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// $Id$
//
// Copyright (C) 2003-2011 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 <RDBoost/PySequenceHolder.h>
#include <RDBoost/python_streambuf.h>
namespace python = boost::python;
using boost_adaptbx::python::streambuf;
namespace RDKit {
SDWriter *getSDWriter(python::object &fileobj) {
// FIX: minor leak here
auto *sb = new streambuf(fileobj);
auto *ost = new streambuf::ostream(*sb);
return new SDWriter(ost, true);
}
void SetSDWriterProps(SDWriter &writer, python::object props) {
// convert the python list to a STR_VECT
STR_VECT propNames;
PySequenceHolder<std::string> seq(props);
for (unsigned int i = 0; i < seq.size(); i++) {
propNames.push_back(seq[i]);
}
writer.setProps(propNames);
}
void WriteMolToSD(SDWriter &writer, ROMol &mol, int confId) {
writer.write(mol, confId);
}
std::string getSDTextHelper(const ROMol &mol, int confId, bool kekulize,
bool force_V3000, int molid) {
return SDWriter::getText(mol, confId, kekulize, force_V3000, molid);
}
struct sdwriter_wrap {
static void wrap() {
std::string docStr =
"A class for writing molecules to SD files.\n\
\n\
Usage examples:\n\
\n\
1) writing to a named file:\n\
>>> writer = SDWriter('out.sdf')\n\
>>> for mol in list_of_mols:\n\
... writer.write(mol)\n\
\n\
2) writing to a file-like object: \n\
>>> import gzip\n\
>>> outf=gzip.open('out.sdf.gz','w+')\n\
>>> writer = SDWriter(outf)\n\
>>> for mol in list_of_mols:\n \
... writer.write(mol)\n\
>>> writer.close()\n\
>>> outf.close()\n\
\n\
By default all non-private molecular properties are written to the SD file.\n\
This can be changed using the SetProps method:\n\
>>> writer = SDWriter('out.sdf')\n\
>>> writer.SetProps(['prop1','prop2'])\n\
\n";
python::class_<SDWriter, boost::noncopyable>("SDWriter", docStr.c_str(),
python::no_init)
.def("__init__", python::make_constructor(&getSDWriter))
.def(python::init<std::string>(python::args("fileName"),
"Constructor.\n\n"
" If a string argument is provided, "
"it will be treated as the name of the "
"output file.\n"
" If a file-like object is provided, "
"output will be sent there.\n\n"))
.def("SetProps", SetSDWriterProps,
"Sets the properties to be written to the output file\n\n"
" ARGUMENTS:\n\n"
" - props: a list or tuple of property names\n\n")
.def("write", WriteMolToSD, (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) ID of the conformation to write\n\n")
.def("flush", &SDWriter::flush,
"Flushes the output file (forces the disk file to be "
"updated).\n\n")
.def("close", &SDWriter::close,
"Flushes the output file and closes it. The Writer cannot be used "
"after this.\n\n")
.def("NumMols", &SDWriter::numMols,
"Returns the number of molecules written so far.\n\n")
.def("SetForceV3000", &SDWriter::setForceV3000,
"Sets whether or not V3000 mol file writing is being forced.\n\n")
.def("GetForceV3000", &SDWriter::getForceV3000,
"Returns whether or not V3000 mol file writing is being "
"forced.\n\n")
.def("SetKekulize", &SDWriter::setKekulize,
"Sets whether or not molecules are kekulized on writing.\n\n")
.def("GetKekulize", &SDWriter::getKekulize,
"Returns whether or not molecules are kekulized on writing.\n\n")
.def("GetText",
//(std::string(*)(const ROMol &, int, bool, bool, int))
getSDTextHelper,
(python::arg("mol"), python::arg("confId") = -1,
python::arg("kekulize") = true,
python::arg("force_v3000") = false, python::arg("molid") = -1),
"returns the SD text for a molecule")
.staticmethod("GetText");
};
};
}
void wrap_sdwriter() { RDKit::sdwriter_wrap::wrap(); }
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