> I got the hash-based algorithm up and running (commit here). I ran it on a
> folder of ~100 cif files, and it’s about 5% faster. I don’t think the small
> performance gain is worth migrating away from tried and tested code, but, if
> there’s another opinion out there, let me know.
>
The current ConnectTheDots is generally N log N since the atoms are sorted. But
my question would be whether the PerceiveBondOrders is being triggered on your
CIF files. Try, for example, running:
obabel file.cif -O file.cml -as #output only single bonds from ConnectTheDots()
I suspect the problem is not in perceiving bonds, but the ring perception and
aromaticity detection needed in the PerceiveBondOrders.
BTW, I'd try benchmarking before and after the commit with -as for perceiving
only single bonds. I'd be curious on large CIF files how much the hash-based
algorithm helps.
> Geoff - This might be more of a question for the Avogadro mailing list, but
> do you think there’s a more elegant way to handle these large cifs in a GUI?
> The example cif currently freezes up Avogadro (and the internal front-end
> software at my job) with a ton of CPU work. Maybe this could be run in a
> background thread with a timeout?
>
Avogadro *does* read molecule files in a background thread. Granted, you can't
do anything until the molecule is read, but the interface still works. Again,
if you're seeing a huge CPU hit, my guess is that it's from PBO. Now if you
have a bit of free time for coding, I've got a great idea there for a huge
performance win. :-)
-Geoff
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