> I found two slightly different datasets: MMFF94_dative.mol2 and
> MMFF94_hypervalent.mol2 . Which one of them is the one I should be
> using?
> …
See test/mmff94validate.cpp and the comments at the top. The easiest to grab is:
MMFF94_dative.mol2
MMFF94_opti.log
> tool(I am using OProfile) is showing that the most intensive computation
> is occurring inside forcefield.cpp rather than forcefieldmmff94.cpp
Well, forcefield.cpp contains implementations for computing interactions,
derivatives, gradients, etc. I spent a bit of time trying to clean up easy
optimizations about a year ago. So it's not surprising. I'll be curious what
you find. (You can also use obminimize on _dative.mol2 as well if you want a
*lot* of profiling.)
I think Tim also started on porting the forcefield.cpp code over to use the
Eigen template matrix/vector library:
https://github.com/timvdm/OBForceField/tree/master/src
One advantage to Eigen is that it uses vector instructions (e.g., SSE3/SSE4,
etc.) where available.
Hope that helps,
-Geoff
------------------------------------------------------------------------------
Live Security Virtual Conference
Exclusive live event will cover all the ways today's security and
threat landscape has changed and how IT managers can respond. Discussions
will include endpoint security, mobile security and the latest in malware
threats. http://www.accelacomm.com/jaw/sfrnl04242012/114/50122263/
_______________________________________________
OpenBabel-Devel mailing list
OpenBabel-Devel@lists.sourceforge.net
https://lists.sourceforge.net/lists/listinfo/openbabel-devel
