/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2019, by the GROMACS development team, led by
+ * Copyright (c) 2019,2020,2021, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
// We don't want Python users to create invalid params objects, so don't
// export a constructor until we can default initialize a valid one.
// mdparams.def(py::init());
- mdparams.def("extract",
- [](const GmxMdParams& self) {
- py::dict dictionary;
- for (const auto& key : gmxapicompat::keys(self))
- {
- try
- {
- // TODO: More complete typing and dispatching.
- // This only handles the two types described in the initial implementation.
- // Less trivial types (strings, maps, arrays) warrant additional
- // design discussion before being exposed through an interface
- // like this one.
- // Also reference https://redmine.gromacs.org/issues/2993
-
- // We can use templates and/or tag dispatch in a more complete
- // future implementation.
- const auto& paramType = gmxapicompat::mdParamToType(key);
- if (paramType == GmxapiType::FLOAT64)
- {
- dictionary[key.c_str()] = extractParam(self, key, double());
- }
- else if (paramType == GmxapiType::INT64)
- {
- dictionary[key.c_str()] = extractParam(self, key, int64_t());
- }
- }
- catch (const gmxapicompat::ValueError& e)
- {
- throw gmxapi::ProtocolError(std::string("Unknown parameter: ") + key);
- }
- }
- return dictionary;
- },
- "Get a dictionary of the parameters.");
+ mdparams.def(
+ "extract",
+ [](const GmxMdParams& self) {
+ py::dict dictionary;
+ for (const auto& key : gmxapicompat::keys(self))
+ {
+ try
+ {
+ // TODO: More complete typing and dispatching.
+ // This only handles the two types described in the initial implementation.
+ // Less trivial types (strings, maps, arrays) warrant additional
+ // design discussion before being exposed through an interface
+ // like this one.
+ // Also reference https://gitlab.com/gromacs/gromacs/-/issues/2993
+
+ // We can use templates and/or tag dispatch in a more complete
+ // future implementation.
+ const auto& paramType = gmxapicompat::mdParamToType(key);
+ if (paramType == GmxapiType::FLOAT64)
+ {
+ dictionary[key.c_str()] = extractParam(self, key, double());
+ }
+ else if (paramType == GmxapiType::INT64)
+ {
+ dictionary[key.c_str()] = extractParam(self, key, int64_t());
+ }
+ }
+ catch (const gmxapicompat::ValueError& e)
+ {
+ throw gmxapi::ProtocolError(std::string("Unknown parameter: ") + key);
+ }
+ }
+ return dictionary;
+ },
+ "Get a dictionary of the parameters.");
// Overload a setter for each known type and None
- mdparams.def("set",
- [](GmxMdParams* self, const std::string& key, int64_t value) {
- gmxapicompat::setParam(self, key, value);
- },
- py::arg("key").none(false), py::arg("value").none(false),
- "Use a dictionary to update simulation parameters.");
- mdparams.def("set",
- [](GmxMdParams* self, const std::string& key, double value) {
- gmxapicompat::setParam(self, key, value);
- },
- py::arg("key").none(false), py::arg("value").none(false),
- "Use a dictionary to update simulation parameters.");
- mdparams.def("set",
- [](GmxMdParams* self, const std::string& key, py::none) {
- // unsetParam(self, key);
- },
- py::arg("key").none(false), py::arg("value"),
- "Use a dictionary to update simulation parameters.");
+ mdparams.def(
+ "set",
+ [](GmxMdParams* self, const std::string& key, int64_t value) {
+ gmxapicompat::setParam(self, key, value);
+ },
+ py::arg("key").none(false),
+ py::arg("value").none(false),
+ "Use a dictionary to update simulation parameters.");
+ mdparams.def(
+ "set",
+ [](GmxMdParams* self, const std::string& key, double value) {
+ gmxapicompat::setParam(self, key, value);
+ },
+ py::arg("key").none(false),
+ py::arg("value").none(false),
+ "Use a dictionary to update simulation parameters.");
+ mdparams.def(
+ "set",
+ [](GmxMdParams* self, const std::string& key, py::none) {
+ // unsetParam(self, key);
+ },
+ py::arg("key").none(false),
+ py::arg("value"),
+ "Use a dictionary to update simulation parameters.");
py::class_<TprReadHandle> tprfile(module, "TprFile");
return params;
});
- module.def("read_tprfile", &readTprFile, py::arg("filename"),
+ module.def("read_tprfile",
+ &readTprFile,
+ py::arg("filename"),
"Get a handle to a TPR file resource for a given file name.");
- module.def("write_tprfile",
- [](std::string filename, const GmxMdParams& parameterObject) {
- auto tprReadHandle = gmxapicompat::getSourceFileHandle(parameterObject);
- auto params = gmxapicompat::getMdParams(tprReadHandle);
- auto structure = gmxapicompat::getStructureSource(tprReadHandle);
- auto state = gmxapicompat::getSimulationState(tprReadHandle);
- auto topology = gmxapicompat::getTopologySource(tprReadHandle);
- gmxapicompat::writeTprFile(filename, *params, *structure, *state, *topology);
- },
- py::arg("filename").none(false), py::arg("parameters"),
- "Write a new TPR file with the provided data.");
-
- module.def("copy_tprfile",
- [](const gmxapicompat::TprReadHandle& input, std::string outFile) {
- return gmxapicompat::copy_tprfile(input, outFile);
- },
- py::arg("source"), py::arg("destination"),
- "Copy a TPR file from ``source`` to ``destination``.");
-
- module.def("rewrite_tprfile",
- [](std::string input, std::string output, double end_time) {
- return gmxapicompat::rewrite_tprfile(input, output, end_time);
- },
- py::arg("source"), py::arg("destination"), py::arg("end_time"),
- "Copy a TPR file from ``source`` to ``destination``, replacing `nsteps` with "
- "``end_time``.");
+ module.def(
+ "write_tprfile",
+ [](std::string filename, const GmxMdParams& parameterObject) {
+ auto tprReadHandle = gmxapicompat::getSourceFileHandle(parameterObject);
+ auto params = gmxapicompat::getMdParams(tprReadHandle);
+ auto structure = gmxapicompat::getStructureSource(tprReadHandle);
+ auto state = gmxapicompat::getSimulationState(tprReadHandle);
+ auto topology = gmxapicompat::getTopologySource(tprReadHandle);
+ gmxapicompat::writeTprFile(filename, *params, *structure, *state, *topology);
+ },
+ py::arg("filename").none(false),
+ py::arg("parameters"),
+ "Write a new TPR file with the provided data.");
+
+ module.def(
+ "copy_tprfile",
+ [](const gmxapicompat::TprReadHandle& input, std::string outFile) {
+ return gmxapicompat::copy_tprfile(input, outFile);
+ },
+ py::arg("source"),
+ py::arg("destination"),
+ "Copy a TPR file from ``source`` to ``destination``.");
+
+ module.def(
+ "rewrite_tprfile",
+ [](std::string input, std::string output, double end_time) {
+ return gmxapicompat::rewrite_tprfile(input, output, end_time);
+ },
+ py::arg("source"),
+ py::arg("destination"),
+ py::arg("end_time"),
+ "Copy a TPR file from ``source`` to ``destination``, replacing `nsteps` with "
+ "``end_time``.");
}
} // end namespace gmxpy
biod.pnpi.spb.ru / alexxy / gromacs.git / blobdiff