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// Copyright 2017 Global Phasing Ltd.
#include "common.h"
#include <pybind11/stl.h>
#include <pybind11/stl_bind.h>
#include <ostream>
#include "gemmi/seqid.hpp"
#include "gemmi/metadata.hpp"
#include "gemmi/enumstr.hpp"
#include "tostr.hpp"
#include "meta.h"
namespace py = pybind11;
using namespace gemmi;
namespace gemmi {
// not inline
std::ostream& operator<< (std::ostream& os, const Entity& ent) {
os << "<gemmi.Entity '" << ent.name << "' "
<< entity_type_to_string(ent.entity_type);
if (ent.polymer_type != PolymerType::Unknown)
os << ' ' << polymer_type_to_qstring(ent.polymer_type);
os << " object at 0x" << std::hex << (size_t)&ent << std::dec << '>';
return os;
}
}
void add_meta(py::module& m) {
// seqid.hpp
py::class_<SeqId>(m, "SeqId")
.def(py::init<int, char>())
.def(py::init<const std::string&>())
.def_readwrite("num", &SeqId::num)
.def_readwrite("icode", &SeqId::icode)
.def("__str__", &SeqId::str)
.def("__repr__", [](const SeqId& self) {
return "<gemmi.SeqId " + self.str() + ">";
})
.def(py::self == py::self)
.def(py::self < py::self)
.def(py::pickle(
[](const SeqId &self) {
return py::make_tuple(self.num, self.icode);
},
[](py::tuple t) {
if (t.size() != 2)
throw std::runtime_error("invalid tuple size");
return SeqId(t[0].cast<int>(), t[1].cast<char>());
}
));
py::class_<ResidueId>(m, "ResidueId")
.def(py::init<>())
.def_readwrite("name", &ResidueId::name)
.def_readwrite("seqid", &ResidueId::seqid)
.def_readwrite("segment", &ResidueId::segment)
.def("__str__", &ResidueId::str)
.def("__repr__", [](const ResidueId& self) {
return "<gemmi.ResidueId " + self.str() + ">";
})
.def(py::self == py::self)
.def(py::pickle(
[](const ResidueId &self) {
return py::make_tuple(self.seqid, self.segment, self.name);
},
[](py::tuple t) {
if (t.size() != 3)
throw std::runtime_error("invalid tuple size");
ResidueId r;
r.seqid = t[0].cast<SeqId>();
r.segment = t[1].cast<std::string>();
r.name = t[2].cast<std::string>();
return r;
}
));
py::class_<AtomAddress>(m, "AtomAddress")
.def(py::init<>())
.def(py::init<const std::string&, const SeqId&, const std::string&,
const std::string&, char>(),
py::arg("chain"), py::arg("seqid"), py::arg("resname"),
py::arg("atom"), py::arg("altloc")='\0')
.def_readwrite("chain_name", &AtomAddress::chain_name)
.def_readwrite("res_id", &AtomAddress::res_id)
.def_readwrite("atom_name", &AtomAddress::atom_name)
.def_readwrite("altloc", &AtomAddress::altloc)
.def("__str__", &AtomAddress::str)
.def("__repr__", [](const AtomAddress& self) {
return tostr("<gemmi.AtomAddress ", self.str(), '>');
})
.def(py::self == py::self)
.def(py::pickle(
[](const AtomAddress &self) {
return py::make_tuple(self.chain_name, self.res_id, self.atom_name, self.altloc);
},
[](py::tuple t) {
if (t.size() != 4)
throw std::runtime_error("invalid tuple size");
return AtomAddress(t[0].cast<std::string>(), t[1].cast<ResidueId>(),
t[2].cast<std::string>(), t[3].cast<char>());
}
));
// metadata.hpp
py::class_<NcsOp>(m, "NcsOp")
.def(py::init<>())
.def(py::init([](const Transform& tr, const std::string& id, bool given) {
NcsOp* op = new NcsOp();
op->tr = tr;
op->id = id;
op->given = given;
return op;
}), py::arg("tr"), py::arg("id")="", py::arg("given")=false)
.def_readwrite("id", &NcsOp::id)
.def_readwrite("given", &NcsOp::given)
.def_readonly("tr", &NcsOp::tr)
.def("apply", &NcsOp::apply)
.def("__repr__", [](const NcsOp& self) {
return tostr("<gemmi.NcsOp ", self.id,
" |shift|=", self.tr.vec.length(),
(self.given ? " (" : " (not "), "given)>");
});
py::bind_vector<std::vector<NcsOp>>(m, "NcsOpList");
py::enum_<EntityType>(m, "EntityType")
.value("Unknown", EntityType::Unknown)
.value("Polymer", EntityType::Polymer)
.value("NonPolymer", EntityType::NonPolymer)
.value("Water", EntityType::Water);
py::enum_<PolymerType>(m, "PolymerType")
.value("PeptideL", PolymerType::PeptideL)
.value("PeptideD", PolymerType::PeptideD)
.value("Dna", PolymerType::Dna)
.value("Rna", PolymerType::Rna)
.value("DnaRnaHybrid", PolymerType::DnaRnaHybrid)
.value("SaccharideD", PolymerType::SaccharideD)
.value("SaccharideL", PolymerType::SaccharideL)
.value("Pna", PolymerType::Pna)
.value("CyclicPseudoPeptide", PolymerType::CyclicPseudoPeptide)
.value("Other", PolymerType::Other)
.value("Unknown", PolymerType::Unknown);
py::class_<Entity>(m, "Entity")
.def(py::init<std::string>())
.def_readwrite("name", &Entity::name)
.def_readwrite("subchains", &Entity::subchains)
.def_readwrite("entity_type", &Entity::entity_type)
.def_readwrite("polymer_type", &Entity::polymer_type)
.def_readwrite("sifts_unp_acc", &Entity::sifts_unp_acc)
.def_readwrite("full_sequence", &Entity::full_sequence)
.def_static("first_mon", &Entity::first_mon)
.def("__repr__", [](const Entity& self) { return tostr(self); });
py::bind_vector<std::vector<Entity>>(m, "EntityList");
py::enum_<Connection::Type>(m, "ConnectionType")
.value("Covale", Connection::Type::Covale)
.value("Disulf", Connection::Type::Disulf)
.value("Hydrog", Connection::Type::Hydrog)
.value("MetalC", Connection::Type::MetalC)
.value("Unknown", Connection::Type::Unknown);
py::class_<Connection>(m, "Connection")
.def(py::init<>())
.def_readwrite("name", &Connection::name)
.def_readwrite("link_id", &Connection::link_id)
.def_readwrite("type", &Connection::type)
.def_readwrite("asu", &Connection::asu)
.def_readwrite("partner1", &Connection::partner1)
.def_readwrite("partner2", &Connection::partner2)
.def_readwrite("reported_distance", &Connection::reported_distance)
.def("__repr__", [](const Connection& self) {
return tostr("<gemmi.Connection ", self.name, " ",
self.partner1.str(), " - ", self.partner2.str(), '>');
});
py::bind_vector<std::vector<Connection>>(m, "ConnectionList");
py::class_<Helix> helix(m, "Helix");
py::enum_<Helix::HelixClass>(helix, "HelixClass")
.value("UnknownHelix", Helix::HelixClass::UnknownHelix)
.value("RAlpha", Helix::HelixClass::RAlpha)
.value("ROmega", Helix::HelixClass::ROmega)
.value("RPi", Helix::HelixClass::RPi)
.value("RGamma", Helix::HelixClass::RGamma)
.value("R310", Helix::HelixClass::R310)
.value("LAlpha", Helix::HelixClass::LAlpha)
.value("LOmega", Helix::HelixClass::LOmega)
.value("LGamma", Helix::HelixClass::LGamma)
.value("Helix27", Helix::HelixClass::Helix27)
.value("HelixPolyProlineNone", Helix::HelixClass::HelixPolyProlineNone);
helix
.def(py::init<>())
.def_readwrite("start", &Helix::start)
.def_readwrite("end", &Helix::end)
.def_readwrite("pdb_helix_class", &Helix::pdb_helix_class)
.def_readwrite("length", &Helix::length);
py::bind_vector<std::vector<Helix>>(m, "HelixList");
py::class_<Sheet> sheet(m, "Sheet");
py::class_<Sheet::Strand>(sheet, "Strand")
.def(py::init<>())
.def_readwrite("start", &Sheet::Strand::start)
.def_readwrite("end", &Sheet::Strand::end)
.def_readwrite("hbond_atom2", &Sheet::Strand::hbond_atom2)
.def_readwrite("hbond_atom1", &Sheet::Strand::hbond_atom1)
.def_readwrite("sense", &Sheet::Strand::sense)
.def_readwrite("name", &Sheet::Strand::name);
py::bind_vector<std::vector<Sheet::Strand>>(sheet, "StrandList");
sheet
.def(py::init<std::string>())
.def_readwrite("name", &Sheet::name)
.def_readwrite("strands", &Sheet::strands);
py::bind_vector<std::vector<Sheet>>(m, "SheetList");
py::class_<Assembly> assembly(m, "Assembly");
py::class_<Assembly::Operator>(assembly, "Operator")
.def(py::init<>())
.def_readwrite("name", &Assembly::Operator::name)
.def_readwrite("type", &Assembly::Operator::type)
.def_readwrite("transform", &Assembly::Operator::transform);
py::bind_vector<std::vector<Assembly::Operator>>(assembly, "OperatorList");
py::class_<Assembly::Gen>(assembly, "Gen")
.def(py::init<>())
.def_readwrite("chains", &Assembly::Gen::chains)
.def_readwrite("subchains", &Assembly::Gen::subchains)
.def_readonly("operators", &Assembly::Gen::operators);
py::bind_vector<std::vector<Assembly::Gen>>(assembly, "GenList");
py::enum_<Assembly::SpecialKind>(m, "AssemblySpecialKind")
.value("NA", Assembly::SpecialKind::NA)
.value("CompleteIcosahedral", Assembly::SpecialKind::CompleteIcosahedral)
.value("RepresentativeHelical", Assembly::SpecialKind::RepresentativeHelical)
.value("CompletePoint", Assembly::SpecialKind::CompletePoint);
assembly
.def(py::init<const std::string&>())
.def_readwrite("name", &Assembly::name)
.def_readwrite("author_determined", &Assembly::author_determined)
.def_readwrite("software_determined", &Assembly::software_determined)
.def_readwrite("oligomeric_details", &Assembly::oligomeric_details)
.def_readonly("generators", &Assembly::generators)
.def_readwrite("special_kind", &Assembly::special_kind)
;
py::bind_vector<std::vector<Assembly>>(m, "AssemblyList");
py::class_<Metadata>(m, "Metadata")
.def_readwrite("authors", &Metadata::authors)
;
}
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