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//
// Copyright (C) 2018 Dan Nealschneider
//
// @@ 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.
//
#define NO_IMPORT_ARRAY
#include <boost/python.hpp>
#include <string>
// ours
#include <RDBoost/Wrap.h>
#include <GraphMol/RDKitBase.h>
#include <GraphMol/StereoGroup.h>
namespace python = boost::python;
namespace RDKit {
namespace {
std::string stereoGroupClassDoc =
"A collection of atoms with a defined stereochemical relationship.\n\n"
"Used to help represent a sample with unknown stereochemistry, or that "
"is a mix\nof diastereomers.\n";
StereoGroup *createStereoGroup(StereoGroupType typ, ROMol &mol,
python::object atomIds, unsigned readId) {
std::vector<Atom *> cppAtoms;
std::vector<Bond *> cppBonds;
python::stl_input_iterator<unsigned int> beg(atomIds), end;
while (beg != end) {
unsigned int v = *beg;
if (v >= mol.getNumAtoms()) {
throw_value_error("atom index exceeds mol.GetNumAtoms()");
}
cppAtoms.push_back(mol.getAtomWithIdx(v));
++beg;
}
auto *sg = new StereoGroup(typ, cppAtoms, cppBonds, readId);
return sg;
}
python::object getAtomsHelper(StereoGroup &sg) {
python::list res;
for (auto at : sg.getAtoms()) {
res.append(boost::ref(*at));
}
return python::tuple(res);
}
} // namespace
struct stereogroup_wrap {
static void wrap() {
python::enum_<RDKit::StereoGroupType>("StereoGroupType")
.value("STEREO_ABSOLUTE", RDKit::StereoGroupType::STEREO_ABSOLUTE)
.value("STEREO_OR", RDKit::StereoGroupType::STEREO_OR)
.value("STEREO_AND", RDKit::StereoGroupType::STEREO_AND)
.export_values();
python::class_<StereoGroup, boost::shared_ptr<StereoGroup>>(
"StereoGroup", stereoGroupClassDoc.c_str(), python::no_init)
.def("GetGroupType", &StereoGroup::getGroupType, python::args("self"),
"Returns the StereoGroupType.\n")
.def("GetAtoms", getAtomsHelper, python::args("self"),
"access the atoms in the StereoGroup.\n")
.def("GetReadId", &StereoGroup::getReadId, python::args("self"),
"return the StereoGroup's original ID.\n"
"Note that the ID only makes sense for AND/OR groups.\n")
.def("GetWriteId", &StereoGroup::getWriteId, python::args("self"),
"return the StereoGroup's ID that will be exported.\n"
"Note that the ID only makes sense for AND/OR groups.\n")
.def("SetWriteId", &StereoGroup::setWriteId, python::args("self", "id"),
"return the StereoGroup's ID that will be exported.\n"
"Note that the ID only makes sense for AND/OR groups.\n");
python::def("CreateStereoGroup", &createStereoGroup,
"creates a StereoGroup associated with a molecule from a list "
"of atom Ids",
(python::arg("stereoGroupType"), python::arg("mol"),
python::arg("atomIds"), python::arg("readId") = 0),
python::return_value_policy<
python::manage_new_object,
python::with_custodian_and_ward_postcall<0, 2>>());
python::def(
"ForwardStereoGroupIds", &RDKit::forwardStereoGroupIds,
python::args("mol"),
"Forward the original Stereo Group IDs when exporting the Mol.");
}
};
} // namespace RDKit
void wrap_stereogroup() { RDKit::stereogroup_wrap::wrap(); }
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