mirror of
https://github.com/rdkit/rdkit.git
synced 2026-06-06 22:39:55 +08:00
19bdd21de1
* add new test (it fails, of course) * isAtomPotentialTetrahedralCenter() there and tested tests cases for molecular stereo written (but failing, of course) create new_chirality.cpp, we will probably want to change this at some point new StereoInfo structure * more infrastructure - isBondPotentialStereoBond() - two getStereoInfo() functions - associated unit tests * backup * oops * backup * switch to always using four atoms for bonds * backup * add new test (it fails, of course) * isAtomPotentialTetrahedralCenter() there and tested tests cases for molecular stereo written (but failing, of course) create new_chirality.cpp, we will probably want to change this at some point new StereoInfo structure * more infrastructure - isBondPotentialStereoBond() - two getStereoInfo() functions - associated unit tests * backup * oops * backup * switch to always using four atoms for bonds * backup * this now actually works * doc update * add a test to demo that ring stereo is not working * more testing * add a fun CIP test * add review note * debugging * remove extraneous debugging turn off tests for ring-double bond stereo * disable the ring-stereo fix... this breaks a few tests, but we will recover * works, needs cleanup, chirality code needs re-testing * nothing works * Fixes #3322 * Python and C++ tests now pass * clang-format * first pass at python wrappers * improve doctest * basic optimization... stop with the copying * rename * all tests passing again * optimization * fix the sort in the tests * looks like this might fix the windows-dll build problems * update tests * the fun never ends * comment cleanup * handle deliberately unspecified atoms/bonds * add cleanIt option * add flagPossible * add option to use the new code to the SMILES parser * additional testing * additional testing * a bit of additional testing never hurts * changes in response to review * fixes a bug with potential parastereo not being cleared other changes in response to review * update docs
60 lines
2.6 KiB
C++
60 lines
2.6 KiB
C++
//
|
|
// Copyright (C) 2020 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 <string>
|
|
#include <GraphMol/RDKitBase.h>
|
|
#include <GraphMol/Chirality.h>
|
|
|
|
#include <RDBoost/Wrap.h>
|
|
|
|
namespace python = boost::python;
|
|
|
|
namespace RDKit {
|
|
struct chirality_wrapper {
|
|
static void wrap() {
|
|
python::enum_<Chirality::StereoType>("StereoType")
|
|
.value("Unspecified", Chirality::StereoType::Unspecified)
|
|
.value("Atom_Tetrahedral", Chirality::StereoType::Atom_Tetrahedral)
|
|
.value("Bond_Double", Chirality::StereoType::Bond_Double)
|
|
.value("Bond_Cumulene_Even", Chirality::StereoType::Bond_Cumulene_Even)
|
|
.value("Bond_Atropisomer", Chirality::StereoType::Bond_Atropisomer);
|
|
python::enum_<Chirality::StereoSpecified>("StereoSpecified")
|
|
.value("Unspecified", Chirality::StereoSpecified::Unspecified)
|
|
.value("Specified", Chirality::StereoSpecified::Specified)
|
|
.value("Unknown", Chirality::StereoSpecified::Unknown);
|
|
python::enum_<Chirality::StereoDescriptor>("StereoDescriptor")
|
|
.value("NoValue",
|
|
Chirality::StereoDescriptor::None) // can't use "None" in Python
|
|
.value("Tet_CW", Chirality::StereoDescriptor::Tet_CW)
|
|
.value("Tet_CCW", Chirality::StereoDescriptor::Tet_CCW)
|
|
.value("Bond_Cis", Chirality::StereoDescriptor::Bond_Cis)
|
|
.value("Bond_Trans", Chirality::StereoDescriptor::Bond_Trans);
|
|
python::class_<Chirality::StereoInfo>("StereoInfo",
|
|
"Class describing stereochemistry")
|
|
.def_readonly("NOATOM", &Chirality::StereoInfo::NOATOM,
|
|
"marker for unspecified int values")
|
|
.def_readwrite("type", &Chirality::StereoInfo::type,
|
|
"the type of stereo")
|
|
.def_readwrite("specified", &Chirality::StereoInfo::specified,
|
|
"whether or not it is specified")
|
|
.def_readwrite("centeredOn", &Chirality::StereoInfo::centeredOn,
|
|
"index of the item the stereo concerns")
|
|
.def_readwrite("descriptor", &Chirality::StereoInfo::descriptor,
|
|
"stereo descriptor")
|
|
.def_readonly("controllingAtoms",
|
|
&Chirality::StereoInfo::controllingAtoms,
|
|
"indices of the atoms controlling the stereo");
|
|
};
|
|
};
|
|
} // namespace RDKit
|
|
|
|
void wrap_chirality() { RDKit::chirality_wrapper::wrap(); }
|