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// Copyright 2017 Global Phasing Ltd.
#include "gemmi/numb.hpp"
#include "gemmi/cifdoc.hpp"
#include "gemmi/cif.hpp"
#include "gemmi/json.hpp"
#include "gemmi/smcif.hpp" // for make_small_structure_from_block
#include "gemmi/small.hpp" // for SmallStructure
#include "gemmi/interop.hpp" // for atom_to_site, mx_to_sx_structure
#include "gemmi/chemcomp_xyz.hpp"
#include "gemmi/remarks.hpp"
#define GEMMI_READ_CIF_IMPLEMENTATION
#include "gemmi/read_cif.hpp" // for read_cif_gz, read_mmjson_gz
#define GEMMI_READ_COOR_IMPLEMENTATION
#include "gemmi/read_coor.hpp" // for read_structure_gz
#include "common.h"
#include <pybind11/stl.h>
#include <pybind11/stl_bind.h>
namespace py = pybind11;
using namespace gemmi;
PYBIND11_MAKE_OPAQUE(std::vector<SmallStructure::Site>)
void add_cif_read(py::module& cif) {
cif.def("read_file", &cif::read_file, py::arg("filename"),
"Reads a CIF file copying data into Document.");
cif.def("read", &read_cif_or_mmjson_gz,
py::arg("filename"), "Reads normal or gzipped CIF file.");
cif.def("read_mmjson", &read_mmjson_gz,
py::arg("filename"), "Reads normal or gzipped mmJSON file.");
cif.def("read_string", &cif::read_string, py::arg("data"),
"Reads a string as a CIF file.");
cif.def("as_string", (std::string (*)(const std::string&)) &cif::as_string,
py::arg("value"), "Get string content (no quotes) from raw string.");
cif.def("as_number", &cif::as_number,
py::arg("value"), py::arg("default")=NAN,
"Returns float number from string");
cif.def("as_int", (int (*)(const std::string&)) &cif::as_int,
py::arg("value"), "Returns int number from string value.");
cif.def("as_int", (int (*)(const std::string&, int)) &cif::as_int,
py::arg("value"), py::arg("default"),
"Returns int number from string value or the second arg if null.");
cif.def("is_null", &cif::is_null, py::arg("value"));
}
void add_read_structure(py::module& m) {
m.def("read_structure", [](const std::string& path, bool merge,
CoorFormat format) {
Structure* st = new Structure(read_structure_gz(path, format));
if (!st->raw_remarks.empty())
read_metadata_from_remarks(*st);
if (merge)
st->merge_chain_parts();
return st;
}, py::arg("path"), py::arg("merge_chain_parts")=true,
py::arg("format")=CoorFormat::Unknown,
"Reads a coordinate file into Structure.");
m.def("make_structure_from_block", &make_structure_from_block,
py::arg("block"), "Takes mmCIF block and returns Structure.");
m.def("read_pdb_string", [](const std::string& s, int max_line_length,
bool split_chain_on_ter) {
PdbReadOptions options;
options.max_line_length = max_line_length;
options.split_chain_on_ter = split_chain_on_ter;
Structure* st = new Structure(read_pdb_string(s, "string", options));
read_metadata_from_remarks(*st);
return st;
}, py::arg("s"), py::arg("max_line_length")=0,
py::arg("split_chain_on_ter")=false, "Reads a string as PDB file.");
m.def("read_pdb", [](const std::string& path, int max_line_length,
bool split_chain_on_ter) {
PdbReadOptions options;
options.max_line_length = max_line_length;
options.split_chain_on_ter = split_chain_on_ter;
Structure* st = new Structure(read_pdb_gz(path, options));
read_metadata_from_remarks(*st);
return st;
}, py::arg("filename"), py::arg("max_line_length")=0,
py::arg("split_chain_on_ter")=false);
// from smcif.hpp
m.def("read_small_structure", [](const std::string& path) {
cif::Block block = cif::read_file(path).sole_block();
return new SmallStructure(make_small_structure_from_block(block));
}, py::arg("path"), "Reads a small molecule CIF file.");
m.def("make_small_structure_from_block", &make_small_structure_from_block,
py::arg("block"), "Takes CIF block and returns SmallStructure.");
// from chemcomp_xyz.hpp
m.def("make_structure_from_chemcomp_block",
&make_structure_from_chemcomp_block, py::arg("block"),
"CIF block from CCD or monomer library -> single-residue Structure.");
// and an unrelated function from gz.hpp
m.def("estimate_uncompressed_size", &estimate_uncompressed_size,
py::arg("path"),
"Returns uncompressed size of a .gz file (not always reliable)");
}
void add_small(py::module& m) {
using gemmi::SmallStructure;
py::class_<SmallStructure> small_structure(m, "SmallStructure");
py::class_<SmallStructure::Site>(small_structure, "Site")
.def(py::init<>())
.def(py::init(&gemmi::atom_to_site))
.def_readwrite("label", &SmallStructure::Site::label)
.def_readwrite("type_symbol", &SmallStructure::Site::type_symbol)
.def_readwrite("fract", &SmallStructure::Site::fract)
.def_readwrite("occ", &SmallStructure::Site::occ)
.def_readwrite("u_iso", &SmallStructure::Site::u_iso)
.def_readwrite("element", &SmallStructure::Site::element)
.def_readwrite("charge", &SmallStructure::Site::charge)
.def_readwrite("disorder_group", &SmallStructure::Site::disorder_group)
.def_readwrite("aniso", &SmallStructure::Site::aniso)
.def("orth", &SmallStructure::Site::orth)
.def("__repr__", [](const SmallStructure::Site& self) {
return "<gemmi.SmallStructure.Site " + self.label + ">";
});
py::bind_vector<std::vector<SmallStructure::Site>>(small_structure, "SiteList");
using AtomType = SmallStructure::AtomType;
py::class_<AtomType>(small_structure, "AtomType")
.def_readonly("symbol", &AtomType::symbol)
.def_readonly("element", &AtomType::element)
.def_readwrite("dispersion_real", &AtomType::dispersion_real)
.def_readwrite("dispersion_imag", &AtomType::dispersion_imag)
.def("__repr__", [](const AtomType& self) {
return "<gemmi.SmallStructure.AtomType " + self.symbol + ">";
});
small_structure
.def(py::init<>())
.def_readwrite("name", &SmallStructure::name)
.def_readwrite("cell", &SmallStructure::cell)
.def_readwrite("spacegroup_hm", &SmallStructure::spacegroup_hm)
.def_readonly("sites", &SmallStructure::sites)
.def_readonly("atom_types", &SmallStructure::atom_types)
.def_readwrite("wavelength", &SmallStructure::wavelength)
.def("add_site", [](SmallStructure& self, const SmallStructure::Site& site) {
self.sites.push_back(site);
})
.def("find_spacegroup", &SmallStructure::find_spacegroup)
.def("get_atom_type", &SmallStructure::get_atom_type)
.def("get_all_unit_cell_sites", &SmallStructure::get_all_unit_cell_sites)
.def("remove_hydrogens", &SmallStructure::remove_hydrogens)
.def("change_occupancies_to_crystallographic",
&SmallStructure::change_occupancies_to_crystallographic,
py::arg("max_dist")=0.4)
.def("setup_cell_images", &SmallStructure::setup_cell_images)
.def("make_cif_block", &make_cif_block_from_small_structure)
.def("__repr__", [](const SmallStructure& self) {
return "<gemmi.SmallStructure: " + std::string(self.name) + ">";
});
m.def("mx_to_sx_structure", &gemmi::mx_to_sx_structure,
py::arg("st"), py::arg("n")=0);
}
// used in cif.cpp
void cif_parse_string(cif::Document& doc, const std::string& data) {
tao::pegtl::memory_input<> in(data, "string");
cif::parse_input(doc, in);
}
void cif_parse_file(cif::Document& doc, const std::string& filename) {
GEMMI_CIF_FILE_INPUT(in, filename);
cif::parse_input(doc, in);
}
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