Unexpected Unspecified Stereochemistry Error in Molecule.from_rdkit #1410
Description
Describe the bug
I have an rdkit molecule object in which I have to set custom SetAtomMapNum for all atoms. Whenever I want to parse that rdkit object to an openff-toolkit Molecule object, I get an UndefinedStereochemistryError. This happens for molecules who don't even have steorecenters by construction and only if I add hydrogen atoms to them. If I set every atommap to 0 on every atom, the erroneous behaviour is not observed.
To Reproduce
from openff.toolkit.topology.molecule import Molecule
from rdkit.Chem import AllChem as Chem
### The following will crash with `UndefinedStereochemistryError`
rdmol = Chem.MolFromSmiles("CCCC")
rdmol = Chem.AddHs(rdmol)
for i, a in enumerate(rdmol.GetAtoms()):
a.SetAtomMapNum(i)
offmol = Molecule.from_rdkit(rdmol)
### The following will not crash
rdmol = Chem.MolFromSmiles("CCCC")
rdmol = Chem.AddHs(rdmol)
for i, a in enumerate(rdmol.GetAtoms()):
a.SetAtomMapNum(0)
offmol = Molecule.from_rdkit(rdmol)
Output
---------------------------------------------------------------------------
UndefinedStereochemistryError Traceback (most recent call last)
Input In [54], in <cell line: 10>()
7 a.SetAtomMapNum(i)
8 #a.SetAtomMapNum(0)
---> 10 offmol = Molecule.from_rdkit(rdmol)
File ~/progs/miniconda3/envs/atomtyping/lib/python3.9/site-packages/openff/toolkit/utils/base_wrapper.py:51, in ToolkitWrapper.requires_toolkit.<locals>.decorator.<locals>.wrapped_function(*args, **kwargs)
47 msg = "This function requires the {} toolkit".format(
48 cls._toolkit_name
49 )
50 raise ToolkitUnavailableException(msg)
---> 51 value = func(*args, **kwargs)
52 return value
File ~/progs/miniconda3/envs/atomtyping/lib/python3.9/site-packages/openff/toolkit/topology/molecule.py:5110, in FrozenMolecule.from_rdkit(cls, rdmol, allow_undefined_stereo, hydrogens_are_explicit)
5079 """
5080 Create a Molecule from an RDKit molecule.
5081
(...)
5107
5108 """
5109 toolkit = RDKitToolkitWrapper()
-> 5110 molecule = toolkit.from_rdkit(
5111 rdmol,
5112 allow_undefined_stereo=allow_undefined_stereo,
5113 hydrogens_are_explicit=hydrogens_are_explicit,
5114 _cls=cls,
5115 )
5116 return molecule
File ~/progs/miniconda3/envs/atomtyping/lib/python3.9/site-packages/openff/toolkit/utils/rdkit_wrapper.py:1458, in RDKitToolkitWrapper.from_rdkit(self, rdmol, allow_undefined_stereo, hydrogens_are_explicit, _cls)
1455 Chem.AssignStereochemistry(rdmol, cleanIt=False)
1457 # Check for undefined stereochemistry.
-> 1458 self._detect_undefined_stereo(
1459 rdmol,
1460 raise_warning=allow_undefined_stereo,
1461 err_msg_prefix="Unable to make OFFMol from RDMol: ",
1462 )
1464 # Create a new OpenFF Molecule
1465 offmol = _cls()
File ~/progs/miniconda3/envs/atomtyping/lib/python3.9/site-packages/openff/toolkit/utils/rdkit_wrapper.py:2280, in RDKitToolkitWrapper._detect_undefined_stereo(cls, rdmol, err_msg_prefix, raise_warning)
2278 else:
2279 msg = "Unable to make OFFMol from RDMol: " + msg
-> 2280 raise UndefinedStereochemistryError(msg)
UndefinedStereochemistryError: Unable to make OFFMol from RDMol: Unable to make OFFMol from RDMol: RDMol has unspecified stereochemistry. Undefined chiral centers are:
- Atom C (index 0)
- Atom C (index 1)
- Atom C (index 2)
- Atom C (index 3)
Computing environment (please complete the following information):
- Operating system:
5.15.0-46-generic #49~20.04.1-Ubuntu SMP Thu Aug 4 19:15:44 UTC 2022 x86_64 x86_64 x86_64 GNU/Linux - Output of running
conda list:
# packages in environment at /scratch/wulsdorf/progs/miniconda3/envs/atomtyping:
#
# Name Version Build Channel
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qtpy 2.0.1 pyhd8ed1ab_0 conda-forge
ray 1.9.2 pypi_0 pypi
rdkit 2021.09.4 py39hccf6a74_0 conda-forge
re2 2022.02.01 h9c3ff4c_0 conda-forge
readline 8.1.2 h7f8727e_1
redis 4.1.0 pypi_0 pypi
regex 2022.3.15 py39h7f8727e_0
reportlab 3.5.68 py39he59360d_1 conda-forge
requests 2.27.1 pyhd8ed1ab_0 conda-forge
s2n 1.0.10 h9b69904_0 conda-forge
sander 16.0 pypi_0 pypi
scikit-learn 1.0.2 py39h51133e4_1
scipy 1.7.3 py39hc147768_0
seaborn 0.12.0 hd8ed1ab_0 conda-forge
seaborn-base 0.12.0 pyhd8ed1ab_0 conda-forge
send2trash 1.8.0 pyhd3eb1b0_1
setuptools 60.9.3 py39hf3d152e_0 conda-forge
simint 0.7 h642920c_1 psi4
six 1.16.0 pyh6c4a22f_0 conda-forge
smirnoff99frosst 1.1.0 pyh44b312d_0 conda-forge
snappy 1.1.8 he1b5a44_3 conda-forge
sniffio 1.2.0 py39hf3d152e_2 conda-forge
soupsieve 2.3.1 pyhd8ed1ab_0 conda-forge
sqlalchemy 1.3.23 py39h3811e60_0 conda-forge
sqlite 3.37.0 hc218d9a_0
stack_data 0.2.0 pyhd3eb1b0_0
statsmodels 0.13.2 py39hd257fcd_0 conda-forge
tbb 2021.5.0 hd09550d_0
tempora 5.0.2 pypi_0 pypi
tenacity 8.0.1 pyhd8ed1ab_0 conda-forge
terminado 0.13.1 py39hf3d152e_0 conda-forge
testpath 0.5.0 pyhd8ed1ab_0 conda-forge
threadpoolctl 3.1.0 pyh8a188c0_0 conda-forge
tinycss2 1.1.1 pyhd8ed1ab_0 conda-forge
tinydb 4.7.0 pyhd8ed1ab_0 conda-forge
tk 8.6.12 h27826a3_0 conda-forge
tmap 1.0.6 py39h2bc3f7f_0 tmap
toml 0.10.2 pyhd8ed1ab_0 conda-forge
tomli 1.2.2 pyhd3eb1b0_0
tornado 6.1 py39h3811e60_2 conda-forge
torsiondrive 1.1.0 pyhd8ed1ab_0 conda-forge
tqdm 4.62.3 pyhd3eb1b0_1
traitlets 5.1.1 pyhd8ed1ab_0 conda-forge
typed-ast 1.5.2 py39h3811e60_0 conda-forge
typing-extensions 4.1.1 hd8ed1ab_0 conda-forge
typing_extensions 4.1.1 pyha770c72_0 conda-forge
tzcode 2021e h7f98852_0 conda-forge
tzdata 2021e hda174b7_0
ujson 5.4.0 pypi_0 pypi
unicodedata2 14.0.0 py39h3811e60_0 conda-forge
urllib3 1.26.8 pyhd8ed1ab_1 conda-forge
wcwidth 0.2.5 pyh9f0ad1d_2 conda-forge
webencodings 0.5.1 py_1 conda-forge
websocket-client 1.2.3 pyhd8ed1ab_0 conda-forge
wheel 0.37.1 pyhd3eb1b0_0
widgetsnbextension 3.5.2 py39h06a4308_0
wrapt 1.13.3 pypi_0 pypi
xmltodict 0.12.0 py_0 conda-forge
xorg-kbproto 1.0.7 h7f98852_1002 conda-forge
xorg-libice 1.0.10 h7f98852_0 conda-forge
xorg-libsm 1.2.3 hd9c2040_1000 conda-forge
xorg-libx11 1.7.2 h7f98852_0 conda-forge
xorg-libxau 1.0.9 h7f98852_0 conda-forge
xorg-libxdmcp 1.1.3 h7f98852_0 conda-forge
xorg-libxext 1.3.4 h7f98852_1 conda-forge
xorg-libxpm 3.5.13 h7f98852_0 conda-forge
xorg-libxrender 0.9.10 h7f98852_1003 conda-forge
xorg-libxt 1.2.1 h7f98852_2 conda-forge
xorg-renderproto 0.11.1 h7f98852_1002 conda-forge
xorg-xextproto 7.3.0 h7f98852_1002 conda-forge
xorg-xproto 7.0.31 h7f98852_1007 conda-forge
xz 5.2.5 h516909a_1 conda-forge
yaml 0.2.5 h7f98852_2 conda-forge
zc-lockfile 2.0 pypi_0 pypi
zeromq 4.3.4 h9c3ff4c_1 conda-forge
zipp 3.7.0 pyhd8ed1ab_1 conda-forge
zlib 1.2.11 h36c2ea0_1013 conda-forge
zstd 1.5.2 ha95c52a_0 conda-forge
Additional context