Hi there, I have hit on some surprising behaviour (to me at least), and I thought to ask for further clarification.
I create a molecule without sanitization (red flag) - because, oh well, I
downloaded this sd file from the web so it must be perfectly curated and
what not.
When I try Chem.AddHs, I get
<rdkit.Chem.rdchem.Mol object at 0x140a3d0>
[11:47:00]
****
Pre-condition Violation
getNumImplicitHs() called without preceding call to calcImplicitValence()
Violation occurred on line 167 in file
/opt/RDKit_trunk/Code/GraphMol/Atom.cpp
Failed Expression: d_implicitValence>-1
****
Traceback (most recent call last):
File "./test.py", line 107, in <module>
Chem.AddHs(m, addCoords=True)
RuntimeError: Pre-condition Violation
I understand that this may be related to having sanitization switched off
(in fact if I turn it on it works), but my question is - is this the
correct error message?
Perhaps calcImplicitValence() should be called regardless of sanitization?
I have attached a reproducible example.
-
Jean-Paul Ebejer
Early Stage Researcher
test.py
Description: Binary data
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