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https://github.com/rdkit/rdkit.git
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ccfb1fa688
* fixleak in CIP labels catch test * fix leak in Murtagh clustering * do not leak writers in streambuf * fix leaks in fingerprintgeneratorwrapper * remove 'minor leak' comments
75 lines
2.7 KiB
C++
75 lines
2.7 KiB
C++
//
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// Copyright (C) 2013-2021 Greg Landrum and Rational Discovery LLC
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//
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// @@ All Rights Reserved @@
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// This file is part of the RDKit.
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// The contents are covered by the terms of the BSD license
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// which is included in the file license.txt, found at the root
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// of the RDKit source tree.
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//
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#define NO_IMPORT_ARRAY
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#include <RDBoost/python.h>
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#include <string>
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// ours
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#include <GraphMol/FileParsers/MolWriters.h>
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#include <GraphMol/RDKitBase.h>
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#include "rdchem.h"
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#include "ContextManagers.h"
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#include <RDBoost/PySequenceHolder.h>
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#include <RDBoost/python_streambuf.h>
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namespace python = boost::python;
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namespace RDKit {
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using boost_adaptbx::python::streambuf;
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namespace {
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PDBWriter *getPDBWriter(python::object &fileobj, unsigned int flavor = 0) {
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auto *sb = new streambuf(fileobj, 't');
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auto *ost = new streambuf::ostream(sb);
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return new PDBWriter(ost, true, flavor);
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}
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} // namespace
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std::string pdbwDocStr =
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"Constructor.\n\n"
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" ARGUMENTS:\n\n"
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" - fileName: name of the output file. ('-' to write to stdout)\n"
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" - flavor: (optional) \n\n";
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struct pdbwriter_wrap {
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static void wrap() {
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python::class_<PDBWriter, boost::noncopyable>(
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"PDBWriter", "A class for writing molecules to PDB files.",
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python::no_init)
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.def("__init__",
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python::make_constructor(
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&getPDBWriter, python::default_call_policies(),
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(python::arg("fileObj"), python::arg("flavor") = 0)))
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.def(python::init<std::string, unsigned int>(
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(python::arg("self"), python::arg("fileName"),
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python::arg("flavor") = 0),
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pdbwDocStr.c_str()))
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.def("__enter__", &MolIOEnter<PDBWriter>,
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python::return_internal_reference<>())
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.def("__exit__", &MolIOExit<PDBWriter>)
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.def("write", &PDBWriter::write,
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(python::arg("self"), python::arg("mol"),
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python::arg("confId") = -1),
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"Writes a molecule to the output file.\n\n"
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" ARGUMENTS:\n\n"
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" - mol: the Mol to be written\n"
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" - confId: (optional) ignored \n\n")
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.def("flush", &PDBWriter::flush, python::args("self"),
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"Flushes the output file (forces the disk file to be "
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"updated).\n\n")
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.def("close", &PDBWriter::close, python::args("self"),
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"Flushes the output file and closes it. The Writer cannot be used "
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"after this.\n\n")
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.def("NumMols", &PDBWriter::numMols, python::args("self"),
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"Returns the number of molecules written so far.\n\n");
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};
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};
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} // namespace RDKit
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void wrap_pdbwriter() { RDKit::pdbwriter_wrap::wrap(); }
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