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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/Validate.h>
namespace python = boost::python;
using namespace RDKit;
namespace {
python::list rdkitValidate(MolStandardize::RDKitValidation &self,
const ROMol &mol, const bool reportAllFailures) {
python::list res;
std::vector<MolStandardize::ValidationErrorInfo> errout =
self.validate(mol, reportAllFailures);
for (auto &query : errout) {
std::string msg = query.message();
res.append(msg);
}
return res;
}
MolStandardize::MolVSValidation *getMolVSValidation(
python::object validations) {
std::vector<boost::shared_ptr<MolStandardize::MolVSValidations>> vs;
std::unique_ptr<
std::vector<boost::shared_ptr<MolStandardize::MolVSValidations>>>
pvect = pythonObjectToVect<
boost::shared_ptr<MolStandardize::MolVSValidations>>(validations);
for (auto v : *pvect) {
vs.push_back(v->copy());
}
return new MolStandardize::MolVSValidation(vs);
}
python::list molVSvalidateHelper(MolStandardize::MolVSValidation &self,
const ROMol &mol, bool reportAllFailures) {
python::list s;
std::vector<MolStandardize::ValidationErrorInfo> errout =
self.validate(mol, reportAllFailures);
for (auto &query : errout) {
s.append(query.message());
}
return s;
}
MolStandardize::AllowedAtomsValidation *getAllowedAtomsValidation(
python::object atoms) {
std::unique_ptr<std::vector<Atom *>> p_atomList =
pythonObjectToVect<Atom *>(atoms);
std::vector<std::shared_ptr<Atom>> satoms;
for (auto ap : *p_atomList) {
satoms.push_back(std::shared_ptr<Atom>(ap->copy()));
}
return new MolStandardize::AllowedAtomsValidation(satoms);
}
python::list allowedAtomsValidate(MolStandardize::AllowedAtomsValidation &self,
const ROMol &mol,
const bool reportAllFailures) {
python::list res;
std::vector<MolStandardize::ValidationErrorInfo> errout =
self.validate(mol, reportAllFailures);
for (auto &query : errout) {
std::string msg = query.message();
res.append(msg);
}
return res;
}
MolStandardize::DisallowedAtomsValidation *getDisallowedAtomsValidation(
python::object atoms) {
std::unique_ptr<std::vector<Atom *>> p_atomList =
pythonObjectToVect<Atom *>(atoms);
std::vector<std::shared_ptr<Atom>> satoms;
for (auto ap : *p_atomList) {
satoms.push_back(std::shared_ptr<Atom>(ap->copy()));
}
return new MolStandardize::DisallowedAtomsValidation(satoms);
}
python::list disallowedAtomsValidate(
MolStandardize::DisallowedAtomsValidation &self, const ROMol &mol,
const bool reportAllFailures) {
python::list res;
std::vector<MolStandardize::ValidationErrorInfo> errout =
self.validate(mol, reportAllFailures);
for (auto &query : errout) {
std::string msg = query.message();
res.append(msg);
}
return res;
}
python::list standardizeSmilesHelper(const std::string &smiles) {
python::list res;
std::vector<MolStandardize::ValidationErrorInfo> errout =
MolStandardize::validateSmiles(smiles);
for (auto &query : errout) {
std::string msg = query.message();
res.append(msg);
}
return res;
}
} // namespace
struct validate_wrapper {
static void wrap() {
std::string docString = "";
python::class_<MolStandardize::RDKitValidation, boost::noncopyable>(
"RDKitValidation", python::init<>())
.def("validate", rdkitValidate,
(python::arg("self"), python::arg("mol"),
python::arg("reportAllFailures") = false),
"");
python::class_<MolStandardize::MolVSValidations, boost::noncopyable>(
"MolVSValidations", python::no_init)
.def("run", &MolStandardize::MolVSValidations::run,
(python::arg("self"), python::arg("mol"),
python::arg("reportAllFailures"), python::arg("errors")),
"");
python::class_<MolStandardize::NoAtomValidation,
python::bases<MolStandardize::MolVSValidations>>(
"NoAtomValidation", python::init<>())
.def("run", &MolStandardize::NoAtomValidation::run,
(python::arg("self"), python::arg("mol"),
python::arg("reportAllFailures"), python::arg("errors")),
"");
python::class_<MolStandardize::FragmentValidation,
python::bases<MolStandardize::MolVSValidations>>(
"FragmentValidation", python::init<>())
.def("run", &MolStandardize::FragmentValidation::run,
(python::arg("self"), python::arg("mol"),
python::arg("reportAllFailures"), python::arg("errors")),
"");
python::class_<MolStandardize::NeutralValidation,
python::bases<MolStandardize::MolVSValidations>>(
"NeutralValidation", python::init<>())
.def("run", &MolStandardize::NeutralValidation::run,
(python::arg("self"), python::arg("mol"),
python::arg("reportAllFailures"), python::arg("errors")),
"");
python::class_<MolStandardize::IsotopeValidation,
python::bases<MolStandardize::MolVSValidations>>(
"IsotopeValidation", python::init<>())
.def("run", &MolStandardize::IsotopeValidation::run,
(python::arg("self"), python::arg("mol"),
python::arg("reportAllFailures"), python::arg("errors")),
"");
python::class_<MolStandardize::MolVSValidation, boost::noncopyable>(
"MolVSValidation")
.def("__init__", python::make_constructor(&getMolVSValidation))
.def("validate", molVSvalidateHelper,
(python::arg("self"), python::arg("mol"),
python::arg("reportAllFailures") = false),
"");
python::class_<MolStandardize::AllowedAtomsValidation, boost::noncopyable>(
"AllowedAtomsValidation", python::no_init)
.def("__init__", python::make_constructor(&getAllowedAtomsValidation))
.def("validate", allowedAtomsValidate,
(python::arg("self"), python::arg("mol"),
python::arg("reportAllFailures") = false),
"");
;
python::class_<MolStandardize::DisallowedAtomsValidation,
boost::noncopyable>("DisallowedAtomsValidation",
python::no_init)
.def("__init__",
python::make_constructor(&getDisallowedAtomsValidation))
.def("validate", disallowedAtomsValidate,
(python::arg("self"), python::arg("mol"),
python::arg("reportAllFailures") = false),
"");
python::def("ValidateSmiles", standardizeSmilesHelper, (python::arg("mol")),
docString.c_str());
}
};
void wrap_validate() { validate_wrapper::wrap(); }
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