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// Copyright 2017 Global Phasing Ltd.
#include "gemmi/symmetry.hpp"
#include "common.h"
#include <pybind11/stl.h>
#include <pybind11/stl_bind.h>
#include <pybind11/numpy.h>
#include "miller_a.h"
namespace py = pybind11;
using namespace gemmi;
void add_symmetry(py::module& m) {
py::enum_<CrystalSystem>(m, "CrystalSystem")
.value("Triclinic", CrystalSystem::Triclinic)
.value("Monoclinic", CrystalSystem::Monoclinic)
.value("Orthorhombic", CrystalSystem::Orthorhombic)
.value("Tetragonal", CrystalSystem::Tetragonal)
.value("Trigonal", CrystalSystem::Trigonal)
.value("Hexagonal", CrystalSystem::Hexagonal)
.value("Cubic", CrystalSystem::Cubic)
;
py::class_<Op>(m, "Op")
.def(py::init<>(&Op::identity))
.def(py::init(&parse_triplet))
.def_property_readonly_static("DEN", [](py::object) { return Op::DEN; },
"Denominator (integer) for the translation vector.")
.def_readwrite("rot", &Op::rot, "3x3 integer matrix.")
.def_readwrite("tran", &Op::tran,
"Numerators (integers) of the translation vector. Denominator DEN=24.")
.def("triplet", &Op::triplet, py::arg("style")='x')
.def("inverse", &Op::inverse, "Returns inverted operator.")
.def("wrap", &Op::wrap, "Wrap the translation part to [0,1)")
.def("translated", &Op::translated, py::arg("a"), "Adds a to tran")
.def("transposed_rot", &Op::transposed_rot)
.def("det_rot", &Op::det_rot, "Determinant of the 3x3 matrix.")
.def("rot_type", &Op::rot_type)
.def("combine", &Op::combine, py::arg("b"),
"Combine two symmetry operations.")
.def("seitz", [](const Op& self) {
auto arr = self.int_seitz();
auto mat = py::list();
py::object fr = py::module::import("fractions").attr("Fraction");
for (int i = 0; i < 4; ++i) {
auto row = py::list();
for (int j = 0; j < 4; ++j) {
auto v = arr[i][j];
if (i == 3 || v == 0)
row.append(v);
else if (std::abs(v) == Op::DEN)
row.append(v / Op::DEN);
else
row.append(fr(v, Op::DEN + 0)); // +0 to avoid linker error
}
mat.append(row);
}
return mat;
}, "Returns Seitz matrix (fractions)")
.def("float_seitz", &Op::float_seitz, "Returns Seitz matrix (floats)")
.def("apply_to_xyz", &Op::apply_to_xyz, py::arg("xyz"))
.def("apply_to_hkl", &Op::apply_to_hkl, py::arg("hkl"))
.def("phase_shift", &Op::phase_shift, py::arg("hkl"))
.def("__mul__", [](const Op& a, const Op& b) { return a * b; },
py::is_operator())
.def("__mul__", [](const Op &a, const std::string& b) {
return a * parse_triplet(b);
}, py::is_operator())
.def("__rmul__", [](const Op& a, const std::string& b) {
return parse_triplet(b) * a;
}, py::is_operator())
.def("__eq__", [](const Op& a, const Op& b) { return a == b; },
py::is_operator())
.def("__eq__", [](const Op& a, const std::string& b) {
return a == parse_triplet(b);
}, py::is_operator())
#if PY_MAJOR_VERSION < 3 // in Py3 != is inferred from ==
.def("__ne__", [](const Op& a, const Op& b) { return a != b; },
py::is_operator())
.def("__ne__", [](const Op& a, const std::string& b) {
return a != parse_triplet(b);
}, py::is_operator())
#endif
.def("__copy__", [](const Op& self) { return Op(self); })
.def("__deepcopy__", [](const Op& self, py::dict) { return Op(self); }, py::arg("memo"))
.def("__hash__", [](const Op& self) { return std::hash<Op>()(self); })
.def("__repr__", [](const Op& self) {
return "<gemmi.Op(\"" + self.triplet() + "\")>";
});
m.def("parse_triplet", &parse_triplet, py::arg("triplet"),
"Parse coordinate triplet into gemmi.Op.");
m.def("parse_triplet_part", &parse_triplet_part, py::arg("s"),
"Parse one of the three parts of a triplet.");
m.def("make_triplet_part", &make_triplet_part,
py::arg("xyz"), py::arg("w"), py::arg("style")='x',
"Make one of the three parts of a triplet.");
py::class_<GroupOps>(m, "GroupOps")
.def(py::init(&split_centering_vectors))
.def("__iter__", [](const GroupOps& self) {
return py::make_iterator(self);
}, py::keep_alive<0, 1>())
.def("__eq__", [](const GroupOps &a, const GroupOps &b) {
return a.is_same_as(b);
}, py::is_operator())
#if PY_MAJOR_VERSION < 3 // in Py3 != is inferred from ==
.def("__ne__", [](const GroupOps &a, const GroupOps &b) {
return !a.is_same_as(b);
}, py::is_operator())
#endif
.def("__len__", [](const GroupOps& g) { return g.order(); })
.def("__deepcopy__", [](const GroupOps& g, py::dict) { return GroupOps(g); },
py::arg("memo"))
.def_readwrite("sym_ops", &GroupOps::sym_ops,
"Symmetry operations (to be combined with centering vectors).")
.def_readwrite("cen_ops", &GroupOps::cen_ops, "Centering vectors.")
.def("add_missing_elements", &GroupOps::add_missing_elements)
.def("find_centering", &GroupOps::find_centering)
.def("has_same_centring", &GroupOps::has_same_centring)
.def("has_same_rotations", &GroupOps::has_same_rotations)
.def("is_centrosymmetric", &GroupOps::is_centrosymmetric)
.def("is_reflection_centric", &GroupOps::is_reflection_centric)
.def("centric_flag_array", [](const GroupOps& g, py::array_t<int> hkl) {
return miller_function<bool>(g, &GroupOps::is_reflection_centric, hkl);
})
.def("epsilon_factor_without_centering", &GroupOps::epsilon_factor_without_centering)
.def("epsilon_factor", &GroupOps::epsilon_factor)
.def("epsilon_factor_array", [](const GroupOps& g, py::array_t<int> hkl) {
return miller_function<int>(g, &GroupOps::epsilon_factor, hkl);
})
.def("epsilon_factor_without_centering_array", [](const GroupOps& g,
py::array_t<int> hkl) {
return miller_function<int>(g, &GroupOps::epsilon_factor_without_centering, hkl);
})
.def("is_systematically_absent", &GroupOps::is_systematically_absent)
.def("systematic_absences", [](const GroupOps& g, py::array_t<int> hkl) {
return miller_function<bool>(g, &GroupOps::is_systematically_absent, hkl);
})
.def("find_grid_factors", &GroupOps::find_grid_factors,
"Minimal multiplicity for real-space grid (e.g. 1,1,6 for P61).")
.def("change_basis_forward", &GroupOps::change_basis_forward, py::arg("cob"),
"Applies the change-of-basis operator (in place).")
.def("change_basis_backward", &GroupOps::change_basis_backward, py::arg("cob"),
"Applies inverse of the change-of-basis operator (in place).")
.def("derive_symmorphic", &GroupOps::derive_symmorphic)
.def("add_inversion", &GroupOps::add_inversion)
;
py::class_<SpaceGroup, std::unique_ptr<SpaceGroup, py::nodelete>>(m, "SpaceGroup")
.def(py::init([](int n) {
return const_cast<SpaceGroup*>(&get_spacegroup_by_number(n));
}), py::arg("ccp4"), py::return_value_policy::reference)
.def(py::init([](const std::string& s) {
return const_cast<SpaceGroup*>(&get_spacegroup_by_name(s));
}), py::arg("hm"), py::return_value_policy::reference)
.def_readonly("number", &SpaceGroup::number, "number 1-230.")
.def_readonly("ccp4", &SpaceGroup::ccp4, "ccp4 number")
// Intel Compiler would not compile .def_readonly("hm", ...),
// the difference with hm, qualifier and hall is that they are char[N]
.def_property_readonly("hm", [](const SpaceGroup &self) -> const char* {
return self.hm;
}, "Hermann-Mauguin name")
.def_readonly("ext", &SpaceGroup::ext, "Extension (1, 2, H, R or none)")
.def_property_readonly("qualifier", [](const SpaceGroup &s) -> const char* {
return s.qualifier;
}, "e.g. 'cab'")
.def_property_readonly("hall", [](const SpaceGroup &self) -> const char* {
return self.hall;
}, "Hall symbol")
.def_property_readonly("basisop", &SpaceGroup::basisop)
.def("xhm", &SpaceGroup::xhm, "extended Hermann-Mauguin name")
.def("centring_type", &SpaceGroup::centring_type)
.def("short_name", &SpaceGroup::short_name,
"H-M name w/o spaces and with 1's removed in '1 ... 1'.")
.def("is_enantiomorphic", &SpaceGroup::is_enantiomorphic)
.def("is_sohncke", &SpaceGroup::is_sohncke)
.def("is_symmorphic", &SpaceGroup::is_symmorphic)
.def("point_group_hm", &SpaceGroup::point_group_hm,
"Returns H-M name of the point group.")
.def("laue_str", &SpaceGroup::laue_str,
"Returns name of the Laue class (for centrosymmetric groups "
"the same as point_group_hm).")
.def("crystal_system", &SpaceGroup::crystal_system)
.def("crystal_system_str", &SpaceGroup::crystal_system_str,
"Returns lower-case name of the crystal system.")
.def("is_centrosymmetric", &SpaceGroup::is_centrosymmetric)
.def("is_reference_setting", &SpaceGroup::is_reference_setting)
.def("centred_to_primitive", &SpaceGroup::centred_to_primitive)
.def("operations", &SpaceGroup::operations, "Group of operations")
.def("switch_to_asu", [](const SpaceGroup& sg, py::array_t<int> hkl) {
auto h = hkl.mutable_unchecked<2>();
if (h.shape(1) < 3)
throw std::domain_error("error: the size of the second dimension < 3");
GroupOps gops = sg.operations();
ReciprocalAsu asu(&sg);
for (py::ssize_t i = 0; i < h.shape(0); ++i) {
Op::Miller hkl = asu.to_asu({{h(i, 0), h(i, 1), h(i, 2)}}, gops).first;
for (int j = 0; j != 3; ++j)
h(i, j) = hkl[j];
}
}, py::arg("miller_array").noconvert())
.def("__repr__", [](const SpaceGroup &self) {
return "<gemmi.SpaceGroup(\"" + self.xhm() + "\")>";
})
.def(py::pickle(
[](const SpaceGroup &self) {
return self.xhm();
},
[](const std::string &s) {
return const_cast<SpaceGroup*>(&get_spacegroup_by_name(s));
}
));
py::class_<ReciprocalAsu>(m, "ReciprocalAsu")
.def(py::init<const SpaceGroup*, bool>(), py::arg(), py::arg("tnt")=false)
.def("is_in", &ReciprocalAsu::is_in, py::arg("hkl"))
.def("condition_str", &ReciprocalAsu::condition_str)
.def("to_asu", &ReciprocalAsu::to_asu, py::arg("hkl"), py::arg("group_ops"))
;
m.def("spacegroup_table", []() {
return py::make_iterator(spacegroup_tables::main);
}, py::return_value_policy::reference);
m.def("spacegroup_table_itb", []() {
return py::make_iterator(spacegroup_tables::main + 0,
spacegroup_tables::main + 530);
}, py::return_value_policy::reference);
m.def("generators_from_hall", &generators_from_hall, py::arg("hall"),
"Parse Hall notation.");
m.def("symops_from_hall", &symops_from_hall, py::arg("hall"),
"Parse Hall notation.");
m.def("find_spacegroup_by_number", &find_spacegroup_by_number,
py::arg("ccp4"), py::return_value_policy::reference,
"Returns space-group of given number.");
m.def("find_spacegroup_by_name", &find_spacegroup_by_name,
py::arg("hm"), py::arg("alpha")=0., py::arg("gamma")=0.,
py::return_value_policy::reference,
"Returns space-group with given name.");
m.def("get_spacegroup_reference_setting", &get_spacegroup_reference_setting,
py::arg("number"), py::return_value_policy::reference);
m.def("find_spacegroup_by_ops", &find_spacegroup_by_ops,
py::arg("group_ops"), py::return_value_policy::reference,
"Returns space-group with identical operations.");
m.def("seitz_to_op", &seitz_to_op);
}
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