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//
// Copyright (C) 2013-2021 Greg Landrum and Rational Discovery LLC
//
// @@ All Rights Reserved @@
// This file is part of the RDKit.
// The contents are covered by the terms of the BSD license
// which is included in the file license.txt, found at the root
// of the RDKit source tree.
//
#define NO_IMPORT_ARRAY
#include <RDBoost/python.h>
#include <string>
// ours
#include <GraphMol/FileParsers/MolWriters.h>
#include <GraphMol/RDKitBase.h>
#include "rdchem.h"
#include "ContextManagers.h"
#include <RDBoost/PySequenceHolder.h>
#include <RDBoost/python_streambuf.h>
namespace python = boost::python;
namespace RDKit {
using boost_adaptbx::python::streambuf;
namespace {
PDBWriter *getPDBWriter(python::object &fileobj, unsigned int flavor = 0) {
auto *sb = new streambuf(fileobj, 't');
auto *ost = new streambuf::ostream(sb);
return new PDBWriter(ost, true, flavor);
}
} // namespace
std::string pdbwDocStr =
"Constructor.\n\n"
" ARGUMENTS:\n\n"
" - fileName: name of the output file. ('-' to write to stdout)\n"
" - flavor: (optional) \n\n";
struct pdbwriter_wrap {
static void wrap() {
python::class_<PDBWriter, boost::noncopyable>(
"PDBWriter", "A class for writing molecules to PDB files.",
python::no_init)
.def("__init__",
python::make_constructor(
&getPDBWriter, python::default_call_policies(),
(python::arg("fileObj"), python::arg("flavor") = 0)))
.def(python::init<std::string, unsigned int>(
(python::arg("self"), python::arg("fileName"),
python::arg("flavor") = 0),
pdbwDocStr.c_str()))
.def("__enter__", &MolIOEnter<PDBWriter>,
python::return_internal_reference<>())
.def("__exit__", &MolIOExit<PDBWriter>)
.def("write", &PDBWriter::write,
(python::arg("self"), python::arg("mol"),
python::arg("confId") = -1),
"Writes a molecule to the output file.\n\n"
" ARGUMENTS:\n\n"
" - mol: the Mol to be written\n"
" - confId: (optional) ignored \n\n")
.def("flush", &PDBWriter::flush, python::args("self"),
"Flushes the output file (forces the disk file to be "
"updated).\n\n")
.def("close", &PDBWriter::close, python::args("self"),
"Flushes the output file and closes it. The Writer cannot be used "
"after this.\n\n")
.def("NumMols", &PDBWriter::numMols, python::args("self"),
"Returns the number of molecules written so far.\n\n");
};
};
} // namespace RDKit
void wrap_pdbwriter() { RDKit::pdbwriter_wrap::wrap(); }
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