mirror of
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
95 lines
3.8 KiB
C++
95 lines
3.8 KiB
C++
//
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// Copyright (C) 2005-2021 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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TDTWriter *getTDTWriter(python::object &fileobj) {
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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 TDTWriter(ost, true);
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}
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void SetTDTWriterProps(TDTWriter &writer, python::object props) {
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// convert the python list to a STR_VECT
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STR_VECT propNames;
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PySequenceHolder<std::string> seq(props);
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for (unsigned int i = 0; i < seq.size(); i++) {
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propNames.push_back(seq[i]);
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}
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writer.setProps(propNames);
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}
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struct tdtwriter_wrap {
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static void wrap() {
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std::string docStr =
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"Constructor.\n\n"
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" If a string argument is provided, it will be treated as the name "
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"of the output file.\n"
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" If a file-like object is provided, output will be sent there.\n\n";
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python::class_<TDTWriter, boost::noncopyable>(
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"TDTWriter", "A class for writing molecules to TDT files.\n",
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python::no_init)
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.def("__init__", python::make_constructor(&getTDTWriter))
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.def(python::init<std::string>(python::args("self", "fileName"),
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docStr.c_str()))
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.def("__enter__", &MolIOEnter<TDTWriter>,
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python::return_internal_reference<>())
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.def("__exit__", &MolIOExit<TDTWriter>)
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.def("SetProps", SetTDTWriterProps, python::args("self", "props"),
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"Sets the properties to be written to the output file\n\n"
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" ARGUMENTS:\n\n"
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" - props: a list or tuple of property names\n\n")
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.def("write", &TDTWriter::write,
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(python::arg("self"), python::arg("mol"),
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python::arg("confId") = defaultConfId),
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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) ID of the conformation to write\n\n")
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.def("flush", &TDTWriter::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", &TDTWriter::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", &TDTWriter::numMols, python::args("self"),
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"Returns the number of molecules written so far.\n\n")
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.def("SetWrite2D", &TDTWriter::setWrite2D,
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(python::arg("self"), python::arg("state") = true),
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"causes 2D conformations to be written (default is 3D "
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"conformations)")
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.def("GetWrite2D", &TDTWriter::getWrite2D, python::args("self"))
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.def("SetWriteNames", &TDTWriter::setWriteNames,
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(python::arg("self"), python::arg("state") = true),
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"causes names to be written to the output file as NAME records")
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.def("GetWriteNames", &TDTWriter::getWriteNames, python::args("self"))
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.def("SetNumDigits", &TDTWriter::setNumDigits,
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python::args("self", "numDigits"),
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"sets the number of digits to be written for coordinates")
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.def("GetNumDigits", &TDTWriter::getNumDigits, python::args("self"));
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};
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};
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} // namespace RDKit
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void wrap_tdtwriter() { RDKit::tdtwriter_wrap::wrap(); }
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