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// $Id: SDMolSupplier.cpp 1955 2012-02-10 16:24:42Z glandrum $
//
// Copyright (C) 2003-2010 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/MolSupplier.h>
#include <GraphMol/RDKitBase.h>
#include <RDBoost/PySequenceHolder.h>
#include "MolSupplier.h"
namespace python = boost::python;
namespace RDKit {
void setStreamIndices(SDMolSupplier &self,python::object arg){
std::vector<std::streampos> loc;
PySequenceHolder<int> seq(arg);
loc.reserve(seq.size());
for(unsigned int i=0;i<seq.size();++i){
loc.push_back(static_cast<std::streampos>(seq[i]));
}
self.setStreamIndices(loc);
}
std::string sdMolSupplierClassDoc="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.sdf')\n \
>>> for mol in suppl:\n \
... mol.GetNumAtoms()\n \
\n \
2) Lazy evaluation 2:\n \
>>> suppl = SDMolSupplier('in.sdf')\n \
>>> mol1 = suppl.next()\n \
>>> mol2 = suppl.next()\n \
>>> suppl.reset()\n \
>>> mol3 = suppl.next()\n \
# mol3 and mol1 are the same: \n \
>>> MolToSmiles(mol3)==MolToSmiles(mol1)\n \
\n \
3) Random Access:\n \
>>> suppl = SDMolSupplier('in.sdf')\n \
>>> mol1 = suppl[0] \n \
>>> mol2 = suppl[1] \n \
NOTE: this will generate an IndexError if the supplier doesn't have that many\n \
molecules.\n \
\n \
4) Random Access 2: looping over all molecules \n \
>>> suppl = SDMolSupplier('in.sdf')\n \
>>> nMols = len(suppl)\n \
>>> for i in range(nMols):\n \
... suppl[i].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 sdmolsup_wrap {
static void wrap() {
python::class_<SDMolSupplier,boost::noncopyable>("SDMolSupplier",
sdMolSupplierClassDoc.c_str(),
python::init<>())
.def(python::init<std::string,bool,bool,bool>((python::arg("fileName"),
python::arg("sanitize")=true,
python::arg("removeHs")=true,
python::arg("strictParsing")=true)))
.def("__iter__", (SDMolSupplier *(*)(SDMolSupplier *))&MolSupplIter,
python::return_internal_reference<1>() )
.def("next", (ROMol *(*)(SDMolSupplier *))&MolSupplNextAcceptNullLastMolecule,
"Returns the next molecule in the file. Raises _StopIteration_ on EOF.\n",
python::return_value_policy<python::manage_new_object>())
.def("__getitem__", (ROMol *(*)(SDMolSupplier *,int))&MolSupplGetItem,
python::return_value_policy<python::manage_new_object>())
.def("reset", &SDMolSupplier::reset,
"Resets our position in the file to the beginning.\n")
.def("__len__", &SDMolSupplier::length)
.def("SetData", &SDMolSupplier::setData,
"Sets the text to be parsed",
(python::arg("self"),python::arg("data"),python::arg("sanitize")=true,
python::arg("removeHs")=true))
.def("_SetStreamIndices", setStreamIndices,
"Sets the locations of mol beginnings in the input stream. Be *very* careful with this method.",
(python::arg("self"),python::arg("locs")))
.def("GetItemText", &SDMolSupplier::getItemText,
"returns the text for an item",
(python::arg("self"),python::arg("index")))
;
};
};
}
void wrap_sdsupplier() {
RDKit::sdmolsup_wrap::wrap();
}
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