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
130 lines
5.1 KiB
C++
130 lines
5.1 KiB
C++
//
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// Copyright (C) 2003-2021 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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using boost_adaptbx::python::streambuf;
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namespace RDKit {
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SDWriter *getSDWriter(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 SDWriter(ost, true);
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}
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void SetSDWriterProps(SDWriter &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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void WriteMolToSD(SDWriter &writer, ROMol &mol, int confId) {
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writer.write(mol, confId);
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}
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std::string getSDTextHelper(const ROMol &mol, int confId, bool kekulize,
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bool force_V3000, int molid) {
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return SDWriter::getText(mol, confId, kekulize, force_V3000, molid);
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}
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struct sdwriter_wrap {
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static void wrap() {
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std::string docStr =
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"A class for writing molecules to SD files.\n\
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\n\
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Usage examples:\n\
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\n\
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1) writing to a named file:\n\n\
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>>> writer = SDWriter('out.sdf')\n\
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>>> for mol in list_of_mols:\n\
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... writer.write(mol)\n\
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\n\
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2) writing to a file-like object: \n\n\
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>>> import gzip\n\
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>>> outf=gzip.open('out.sdf.gz','wt+')\n\
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>>> writer = SDWriter(outf)\n\
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>>> for mol in list_of_mols:\n\
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... writer.write(mol)\n\
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>>> writer.close()\n\
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>>> outf.close()\n\
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\n\
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By default all non-private molecular properties are written to the SD file.\n\
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This can be changed using the SetProps method:\n\n\
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>>> writer = SDWriter('out.sdf')\n\
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>>> writer.SetProps(['prop1','prop2'])\n\
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\n";
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python::class_<SDWriter, boost::noncopyable>("SDWriter", docStr.c_str(),
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python::no_init)
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.def("__init__", python::make_constructor(&getSDWriter))
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.def(python::init<std::string>(python::args("self", "fileName"),
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"Constructor.\n\n"
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" If a string argument is provided, "
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"it will be treated as the name of the "
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"output file.\n"
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" If a file-like object is provided, "
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"output will be sent there.\n\n"))
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.def("__enter__", &MolIOEnter<SDWriter>,
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python::return_internal_reference<>())
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.def("__exit__", &MolIOExit<SDWriter>)
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.def("SetProps", SetSDWriterProps, 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", WriteMolToSD,
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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) ID of the conformation to write\n\n")
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.def("flush", &SDWriter::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", &SDWriter::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", &SDWriter::numMols, python::args("self"),
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"Returns the number of molecules written so far.\n\n")
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.def("SetForceV3000", &SDWriter::setForceV3000,
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python::args("self", "val"),
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"Sets whether or not V3000 mol file writing is being forced.\n\n")
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.def("GetForceV3000", &SDWriter::getForceV3000, python::args("self"),
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"Returns whether or not V3000 mol file writing is being "
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"forced.\n\n")
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.def("SetKekulize", &SDWriter::setKekulize, python::args("self", "val"),
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"Sets whether or not molecules are kekulized on writing.\n\n")
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.def("GetKekulize", &SDWriter::getKekulize, python::args("self"),
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"Returns whether or not molecules are kekulized on writing.\n\n")
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.def("GetText", getSDTextHelper,
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(python::arg("mol"), python::arg("confId") = -1,
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python::arg("kekulize") = true,
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python::arg("force_v3000") = false, python::arg("molid") = -1),
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"returns the SD text for a molecule")
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.staticmethod("GetText");
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};
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};
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} // namespace RDKit
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void wrap_sdwriter() { RDKit::sdwriter_wrap::wrap(); }
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