On 2012-10-10 10:30, Noel O'Boyle wrote: > On 9 October 2012 18:58, David van der Spoel <sp...@xray.bmc.uu.se> wrote: >> On 2012-10-09 19:44, Geoff Hutchison wrote: >>>> Apparently it did more than just that and fixed some issue >>>> along the way. >>>> >>>> Geoff, could this be considered for maintenance release? >>> >>> Not as-is. It changes API / ABI, so it must be confined for trunk. There >>> are usually bugs like this which are fixed by 2.x releases which cannot be >>> fixed by maintenance releases. >>> >> So is there any defined plan for what goes into 2.4 and when it should >> be ready? >> >> I can live with a development version as well (trunk?) for a while but >> since we're considering linking openbabel in with gromacs at some stage >> (to be released in a year or so) it would be good to have an idea of >> whether it is feasible to have this kind of features in a stable >> version. I realize that it is difficult to predict, but asking is easy :). > > What is the link between Gaussian files and Gromacs? Or is this a > separate issue? I would have thought that Gromacs has the complete > structure with bond orders and explicit hydrogens. If so, it could > read the Gaussian file and set this information based on that (in > general, the atom order is preserved on reading/writing with OB). > > - Noel > This is for generating topologies based on Gaussian calculations. Since one only has element names and coordinates and overall charge in such files it would be handy to use OB to extract bond orders.
Geoff was mentioning that the API would have to change to support this, but in fact it says in the OB documentation that all info is extracted from the input file, and reading the charge from a gaussian file could be used in OB internals without changing API I would expect, but I'm not familiar with the API yet. In general open babel is useful for file conversion as well, so gromacs could use it for reading/writing files, rather than implementing stuff ourselves. -- 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 ------------------------------------------------------------------------------ Don't let slow site performance ruin your business. Deploy New Relic APM Deploy New Relic app performance management and know exactly what is happening inside your Ruby, Python, PHP, Java, and .NET app Try New Relic at no cost today and get our sweet Data Nerd shirt too! http://p.sf.net/sfu/newrelic-dev2dev _______________________________________________ OpenBabel-discuss mailing list OpenBabel-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/openbabel-discuss
