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//
// Copyright (C) 2011-2019 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 <RDBoost/python.h>
#include <string>
#include <fstream>
// ours
#include <RDGeneral/BadFileException.h>
#include <GraphMol/FileParsers/MolSupplier.h>
#include <GraphMol/RDKitBase.h>
#include <RDBoost/python_streambuf.h>
#include "ContextManagers.h"
#include "MolSupplier.h"
namespace python = boost::python;
using boost_adaptbx::python::streambuf;
namespace {
class LocalForwardSDMolSupplier : public RDKit::ForwardSDMolSupplier {
private:
std::unique_ptr<streambuf> dp_streambuf;
public:
LocalForwardSDMolSupplier(python::object &input, bool sanitize, bool removeHs,
bool strictParsing) {
dp_streambuf.reset(new streambuf(input, 'b'));
auto sbis = new streambuf::istream(*dp_streambuf);
bool owner = true;
RDKit::v2::FileParsers::MolFileParserParams params;
params.sanitize = sanitize;
params.removeHs = removeHs;
params.strictParsing = strictParsing;
dp_supplier.reset(
new RDKit::v2::FileParsers::ForwardSDMolSupplier(sbis, owner, params));
POSTCONDITION(sbis, "bad instream");
}
LocalForwardSDMolSupplier(streambuf &input, bool sanitize, bool removeHs,
bool strictParsing) {
auto sbis = new streambuf::istream(input);
bool owner = true;
RDKit::v2::FileParsers::MolFileParserParams params;
params.sanitize = sanitize;
params.removeHs = removeHs;
params.strictParsing = strictParsing;
dp_supplier.reset(
new RDKit::v2::FileParsers::ForwardSDMolSupplier(sbis, owner, params));
POSTCONDITION(sbis, "bad instream");
}
LocalForwardSDMolSupplier(std::string filename, bool sanitize, bool removeHs,
bool strictParsing) {
std::istream *tmpStream = nullptr;
tmpStream = static_cast<std::istream *>(
new std::ifstream(filename.c_str(), std::ios_base::binary));
if (!(*tmpStream) || tmpStream->bad()) {
delete tmpStream;
std::ostringstream errout;
errout << "Bad input file " << filename;
throw RDKit::BadFileException(errout.str());
}
bool owner = true;
RDKit::v2::FileParsers::MolFileParserParams params;
params.sanitize = sanitize;
params.removeHs = removeHs;
params.strictParsing = strictParsing;
dp_supplier.reset(new RDKit::v2::FileParsers::ForwardSDMolSupplier(
tmpStream, owner, params));
POSTCONDITION(tmpStream, "bad instream");
}
};
LocalForwardSDMolSupplier *FwdMolSupplIter(LocalForwardSDMolSupplier *self) {
return self;
}
} // namespace
namespace RDKit {
std::string fsdMolSupplierClassDoc =
"A class which supplies molecules from file-like object containing SD data.\n\
\n\
Usage examples:\n\
\n\
1) Lazy evaluation: the molecules are not constructed until we ask for them:\n\n\
>>> suppl = ForwardSDMolSupplier(file('in.sdf'))\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 = ForwardSDMolSupplier(gzip.open('in.sdf.gz'))\n\
>>> for mol in suppl:\n\
... if mol is not None: print 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 forwardsdmolsup_wrap {
static void wrap() {
python::class_<LocalForwardSDMolSupplier, boost::noncopyable>(
"ForwardSDMolSupplier", fsdMolSupplierClassDoc.c_str(), python::no_init)
.def(python::init<python::object &, bool, bool, bool>(
(python::arg("self"), python::arg("fileobj"),
python::arg("sanitize") = true, python::arg("removeHs") = true,
python::arg("strictParsing") =
true))[python::with_custodian_and_ward_postcall<0, 2>()])
.def(python::init<streambuf &, bool, bool, bool>(
(python::arg("self"), python::arg("streambuf"),
python::arg("sanitize") = true, python::arg("removeHs") = true,
python::arg("strictParsing") =
true))[python::with_custodian_and_ward_postcall<0, 2>()])
.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__",
(LocalForwardSDMolSupplier * (*)(LocalForwardSDMolSupplier *)) &
MolIOEnter,
python::return_internal_reference<>())
.def("__exit__", (bool (*)(LocalForwardSDMolSupplier *, python::object,
python::object, python::object)) &
MolIOExit)
.def("__next__",
(ROMol * (*)(LocalForwardSDMolSupplier *)) & MolForwardSupplNext,
"Returns the next molecule in the file. Raises _StopIteration_ "
"on EOF.\n",
python::return_value_policy<python::manage_new_object>(),
python::args("self"))
.def("atEnd", &ForwardSDMolSupplier::atEnd, python::args("self"),
"Returns whether or not we have hit EOF.\n")
.def("GetEOFHitOnRead", &ForwardSDMolSupplier::getEOFHitOnRead,
python::args("self"),
"Returns whether or EOF was hit while parsing the previous "
"entry.\n")
.def("__iter__", &FwdMolSupplIter,
python::return_internal_reference<1>(), python::args("self"))
.def("GetProcessPropertyLists",
&ForwardSDMolSupplier::getProcessPropertyLists,
python::args("self"),
"returns whether or not any property lists that are present will "
"be processed when reading molecules")
.def("SetProcessPropertyLists",
&ForwardSDMolSupplier::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_forwardsdsupplier() { RDKit::forwardsdmolsup_wrap::wrap(); }
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