Re: [Open Babel] protonation and structure normalization

2010-09-09 Thread david.lagorce
> 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. >Well yes, if you're comparing AddHydrogens() with and without correctForPH, then the results are >different.

Re: [Open Babel] protonation and structure normalization

2010-09-06 Thread Geoffrey Hutchison
> 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. Well yes, if you're comparing AddHydrogens() with and without correctForPH, then the results are different.

[Open Babel] protonation and structure normalization

2010-09-06 Thread David Lagorce
Dear All, 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/phmod