static void writeKeyValueMap(
PolymorphicSharedPtr<KeyspaceStorage>& inStorage,
boost::python::dict& keysAndValues
)
{
map<SharedState::Key, KeyState> state;
boost::python::list keys = keysAndValues.keys();
long len = boost::python::len(keys);
for (long k = 0; k < len; k++)
{
state[boost::python::extract<SharedState::Key>(keys[k])()] =
KeyState(
null() << ValueType(
null() << PythonWrapper<SharedState::View>::pyToJsonOrError(keysAndValues[keys[k]]),
UniqueId()
),
null() << UniqueId(),
std::map<UniqueId, PartialEvent>()
);
}
inStorage->writeStateExternal(state);
}
INT_VECT EmbedMultipleConfs(
ROMol &mol, unsigned int numConfs, unsigned int maxAttempts, int seed,
bool clearConfs, bool useRandomCoords, double boxSizeMult, bool randNegEig,
unsigned int numZeroFail, double pruneRmsThresh, python::dict &coordMap,
double forceTol, bool ignoreSmoothingFailures, bool enforceChirality,
int numThreads, bool useExpTorsionAnglePrefs, bool useBasicKnowledge,
bool printExpTorsionAngles) {
std::map<int, RDGeom::Point3D> pMap;
python::list ks = coordMap.keys();
unsigned int nKeys = python::extract<unsigned int>(ks.attr("__len__")());
for (unsigned int i = 0; i < nKeys; ++i) {
unsigned int id = python::extract<unsigned int>(ks[i]);
pMap[id] = python::extract<RDGeom::Point3D>(coordMap[id]);
}
std::map<int, RDGeom::Point3D> *pMapPtr = 0;
if (nKeys) {
pMapPtr = &pMap;
}
INT_VECT res;
{
NOGIL gil;
DGeomHelpers::EmbedMultipleConfs(
mol, res, numConfs, numThreads, maxAttempts, seed, clearConfs,
useRandomCoords, boxSizeMult, randNegEig, numZeroFail, pruneRmsThresh,
pMapPtr, forceTol, ignoreSmoothingFailures, enforceChirality,
useExpTorsionAnglePrefs, useBasicKnowledge, printExpTorsionAngles);
}
return res;
}
unsigned int Compute2DCoords(RDKit::ROMol &mol, bool canonOrient,
bool clearConfs, python::dict &coordMap,
unsigned int nFlipsPerSample = 3,
unsigned int nSamples = 100, int sampleSeed = 100,
bool permuteDeg4Nodes = false,
double bondLength = -1.0) {
RDGeom::INT_POINT2D_MAP cMap;
cMap.clear();
python::list ks = coordMap.keys();
for (unsigned int i = 0;
i < python::extract<unsigned int>(ks.attr("__len__")()); i++) {
unsigned int id = python::extract<unsigned int>(ks[i]);
if (id >= mol.getNumAtoms()) {
throw_value_error("atom index out of range");
}
cMap[id] = python::extract<RDGeom::Point2D>(coordMap[id]);
}
double oBondLen = RDDepict::BOND_LEN;
if (bondLength > 0) {
RDDepict::BOND_LEN = bondLength;
}
unsigned int res;
res = RDDepict::compute2DCoords(mol, &cMap, canonOrient, clearConfs,
nFlipsPerSample, nSamples, sampleSeed,
permuteDeg4Nodes);
if (bondLength > 0) {
RDDepict::BOND_LEN = oBondLen;
}
return res;
}
void clientW::connect(const std::string& uri, const boost::python::dict& query){
std::map<std::string, std::string> newmap;
int len = boost::python::len(query);
boost::python::list keys = query.keys();
for(int i=0; i < len; i++) {
std::string k = boost::python::extract<std::string>(keys[i]);
newmap[k] = boost::python::extract<std::string>(query[k]);
}
this->client::connect(uri,newmap);
}
map<string,double> extract_solution(boost::python::dict pySol)
{
boost::python::list sol_keys = pySol.keys();
map<string,double> sol;
for(int iter = 0; iter < len(sol_keys); ++iter)
{
boost::python::extract<std::string> key(sol_keys[iter]);
boost::python::extract<double> value(pySol[sol_keys[iter]]);
sol[key] = value;
}
return sol;
}
static mapnik::attributes dict2attr(boost::python::dict const& d)
{
using namespace boost::python;
mapnik::attributes vars;
mapnik::transcoder tr_("utf8");
boost::python::list keys=d.keys();
for (int i=0; i < len(keys); ++i)
{
std::string key = extract<std::string>(keys[i]);
object obj = d[key];
if (PyUnicode_Check(obj.ptr()))
{
PyObject* temp = PyUnicode_AsUTF8String(obj.ptr());
if (temp)
{
#if PY_VERSION_HEX >= 0x03000000
char* c_str = PyBytes_AsString(temp);
#else
char* c_str = PyString_AsString(temp);
#endif
vars[key] = tr_.transcode(c_str);
Py_DecRef(temp);
}
continue;
}
extract<std::string> ex0(obj);
if (ex0.check())
{
vars[key] = tr_.transcode(ex0().c_str());
continue;
}
extract<mapnik::value_integer> ex2(obj);
if (ex2.check())
{
vars[key] = ex2();
continue;
}
extract<double> ex3(obj);
if (ex3.check())
{
vars[key] = ex3();
continue;
}
extract<mapnik::value_bool> ex1(obj);
if (ex1.check())
{
vars[key] = ex1();
continue;
}
}
return vars;
}
map<string,Vec4d> extract_targets(boost::python::dict target_positions)
{
boost::python::list target_keys = target_positions.keys();
map<string,Vec4d> target;
for( int iter = 0; iter < len(target_keys); ++iter)
{
boost::python::extract<std::string> key(target_keys[iter]);
boost::python::list value = boost::python::extract<boost::python::list>(target_positions[target_keys[iter]]);
Vec4d v;
assert(len(value) == 4);
for(int jter = 0; jter < len(value); ++jter)
v.values[jter] = boost::python::extract<double>(value[jter]);
target[key] = v;
}
return target;
}
