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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/Charge.h>
namespace python = boost::python;
using namespace RDKit;
namespace {
std::vector<MolStandardize::ChargeCorrection> defaultChargeCorrections() {
return MolStandardize::CHARGE_CORRECTIONS;
}
ROMol *reionizeHelper(MolStandardize::Reionizer &self, const ROMol &mol) {
return self.reionize(mol);
}
void reionizeInPlaceHelper(MolStandardize::Reionizer &self, ROMol &mol) {
self.reionizeInPlace(static_cast<RWMol &>(mol));
}
MolStandardize::Reionizer *reionizerFromData(const std::string &data,
python::object chargeCorrections) {
std::istringstream sstr(data);
auto corrections =
pythonObjectToVect<MolStandardize::ChargeCorrection>(chargeCorrections);
MolStandardize::Reionizer *res;
if (corrections) {
res = new MolStandardize::Reionizer(sstr, *corrections);
} else {
res = new MolStandardize::Reionizer(
sstr, std::vector<MolStandardize::ChargeCorrection>());
}
return res;
}
void unchargeInPlaceHelper(MolStandardize::Uncharger &self, ROMol &mol) {
self.unchargeInPlace(static_cast<RWMol &>(mol));
}
} // namespace
struct charge_wrapper {
static void wrap() {
python::scope().attr("__doc__") =
"Module containing functions for charge corrections";
std::string docString = "";
python::class_<MolStandardize::ChargeCorrection, boost::noncopyable>(
"ChargeCorrection",
python::init<std::string, std::string, int>(
python::args("self", "name", "smarts", "charge")))
.def_readwrite("Name", &MolStandardize::ChargeCorrection::Name)
.def_readwrite("Smarts", &MolStandardize::ChargeCorrection::Smarts)
.def_readwrite("Charge", &MolStandardize::ChargeCorrection::Charge);
python::def("CHARGE_CORRECTIONS", defaultChargeCorrections);
python::class_<MolStandardize::Reionizer, boost::noncopyable>(
"Reionizer", python::init<>(python::args("self")))
.def(python::init<std::string>(python::args("self", "acidbaseFile")))
.def(python::init<std::string,
std::vector<MolStandardize::ChargeCorrection>>(
python::args("self", "acidbaseFile", "ccs")))
.def("reionize", &reionizeHelper,
(python::arg("self"), python::arg("mol")), "",
python::return_value_policy<python::manage_new_object>())
.def("reionizeInPlace", reionizeInPlaceHelper,
(python::arg("self"), python::arg("mol")),
"modifies the input molecule");
python::def("ReionizerFromData", &reionizerFromData,
(python::arg("paramData"),
python::arg("chargeCorrections") = python::list()),
"creates a reionizer from a string containing parameter data "
"and a list of charge corrections",
python::return_value_policy<python::manage_new_object>());
python::class_<MolStandardize::Uncharger, boost::noncopyable>(
"Uncharger",
python::init<bool, bool, bool>(
(python::arg("self"), python::arg("canonicalOrder") = true,
python::arg("force") = false,
python::arg("protonationOnly") = false)))
.def("uncharge", &MolStandardize::Uncharger::uncharge,
(python::arg("self"), python::arg("mol")), "",
python::return_value_policy<python::manage_new_object>())
.def("unchargeInPlace", unchargeInPlaceHelper,
(python::arg("self"), python::arg("mol")),
"modifies the input molecule");
}
};
void wrap_charge() { charge_wrapper::wrap(); }
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