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// Copyright 2020 Global Phasing Ltd.
#include "common.h"
#include <nanobind/operators.h>
#include <nanobind/stl/array.h>
#include <nanobind/stl/string.h>
#include <nanobind/stl/vector.h> // for expand_one_letter_sequence
#include <nanobind/make_iterator.h>
#include "gemmi/elem.hpp"
#include "gemmi/resinfo.hpp"
#include "gemmi/it92.hpp"
#include "gemmi/c4322.hpp"
#include "gemmi/neutron92.hpp"
#include "gemmi/dencalc.hpp" // for it92_radius_approx, determine_cutoff_radius
#include "gemmi/util.hpp" // for cat
#include "gemmi/xds_ascii.hpp" // for XdsAscii
#include "gemmi/xds2mtz.hpp" // for xds_to_mtz
#include "array.h" // for vector_member_array
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.
static 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(nb::module_& m) {
// it92.hpp
using IT92 = gemmi::IT92<float>;
nb::class_<IT92::Coef>(m, "IT92Coef")
.def(nb::init<>())
.def_prop_ro("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_prop_ro("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_prop_ro("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", &IT92::Coef::calculate_sf, nb::arg("stol2"))
.def("calculate_density_iso", &IT92::Coef::calculate_density_iso,
nb::arg("r2"), nb::arg("B"))
.def("precalculate_density_iso", &IT92::Coef::precalculate_density_iso,
nb::arg("B"), nb::arg("addend")=0.0f)
;
m.def("IT92_normalize", &IT92::normalize);
// can't define property for nb::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; });
// ExpSum for precalculated density (5 gaussians + constant for IT92)
using ExpSum5 = gemmi::ExpSum<5, float>;
nb::class_<ExpSum5>(m, "ExpSum5")
.def("calculate", &ExpSum5::calculate, nb::arg("r2"))
.def("calculate_with_derivative", &ExpSum5::calculate_with_derivative, nb::arg("r"))
;
// Helper functions from dencalc.hpp
m.def("it92_radius_approx", &gemmi::it92_radius_approx<float>, nb::arg("b"));
m.def("determine_cutoff_radius", &gemmi::determine_cutoff_radius<5, float>,
nb::arg("x1"), nb::arg("precal"), nb::arg("cutoff_level"));
// c4322.hpp
using C4322 = gemmi::C4322<float>;
nb::class_<C4322::Coef>(m, "C4322Coef")
.def_prop_ro("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_prop_ro("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, nb::arg("stol2"))
.def("calculate_density_iso", &C4322::Coef::calculate_density_iso,
nb::arg("r2"), nb::arg("B"))
;
using CustomCoef = CustomCoef<double>;
m.def("set_custom_form_factors", [](const std::vector<decltype(CustomCoef::Coef::coefs)>& pp) {
CustomCoef::data.clear();
CustomCoef::Coef item;
for (const auto& p : pp) {
item.set_coefs(p);
CustomCoef::data.push_back(item);
}
});
// neutron92.hpp
using Neutron92 = gemmi::Neutron92<double>;
nb::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, nb::arg("stol2"))
.def("calculate_density_iso", &Neutron92::Coef::calculate_density_iso,
nb::arg("r2"), nb::arg("B"))
;
// elem.hpp (w/ properties from it92.hpp, ...)
nb::class_<Element>(m, "Element")
.def(nb::init<const std::string &>())
.def(nb::init<int>())
// NOLINTNEXTLINE(misc-redundant-expression)
.def(nb::self == nb::self, nb::sig("def __eq__(self, arg: object, /) -> bool"))
.def_prop_ro("name", &Element::name)
.def_prop_ro("weight", &Element::weight)
.def_prop_ro("covalent_r", &Element::covalent_r)
.def_prop_ro("vdw_r", &Element::vdw_r)
.def_prop_ro("atomic_number", &Element::atomic_number)
.def_prop_ro("is_hydrogen", &Element::is_hydrogen)
.def_prop_ro("is_metal", &Element::is_metal)
.def_prop_ro("it92", [](const Element& self) {
return IT92::has(self.elem) ? &IT92::get(self.elem, 0) : nullptr;
}, nb::rv_policy::reference)
.def_prop_ro("c4322", [](const Element& self) {
return C4322::has(self.elem) ? &C4322::get(self.elem) : nullptr;
}, nb::rv_policy::reference)
.def_prop_ro("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);
}, nb::rv_policy::reference);
m.def("set_is_metal", [](const char* el, bool value) {
set_is_metal(find_element(el), value);
});
// resinfo.hpp
nb::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);
nb::class_<ResidueInfo>(m, "ResidueInfo")
.def_ro("name", &ResidueInfo::name)
.def_rw("kind", &ResidueInfo::kind)
.def_ro("one_letter_code", &ResidueInfo::one_letter_code)
.def_ro("hydrogen_count", &ResidueInfo::hydrogen_count)
.def_ro("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, nb::arg("name"),
"Find chemical component information in the internal table.");
m.def("find_tabulated_residue_idx", &find_tabulated_residue_idx, nb::arg("name"));
m.def("expand_one_letter", &expand_one_letter);
m.def("expand_one_letter_sequence", &expand_one_letter_sequence);
nb::handle mod = m;
m.def("resinfo_table", [mod]() {
ResidueInfo* start = &gemmi::get_residue_info(0);
return nb::make_iterator<nb::rv_policy::reference>(mod, "resinfo_table_iterator",
start, start+362);
});
}
void add_xds(nb::module_& m) {
nb::class_<XdsAscii>(m, "XdsAscii")
.def_ro("source_path", &XdsAscii::source_path)
.def_ro("read_columns", &XdsAscii::read_columns)
.def_ro("spacegroup_number", &XdsAscii::spacegroup_number)
.def_ro("wavelength", &XdsAscii::wavelength)
.def_ro("cell_constants", &XdsAscii::cell_constants)
.def_ro("rotation_axis", &XdsAscii::rotation_axis)
.def_ro("friedels_law", &XdsAscii::friedels_law)
.def_ro("generated_by", &XdsAscii::generated_by)
.def_prop_ro("data_size", [](XdsAscii& self) { return self.data.size(); })
.def_prop_ro("miller_array", [](XdsAscii& self) {
constexpr int64_t stride = int64_t(sizeof(XdsAscii::Refl) / sizeof(int));
return nb::ndarray<nb::numpy, int, nb::shape<-1,3>>(
&self.data[0].hkl[0], {self.data.size(), 3}, nb::handle(), {stride, 1});
}, nb::rv_policy::reference_internal)
.def_prop_ro("iset_array", [](XdsAscii& self) {
return vector_member_array(self.data, &XdsAscii::Refl::iset);
}, nb::rv_policy::reference_internal)
.def_prop_ro("iobs_array", [](XdsAscii& self) {
return vector_member_array(self.data, &XdsAscii::Refl::iobs);
}, nb::rv_policy::reference_internal)
.def_prop_ro("sigma_array", [](XdsAscii& self) {
return vector_member_array(self.data, &XdsAscii::Refl::sigma);
}, nb::rv_policy::reference_internal)
.def_prop_ro("xd_array", [](XdsAscii& self) {
return vector_member_array(self.data, &XdsAscii::Refl::xd);
}, nb::rv_policy::reference_internal)
.def_prop_ro("yd_array", [](XdsAscii& self) {
return vector_member_array(self.data, &XdsAscii::Refl::yd);
}, nb::rv_policy::reference_internal)
.def_prop_ro("zd_array", [](XdsAscii& self) {
return vector_member_array(self.data, &XdsAscii::Refl::zd);
}, nb::rv_policy::reference_internal)
.def("filtered", [](XdsAscii& self, const cpu_array<bool>& selection) {
auto v = selection.view();
size_t n = self.data.size();
if (v.shape(0) != n)
throw nb::value_error("boolean array must match the number of reflections");
XdsAscii ret((const XdsAsciiMetadata&) self);
size_t count = 0;
for (size_t i = 0; i < v.shape(0); ++i)
count += (size_t) v(i);
ret.data.reserve(count);
for (size_t i = 0; i < v.shape(0); ++i)
if (v(i))
ret.data.push_back(self.data[i]);
return ret;
})
.def("apply_polarization_correction", &XdsAscii::apply_polarization_correction,
nb::arg("p"), nb::arg("normal"))
.def("to_mtz", &gemmi::xds_to_mtz)
;
m.def("read_xds_ascii", &read_xds_ascii);
}
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