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//
// Copyright (C) 2003-2019 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/MolSupplier.h>
#include <GraphMol/RDKitBase.h>
#include <RDBoost/PySequenceHolder.h>
#include "MolSupplier.h"
#include "ContextManagers.h"
namespace python = boost::python;
namespace RDKit {
void setDataHelper(SDMolSupplier &self, const std::string &text, bool sanitize,
bool removeHs, bool strictParsing) {
self.setData(text, sanitize, removeHs, strictParsing);
}
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\n\
>>> suppl = SDMolSupplier('in.sdf')\n\
>>> for mol in suppl:\n\
... mol.GetNumAtoms()\n\
\n\
2) Lazy evaluation 2:\n\n\
>>> suppl = SDMolSupplier('in.sdf')\n\
>>> mol1 = next(suppl)\n\
>>> mol2 = next(suppl)\n\
>>> suppl.reset()\n\
>>> mol3 = next(suppl)\n\
# mol3 and mol1 are the same:\n\
>>> MolToSmiles(mol3)==MolToSmiles(mol1)\n\
\n\
3) Random Access:\n\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\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<>(python::args("self")))
.def(python::init<std::string, bool, bool, bool>(
(python::arg("self"), python::arg("fileName"),
python::arg("sanitize") = true, python::arg("removeHs") = true,
python::arg("strictParsing") = true)))
.def("__enter__", &MolIOEnter<SDMolSupplier>,
python::return_internal_reference<>())
.def("__exit__", &MolIOExit<SDMolSupplier>)
.def("__iter__", &MolSupplIter<SDMolSupplier>,
python::return_internal_reference<1>(), python::args("self"))
.def("__next__", &MolSupplNext<SDMolSupplier>,
"Returns the next molecule in the file. Raises _StopIteration_ "
"on EOF.\n",
python::return_value_policy<python::manage_new_object>(),
python::args("self"))
.def("__getitem__", &MolSupplGetItem<SDMolSupplier>,
python::return_value_policy<python::manage_new_object>(),
python::args("self", "idx"))
.def("reset", &SDMolSupplier::reset, python::args("self"),
"Resets our position in the file to the beginning.\n")
.def("__len__", &SDMolSupplier::length, python::args("self"))
.def("SetData", setDataHelper, "Sets the text to be parsed",
(python::arg("self"), python::arg("data"),
python::arg("sanitize") = true, python::arg("removeHs") = true,
python::arg("strictParsing") = 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")))
.def("atEnd", &SDMolSupplier::atEnd, python::args("self"),
"Returns whether or not we have hit EOF.\n")
.def("GetProcessPropertyLists", &SDMolSupplier::getProcessPropertyLists,
python::args("self"),
"returns whether or not any property lists that are present will "
"be processed when reading molecules")
.def("SetProcessPropertyLists", &SDMolSupplier::setProcessPropertyLists,
python::args("self", "val"),
"sets whether or not any property lists that are present will be "
"processed when reading molecules");
};
};
} // namespace RDKit
void wrap_sdsupplier() { RDKit::sdmolsup_wrap::wrap(); }
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