Bug in IPython display after setting a molecule property #5192
Comments
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confirmed. thanks for the detailed report @dwhswenson |
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FWIW: a workaround until the next patch release is to set |
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Describe the bug
After setting a property on a molecule, the IPython display code takes a code path that leads to an unbound variable.
To Reproduce
In Jupyter notebook:
Expected behavior
No error.
Screenshots (well, traceback, since that's searchable)
--------------------------------------------------------------------------- UnboundLocalError Traceback (most recent call last) File ~/mambaforge/envs/openfe-notebooks/lib/python3.9/site-packages/IPython/core/formatters.py:343, in BaseFormatter.__call__(self, obj) 341 method = get_real_method(obj, self.print_method) 342 if method is not None: --> 343 return method() 344 return None 345 else: File ~/mambaforge/envs/openfe-notebooks/lib/python3.9/site-packages/rdkit/Chem/Draw/IPythonConsole.py:130, in _toHTML(mol) 127 else: 128 content = Draw._moltoSVG(mol, molSize, [], nm, kekulize=kekulizeStructures, 129 drawOptions=drawOptions) --> 130 res.append(f'<tr><td colspan=2 style="text-align:center">{content}</td></tr>') 132 for i, (pn, pv) in enumerate(props.items()): 133 if ipython_maxProperties >= 0 and i >= ipython_maxProperties: UnboundLocalError: local variable 'content' referenced before assignmentNote: The image does show in the output as well, but obviously the error isn't desirable.
Configuration (please complete the following information):
conda list
Additional context
I think the bug is in lines 124-126 here, where
resis appended to instead of setting the value ofcontent. I'm not sure why this process triggers that code path, but it sure looks like that's the issue.rdkit/rdkit/Chem/Draw/IPythonConsole.py
Lines 117 to 130 in 44a91e1
See also OpenFreeEnergy/gufe#20.
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