After analysis of some compounds whose protonation is carried out by openbabel command line, it would seem that the results are different from those obtained with the AddHydrogens() method embedded in the pybel library, with the correctforpH option.
Does pybel use also the /data/phmodel.txt file? If not, which file is employed in order to check the involved SMARTS pattern…??
In a same way, I want to know of it possible to use pybel (maybe by the ConvertDativeBonds method ??) to standardize a whole file for some specials groups, e.g. nitro, carboxylic acids...
It is documented that it is possible to convert [N+]([O-])=O to N(=O)=O, but it doesn't work for the other representations of the nitro groups, like [N](-OH)=O.
To this end, which file (containing the SMARTS patterns) is employed in the pybel method?
Does anybody know a alternative way to perform a structure normalization using pybel ??