double AlignMolecule(ROMol &prbMol, const ROMol &refMol, int prbCid = -1,
int refCid = -1, python::object atomMap = python::list(),
python::object weights = python::list(),
bool reflect = false, unsigned int maxIters = 50) {
MatchVectType *aMap = _translateAtomMap(atomMap);
unsigned int nAtms;
if (aMap) {
nAtms = aMap->size();
} else {
nAtms = prbMol.getNumAtoms();
}
RDNumeric::DoubleVector *wtsVec = _translateWeights(weights);
if (wtsVec) {
if (wtsVec->size() != nAtms) {
throw_value_error("Incorrect number of weights specified");
}
}
double rmsd;
{
NOGIL gil;
rmsd = MolAlign::alignMol(prbMol, refMol, prbCid, refCid, aMap, wtsVec,
reflect, maxIters);
}
if (aMap) {
delete aMap;
}
if (wtsVec) {
delete wtsVec;
}
return rmsd;
}
PyObject *getMolAlignTransform(const ROMol &prbMol, const ROMol &refMol,
int prbCid = -1, int refCid = -1,
python::object atomMap = python::list(),
python::object weights = python::list(),
bool reflect = false,
unsigned int maxIters = 50) {
MatchVectType *aMap = _translateAtomMap(atomMap);
unsigned int nAtms;
if (aMap) {
nAtms = aMap->size();
} else {
nAtms = prbMol.getNumAtoms();
}
RDNumeric::DoubleVector *wtsVec = _translateWeights(weights);
if (wtsVec) {
if (wtsVec->size() != nAtms) {
throw_value_error("Incorrect number of weights specified");
}
}
RDGeom::Transform3D trans;
double rmsd;
{
NOGIL gil;
rmsd = MolAlign::getAlignmentTransform(
prbMol, refMol, trans, prbCid, refCid, aMap, wtsVec, reflect, maxIters);
}
if (aMap) {
delete aMap;
}
if (wtsVec) {
delete wtsVec;
}
return generateRmsdTransPyTuple(rmsd, trans);
}
std::vector<MatchVectType> _translateAtomMapVector(python::object atomMapVec) {
std::vector<MatchVectType> aMapVec;
PySequenceHolder<python::object> aMapVecSeq(atomMapVec);
for (size_t i = 0; i < aMapVecSeq.size(); ++i) {
MatchVectType *aMap = _translateAtomMap(aMapVecSeq[i]);
aMapVec.push_back(*aMap);
delete aMap;
}
return aMapVec;
}
python::tuple getCrippenO3AForConfs(
ROMol &prbMol, ROMol &refMol, int numThreads,
python::list prbCrippenContribs, python::list refCrippenContribs,
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");
}
}
}
unsigned int prbNAtoms = prbMol.getNumAtoms();
std::vector<double> prbLogpContribs(prbNAtoms);
unsigned int refNAtoms = refMol.getNumAtoms();
std::vector<double> refLogpContribs(refNAtoms);
if ((prbCrippenContribs != python::list()) &&
(python::len(prbCrippenContribs) == prbNAtoms)) {
for (unsigned int i = 0; i < prbNAtoms; ++i) {
python::tuple logpMRTuple =
python::extract<python::tuple>(prbCrippenContribs[i]);
prbLogpContribs[i] = python::extract<double>(logpMRTuple[0]);
}
} else {
std::vector<double> prbMRContribs(prbNAtoms);
std::vector<unsigned int> prbAtomTypes(prbNAtoms);
std::vector<std::string> prbAtomTypeLabels(prbNAtoms);
Descriptors::getCrippenAtomContribs(prbMol, prbLogpContribs, prbMRContribs,
true, &prbAtomTypes,
&prbAtomTypeLabels);
}
if ((refCrippenContribs != python::list()) &&
(python::len(refCrippenContribs) == refNAtoms)) {
for (unsigned int i = 0; i < refNAtoms; ++i) {
python::tuple logpMRTuple =
python::extract<python::tuple>(refCrippenContribs[i]);
refLogpContribs[i] = python::extract<double>(logpMRTuple[0]);
}
} else {
std::vector<double> refMRContribs(refNAtoms);
std::vector<unsigned int> refAtomTypes(refNAtoms);
std::vector<std::string> refAtomTypeLabels(refNAtoms);
Descriptors::getCrippenAtomContribs(refMol, refLogpContribs, refMRContribs,
true, &refAtomTypes,
&refAtomTypeLabels);
}
std::vector<boost::shared_ptr<O3A> > res;
{
NOGIL gil;
getO3AForProbeConfs(prbMol, refMol, &prbLogpContribs, &refLogpContribs, res,
numThreads, MolAlign::O3A::CRIPPEN, 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 (cMap) {
delete cMap;
}
if (cWts) {
delete cWts;
}
return python::tuple(pyres);
}
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);
}
PyO3A *getCrippenO3A(ROMol &prbMol, ROMol &refMol,
python::list prbCrippenContribs,
python::list refCrippenContribs, 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");
}
}
}
unsigned int prbNAtoms = prbMol.getNumAtoms();
std::vector<double> prbLogpContribs(prbNAtoms);
unsigned int refNAtoms = refMol.getNumAtoms();
std::vector<double> refLogpContribs(refNAtoms);
if ((prbCrippenContribs != python::list()) &&
(python::len(prbCrippenContribs) == prbNAtoms)) {
for (unsigned int i = 0; i < prbNAtoms; ++i) {
python::tuple logpMRTuple =
python::extract<python::tuple>(prbCrippenContribs[i]);
prbLogpContribs[i] = python::extract<double>(logpMRTuple[0]);
}
} else {
std::vector<double> prbMRContribs(prbNAtoms);
std::vector<unsigned int> prbAtomTypes(prbNAtoms);
std::vector<std::string> prbAtomTypeLabels(prbNAtoms);
Descriptors::getCrippenAtomContribs(prbMol, prbLogpContribs, prbMRContribs,
true, &prbAtomTypes,
&prbAtomTypeLabels);
}
if ((refCrippenContribs != python::list()) &&
(python::len(refCrippenContribs) == refNAtoms)) {
for (unsigned int i = 0; i < refNAtoms; ++i) {
python::tuple logpMRTuple =
python::extract<python::tuple>(refCrippenContribs[i]);
refLogpContribs[i] = python::extract<double>(logpMRTuple[0]);
}
} else {
std::vector<double> refMRContribs(refNAtoms);
std::vector<unsigned int> refAtomTypes(refNAtoms);
std::vector<std::string> refAtomTypeLabels(refNAtoms);
Descriptors::getCrippenAtomContribs(refMol, refLogpContribs, refMRContribs,
true, &refAtomTypes,
&refAtomTypeLabels);
}
O3A *o3a;
{
NOGIL gil;
o3a = new MolAlign::O3A(prbMol, refMol, &prbLogpContribs, &refLogpContribs,
MolAlign::O3A::CRIPPEN, prbCid, refCid, reflect,
maxIters, options, cMap, cWts);
}
auto *pyO3A = new PyO3A(o3a);
if (cMap) {
delete cMap;
}
if (cWts) {
delete cWts;
}
return pyO3A;
}
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;
}
