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#include <pybind11/pybind11.h>
#include <pybind11/stl.h>
#include <avogadro/core/molecule.h>
#include <avogadro/io/fileformatmanager.h>
#include <avogadro/quantumio/gamessus.h>
#include <avogadro/quantumio/gaussiancube.h>
#include <avogadro/quantumio/gaussianfchk.h>
#include <avogadro/quantumio/molden.h>
#include <avogadro/quantumio/mopacaux.h>
#include <avogadro/quantumio/nwchemjson.h>
#include <avogadro/quantumio/nwchemlog.h>
#include <avogadro/quantumio/orca.h>
namespace py = pybind11;
using namespace Avogadro;
using namespace Avogadro::Core;
using namespace Avogadro::Io;
using namespace Avogadro::QuantumIO;
namespace {
// Add a proxy class for Python that exposes the file format manager singleton.
class ffm
{
public:
ffm() : m_ffm(FileFormatManager::instance()) {}
bool readFile(Core::Molecule& molecule, const std::string& fileName,
const std::string& fileExtension = std::string(),
const std::string& options = std::string()) const
{
return m_ffm.readFile(molecule, fileName, fileExtension, options);
}
bool writeFile(const Core::Molecule& molecule, const std::string& fileName,
const std::string& fileExtension = std::string(),
const std::string& options = std::string()) const
{
return m_ffm.writeFile(molecule, fileName, fileExtension, options);
}
bool readString(Core::Molecule& molecule, const std::string& string,
const std::string& fileExtension,
const std::string& options = std::string()) const
{
return m_ffm.readString(molecule, string, fileExtension, options);
}
std::string writeString(const Molecule& mol, const std::string& ext,
const std::string& options = std::string())
{
std::string fileStr;
bool ok = m_ffm.writeString(mol, fileStr, ext, options);
if (!ok)
fileStr = "Error: " + FileFormatManager::instance().error();
return fileStr;
}
private:
FileFormatManager& m_ffm;
};
} // namespace
PYBIND11_MODULE(io, m)
{
m.doc() = "AvogadroIo Python binding";
/// Add the quantum IO formats, we should probably move them over soon, but
/// get things working for now...
Io::FileFormatManager::registerFormat(new GAMESSUSOutput);
Io::FileFormatManager::registerFormat(new GaussianFchk);
Io::FileFormatManager::registerFormat(new GaussianCube);
Io::FileFormatManager::registerFormat(new MoldenFile);
Io::FileFormatManager::registerFormat(new MopacAux);
Io::FileFormatManager::registerFormat(new NWChemJson);
Io::FileFormatManager::registerFormat(new NWChemLog);
Io::FileFormatManager::registerFormat(new ORCAOutput);
/// This class uses a singleton pattern, make it accessible through Python.
py::class_<ffm>(m, "FileFormatManager")
.def(py::init<>())
.def("read_file", &ffm::readFile,
"Read in a molecule from the supplied file path", py::arg("molecule"),
py::arg("file_name"), py::arg("file_extension") = std::string(),
py::arg("options") = std::string())
.def("write_file", &ffm::writeFile,
"Write the molecule to the supplied file path", py::arg("molecule"),
py::arg("file_name"), py::arg("file_extension") = std::string(),
py::arg("options") = std::string())
.def("read_string", &ffm::readString,
"Read in a molecule from the supplied string", py::arg("molecule"),
py::arg("string"), py::arg("file_extension"),
py::arg("options") = std::string())
.def("write_string", &ffm::writeString,
"Write a molecule to the supplied string", py::arg("mol"),
py::arg("file_extension"), py::arg("options") = std::string());
}
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