Dear all,
I noticed a strange behavior when extracting murcko scaffolds from
preprocessed molecules with an inhouse standardization protocol.
I made a gist to illustrate the problem:
https://gist.github.com/jose-manuel/04d69dd3ac52cca74449e73d614df42e
This leaves me with several questions:
1. When working with the standardized molecule, I get a drawing of the
murcko scaffold without Hs on the terminal nitrogen.
Why is that? I would expect either a radical (so with '.') or an
additional hydrogen. The smiles does not indicate the molecule is a
radical either.
2. When sanitizing the molecule to update the smiles, I get a radical
by default, instead of a H bound to the nitrogen. Why is not a H
added instead? If I switch off the FINDRADICALS sanitization flag, I
do not get an extra hydrogen either...
3. When I apply the default Sanitization to the murcko scaffold and try
to display it, I get an UnicodeEncodeError.
If I manually replace [N] by N in the smiles and create a new
molecule from it, I don't get an error anymore. Is there a
workaround? Interestingly, the function Draw.MolsToGridImage works
just fine but I could not find how to change the atom label size and
bond width.
Am I missing something obvious?
Many thanks in advance as any feedback would be much appreciated!
Cheers,
Jose Manuel
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