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// Copyright 2024 DeepMind Technologies Limited
//
// AlphaFold 3 source code is licensed under CC BY-NC-SA 4.0. To view a copy of
// this license, visit https://creativecommons.org/licenses/by-nc-sa/4.0/
//
// To request access to the AlphaFold 3 model parameters, follow the process set
// out at https://github.com/google-deepmind/alphafold3. You may only use these
// if received directly from Google. Use is subject to terms of use available at
// https://github.com/google-deepmind/alphafold3/blob/main/WEIGHTS_TERMS_OF_USE.md
#include "alphafold3/model/mkdssp_pybind.h"
#include <cif++/file.hpp>
#include <cif++/pdb.hpp>
#include <dssp.hpp>
#include <sstream>
#include "absl/strings/string_view.h"
#include "pybind11/pybind11.h"
namespace alphafold3 {
namespace py = pybind11;
void RegisterModuleMkdssp(pybind11::module m) {
py::module site = py::module::import("site");
py::list paths = py::cast<py::list>(site.attr("getsitepackages")());
// Find the first path that contains the libcifpp components.cif file.
bool found = false;
for (const auto& py_path : paths) {
auto path_str =
std::filesystem::path(py::cast<absl::string_view>(py_path)) /
"share/libcifpp/components.cif";
if (std::filesystem::exists(path_str)) {
setenv("LIBCIFPP_DATA_DIR", path_str.parent_path().c_str(), 0);
found = true;
break;
}
}
if (!found) {
throw py::type_error("Could not find the libcifpp components.cif file.");
}
m.def(
"get_dssp",
[](absl::string_view mmcif, int model_no,
int min_poly_proline_stretch_length,
bool calculate_surface_accessibility) {
cif::file cif_file(mmcif.data(), mmcif.size());
dssp result(cif_file.front(), model_no, min_poly_proline_stretch_length,
calculate_surface_accessibility);
std::stringstream sstream;
result.write_legacy_output(sstream);
return sstream.str();
},
py::arg("mmcif"), py::arg("model_no") = 1,
py::arg("min_poly_proline_stretch_length") = 3,
py::arg("calculate_surface_accessibility") = false,
py::doc("Gets secondary structure from an mmCIF file."));
}
} // namespace alphafold3