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// $Id: SDMolSupplier.cpp 585 2008-03-30 13:36:56Z glandrum $
//
// Copyright (C) 2009 Greg Landrum
//
// @@ 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>
#include <boost/iostreams/device/file.hpp>
#include <boost/iostreams/filtering_stream.hpp>
#include <boost/iostreams/filter/gzip.hpp>
#include <boost/iostreams/filter/bzip2.hpp>
#include <boost/algorithm/string.hpp>
namespace io=boost::iostreams;
//ours
#include <GraphMol/FileParsers/MolSupplier.h>
#include <GraphMol/RDKitBase.h>
#include <RDBoost/Wrap.h>
#include "MolSupplier.h"
namespace python = boost::python;
namespace RDKit {
// Note that this returns a pointer to the supplier itself, so be careful
// that it doesn't get deleted by python!
ForwardSDMolSupplier *MolSupplIter(ForwardSDMolSupplier *suppl){
return suppl;
}
ROMol *MolSupplNext(ForwardSDMolSupplier *suppl){
ROMol *res=0;
if (!suppl->atEnd()) {
try {
res=suppl->next();
} catch(...){
res=0;
}
}
if(!res && suppl->atEnd()) {
PyErr_SetString(PyExc_StopIteration,"End of supplier hit");
throw boost::python::error_already_set();
}
return res;
}
ForwardSDMolSupplier *createForwardSupplier(std::string filename,bool sanitize,
bool removeHs){
std::vector<std::string> splitName;
boost::split(splitName,filename,boost::is_any_of("."));
io::filtering_istream *strm=new io::filtering_istream();
if(splitName.back()=="sdf"){
}
else if(splitName.back()=="gz"){
#ifndef RDK_NOGZIP
strm->push(io::gzip_decompressor());
#else
throw_value_error("gzip support not enabled");
#endif
}
else if(splitName.back()=="bz2"){
#ifndef RDK_NOBZIP2
strm->push(io::bzip2_decompressor());
#else
throw_value_error("bzip2 support not enabled");
#endif
}
else {
std::string errorTxt="Unrecognized extension: "+splitName.back();
throw_value_error(errorTxt);
}
io::file_source fileSource(filename);
if(!fileSource.is_open()){
std::string errorTxt="could not open file: "+filename;
throw_value_error(errorTxt);
}
strm->push(fileSource);
ForwardSDMolSupplier *res=new ForwardSDMolSupplier(strm,true,sanitize,removeHs);
return res;
}
std::string csdMolSupplierClassDoc="A class which supplies molecules from an SD file.\n \
\n \
Usage examples:\n \
\n \
1) Lazy evaluation: the molecules are not constructed until we ask for them:\n \
>>> suppl = SDMolSupplier('in.smi')\n \
>>> for mol in suppl:\n \
... mol.GetNumAtoms()\n \
\n \
Properties in the SD file are used to set properties on each molecule.\n\
The properties are accessible using the mol.GetProp(propName) method.\n\
\n";
struct compressedsdmolsup_wrap {
static void wrap() {
python::class_<ForwardSDMolSupplier,boost::noncopyable>("_CompressedSDMolSupplier",
csdMolSupplierClassDoc.c_str(),
python::no_init)
.def("__iter__", (ForwardSDMolSupplier *(*)(ForwardSDMolSupplier *))&MolSupplIter,
python::return_internal_reference<1>() )
.def("next", (ROMol *(*)(ForwardSDMolSupplier *))&MolSupplNext,
"Returns the next molecule in the file. Raises _StopIteration_ on EOF.\n",
python::return_value_policy<python::manage_new_object>())
;
python::def("CompressedSDMolSupplier",createForwardSupplier,
(python::arg("fileName"),python::arg("sanitize")=true,
python::arg("removeHs")=true),
python::return_value_policy<python::manage_new_object>());
};
};
}
void wrap_compressedsdsupplier() {
RDKit::compressedsdmolsup_wrap::wrap();
}
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