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//------------------------------------------------------------------------------
// This file is part of the OpenStructure project <www.openstructure.org>
//
// Copyright (C) 2008-2020 by the OpenStructure authors
//
// This library is free software; you can redistribute it and/or modify it under
// the terms of the GNU Lesser General Public License as published by the Free
// Software Foundation; either version 3.0 of the License, or (at your option)
// any later version.
// This library is distributed in the hope that it will be useful, but WITHOUT
// ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS
// FOR A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
// details.
//
// You should have received a copy of the GNU Lesser General Public License
// along with this library; if not, write to the Free Software Foundation, Inc.,
// 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA
//------------------------------------------------------------------------------
#include <boost/python.hpp>
using namespace boost::python;
#include <ost/io/mol/io_profile.hh>
#include <ost/io/mol/pdb_reader.hh>
#include <ost/io/mol/pdb_writer.hh>
#include <ost/io/mol/pdb_str.hh>
using namespace ost;
using namespace ost::io;
BOOST_PYTHON_MEMBER_FUNCTION_OVERLOADS(X_import,
PDBReader::Import, 1, 2)
BOOST_PYTHON_FUNCTION_OVERLOADS(load_PDB_ov, LoadPDB, 1, 2)
void (PDBWriter::*write_a)(const mol::EntityHandle&)=&PDBWriter::Write;
void (PDBWriter::*write_b)(const mol::EntityView&)=&PDBWriter::Write;
String (*pdb_str_a)(const mol::EntityHandle&, const IOProfile&)=&EntityToPDBString;
String (*pdb_str_b)(const mol::EntityView&, const IOProfile&)=&EntityToPDBString;
void remove_profiles() {
IOProfileRegistry::RemoveProfiles();
}
void export_pdb_io()
{
class_<IOProfile>("IOProfile",
init<String,bool,bool,bool,bool,bool,
conop::ProcessorPtr>((arg("dialect")="PDB",
arg("fault_tolerant")=false,
arg("join_spread_atom_records")=false,
arg("no_hetatms")=false,
arg("calpha_only")=false,
arg("read_conect")=false,
arg("processor")=conop::ProcessorPtr())))
.def(init<const IOProfile&>())
.def_readwrite("dialect", &IOProfile::dialect)
.def_readwrite("fault_tolerant", &IOProfile::fault_tolerant)
.def_readwrite("no_hetatms", &IOProfile::no_hetatms)
.def_readwrite("calpha_only", &IOProfile::calpha_only)
.def_readwrite("join_spread_atom_records", &IOProfile::join_spread_atom_records)
.def_readwrite("read_conect", &IOProfile::read_conect)
.def_readwrite("processor", &IOProfile::processor)
.def("Copy", &IOProfile::Copy)
.def(self_ns::str(self))
;
class_<IOProfileRegistry>("IOProfileRegistry", no_init)
.def("Get", &IOProfileRegistry::Get,
return_internal_reference<>())
.def("Set", &IOProfileRegistry::Set)
.def("Instance", &IOProfileRegistry::Instance,
//return_internal_reference).staticmethod("Instance")
return_value_policy<reference_existing_object>()).staticmethod("Instance")
.def("GetDefault", &IOProfileRegistry::GetDefault,
return_internal_reference<>())
;
class_<PDBReader, boost::noncopyable>("PDBReader", init<String, const IOProfile&>())
.def("HasNext", &PDBReader::HasNext)
.def("Import", &PDBReader::Import,
X_import(args("entity", "restrict_chains")))
.add_property("read_seqres", &PDBReader::GetReadSeqRes,
&PDBReader::SetReadSeqRes)
.add_property("seqres", &PDBReader::GetSeqRes)
;
class_<PDBWriter, boost::noncopyable>("PDBWriter", init<String, const IOProfile&>())
.def("Write", write_a)
.def("SetIsPQR", &PDBWriter::SetIsPQR)
.def("IsPQR", &PDBWriter::IsPQR)
.def("SetWriteMultiModel", &PDBWriter::SetWriteMultiModel)
.def("GetWriteMultiModel", &PDBWriter::GetWriteMultiModel)
.add_property("write_multi_model", &PDBWriter::GetWriteMultiModel,
&PDBWriter::SetWriteMultiModel)
.def("Write", write_b)
;
def("EntityToPDBStr", pdb_str_a,
(arg("entity"), arg("profile")=IOProfile()));
def("EntityToPDBStr", pdb_str_b,
(arg("entity"), arg("profile")=IOProfile()));
def("PDBStrToEntity", &PDBStringToEntity, (arg("pdb_string"),
arg("profile")=IOProfile(),
arg("process")=false));
// we need to make sure there are no pending references to Python objects
// tied to the IOProfileRegistry singleton. The destructor of
// IOProfileRegistry may be called after Python is shutdown which results
// in a segfault.
scope().attr("__dict__")["atexit"]=handle<>(PyImport_ImportModule("atexit"));
def("_remove_profiles", &remove_profiles);
object r=scope().attr("_remove_profiles");
scope().attr("atexit").attr("register")(r);
}
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