> 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
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