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//
// Copyright (C) 2018 Susan H. Leung
//
// @@ 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.
//
#include <RDBoost/Wrap.h>
#include <GraphMol/RDKitBase.h>
#include <GraphMol/MolStandardize/Fragment.h>
namespace python = boost::python;
using namespace RDKit;
namespace {
ROMol *removeHelper(MolStandardize::FragmentRemover &self, const ROMol &mol) {
return self.remove(mol);
}
void removeInPlaceHelper(MolStandardize::FragmentRemover &self, ROMol &mol) {
self.removeInPlace(static_cast<RWMol &>(mol));
}
ROMol *chooseHelper(MolStandardize::LargestFragmentChooser &self,
const ROMol &mol) {
return self.choose(mol);
}
void chooseInPlaceHelper(MolStandardize::LargestFragmentChooser &self,
ROMol &mol) {
self.chooseInPlace(static_cast<RWMol &>(mol));
}
MolStandardize::FragmentRemover *removerFromParams(const std::string &data,
bool leave_last,
bool skip_if_all_match) {
std::istringstream sstr(data);
return new MolStandardize::FragmentRemover(sstr, leave_last,
skip_if_all_match);
}
} // namespace
struct fragment_wrapper {
static void wrap() {
python::scope().attr("__doc__") =
"Module containing tools for dealing with molecules with more than \
one covalently bonded unit";
std::string docString = "";
python::class_<MolStandardize::FragmentRemover, boost::noncopyable>(
"FragmentRemover", python::init<>(python::args("self")))
.def(python::init<std::string, bool, bool>(
(python::arg("self"), python::arg("fragmentFilename") = "",
python::arg("leave_last") = true,
python::arg("skip_if_all_match") = false)))
.def("remove", &removeHelper, (python::arg("self"), python::arg("mol")),
"", python::return_value_policy<python::manage_new_object>())
.def("removeInPlace", &removeInPlaceHelper,
(python::arg("self"), python::arg("mol")),
"modifies the molecule in place");
python::def(
"FragmentRemoverFromData", &removerFromParams,
(python::arg("fragmentData"), python::arg("leave_last") = true,
python::arg("skip_if_all_match") = false),
"creates a FragmentRemover from a string containing parameter data",
python::return_value_policy<python::manage_new_object>());
python::class_<MolStandardize::LargestFragmentChooser, boost::noncopyable>(
"LargestFragmentChooser",
python::init<bool>(
(python::arg("self"), python::arg("preferOrganic") = false)))
.def(python::init<const MolStandardize::CleanupParameters &>(
(python::arg("self"), python::arg("params"))))
.def("choose", &chooseHelper, (python::arg("self"), python::arg("mol")),
"", python::return_value_policy<python::manage_new_object>())
.def("chooseInPlace", &chooseInPlaceHelper,
(python::arg("self"), python::arg("mol")), "",
python::return_value_policy<python::manage_new_object>());
;
}
};
void wrap_fragment() { fragment_wrapper::wrap(); }
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