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// Copyright 2018 Global Phasing Ltd.
#include <cassert>
#include <sstream> // for ostringstream
#include "gemmi/to_mmcif.hpp"
#include "gemmi/to_pdb.hpp"
#include "gemmi/fstream.hpp"
#include "common.h"
#include <nanobind/stl/string.h>
using namespace gemmi;
void add_write(nb::module_& m, nb::class_<Structure>& structure) {
nb::class_<MmcifOutputGroups>(m, "MmcifOutputGroups")
.def(nb::init<bool>())
.def("__init__", [](MmcifOutputGroups* p, bool all, const nb::kwargs& kwargs) {
nb::object obj = nb::type<MmcifOutputGroups>()(all);
for (auto [key, value] : kwargs)
obj.attr(key) = nb::cast<bool>(value);
new(p) MmcifOutputGroups(nb::cast<const MmcifOutputGroups&>(obj));
}, nb::arg("all"), nb::arg("kwargs"))
#define DEF_BIT_PROPERTY(name) \
.def_prop_rw(#name, [](MmcifOutputGroups g) { return g.name; }, \
[](MmcifOutputGroups& g, bool v) { g.name = v; })
DEF_BIT_PROPERTY(atoms)
DEF_BIT_PROPERTY(block_name)
DEF_BIT_PROPERTY(entry)
DEF_BIT_PROPERTY(database_status)
DEF_BIT_PROPERTY(author)
DEF_BIT_PROPERTY(cell)
DEF_BIT_PROPERTY(symmetry)
DEF_BIT_PROPERTY(entity)
DEF_BIT_PROPERTY(entity_poly)
DEF_BIT_PROPERTY(struct_ref)
DEF_BIT_PROPERTY(chem_comp)
DEF_BIT_PROPERTY(exptl)
DEF_BIT_PROPERTY(diffrn)
DEF_BIT_PROPERTY(reflns)
DEF_BIT_PROPERTY(refine)
DEF_BIT_PROPERTY(title_keywords)
DEF_BIT_PROPERTY(ncs)
DEF_BIT_PROPERTY(struct_asym)
DEF_BIT_PROPERTY(origx)
DEF_BIT_PROPERTY(struct_conf)
DEF_BIT_PROPERTY(struct_sheet)
DEF_BIT_PROPERTY(struct_biol)
DEF_BIT_PROPERTY(assembly)
DEF_BIT_PROPERTY(conn)
DEF_BIT_PROPERTY(cis)
DEF_BIT_PROPERTY(scale)
DEF_BIT_PROPERTY(atom_type)
DEF_BIT_PROPERTY(entity_poly_seq)
DEF_BIT_PROPERTY(tls)
DEF_BIT_PROPERTY(software)
DEF_BIT_PROPERTY(group_pdb)
DEF_BIT_PROPERTY(auth_all)
;
#undef DEF_BIT_PROPERTY
nb::class_<PdbWriteOptions>(m, "PdbWriteOptions")
.def("__init__", [](PdbWriteOptions* opt, bool minimal, bool headers_only) {
new(opt) PdbWriteOptions;
if (minimal)
*opt = PdbWriteOptions::minimal();
else if (headers_only)
*opt = PdbWriteOptions::headers_only();
}, nb::arg("minimal")=false, nb::arg("headers_only")=false)
.def("__init__", [](PdbWriteOptions* p, bool minimal, bool headers_only,
const nb::kwargs& kwargs) {
nb::object obj = nb::type<PdbWriteOptions>()(minimal, headers_only);
for (auto [key, value] : kwargs)
obj.attr(key) = nb::cast<bool>(value);
new(p) PdbWriteOptions(nb::cast<const PdbWriteOptions&>(obj));
}, nb::arg("minimal")=false, nb::arg("headers_only")=false, nb::arg("kwargs"))
#define DEF_PROPERTY(name) \
.def_prop_rw(#name, [](PdbWriteOptions g) { return g.name; }, \
[](PdbWriteOptions& g, bool v) { g.name = v; })
DEF_PROPERTY(minimal_file)
DEF_PROPERTY(atom_records)
DEF_PROPERTY(seqres_records)
DEF_PROPERTY(ssbond_records)
DEF_PROPERTY(link_records)
DEF_PROPERTY(cispep_records)
DEF_PROPERTY(cryst1_record)
DEF_PROPERTY(ter_records)
DEF_PROPERTY(conect_records)
DEF_PROPERTY(end_record)
DEF_PROPERTY(numbered_ter)
DEF_PROPERTY(ter_ignores_type)
DEF_PROPERTY(use_linkr)
DEF_PROPERTY(use_link_id)
DEF_PROPERTY(preserve_serial)
;
#undef DEF_PROPERTY
structure
.def("make_pdb_string", &make_pdb_string,
nb::arg("options").sig("PdbWriteOptions()")=PdbWriteOptions())
.def("write_pdb", [](const Structure& st, const std::string& path, PdbWriteOptions options) {
Ofstream f(path);
write_pdb(st, f.ref(), options);
})
// deprecated - kept for compatibility
.def("write_pdb", [](const Structure& st, const std::string& path, const nb::kwargs& kwargs) {
Ofstream f(path);
nb::object options = nb::type<PdbWriteOptions>()(**kwargs);
write_pdb(st, f.ref(), nb::cast<const PdbWriteOptions&>(options));
}, nb::arg("path"), nb::arg("kwargs"))
// deprecated
.def("make_pdb_headers", &make_pdb_headers)
// deprecated
.def("write_minimal_pdb", [](const Structure& st, const std::string& path) {
Ofstream f(path);
write_minimal_pdb(st, f.ref());
}, nb::arg("path"))
// deprecated
.def("make_minimal_pdb", [](const Structure& st) {
std::ostringstream os;
write_minimal_pdb(st, os);
return os.str();
})
.def("make_mmcif_document", &make_mmcif_document,
nb::arg("groups").sig("MmcifOutputGroups(True)")=MmcifOutputGroups(true))
.def("make_mmcif_block", &make_mmcif_block,
nb::arg("groups").sig("MmcifOutputGroups(True)")=MmcifOutputGroups(true))
.def("update_mmcif_block", &update_mmcif_block, nb::arg("block"),
nb::arg("groups").sig("MmcifOutputGroups(True)")=MmcifOutputGroups(true))
.def("make_mmcif_headers", &make_mmcif_headers)
;
}
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