(ccing to the list) Good question. The PDB format actually doesn't have an implicit valence model but it's true that we do infer the structure. And in fact the same could be done for an XYZ file (apparently OEChem does this) but it requires a lot of clever guesswork and works best for structures where you already have a good idea what the answer is (e.g. proteins in PDB files). And even then, no-one has any idea whether for example Histidine is protonated or where the hydrogen is (although there is a paper on this topic).
Anyway, I'm not sure what your application is, but the general rule of chemical file formats is that if you have information on bond orders and charges, don't throw it away and expect a toolkit to work it out correctly. It may do this in some cases, but there's a certain error rate (there's a paper on this also). Regards, - Noel On 7 April 2015 at 19:36, eric henon <eric.he...@univ-reims.fr> wrote: > Dear Noel, > > Thanks a lot for your answer. > I fully agree with you that "implicit hydrogen" is a sensitive concept. > I thought that the xyz format had an implicit > hydrogen model based on closed shells for neutral species. > > However, it is not clear for me why openbabel > successfully adds properly hydrogens from this short pdb file, > without any explicit information of charge nor spin : > > HETATM 1 O 2 2 -13.792 5.005 -6.266 0.00 0.00 > O > HETATM 2 C 2 2 -12.612 5.149 -6.445 0.00 0.00 > C > HETATM 3 N 2 2 -12.095 5.442 -7.679 0.00 0.00 > N > HETATM 4 N 2 2 -10.800 5.578 -7.968 0.00 0.00 > N > HETATM 5 C 2 2 -9.917 5.465 -7.053 0.00 0.00 > C > HETATM 6 C 2 2 -10.306 5.172 -5.690 0.00 0.00 > C > HETATM 7 C 2 2 -11.597 5.024 -5.395 0.00 0.00 > C > HETATM 8 C 2 2 -13.006 5.586 -8.816 0.00 0.00 > C > > I guess openbabel uses an implicit valence model in this case, while for the > same system > it does not handle the corresponding xyz file format ? > > Regards. > Ric > > > > Le 6 avr. 2015 à 21:08, Noel O'Boyle <baoille...@gmail.com> a écrit : > > That XYZ file does not represent ethanol. It describes some sort of > radical species involving C-C-O. The XYZ format does not have an > implicit valence model - if the atoms are present, they are in the > file - if not, they don't exist. > > You may be confusing this with a MOL file which has an implicit > valence model and a way of describing the formal charge on each atom > (how do we know how many hydrogens to add otherwise?). > > > > But, without any information in this pdb file: > > > > > If interested, > you can read more about these issues at > http://nextmovesoftware.com/blog/2013/02/27/explicit-and-implicit-hydrogens-taking-liberties-with-valence/ > > Regards, > Noel > > On 5 April 2015 at 15:46, eric henon <eric.he...@univ-reims.fr> wrote: > > Hello, > > I' m using open babel (2.3.1 on Mac Os and I tried also 2.2.3 on a Linux > machine) > to add hydrogen atoms on a ligand, and it does not work. > > The command I entered is: > > babel -iXYZ ligand.xyz -oXYZ ligandH.xyz -h > > as specified in the "help" list. > > The generated file is exactly the same as the input file, > ... without any hydrogen atoms added. > > Then, I tried on a very simple case: > > 3 > ethanol "backbone" > C 0.00000 0.00000 0.00000 > C -0.68400 -1.18400 -0.48300 > O -0.02400 -2.32700 -0.01700 > > It does not work either (either on Mac OS or a Linux machine). > > I probably missed something when using openbabel. > Any help will be appreciated. > Thanks. > > Ric > > ------------------------------------------------------------------------------ > Dive into the World of Parallel Programming The Go Parallel Website, > sponsored > by Intel and developed in partnership with Slashdot Media, is your hub for > all > things parallel software development, from weekly thought leadership blogs > to > news, videos, case studies, tutorials and more. Take a look and join the > conversation now. http://goparallel.sourceforge.net/ > _______________________________________________ > OpenBabel-discuss mailing list > OpenBabel-discuss@lists.sourceforge.net > https://lists.sourceforge.net/lists/listinfo/openbabel-discuss > > ------------------------------------------------------------------------------ BPM Camp - Free Virtual Workshop May 6th at 10am PDT/1PM EDT Develop your own process in accordance with the BPMN 2 standard Learn Process modeling best practices with Bonita BPM through live exercises http://www.bonitasoft.com/be-part-of-it/events/bpm-camp-virtual- event?utm_ source=Sourceforge_BPM_Camp_5_6_15&utm_medium=email&utm_campaign=VA_SF _______________________________________________ OpenBabel-discuss mailing list OpenBabel-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/openbabel-discuss
