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// Copyright 2020 Global Phasing Ltd.
#include "common.h"
#include "gemmi/elem.hpp"
#include "gemmi/resinfo.hpp"
#include "gemmi/it92.hpp"
#include "gemmi/c4322.hpp"
#include "gemmi/neutron92.hpp"
#include "gemmi/util.hpp" // for cat
#include <pybind11/stl.h>
#include <pybind11/numpy.h>
#include <pybind11/operators.h>
namespace py = pybind11;
using namespace gemmi;
// Round coefficients.
// Decimal number from tables, such as 11.7695, after -> 32-bit float -> double
// becomes 11.769499778747559. Let's round it, it's for printing only anyway.
double roc(float x) {
float ax = std::abs(x);
double n = ax < 16.f ? 1e6 : ax < 128.f ? 1e5 : 1e4;
return std::round(x * n) / n;
}
void add_elem(py::module& m) {
// it92.hpp
using IT92 = gemmi::IT92<float>;
py::class_<IT92::Coef>(m, "IT92Coef")
.def_property_readonly("a", [](IT92::Coef& c) -> std::array<double,4> {
return {{ roc(c.a(0)), roc(c.a(1)), roc(c.a(2)), roc(c.a(3)) }};
})
.def_property_readonly("b", [](IT92::Coef& c) -> std::array<double,4> {
return {{ roc(c.b(0)), roc(c.b(1)), roc(c.b(2)), roc(c.b(3)) }};
})
.def_property_readonly("c", [](IT92::Coef& c) { return roc(c.c()); })
.def("get_coefs", [](const IT92::Coef &self) { return self.coefs; })
.def("set_coefs", &IT92::Coef::set_coefs)
.def("calculate_sf", py::vectorize(&IT92::Coef::calculate_sf), py::arg("stol2"))
.def("calculate_density_iso",
[](const IT92::Coef &self, py::array_t<float> r2, float B) {
return py::vectorize([&self,B](float r2) {
return self.calculate_density_iso(r2, B);
})(r2);
}, py::arg("r2"), py::arg("B"))
;
m.def("IT92_normalize", &IT92::normalize);
// can't define property for py::module_, and we don't expose IT92 as class
m.def("IT92_get_ignore_charge", []() { return IT92::ignore_charge; });
m.def("IT92_set_ignore_charge", [](bool v) { IT92::ignore_charge = v; });
// c4322.hpp
using C4322 = gemmi::C4322<float>;
py::class_<C4322::Coef>(m, "C4322Coef")
.def_property_readonly("a", [](C4322::Coef& c) -> std::array<double,5> {
return {{ roc(c.a(0)), roc(c.a(1)), roc(c.a(2)), roc(c.a(3)), roc(c.a(4)) }};
})
.def_property_readonly("b", [](C4322::Coef& c) -> std::array<double,5> {
return {{ roc(c.b(0)), roc(c.b(1)), roc(c.b(2)), roc(c.b(3)), roc(c.b(4)) }};
})
.def("get_coefs", [](const C4322::Coef &self) { return self.coefs; })
.def("set_coefs", &C4322::Coef::set_coefs)
.def("calculate_sf", &C4322::Coef::calculate_sf, py::arg("stol2"))
.def("calculate_density_iso", &C4322::Coef::calculate_density_iso,
py::arg("r2"), py::arg("B"))
;
// neutron92.hpp
using Neutron92 = gemmi::Neutron92<double>;
py::class_<Neutron92::Coef>(m, "Neutron92")
.def("get_coefs", [](const Neutron92::Coef &self) { return self.coefs; })
// the same arguments as above - for consistency
.def("calculate_sf", &Neutron92::Coef::calculate_sf, py::arg("stol2"))
.def("calculate_density_iso", &Neutron92::Coef::calculate_density_iso,
py::arg("r2"), py::arg("B"))
;
// elem.hpp (w/ properties from it92.hpp, ...)
py::class_<Element>(m, "Element")
.def(py::init<const std::string &>())
.def(py::init<int>())
.def(py::self == py::self)
.def_property_readonly("name", &Element::name)
.def_property_readonly("weight", &Element::weight)
.def_property_readonly("covalent_r", &Element::covalent_r)
.def_property_readonly("vdw_r", &Element::vdw_r)
.def_property_readonly("atomic_number", &Element::atomic_number)
.def_property_readonly("is_hydrogen", &Element::is_hydrogen)
.def_property_readonly("is_metal", &Element::is_metal)
.def_property_readonly("it92", [](const Element& self) {
return IT92::has(self.elem) ? &IT92::get(self.elem, 0) : nullptr;
}, py::return_value_policy::reference_internal)
.def_property_readonly("c4322", [](const Element& self) {
return C4322::has(self.elem) ? &C4322::get(self.elem) : nullptr;
}, py::return_value_policy::reference_internal)
.def_property_readonly("neutron92", [](const Element& self) {
return Neutron92::get(self.elem); // a copy is created
})
.def("__hash__", [](const Element &self) { return self.ordinal(); })
.def("__repr__", [](const Element& self) {
return gemmi::cat("gemmi.Element('", self.name(), "')");
});
m.def("IT92_get_exact", [](gemmi::Element el, signed char charge) {
return IT92::get_exact(el.elem, charge);
}, py::return_value_policy::reference_internal);
// resinfo.hpp
py::enum_<ResidueKind>(m, "ResidueKind")
.value("UNKNOWN", ResidueKind::UNKNOWN)
.value("AA", ResidueKind::AA)
.value("AAD", ResidueKind::AAD)
.value("PAA", ResidueKind::PAA)
.value("MAA", ResidueKind::MAA)
.value("RNA", ResidueKind::RNA)
.value("DNA", ResidueKind::DNA)
.value("BUF", ResidueKind::BUF)
.value("HOH", ResidueKind::HOH)
.value("PYR", ResidueKind::PYR)
.value("KET", ResidueKind::KET)
.value("ELS", ResidueKind::ELS);
py::class_<ResidueInfo>(m, "ResidueInfo")
.def_readonly("kind", &ResidueInfo::kind)
.def_readonly("one_letter_code", &ResidueInfo::one_letter_code)
.def_readonly("hydrogen_count", &ResidueInfo::hydrogen_count)
.def_readonly("weight", &ResidueInfo::weight)
.def("found", &ResidueInfo::found)
.def("is_standard", &ResidueInfo::is_standard)
.def("fasta_code", &ResidueInfo::fasta_code)
.def("is_water", &ResidueInfo::is_water)
.def("is_nucleic_acid", &ResidueInfo::is_nucleic_acid)
.def("is_amino_acid", &ResidueInfo::is_amino_acid);
m.def("find_tabulated_residue", &find_tabulated_residue, py::arg("name"),
"Find chemical component information in the internal table.");
m.def("expand_one_letter", &expand_one_letter);
m.def("expand_one_letter_sequence", &expand_one_letter_sequence);
}
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