> 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. But I can assure you that Pybel calls the same calls as the command-line when you supply the same options. > Does pybel use also the /data/phmodel.txt file? Yes. > 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. I have never seen a nitro group represented with an explicit H. Can you give us a real example? Or a list of the "other representations of nitro groups" that you expect? > To this end, which file (containing the SMARTS patterns) is employed in > the pybel method? CorrectDativeBonds does not use SMARTS patterns. Instead, it looks for atom pairs with neighboring "+" and "-" formal charges and it increases the bond order to remove the formal charges. Hope that helps, -Geoff ------------------------------------------------------------------------------ This SF.net Dev2Dev email is sponsored by: Show off your parallel programming skills. Enter the Intel(R) Threading Challenge 2010. http://p.sf.net/sfu/intel-thread-sfd _______________________________________________ OpenBabel-discuss mailing list OpenBabel-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/openbabel-discuss
