Albert, I think CML will continue to be very much a first class citizen too. JSON feels much easier to change/augment, and Python support for JSON is very good - it would be great to add it, but I don't think it is critical. We could add some simple Python glue too, the format is super-simple. With Open Babel we ended up using CML, MDL and XYZ to get data into Avogadro 2.
Marcus On Thu, Dec 18, 2014 at 9:59 AM, Defusco III, Albert A <defu...@pitt.edu> wrote: > Hi Karol, > > It looks Avogadro2 will be using Chemical JSON whenever possible to transfer > data. Do you think this would be possible with cclib? > > http://wiki.openchemistry.org/Chemical_JSON > > > > Albert > > > > ------------------------------------------------------ > Albert DeFusco, Ph.D. > Research Assistant Professor > Technical Director, Center for Simulation and Modeling > University of Pittsburgh > Pittsburgh, PA 15260 > 412-648-3094 > http://www.pitt.edu/~defusco > http://www.sam.pitt.edu > > On Dec 17, 2014, at 11:22 PM, Karol Langner <karol.lang...@gmail.com> wrote: > >> One of the things I want to do soon is give cclib the ability to output CML. >> That would be an easy way to communicate between programs in a standard >> format. >> >> Karol >> >> On Fri, Dec 12, 2014 at 12:33 PM, Geoffrey Hutchison >> <geoff.hutchi...@gmail.com> wrote: >> > It sounds like you think of these things as exclusive, and I don't see >> > why they should be. >> >> The current state of the code is >> https://github.com/OpenChemistry/avogadrolibs/tree/master/avogadro/quantumio >> >> That is, these things are *separate* from “regular” IO. Reading files and >> finding quantum data are currently in different parts of the code. >> >> Now, one may question whether “regular” and quantum IO *should* be separate. >> But I’m not talking about throwing away existing code - I believe Albert was >> saying that rather than adding X new implementations to >> avogadrolibs/avogadro/quantumio, it would be helpful to have an interface to >> cclib for parsing quantum data. >> >> > is demonstrably much more efficient than going through Open Babel for >> > "regular" input for example. We can certainly tweak defaults, so the >> >> I certainly wasn’t talking about changing the current pattern for regular >> IO, although I’d certainly suggest that the interface could merge “import” >> and “open” commands. In the case of CML or other formats that Avogadro >> directly handles, preference can go to the internal implementation, and >> other formats could be handled through Open Babel. >> >> I’d be happy to make that change. >> >> I thought the discussion was about Summer of Code projects, and certainly >> improving quantum IO would be great. (Adding features to read and visualize >> other “cube” formats would be nice too.) >> >> -Geoff >> >> >> ------------------------------------------------------------------------------ >> Download BIRT iHub F-Type - The Free Enterprise-Grade BIRT Server >> from Actuate! Instantly Supercharge Your Business Reports and Dashboards >> with Interactivity, Sharing, Native Excel Exports, App Integration & more >> Get technology previously reserved for billion-dollar corporations, FREE >> http://pubads.g.doubleclick.net/gampad/clk?id=164703151&iu=/4140/ostg.clktrk >> _______________________________________________ >> Avogadro-devel mailing list >> Avogadro-devel@lists.sourceforge.net >> https://lists.sourceforge.net/lists/listinfo/avogadro-devel >> ------------------------------------------------------------------------------ >> Download BIRT iHub F-Type - The Free Enterprise-Grade BIRT Server >> from Actuate! Instantly Supercharge Your Business Reports and Dashboards >> with Interactivity, Sharing, Native Excel Exports, App Integration & more >> Get technology previously reserved for billion-dollar corporations, FREE >> http://pubads.g.doubleclick.net/gampad/clk?id=164703151&iu=/4140/ostg.clktrk_______________________________________________ >> Avogadro-devel mailing list >> Avogadro-devel@lists.sourceforge.net >> https://lists.sourceforge.net/lists/listinfo/avogadro-devel > > > ------------------------------------------------------------------------------ > Download BIRT iHub F-Type - The Free Enterprise-Grade BIRT Server > from Actuate! Instantly Supercharge Your Business Reports and Dashboards > with Interactivity, Sharing, Native Excel Exports, App Integration & more > Get technology previously reserved for billion-dollar corporations, FREE > http://pubads.g.doubleclick.net/gampad/clk?id=164703151&iu=/4140/ostg.clktrk > _______________________________________________ > Avogadro-devel mailing list > Avogadro-devel@lists.sourceforge.net > https://lists.sourceforge.net/lists/listinfo/avogadro-devel ------------------------------------------------------------------------------ Download BIRT iHub F-Type - The Free Enterprise-Grade BIRT Server from Actuate! Instantly Supercharge Your Business Reports and Dashboards with Interactivity, Sharing, Native Excel Exports, App Integration & more Get technology previously reserved for billion-dollar corporations, FREE http://pubads.g.doubleclick.net/gampad/clk?id=164703151&iu=/4140/ostg.clktrk _______________________________________________ Avogadro-devel mailing list Avogadro-devel@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/avogadro-devel
