On 2013-04-26 07:36, David van der Spoel wrote: > On 2013-04-26 05:38, Geoffrey Hutchison wrote: >>> I'm looking at types.txt and wondering whether not the internal >>> representation of atom types (INT) should be unique? Now there are three >>> HO, two H, three C3 etc. >> >> IIRC, the issue is that some programs have different distinctions. For >> example PCModel (PCM) separates between multiple HO types. >> >> Now that's not saying it's perfect. I think I did a "sort -u" at one point, >> because people kept adding to the bottom and there would be duplicate >> entries, etc. So if you spot good simplifications, please suggest them. >> > I assume it works like this that OB determines the atom type to be HO (H > bound to O). Now you can in principle subdivide this into different HO, > depending on what the O is bound to. However if you don't use different > names for these HO (HO1, HO2 etc.) then the information gets lost, right? > > I would suggest that > 1) no double internal names should be allowed > 2) a description of each atom type should be included in the file
How about the following file format: # Comment text # More Comment text # Internal|Description|FF1|FF2|.... H|Generic hydrogen|H1|H3|... HO|Hydrogen bound to oxygen|HO1|HP|... where the internal names are unique (and this should be enforced). I'm happy to implement it, so please let me know if there are grave objections. > > >> For example, I don't remember the difference between MM2 "H" type 5 and type >> 28. We could certainly separate these. >> >> -Geoff >> > > -- David van der Spoel, Ph.D., Professor of Biology Dept. of Cell & Molec. Biol., Uppsala University. Box 596, 75124 Uppsala, Sweden. Phone: +46184714205. sp...@xray.bmc.uu.se http://folding.bmc.uu.se ------------------------------------------------------------------------------ Try New Relic Now & We'll Send You this Cool Shirt New Relic is the only SaaS-based application performance monitoring service that delivers powerful full stack analytics. Optimize and monitor your browser, app, & servers with just a few lines of code. Try New Relic and get this awesome Nerd Life shirt! http://p.sf.net/sfu/newrelic_d2d_apr _______________________________________________ OpenBabel-Devel mailing list OpenBabel-Devel@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/openbabel-devel
