I guess I spoke without thinking. What I'm getting at is that it would be nice to see test cases to verify that everything's working as it said before and after. Next time I'll just come out and say it :-)
- Noel On 26 April 2013 10:37, David van der Spoel <sp...@xray.bmc.uu.se> wrote: > On 2013-04-26 11:17, Noel O'Boyle wrote: >> It's always good to link changes in the code to specific bugs that >> need fixing. It may be useful to see whether you identify such cases >> here before you spend time on this. If you decide to go ahead, I would >> suggest that you add some test cases to ensure that existing correct >> behaviour is retained. > Wouldn't you agree it is a bug that an OB atom type has an undefined > mapping to other force fields? > >> >> - Noel >> >> On 26 April 2013 09:08, David van der Spoel <sp...@xray.bmc.uu.se> wrote: >>> 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 > > > -- > 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 ------------------------------------------------------------------------------ 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
