Can you check the code into a branch? Do you mean 5% faster at ConnectTheDots, or 5% faster over the whole reading in?
- Noel On 10 February 2014 02:40, Geoffrey Hutchison <geoff.hutchi...@gmail.com> wrote: > 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 ------------------------------------------------------------------------------ Managing the Performance of Cloud-Based Applications Take advantage of what the Cloud has to offer - Avoid Common Pitfalls. Read the Whitepaper. http://pubads.g.doubleclick.net/gampad/clk?id=121051231&iu=/4140/ostg.clktrk _______________________________________________ OpenBabel-Devel mailing list OpenBabel-Devel@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/openbabel-devel
