JSON might be more realistic due to excellent Python support. Created a
cclib issue for that, too: https://github.com/cclib/cclib/issues/156
I think both CML and chemical JSON will still change with time, and it's
not clear what will emerge as the standard in compchem. So it would be
great to support both in some way. Nonetheless, the two can pretty much be
converted between each other, right?
On Thu, Dec 18, 2014 at 10:31 AM, Marcus D. Hanwell <
[email protected]> wrote:
>
> 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 <[email protected]>
> 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 <[email protected]>
> 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 <
> [email protected]> 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
> >> [email protected]
> >> 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
> >> [email protected]
> >> 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
> > [email protected]
> > 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
[email protected]
https://lists.sourceforge.net/lists/listinfo/avogadro-devel
