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// Copyright 2021 Global Phasing Ltd.
#include "gemmi/topo.hpp"
#include "gemmi/placeh.hpp" // for adjust_hydrogen_distances
#include "gemmi/crd.hpp" // for prepare_crd, prepare_rst
#include "common.h"
#include <pybind11/stl.h>
#include <pybind11/stl_bind.h>
#include <pybind11/iostream.h> // for detail::pythonbuf
namespace py = pybind11;
using namespace gemmi;
PYBIND11_MAKE_OPAQUE(std::vector<Topo::Bond>)
PYBIND11_MAKE_OPAQUE(std::vector<Topo::Angle>)
PYBIND11_MAKE_OPAQUE(std::vector<Topo::Torsion>)
PYBIND11_MAKE_OPAQUE(std::vector<Topo::Chirality>)
PYBIND11_MAKE_OPAQUE(std::vector<Topo::Plane>)
PYBIND11_MAKE_OPAQUE(std::vector<Topo::Link>)
void add_topo(py::module& m) {
py::class_<Topo> topo(m, "Topo");
py::enum_<HydrogenChange>(m, "HydrogenChange")
.value("NoChange", HydrogenChange::NoChange)
.value("Shift", HydrogenChange::Shift)
.value("Remove", HydrogenChange::Remove)
.value("ReAdd", HydrogenChange::ReAdd)
.value("ReAddButWater", HydrogenChange::ReAddButWater);
py::class_<Topo::Bond>(topo, "Bond")
.def_readonly("restr", &Topo::Bond::restr)
.def_readonly("atoms", &Topo::Bond::atoms)
.def("calculate", &Topo::Bond::calculate)
.def("calculate_z", &Topo::Bond::calculate_z)
;
py::class_<Topo::Angle>(topo, "Angle")
.def_readonly("restr", &Topo::Angle::restr)
.def_readonly("atoms", &Topo::Angle::atoms)
.def("calculate", &Topo::Angle::calculate)
.def("calculate_z", &Topo::Angle::calculate_z)
;
py::class_<Topo::Torsion>(topo, "Torsion")
.def_readonly("restr", &Topo::Torsion::restr)
.def_readonly("atoms", &Topo::Torsion::atoms)
.def("calculate", &Topo::Torsion::calculate)
.def("calculate_z", &Topo::Torsion::calculate_z)
;
py::class_<Topo::Chirality>(topo, "Chirality")
.def_readonly("restr", &Topo::Chirality::restr)
.def_readonly("atoms", &Topo::Chirality::atoms)
.def("calculate", &Topo::Chirality::calculate)
.def("calculate_z", &Topo::Chirality::calculate_z,
py::arg("ideal_abs_vol"), py::arg("esd"))
.def("check", &Topo::Chirality::check)
;
py::class_<Topo::Plane>(topo, "Plane")
.def_readonly("restr", &Topo::Plane::restr)
.def_readonly("atoms", &Topo::Plane::atoms)
.def("has", &Topo::Plane::has)
;
py::class_<Topo::Link>(topo, "Link")
.def_readonly("link_id", &Topo::Link::link_id)
.def_readonly("res1", &Topo::Link::res1)
.def_readonly("res2", &Topo::Link::res2)
.def_readonly("alt1", &Topo::Link::alt1)
.def_readonly("alt2", &Topo::Link::alt2)
;
py::bind_vector<std::vector<Topo::Bond>>(m, "TopoBonds");
py::bind_vector<std::vector<Topo::Angle>>(m, "TopoAngles");
py::bind_vector<std::vector<Topo::Torsion>>(m, "TopoTorsions");
py::bind_vector<std::vector<Topo::Chirality>>(m, "TopoChirs");
py::bind_vector<std::vector<Topo::Plane>>(m, "TopoPlanes");
py::bind_vector<std::vector<Topo::Link>>(m, "TopoLinks");
topo
.def(py::init<>())
.def("adjust_hydrogen_distances", &adjust_hydrogen_distances,
py::arg("of"), py::arg("default_scale")=1.)
.def_readonly("bonds", &Topo::bonds)
.def_readonly("angles", &Topo::angles)
.def_readonly("torsions", &Topo::torsions)
.def_readonly("chirs", &Topo::chirs)
.def_readonly("planes", &Topo::planes)
.def_readonly("extras", &Topo::extras)
.def("ideal_chiral_abs_volume", &Topo::ideal_chiral_abs_volume)
.def("links_to_previous", [](Topo& self, Residue* res) {
if (Topo::ResInfo* ri = self.find_resinfo(res))
return ri->prev;
fail("links_to_previous(): Residue not found");
}, py::return_value_policy::reference_internal)
.def("first_bond_in_link", &Topo::first_bond_in_link,
py::return_value_policy::reference_internal)
;
m.def("prepare_topology",
[](Structure& st, MonLib& monlib, size_t model_index,
HydrogenChange h_change, bool reorder,
const py::object& pywarnings, bool ignore_unknown_links) {
std::ostream* warnings = nullptr;
std::ostream os(nullptr);
std::unique_ptr<py::detail::pythonbuf> buffer;
if (!pywarnings.is_none()) {
buffer.reset(new py::detail::pythonbuf(pywarnings));
os.rdbuf(buffer.get());
warnings = &os;
}
return prepare_topology(st, monlib, model_index, h_change, reorder,
warnings, ignore_unknown_links);
}, py::arg("st"), py::arg("monlib"), py::arg("model_index")=0,
py::arg("h_change")=HydrogenChange::NoChange, py::arg("reorder")=false,
py::arg("warnings")=py::none(), py::arg("ignore_unknown_links")=false);
// crd.hpp
m.def("prepare_crd", &prepare_crd);
m.def("prepare_rst", &prepare_rst);
}
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