Beispiel #1
0
void list_keys(py::dict dict)
{
	std::cout << py::len(dict.items()) << " keys in dict:" << std::endl;
	for(int i=0; i<py::len(dict.items()); ++i)
	{
		std::cout << std::string(py::extract<std::string>(dict.items()[i][0]))
			<< std::endl;
	}
}
Beispiel #2
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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;
}
Beispiel #3
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  boost::shared_ptr<ecto::module_<T> > inspect(boost::python::tuple args,
                                               boost::python::dict kwargs)
  {
    typedef ecto::module_<T> module_t;

    namespace bp = boost::python;

    //SHOW();
    boost::shared_ptr<module_t> mm(new module_t());
    ecto::module * m = mm.get();
    m->declare_params();

    bp::list l = kwargs.items();
    for (int j = 0; j < bp::len(l); ++j)
      {
        bp::object key = l[j][0];
        bp::object value = l[j][1];
        std::string keystring = bp::extract<std::string>(key);
        std::string valstring =
            bp::extract<std::string>(value.attr("__repr__")());
        m->parameters.at(keystring).set(value);
      }
    m->declare_io();
    return mm;
  }
Beispiel #4
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	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);
		}
Beispiel #5
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/**
 * If an output workspace was created then extract it from the given dictionary
 * @param locals A dictionary possibly containing an 'output' reference
 * @return A pointer to the output workspace if created, otherwise an empty
 * pointer
 */
boost::shared_ptr<API::Workspace> RunPythonScript::extractOutputWorkspace(
    const boost::python::dict &locals) const {
  using namespace API;
  using namespace boost::python;

  // Might be None, string or a workspace object
  auto pyoutput = locals.get("output");
  if (isNone(pyoutput))
    return Workspace_sptr();

  auto ptrExtract = ExtractWorkspace(pyoutput);
  if (ptrExtract.check()) {
    return ptrExtract();
  } else {
    extract<std::string> extractString(pyoutput);
    if (extractString.check()) {
      // Will raise an error if the workspace does not exist as the user
      // requested
      // an output workspace
      // but didn't create one.
      return AnalysisDataService::Instance().retrieve(extractString());
    } else {
      throw std::runtime_error(
          "Invalid type assigned to 'output' variable. Must "
          "be a string or a Workspace object");
    }
  }
}
Beispiel #6
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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;
}
Beispiel #7
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void Serializable::pyUpdateAttrs(const boost::python::dict& d){	
	boost::python::list l=d.items(); size_t ll=boost::python::len(l); if(ll==0) return;
	for(size_t i=0; i<ll; i++){
		boost::python::tuple t=boost::python::extract<boost::python::tuple>(l[i]);
		string key=boost::python::extract<string>(t[0]);
		pySetAttr(key,t[1]);
	}
	callPostLoad();
}
/**
 * @param mapping A Python dictionary instance
 * @return A new C++ PropertyManager instance
 */
boost::shared_ptr<Kernel::PropertyManager>
createPropertyManager(const boost::python::dict &mapping) {
  auto pmgr = boost::make_shared<PropertyManager>();
#if PY_MAJOR_VERSION >= 3
  object view(mapping.attr("items")());
  object itemIter(handle<>(PyObject_GetIter(view.ptr())));
#else
  object itemIter(mapping.attr("iteritems")());
#endif
  auto length = len(mapping);
  for (ssize_t i = 0; i < length; ++i) {
    const object keyValue(handle<>(PyIter_Next(itemIter.ptr())));
    const std::string cppkey = extract<std::string>(keyValue[0])();
    pmgr->declareProperty(PropertyWithValueFactory::create(cppkey, keyValue[1],
                                                           Direction::Input));
  }
  return pmgr;
}
Beispiel #9
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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);
}
Beispiel #10
0
 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;
 }
Beispiel #11
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    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;
    }
Beispiel #12
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  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;
  }
Beispiel #13
0
//---------------------------------------------------------------------------
boost::property_tree::ptree make_ptree(const boost::python::dict &args) {
    using namespace boost::python;
    boost::property_tree::ptree p;

    for(stl_input_iterator<tuple> arg(args.items()), end; arg != end; ++arg) {
        const char *name = extract<const char*>((*arg)[0]);
        const char *type = extract<const char*>((*arg)[1].attr("__class__").attr("__name__"));

        if (strcmp(type, "int") == 0)
            p.put(name, extract<int>((*arg)[1]));
        else
            p.put(name, extract<float>((*arg)[1]));
    }

    return p;
}
Beispiel #14
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const std::string PugAPI::map(const std::string node, const boost::python::dict& d) const
{
    QVariantMap qmap;
    boost::python::list keys = (boost::python::list)d.iterkeys();
    for (int i = 0; i < boost::python::len(keys); i++) {
        boost::python::object obj = d[keys[i]];
        if (PyString_Check(obj.ptr())) {
            qmap[QString::fromStdString(boost::python::extract<std::string>(keys[i]))] = QString::fromStdString(boost::python::extract<std::string>(obj));
        } else if (PyInt_Check(obj.ptr())) {
            qmap[QString::fromStdString(boost::python::extract<std::string>(keys[i]))] = QVariant(boost::python::extract<int>(obj));
        }
        // ignore things we can't convert
    }

    QString qresult = m_root->map(QString::fromStdString(node), qmap);

    return qresult.toStdString();
}
Beispiel #15
0
void add_mrfenergy_class(py::dict cls_dict, py::object key, const std::string& suffix)
{
    typedef typename T::LocalSize LocalSize;
    typedef typename T::NodeData NodeData;
    typedef typename T::EdgeData EdgeData;
    
    // NodeId is a pointer to a private struct Node. These lines
    // mask NodeId as an integer value (numeric_pointer).
    typedef numeric_pointer (MRFEnergy<T>::*add_node_type)(LocalSize, NodeData);
    typedef void (MRFEnergy<T>::*add_edge_type)(numeric_pointer, numeric_pointer, EdgeData);
    
    // Export the MRFEnergy class for the given T.
    py::object c = py::class_<MRFEnergy<T> >(("MRFEnergy"+suffix).c_str(), "MRF energy representation.",
            py::init<typename T::GlobalSize>())
        .def("add_node", (add_node_type)(&MRFEnergy<T>::AddNode),
            (py::arg("local_size"), py::arg("node_data")))
        .def("add_edge", (add_edge_type)(&MRFEnergy<T>::AddEdge),
            (py::arg("nodeid1"), py::arg("nodeid2"), py::arg("edge_data")))
        .def("minimize_trw", &minimize_trw<T>,
            "Minimize the energy of the MRF using TRW.",
            (py::arg("self"), py::arg("eps")=-1, py::arg("itermax")=50,
                py::arg("printiter")=5, py::arg("printminiter")=0, py::arg("details")=false))
        .def("minimize_bp", &minimize_bp<T>,
            "Minimize the energy of the MRF using BP.",
            (py::arg("self"), py::arg("eps")=-1, py::arg("itermax")=50,
                py::arg("printiter")=5, py::arg("printminiter")=0, py::arg("details")=false))
        .def("zero_messages", &MRFEnergy<T>::ZeroMessages)
        .def("set_automatic_ordering", &MRFEnergy<T>::SetAutomaticOrdering)
        .def("add_grid_nodes", &add_grid_nodes<T>,
            (py::arg("unary_terms"), py::arg("axis")=0))
        .def("add_grid_edges", &add_grid_edges<T>,
            (py::arg("nodeids"), py::arg("edge_data")))
        .def("add_grid_edges_direction", &add_grid_edges_direction<T>,
            (py::arg("nodeis"), py::arg("edge_data"), py::arg("direction")))
        .def("add_grid_edges_direction_local", &add_grid_edges_direction_local<T>,
            (py::arg("nodeis"), py::arg("edge_data"), py::arg("direction"), py::arg("axis")=0))
        .def("get_solution", &get_solution<T>,
            (py::arg("nodeids")));
    
    cls_dict.attr("__setitem__")(key, c);
}
Beispiel #16
0
PXR_NAMESPACE_OPEN_SCOPE

bool
SdfFileFormatArgumentsFromPython(
    const boost::python::dict& dict,
    SdfLayer::FileFormatArguments* args,
    std::string* errMsg)
{
    SdfLayer::FileFormatArguments argsMap;
    typedef SdfLayer::FileFormatArguments::key_type ArgKeyType;
    typedef SdfLayer::FileFormatArguments::mapped_type ArgValueType;

    const boost::python::object items = dict.items();
    for (boost::python::ssize_t i = 0; i < len(items); ++i) {
        boost::python::extract<ArgKeyType> keyExtractor(items[i][0]);
        if (!keyExtractor.check()) {
            if (errMsg) {
                *errMsg = "All file format argument keys must be strings";
            }
            return false;
        }

        boost::python::extract<ArgValueType> valueExtractor(items[i][1]);
        if (!valueExtractor.check()) {
            if (errMsg) {
                *errMsg = "All file format argument values must be strings";
            }
            return false;
        }
            
        argsMap[keyExtractor()] = valueExtractor();
    }

    args->swap(argsMap);
    return true;
}