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//
// Copyright (C) 2020-2021 Greg Landrum and T5 Informatics GmbH
//
// @@ 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/python.h>
#include <GraphMol/MolEnumerator/MolEnumerator.h>
namespace python = boost::python;
using namespace RDKit;
namespace {
enum class EnumeratorTypes { LinkNode, PositionVariation, RepeatUnit };
std::shared_ptr<MolEnumerator::MolEnumeratorOp> opFromName(
EnumeratorTypes typ) {
std::shared_ptr<MolEnumerator::MolEnumeratorOp> res;
switch (typ) {
case EnumeratorTypes::LinkNode:
res.reset(new MolEnumerator::LinkNodeOp());
break;
case EnumeratorTypes::PositionVariation:
res.reset(new MolEnumerator::PositionVariationOp());
break;
case EnumeratorTypes::RepeatUnit:
res.reset(new MolEnumerator::RepeatUnitOp());
break;
default:
throw ValueErrorException("unrecognized operator type");
}
return res;
}
MolEnumerator::MolEnumeratorParams *createParamsFromName(EnumeratorTypes typ) {
auto res = new MolEnumerator::MolEnumeratorParams();
res->dp_operation = opFromName(typ);
return res;
}
void setEnumerationHelper(MolEnumerator::MolEnumeratorParams *self,
EnumeratorTypes typ) {
self->dp_operation = opFromName(typ);
}
MolBundle *enumerateHelper1(const ROMol &mol, unsigned int maxPerOperation) {
auto res = MolEnumerator::enumerate(mol, maxPerOperation);
return new MolBundle(res);
}
MolBundle *enumerateHelper2(const ROMol &mol,
const MolEnumerator::MolEnumeratorParams &ps) {
auto res = MolEnumerator::enumerate(mol, ps);
return new MolBundle(res);
}
} // namespace
BOOST_PYTHON_MODULE(rdMolEnumerator) {
python::scope().attr("__doc__") =
"Module containing classes and functions for enumerating molecules";
python::enum_<EnumeratorTypes>("EnumeratorType")
.value("LinkNode", EnumeratorTypes::LinkNode)
.value("PositionVariation", EnumeratorTypes::PositionVariation)
.value("RepeatUnit", EnumeratorTypes::RepeatUnit);
python::class_<MolEnumerator::MolEnumeratorParams>(
"MolEnumeratorParams", "Molecular enumerator parameters",
python::init<>(python::args("self")))
.def("__init__", python::make_constructor(createParamsFromName))
.def_readwrite("sanitize", &MolEnumerator::MolEnumeratorParams::sanitize,
"sanitize molecules after enumeration")
.def_readwrite("maxToEnumerate",
&MolEnumerator::MolEnumeratorParams::maxToEnumerate,
"maximum number of molecules to enumerate")
.def_readwrite("doRandom", &MolEnumerator::MolEnumeratorParams::doRandom,
"do random enumeration (not yet implemented")
.def_readwrite("randomSeed",
&MolEnumerator::MolEnumeratorParams::randomSeed,
"seed for the random enumeration (not yet implemented")
.def("SetEnumerationOperator", &setEnumerationHelper,
python::args("self", "typ"),
"set the operator to be used for enumeration");
python::def("Enumerate", &enumerateHelper1,
(python::arg("mol"), python::arg("maxPerOperation") = 0),
python::return_value_policy<python::manage_new_object>(),
R"DOC(do an enumeration and return a MolBundle.
If maxPerOperation is >0 that will be used as the maximum number of molecules which
can be returned by any given operation.
Limitations:
- the current implementation does not support molecules which include both
SRUs and LINKNODEs
- Overlapping SRUs, i.e. where one monomer is contained within another, are
not supported)DOC");
python::def(
"Enumerate", &enumerateHelper2,
(python::arg("mol"), python::arg("enumParams")),
python::return_value_policy<python::manage_new_object>(),
R"DOC(do an enumeration for the supplied parameter type and return a MolBundle
Limitations:
- Overlapping SRUs, i.e. where one monomer is contained within another, are
not supported)DOC");
}
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