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// Copyright (c) 2016, Novartis Institutes for BioMedical Research Inc.
// All rights reserved.
//
// Redistribution and use in source and binary forms, with or without
// modification, are permitted provided that the following conditions are
// met:
//
// * Redistributions of source code must retain the above copyright
// notice, this list of conditions and the following disclaimer.
// * Redistributions in binary form must reproduce the above
// copyright notice, this list of conditions and the following
// disclaimer in the documentation and/or other materials provided
// with the distribution.
// * Neither the name of Novartis Institutes for BioMedical Research Inc.
// nor the names of its contributors may be used to endorse or promote
// products derived from this software without specific prior written
// permission.
//
// THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS
// "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT
// LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR
// A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT
// OWNER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL,
// SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT
// LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE,
// DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY
// THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT
// (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE
// OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
//
#include <RDBoost/python.h>
#include <RDBoost/Wrap.h>
#include <GraphMol/StructChecker/StructChecker.h>
#include <GraphMol/RDKitBase.h>
namespace python = boost::python;
namespace RDKit {
namespace StructureCheck {
unsigned int checkMolStructureHelper(const StructChecker &checker, ROMol &m) {
RWMol &fixer = static_cast<RWMol &>(m);
return checker.checkMolStructure(fixer);
}
}
}
struct struct_wrapper {
static void wrap() {
python::enum_<RDKit::StructureCheck::StructChecker::StructureFlags>(
"StructureFlags")
.value("NO_CHANGE", RDKit::StructureCheck::StructChecker::NO_CHANGE)
.value("BAD_MOLECULE",
RDKit::StructureCheck::StructChecker::BAD_MOLECULE)
.value("ALIAS_CONVERSION_FAILED",
RDKit::StructureCheck::StructChecker::ALIAS_CONVERSION_FAILED)
.value("STEREO_ERROR",
RDKit::StructureCheck::StructChecker::STEREO_ERROR)
.value("STEREO_FORCED_BAD",
RDKit::StructureCheck::StructChecker::STEREO_FORCED_BAD)
.value("ATOM_CLASH", RDKit::StructureCheck::StructChecker::ATOM_CLASH)
.value("ATOM_CHECK_FAILED",
RDKit::StructureCheck::StructChecker::ATOM_CHECK_FAILED)
.value("SIZE_CHECK_FAILED",
RDKit::StructureCheck::StructChecker::SIZE_CHECK_FAILED)
.value("TRANSFORMED", RDKit::StructureCheck::StructChecker::TRANSFORMED)
.value("FRAGMENTS_FOUND",
RDKit::StructureCheck::StructChecker::FRAGMENTS_FOUND)
.value("EITHER_WARNING",
RDKit::StructureCheck::StructChecker::EITHER_WARNING)
.value("DUBIOUS_STEREO_REMOVED",
RDKit::StructureCheck::StructChecker::DUBIOUS_STEREO_REMOVED)
.value("RECHARGED", RDKit::StructureCheck::StructChecker::RECHARGED)
.value("STEREO_TRANSFORMED",
RDKit::StructureCheck::StructChecker::STEREO_TRANSFORMED)
.value("TEMPLATE_TRANSFORMED",
RDKit::StructureCheck::StructChecker::TEMPLATE_TRANSFORMED)
.value("TAUTOMER_TRANSFORMED",
RDKit::StructureCheck::StructChecker::TAUTOMER_TRANSFORMED);
python::class_<RDKit::StructureCheck::StructCheckerOptions,
RDKit::StructureCheck::StructCheckerOptions *>(
"StructCheckerOptions", python::init<>())
.def_readwrite(
"AcidityLimit",
&RDKit::StructureCheck::StructCheckerOptions::AcidityLimit)
.def_readwrite(
"RemoveMinorFragments",
&RDKit::StructureCheck::StructCheckerOptions::RemoveMinorFragments)
.def_readwrite(
"DesiredCharge",
&RDKit::StructureCheck::StructCheckerOptions::DesiredCharge)
.def_readwrite(
"CheckCollisions",
&RDKit::StructureCheck::StructCheckerOptions::CheckCollisions)
.def_readwrite(
"CollisionLimitPercent",
&RDKit::StructureCheck::StructCheckerOptions::CollisionLimitPercent)
.def_readwrite("MaxMolSize",
&RDKit::StructureCheck::StructCheckerOptions::MaxMolSize)
.def_readwrite(
"ConvertSText",
&RDKit::StructureCheck::StructCheckerOptions::ConvertSText)
.def_readwrite("StripZeros",
&RDKit::StructureCheck::StructCheckerOptions::StripZeros)
.def_readwrite(
"CheckStereo",
&RDKit::StructureCheck::StructCheckerOptions::CheckStereo)
.def_readwrite(
"ConvertAtomTexts",
&RDKit::StructureCheck::StructCheckerOptions::ConvertAtomTexts)
.def_readwrite(
"GroupsToSGroups",
&RDKit::StructureCheck::StructCheckerOptions::GroupsToSGroups)
.def_readwrite("Verbose",
&RDKit::StructureCheck::StructCheckerOptions::Verbose)
.def(
"LoadGoodAugmentedAtoms",
&RDKit::StructureCheck::StructCheckerOptions::
loadGoodAugmentedAtoms,
(python::arg("path")),
"Load the set of good augmented atoms from the specified file path")
.def("LoadAcidicAugmentedAtoms",
&RDKit::StructureCheck::StructCheckerOptions::
loadAcidicAugmentedAtoms,
(python::arg("path")),
"Load the set of acidic augmented atoms from the specified file "
"path")
.def("LoadAugmentedAtomTranslations",
&RDKit::StructureCheck::StructCheckerOptions::
loadAugmentedAtomTranslations,
(python::arg("path")),
"Load the set of acidic augmented atoms from the specified file "
"path");
python::class_<RDKit::StructureCheck::StructChecker>("StructChecker",
python::init<>())
.def(
python::init<const RDKit::StructureCheck::StructCheckerOptions &>())
.def("CheckMolStructure",
&RDKit::StructureCheck::checkMolStructureHelper,
(python::arg("mol")),
"Check the structure and return a set of structure flags")
.def("StructureFlagsToString",
&RDKit::StructureCheck::StructChecker::StructureFlagsToString,
(python::arg("flags")),
"Return the structure flags as a human readable string")
.staticmethod("StructureFlagsToString")
.def("StringToStructureFlags",
&RDKit::StructureCheck::StructChecker::StringToStructureFlags,
(python::arg("str")),
"Convert a comma seperated string to the appropriate structure "
"flags")
.staticmethod("StringToStructureFlags");
}
};
BOOST_PYTHON_MODULE(rdStructChecker) { struct_wrapper::wrap(); }
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