Hi!
I have a problem understanding the behaviour of hydrogen bond donor
detection in OpenBabel / Pybel and would appreciate your help.
In my example, I have a fucose molecule, given by the SMILES string C[C@
@H]1O[C@@H](O)[C@@H](O)[C@H](O)[C@@H]1O
and want to detect all H-bond donors.
Using the OpenBabel command line (SMILES stored in fucose.smi) and using
$ babel fucose.smi -osmi --append HBD
I get as an output :
C[C@@H]1O[C@@H](O)[C@@H](O)[C@H](O)[C@@H]1O 4
When trying to do the same in Pybel using the IsHbondDonor function of the
OBAtom class, I get 0 donors instead of 4.
import pybel
molecule = "C[C@@H]1O[C@@H](O)[C@@H](O)[C@H](O)[C@@H]1O"
print(molecule)
mol = pybel.readstring("smi", molecule)
print([atom.OBAtom.IsHbondDonor() for atom in mol].count(True))
Is this expected behaviour, i.e. are there differences in the hydrogen bond
detection?
Best
Sebastian
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