Thanks Noel for your reply. Sincerely. Eric Le 8 avr. 2015 à 21:26, Noel O'Boyle <baoille...@gmail.com> a écrit :
> (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
