[OpenBabel-Devel] types.txt
Hi, 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. Cheers, -- 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.sehttp://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
Re: [OpenBabel-Devel] types.txt
On 2013-04-25 09:45, David van der Spoel wrote: Hi, 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. Cheers, And is there a description of each of the types somewhere? -- 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.sehttp://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
Re: [OpenBabel-Devel] types.txt
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 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.sehttp://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
