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9f103a9913
* Fixes #2383 (tests coming in the next commit) Minor typo fix Fixes a "bug" in one of the default transforms * Adds support for directly providing normalization parameter data instead of requiring the use of a text file. * allow fragment removers to be initialized with string data * remove unicode * allow the reionizer to be initialized from a stream
85 lines
3.1 KiB
C++
85 lines
3.1 KiB
C++
//
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// Copyright (C) 2018 Susan H. Leung
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//
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// @@ All Rights Reserved @@
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// This file is part of the RDKit.
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// The contents are covered by the terms of the BSD license
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// which is included in the file license.txt, found at the root
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// of the RDKit source tree.
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//
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#include <RDBoost/Wrap.h>
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#include <GraphMol/RDKitBase.h>
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#include <GraphMol/MolStandardize/Charge.h>
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namespace python = boost::python;
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using namespace RDKit;
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namespace {
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std::vector<MolStandardize::ChargeCorrection> defaultChargeCorrections() {
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return MolStandardize::CHARGE_CORRECTIONS;
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}
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ROMol *reionizeHelper(MolStandardize::Reionizer &self, const ROMol &mol) {
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return self.reionize(mol);
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}
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MolStandardize::Reionizer *reionizerFromData(const std::string &data,
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python::object chargeCorrections) {
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std::istringstream sstr(data);
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auto corrections =
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pythonObjectToVect<MolStandardize::ChargeCorrection>(chargeCorrections);
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MolStandardize::Reionizer *res;
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if (corrections) {
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res = new MolStandardize::Reionizer(sstr, *corrections);
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} else {
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res = new MolStandardize::Reionizer(
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sstr, std::vector<MolStandardize::ChargeCorrection>());
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}
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return res;
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}
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} // namespace
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struct charge_wrapper {
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static void wrap() {
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python::scope().attr("__doc__") =
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"Module containing functions for charge corrections";
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std::string docString = "";
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python::class_<MolStandardize::ChargeCorrection, boost::noncopyable>(
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"ChargeCorrection", python::init<std::string, std::string, int>())
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.def_readwrite("Name", &MolStandardize::ChargeCorrection::Name)
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.def_readwrite("Smarts", &MolStandardize::ChargeCorrection::Smarts)
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.def_readwrite("Charge", &MolStandardize::ChargeCorrection::Charge);
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python::def("CHARGE_CORRECTIONS", defaultChargeCorrections);
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python::class_<MolStandardize::Reionizer, boost::noncopyable>(
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"Reionizer", python::init<>())
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.def(python::init<std::string>())
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.def(python::init<std::string,
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std::vector<MolStandardize::ChargeCorrection>>())
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.def("reionize", &reionizeHelper,
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(python::arg("self"), python::arg("mol")), "",
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python::return_value_policy<python::manage_new_object>());
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python::def("ReionizerFromData", &reionizerFromData,
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(python::arg("paramData"),
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python::arg("chargeCorrections") = python::list()),
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"creates a reionizer from a string containing parameter data "
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"and a list of charge corrections",
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python::return_value_policy<python::manage_new_object>());
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python::class_<MolStandardize::Uncharger, boost::noncopyable>(
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"Uncharger", python::init<bool>((python::arg("self"),
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python::arg("canonicalOrder") = true)))
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.def("uncharge", &MolStandardize::Uncharger::uncharge,
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(python::arg("self"), python::arg("mol")), "",
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python::return_value_policy<python::manage_new_object>());
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}
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};
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void wrap_charge() { charge_wrapper::wrap(); }
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