Hi Jose Manuel,
the problem is just that the scaffold returned by
MurckoScaffold.GetScaffoldForMol() has no explicit hydrogens on the imino N:
for atom in ms.GetAtoms():
print(atom.GetIdx(), atom.GetAtomicNum(), atom.GetNumExplicitHs(),
atom.GetNumImplicitHs(),
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:
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