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284012bd3e
* Modify createStereoGroup add bondIdx list * update python wrapper * Add CreateStereoGroup tests w/ bonds * Update StereoGroup.cpp * Update StereoGroup.cpp * Update StereoGroup.cpp * Update rough_test.py * Update StereoGroup.cpp added check if atom and bond lists are both empty * aded test for empty stereogroup creation
120 lines
4.3 KiB
C++
120 lines
4.3 KiB
C++
//
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// Copyright (C) 2018-2025 Dan Nealschneider and other RDKit contributors
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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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#define NO_IMPORT_ARRAY
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#include <boost/python.hpp>
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#include <string>
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// ours
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#include <RDBoost/Wrap.h>
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#include <GraphMol/RDKitBase.h>
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#include <GraphMol/StereoGroup.h>
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namespace python = boost::python;
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namespace RDKit {
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namespace {
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std::string stereoGroupClassDoc =
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"A collection of atoms with a defined stereochemical relationship.\n\n"
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"Used to help represent a sample with unknown stereochemistry, or that "
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"is a mix\nof diastereomers.\n";
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StereoGroup *createStereoGroup(StereoGroupType typ, ROMol &mol,
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python::object atomIds, python::object bondIds, unsigned readId) {
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std::vector<Atom *> cppAtoms;
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std::vector<Bond *> cppBonds;
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python::stl_input_iterator<unsigned int> beg(atomIds), end;
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while (beg != end) {
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unsigned int v = *beg;
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if (v >= mol.getNumAtoms()) {
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throw_value_error("atom index exceeds mol.GetNumAtoms()");
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}
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cppAtoms.push_back(mol.getAtomWithIdx(v));
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++beg;
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}
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python::stl_input_iterator<unsigned int> bbeg(bondIds), bend;
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while (bbeg != bend) {
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unsigned int v = *bbeg;
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if (v >= mol.getNumBonds()) {
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throw_value_error("bond index exceeds mol.GetNumBonds()");
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}
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cppBonds.push_back(mol.getBondWithIdx(v));
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++bbeg;
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}
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if (cppAtoms.empty() && cppBonds.empty()) {
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throw_value_error("New StereoGroup must contain at least one atom or bond.");
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}
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auto *sg = new StereoGroup(typ, cppAtoms, cppBonds, readId);
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return sg;
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}
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python::object getAtomsHelper(StereoGroup &sg) {
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python::list res;
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for (auto at : sg.getAtoms()) {
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res.append(boost::ref(*at));
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}
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return python::tuple(res);
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}
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python::object getBondsHelper(StereoGroup &sg) {
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python::list res;
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for (auto bnd : sg.getBonds()) {
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res.append(boost::ref(*bnd));
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}
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return python::tuple(res);
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}
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} // namespace
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struct stereogroup_wrap {
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static void wrap() {
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python::enum_<RDKit::StereoGroupType>("StereoGroupType")
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.value("STEREO_ABSOLUTE", RDKit::StereoGroupType::STEREO_ABSOLUTE)
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.value("STEREO_OR", RDKit::StereoGroupType::STEREO_OR)
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.value("STEREO_AND", RDKit::StereoGroupType::STEREO_AND)
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.export_values();
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python::class_<StereoGroup, boost::shared_ptr<StereoGroup>>(
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"StereoGroup", stereoGroupClassDoc.c_str(), python::no_init)
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.def("GetGroupType", &StereoGroup::getGroupType, python::args("self"),
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"Returns the StereoGroupType.\n")
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.def("GetAtoms", getAtomsHelper, python::args("self"),
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"access the atoms in the StereoGroup.\n")
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.def("GetBonds", getBondsHelper, python::args("self"),
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"access the bonds in the StereoGroup.\n")
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.def("GetReadId", &StereoGroup::getReadId, python::args("self"),
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"return the StereoGroup's original ID.\n"
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"Note that the ID only makes sense for AND/OR groups.\n")
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.def("GetWriteId", &StereoGroup::getWriteId, python::args("self"),
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"return the StereoGroup's ID that will be exported.\n"
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"Note that the ID only makes sense for AND/OR groups.\n")
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.def("SetWriteId", &StereoGroup::setWriteId, python::args("self", "id"),
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"return the StereoGroup's ID that will be exported.\n"
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"Note that the ID only makes sense for AND/OR groups.\n");
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python::def("CreateStereoGroup", &createStereoGroup,
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"creates a StereoGroup associated with a molecule from a list "
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"of atom Ids",
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(python::arg("stereoGroupType"), python::arg("mol"),
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python::arg("atomIds") = boost::python::list(), python::arg("bondIds") = boost::python::list(),
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python::arg("readId") = 0),
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python::return_value_policy<
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python::manage_new_object,
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python::with_custodian_and_ward_postcall<0, 2>>());
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python::def(
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"ForwardStereoGroupIds", &RDKit::forwardStereoGroupIds,
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python::args("mol"),
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"Forward the original Stereo Group IDs when exporting the Mol.");
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}
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};
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} // namespace RDKit
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void wrap_stereogroup() { RDKit::stereogroup_wrap::wrap(); }
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