Hi All,
I've recently been writing some code to automatically write GAMESS input files
for me. As these files require a point group it would be advantageous to
determine this automatically from a geometry. Unfortunately I'm having some
difficulty accessing the OBPointGroup class with the python
On 09/07/2012 20:59, Jeff Janes wrote:
> If I make a file foo.smi with just this in it:
>
> [N-]=[N+]=c1c(=O)ccc2=c1c(=O)c1c1c2=O
>
> And then make and use an index file:
>
> ~/openbabel/bin/obabel foo.smi -ofs
> ~/openbabel/bin/obabel foo.fs -ocan -sfoo.smi -at5 -aa --title ""
>
> I find tha
I've just seen a demo of the impact of running applications on the GPU and it
does seem for some operations you can get striking performance gains. Would it
be worth considering porting openbabel to OpenCL?
Chris
--
Liv
> I've recently been writing some code to automatically write GAMESS input
> files for me. As these files require a point group it would be advantageous
> to determine this automatically from a geometry. Unfortunately I'm having
> some difficulty accessing the OBPointGroup class with the python
> I've just seen a demo of the impact of running applications on the GPU and it
> does seem for some operations you can get striking performance gains. Would
> it be worth considering porting openbabel to OpenCL?
Much like muti-threading, it's not clear how some operations in Open Babel
would w
Hi Geoff,
Thanks for the response. Is it not possible to rotate the molecule into the
correct frame once you have determined its point group?
Yours
Ed
On 12 Jul 2012, at 13:12, Geoff Hutchison wrote:
>> I've recently been writing some code to automatically write GAMESS input
>> files for m
> Thanks for the response. Is it not possible to rotate the molecule into the
> correct frame once you have determined its point group?
That could probably be done (but isn't implemented). Reducing to the symmetry
unique atoms would take a decent amount of implementation work, which I don't
pe
Is it possible to do a weighted rotor search in pybel? I have been using
openbabel and the WeightedRotorSearch function. I couldn't find any simple
example online and wanted to find out if the approach below is ok and if
anyone would advise changes. Am I right in saying that the mol is updated to
t
Thanks for the input Geoff.
The example I saw was a proprietary similarity search, I've no idea if a
similar increase is speed would be possible for fastsearch?
Cheers,
Chris
On 12 Jul 2012, at 13:16, Geoff Hutchison wrote:
>> I've just seen a demo of the impact of running applications on the
Hi Chris,
On 12.07.2012 13:16, Geoff Hutchison wrote:
I've just seen a demo of the impact of running applications on the
GPU and it does seem for some operations you can get striking
performance gains. Would it be worth considering porting openbabel to
OpenCL?
Much like muti-threading, it's
A sidepoint from GPU development - and directly related to Geoff's
earlier point.
Perhaps multicore awareness is the way to go...
In the most reductionist of approaches -- you could launch n threads
(instead of one) and have each generate a conformer each since these
are really independent proces
This seems like a good compromise to me, especially if it means we see
it sooner ...
Quoting JP on Thu, 12 Jul 2012 19:07:06 +0100:
> A sidepoint from GPU development - and directly related to Geoff's
> earlier point.
>
> Perhaps multicore awareness is the way to go...
>
> In the most reducti
On Thu, Jul 12, 2012 at 6:40 PM, Chris Swain wrote:
> Thanks for the input Geoff.
>
> The example I saw was a proprietary similarity search, I've no idea if a
> similar increase is speed would be possible for fastsearch?
I'm currently working on improving the algorithm for fastsearch like
operat
> anyone would advise changes. Am I right in saying that the mol is updated to
> the best conformer and this is what will be written to the output file?
Yup. This is very similar to my version of this -- I usually usually something
like:
ff.SteepestDescent(1500, 1.0e-4)
ff.WeightedRo
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