> 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. ok, thanks a lot > 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? I am also agree with you, a nitro with an explicit H, by definition is not a cleary possible, but you can sometimes find it in some databases....Thus, how to correclty re-write it....with babel? In the same way, a nitro group as N(=O)=O loaded in pybel is converted internaly in background to N(OH)OH.... N(=O)=O is possible, so pybel will found 2 H-Bond Donors (lipinski definition) but in fact there is no one... > 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 Thanks a lot for your help... David -- View this message in context: http://open-babel.957263.n4.nabble.com/protonation-and-structure-normalization-tp2528314p2532557.html Sent from the openbabel-discuss mailing list archive at Nabble.com. ------------------------------------------------------------------------------ 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
