost::math::round(mmffVdWParams.epsilon * 1000) == 17));
}
}
void testMMFFBuilder1() {
BOOST_LOG(rdErrorLog) << "-------------------------------------" << std::endl;
BOOST_LOG(rdErrorLog) << " Testing MMFF builder tools." << std::endl;
ROMol *mol, *mol2;
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);
MMFF::MMFFMolProperties *mmffMolProperties =
new MMFF::MMFFMolProperties(*mol);
TEST_ASSERT(mmffMolProperties);
TEST_ASSERT(mmffMolProperties->isValid());
field = new ForceFields::ForceField();
MMFF::Tools::addBonds(*mol, mmffMolProperties, field);
TEST_ASSERT(field->contribs().size() == 3);
nbrMat = MMFF::Tools::buildNeighborMatrix(*mol);
// the neighbor matrix is an upper triangular matrix
// position indices are as follows:
// 0 1 2 3
// 4 5 6
// 7 8
// 9
TEST_ASSERT(MMFF::Tools::twoBitCellPos(mol->getNumAtoms(), 1, 1) == 4);
TEST_ASSERT(MMFF::Tools::twoBitCellPos(mol->getNumAtoms(), 2, 1) == 5);
TEST_ASSERT(MMFF::Tools::twoBitCellPos(mol->getNumAtoms(), 1, 2) == 5);
TEST_ASSERT(MMFF::Tools::getTwoBitCell(nbrMat, 0) ==
MMFF::Tools::RELATION_1_X);
TEST_ASSERT(MMFF::Tools::getTwoBitCell(nbrMat, 1) ==
MMFF::Tools::RELATION_1_2);
TEST_ASSERT(MMFF::Tools::getTwoBitCell(nbrMat, 2) ==
MMFF::Tools::RELATION_1_3);
TEST_ASSERT(MMFF::Tools::getTwoBitCell(nbrMat, 3) ==
MMFF::Tools::RELATION_1_3);
MMFF::Tools::addAngles(*mol, mmffMolProperties, field);
TEST_ASSERT(field->contribs().size() == 6);
// there are no non-bonded terms here:
MMFF::Tools::addVdW(*mol, cid, mmffMolProperties, field, nbrMat);
TEST_ASSERT(field->contribs().size() == 6);
// and no torsions either, until we add Hs:
MMFF::Tools::addTorsions(*mol, mmffMolProperties, field);
TEST_ASSERT(field->contribs().size() == 6);
delete mol;
delete field;
delete mmffMolProperties;
mol = SmilesToMol("CCOC");
Conformer *conf2 = new Conformer(mol->getNumAtoms());
cid = static_cast<int>(mol->addConformer(conf2, true));
TEST_ASSERT(mol);
mmffMolProperties = new MMFF::MMFFMolProperties(*mol);
TEST_ASSERT(mmffMolProperties);
TEST_ASSERT(mmffMolProperties->isValid());
field = new ForceFields::ForceField();
MMFF::Tools::addBonds(*mol, mmffMolProperties, field);
TEST_ASSERT(field->contribs().size() == 3);
nbrMat = MMFF::Tools::buildNeighborMatrix(*mol);
TEST_ASSERT(MMFF::Tools::getTwoBitCell(nbrMat, 0) ==
MMFF::Tools::RELATION_1_X);
TEST_ASSERT(MMFF::Tools::getTwoBitCell(nbrMat, 1) ==
MMFF::Tools::RELATION_1_2);
TEST_ASSERT(MMFF::Tools::getTwoBitCell(nbrMat, 2) ==
MMFF::Tools::RELATION_1_3);
TEST_ASSERT(MMFF::Tools::getTwoBitCell(nbrMat, 3) ==
MMFF::Tools::RELATION_1_4);
MMFF::Tools::addAngles(*mol, mmffMolProperties, field);
TEST_ASSERT(field->contribs().size() == 5);
MMFF::Tools::addVdW(*mol, cid, mmffMolProperties, field, nbrMat);
TEST_ASSERT(field->contribs().size() == 6);
MMFF::Tools::addTorsions(*mol, mmffMolProperties, field);
TEST_ASSERT(field->contribs().size() == 7);
delete mol;
delete field;
delete mmffMolProperties;
mol = SmilesToMol("CO");
Conformer *conf3 = new Conformer(mol->getNumAtoms());
cid = static_cast<int>(mol->addConformer(conf3, true));
TEST_ASSERT(mol);
mmffMolProperties = new MMFF::MMFFMolProperties(*mol);
TEST_ASSERT(mmffMolProperties);
TEST_ASSERT(mmffMolProperties->isValid());
field = new ForceFields::ForceField();
MMFF::Tools::addBonds(*mol, mmffMolProperties, field);
TEST_ASSERT(field->contribs().size() == 1);
nbrMat = MMFF::Tools::buildNeighborMatrix(*mol);
TEST_ASSERT(MMFF::Tools::getTwoBitCell(nbrMat, 0) ==
MMFF::Tools::RELATION_1_X);
TEST_ASSERT(MMFF::Tools::getTwoBitCell(nbrMat, 1) ==
MMFF::Tools::RELATION_1_2);
MMFF::Tools::addAngles(*mol, mmffMolProperties, field);
TEST_ASSERT(field->contribs().size() == 1);
MMFF::Tools::addVdW(*mol, cid, mmffMolProperties, field, nbrMat);
TEST_ASSERT(field->contribs().size() == 1);
MMFF::Tools::addTorsions(*mol, mmffMolProperties, field);
TEST_ASSERT(field->contribs().size() == 1);
mol2 = MolOps::addHs(*mol);
TEST_ASSERT(mol2->getNumAtoms() == 6);
delete field;
delete mmffMolProperties;
mmffMolProperties = new MMFF::MMFFMolProperties(*mol2);
TEST_ASSERT(mmffMolProperties);
TEST_ASSERT(mmffMolProperties->isValid());
field = new ForceFields::ForceField();
MMFF::Tools::addBonds(*mol2, mmffMolProperties, field);
TEST_ASSERT(field->contribs().size() == 5);
nbrMat = MMFF::Tools::buildNeighborMatrix(*mol2);
MMFF::Tools::addAngles(*mol2, mmffMolProperties, field);
TEST_ASSERT(field->contribs().size() == 12);
MMFF::Tools::addVdW(*mol2, cid, mmffMolProperties, field, nbrMat);
TEST_ASSERT(field->contribs().size() == 15);
MMFF::Tools::addTorsions(*mol2, mmffMolProperties, field);
TEST_ASSERT(field->contribs().size() == 18);
delete mol2;
delete mol;
delete field;
delete mmffMolProperties;
BOOST_LOG(rdErrorLog) << " done" << std::endl;
}
PyO3A *getMMFFO3A(ROMol &prbMol, ROMol &refMol, python::object prbProps,
python::object refProps, int prbCid = -1, int refCid = -1,
bool reflect = false, unsigned int maxIters = 50,
unsigned int options = 0,
python::list constraintMap = python::list(),
python::list constraintWeights = python::list()) {
MatchVectType *cMap =
(python::len(constraintMap) ? _translateAtomMap(constraintMap) : nullptr);
RDNumeric::DoubleVector *cWts = nullptr;
if (cMap) {
cWts = _translateWeights(constraintWeights);
if (cWts) {
if ((*cMap).size() != (*cWts).size()) {
throw_value_error(
"The number of weights should match the number of constraints");
}
}
for (auto &i : (*cMap)) {
if ((i.first < 0) || (i.first >= rdcast<int>(prbMol.getNumAtoms())) ||
(i.second < 0) || (i.second >= rdcast<int>(refMol.getNumAtoms()))) {
throw_value_error("Constrained atom idx out of range");
}
if ((prbMol[i.first]->getAtomicNum() == 1) ||
(refMol[i.second]->getAtomicNum() == 1)) {
throw_value_error("Constrained atoms must be heavy atoms");
}
}
}
ForceFields::PyMMFFMolProperties *prbPyMMFFMolProperties = nullptr;
MMFF::MMFFMolProperties *prbMolProps = nullptr;
ForceFields::PyMMFFMolProperties *refPyMMFFMolProperties = nullptr;
MMFF::MMFFMolProperties *refMolProps = nullptr;
if (prbProps != python::object()) {
prbPyMMFFMolProperties =
python::extract<ForceFields::PyMMFFMolProperties *>(prbProps);
prbMolProps = prbPyMMFFMolProperties->mmffMolProperties.get();
} else {
prbMolProps = new MMFF::MMFFMolProperties(prbMol);
if (!prbMolProps->isValid()) {
throw_value_error("missing MMFF94 parameters for probe molecule");
}
}
if (refProps != python::object()) {
refPyMMFFMolProperties =
python::extract<ForceFields::PyMMFFMolProperties *>(refProps);
refMolProps = refPyMMFFMolProperties->mmffMolProperties.get();
} else {
refMolProps = new MMFF::MMFFMolProperties(refMol);
if (!refMolProps->isValid()) {
throw_value_error("missing MMFF94 parameters for reference molecule");
}
}
O3A *o3a;
{
NOGIL gil;
o3a = new MolAlign::O3A(prbMol, refMol, prbMolProps, refMolProps,
MolAlign::O3A::MMFF94, prbCid, refCid, reflect,
maxIters, options, cMap, cWts);
}
auto *pyO3A = new PyO3A(o3a);
if (!prbPyMMFFMolProperties) delete prbMolProps;
if (!refPyMMFFMolProperties) delete refMolProps;
if (cMap) {
delete cMap;
}
if (cWts) {
delete cWts;
}
return pyO3A;
}