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// Copyright (C) 2018 Lorton
//
// @@ 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>
#include <fstream>
#include <memory>
#include <maeparser/MaeConstants.hpp>
#include <maeparser/Reader.hpp>
#include <GraphMol/FileParsers/MolSupplier.h>
#include <GraphMol/RDKitBase.h>
#include <RDBoost/python_streambuf.h>
#include <RDGeneral/BadFileException.h>
#include <RDGeneral/FileParseException.h>
#include "MolSupplier.h"
#include "ContextManagers.h"
namespace python = boost::python;
using namespace schrodinger;
using boost_adaptbx::python::streambuf;
namespace {
bool streamIsGoodOrExhausted(std::istream *stream) {
PRECONDITION(stream, "bad stream");
return stream->good() || (stream->eof() && stream->fail() && !stream->bad());
}
class LocalMaeMolSupplier : public RDKit::MaeMolSupplier {
public:
LocalMaeMolSupplier() : RDKit::MaeMolSupplier() {}
LocalMaeMolSupplier(python::object &input, bool sanitize, bool removeHs)
: dp_streambuf(new streambuf(input)) {
auto inStream = new streambuf::istream(*dp_streambuf);
bool owner = true;
RDKit::v2::FileParsers::MaeMolSupplierParams params;
params.sanitize = sanitize;
params.removeHs = removeHs;
dp_supplier.reset(
new RDKit::v2::FileParsers::MaeMolSupplier(inStream, owner, params));
}
LocalMaeMolSupplier(streambuf &input, bool sanitize, bool removeHs) {
auto inStream = new streambuf::istream(input);
bool owner = true;
RDKit::v2::FileParsers::MaeMolSupplierParams params;
params.sanitize = sanitize;
params.removeHs = removeHs;
dp_supplier.reset(
new RDKit::v2::FileParsers::MaeMolSupplier(inStream, owner, params));
}
LocalMaeMolSupplier(const std::string &fname, bool sanitize = true,
bool removeHs = true)
: RDKit::MaeMolSupplier(fname, sanitize, removeHs) {}
private:
std::unique_ptr<streambuf> dp_streambuf = nullptr;
};
LocalMaeMolSupplier *FwdMolSupplIter(LocalMaeMolSupplier *self) { return self; }
} // namespace
namespace RDKit {
std::string maeMolSupplierClassDoc =
"A class which supplies molecules from file-like object containing Maestro data.\n\
\n\
Usage examples:\n\
\n\
1) Lazy evaluation: the molecules are not constructed until we ask for them:\n\n\
>>> suppl = MaeMolSupplier(file('in.mae'))\n\
>>> for mol in suppl:\n\
... if mol is not None: mol.GetNumAtoms()\n\
\n\
2) we can also read from compressed files: \n\n\
>>> import gzip\n\
>>> suppl = MaeMolSupplier(gzip.open('in.maegz'))\n\
>>> for mol in suppl:\n\
... if mol is not None: print mol.GetNumAtoms()\n\
\n\
Properties in the Maestro file are used to set properties on each molecule.\n\
The properties are accessible using the mol.GetProp(propName) method.\n\
\n";
struct maemolsup_wrap {
static void wrap() {
python::class_<LocalMaeMolSupplier, boost::noncopyable>(
"MaeMolSupplier", maeMolSupplierClassDoc.c_str(),
python::init<>(python::args("self")))
.def(python::init<python::object &, bool, bool>(
(python::arg("self"), python::arg("fileobj"),
python::arg("sanitize") = true,
python::arg("removeHs") =
true))[python::with_custodian_and_ward_postcall<0, 2>()])
.def(python::init<streambuf &, bool, bool>(
(python::arg("self"), python::arg("streambuf"),
python::arg("sanitize") = true,
python::arg("removeHs") =
true))[python::with_custodian_and_ward_postcall<0, 2>()])
.def(python::init<std::string, bool, bool>(
(python::arg("self"), python::arg("filename"),
python::arg("sanitize") = true, python::arg("removeHs") = true)))
.def("__enter__", &MolIOEnter<LocalMaeMolSupplier>,
python::return_internal_reference<>())
.def("__exit__", &MolIOExit<LocalMaeMolSupplier>)
.def("__iter__", &FwdMolSupplIter,
python::return_internal_reference<1>(), python::args("self"))
.def("__next__", &MolSupplNext<LocalMaeMolSupplier>,
"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<LocalMaeMolSupplier>,
python::return_value_policy<python::manage_new_object>(),
python::args("self", "idx"))
.def("reset", &MaeMolSupplier::reset, python::args("self"),
"Resets our position in the file to the beginning.\n")
.def("__len__", &MaeMolSupplier::length, python::args("self"))
.def("SetData", &MaeMolSupplier::setData, "Sets the text to be parsed",
((python::arg("self"), python::arg("data")),
python::arg("sanitize") = true, python::arg("removeHs") = true))
.def("atEnd", &MaeMolSupplier::atEnd, python::args("self"),
"Returns whether or not we have hit EOF.\n");
};
};
} // namespace RDKit
void wrap_maesupplier() { RDKit::maemolsup_wrap::wrap(); }
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