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// $Id: SmilesWriter.cpp 1885 2011-12-09 04:59:46Z glandrum $
//
// 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 <boost/python.hpp>
#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;
namespace RDKit {
using boost_adaptbx::python::streambuf;
SmilesWriter *getSmilesWriter(python::object &fileobj,
std::string delimiter=" ",
std::string nameHeader="Name",
bool includeHeader=true,
bool isomericSmiles=false,
bool kekuleSmiles=false){
// FIX: minor leak here
streambuf *sb=new streambuf(fileobj);
streambuf::ostream *ost=new streambuf::ostream(*sb);
return new SmilesWriter(ost,delimiter,nameHeader,includeHeader,true,isomericSmiles,kekuleSmiles);
}
void SetSmiWriterProps(SmilesWriter &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);
}
std::string swDocStr="Constructor.\n\n"
" ARGUMENTS:\n\n"
" - fileName: name of the output file. ('-' to write to stdout)\n"
" - delimiter: (optional) delimiter to be used to separate entries on each line.\n"
" - nameHeader: (optional) text to use for the name column in the header line.\n"
" If this is blank, names will not be dumped.\n"
" - includeHeader: (optional) toggles inclusion of a header line in the output file.\n"
" - isomericSmiles: (optional) toggles output of isomeric smiles (includes stereochem information).\n"
" - includeHeader: (optional) toggles output of kekule smiles (no aromatic bonds for molecules that have been kekulized).\n\n";
struct smiwriter_wrap {
static void wrap() {
python::class_<SmilesWriter>("SmilesWriter",
"A class for writing molecules to text files.",
python::no_init)
.def("__init__",python::make_constructor(&getSmilesWriter,python::default_call_policies(),
(python::arg("fileObj"),
python::arg("delimiter")=" ",
python::arg("nameHeader")="Name",
python::arg("includeHeader")=true,
python::arg("isomericSmiles")=false,
python::arg("kekuleSmiles")=false)))
.def(python::init<std::string,std::string,std::string,bool,bool,bool>((python::arg("fileName"),
python::arg("delimiter")=" ",
python::arg("nameHeader")="Name",
python::arg("includeHeader")=true,
python::arg("isomericSmiles")=false,
python::arg("kekuleSmiles")=false),
swDocStr.c_str()))
.def("SetProps", SetSmiWriterProps,
"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", &SmilesWriter::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", &SmilesWriter::flush,
"Flushes the output file (forces the disk file to be updated).\n\n"
)
.def("close", &SmilesWriter::close,
"Flushes the output file and closes it. The Writer cannot be used after this.\n\n"
)
.def("NumMols", &SmilesWriter::numMols,
"Returns the number of molecules written so far.\n\n"
)
;
};
};
}
void wrap_smiwriter() {
RDKit::smiwriter_wrap::wrap();
}
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