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https://github.com/rdkit/rdkit.git
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ac54eb3209
* reionizer and uncharger and normalizer can now operate in place * add removeUnmatchedAtoms argument to in-place version of runReactant When set to false atoms which are not explicitly removed by the reaction are preserved * Fix a case where transforms were incorrectly updating atomic numbers * add more inplace operations to MolStandardize * support those in the Python layer * support inplace for the rest of the python wrappers * move a few more functions over to the inplace code
68 lines
2.3 KiB
C++
68 lines
2.3 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/Normalize.h>
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#include <sstream>
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namespace python = boost::python;
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using namespace RDKit;
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namespace {
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ROMol *normalizeHelper(MolStandardize::Normalizer &self, const ROMol &mol) {
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return self.normalize(mol);
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}
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void normalizeInPlaceHelper(MolStandardize::Normalizer &self, ROMol &mol) {
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self.normalizeInPlace(static_cast<RWMol &>(mol));
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}
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MolStandardize::Normalizer *normalizerFromDataAndParams(
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const std::string &data, const MolStandardize::CleanupParameters ¶ms) {
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std::istringstream sstr(data);
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return new MolStandardize::Normalizer(sstr, params.maxRestarts);
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}
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} // namespace
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struct normalize_wrapper {
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static void wrap() {
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python::scope().attr("__doc__") =
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"Module containing tools for normalizing molecules defined by SMARTS "
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"patterns";
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std::string docString = "";
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python::class_<MolStandardize::Normalizer, boost::noncopyable>(
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"Normalizer", python::init<>())
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.def(python::init<std::string, unsigned int>(
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python::args("normalizeFilename", "maxRestarts")))
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.def("normalize", &normalizeHelper,
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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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.def("normalizeInPlace", &normalizeInPlaceHelper,
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(python::arg("self"), python::arg("mol")),
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"modifies the input molecule");
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python::def(
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"NormalizerFromData", &normalizerFromDataAndParams,
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(python::arg("paramData"), python::arg("params")),
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"creates a Normalizer from a string containing normalization SMARTS",
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python::return_value_policy<python::manage_new_object>());
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python::def("NormalizerFromParams", &MolStandardize::normalizerFromParams,
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(python::arg("params")),
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"creates a Normalizer from CleanupParameters",
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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_normalize() { normalize_wrapper::wrap(); }
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