Open bannanc opened 6 years ago
I did not bring this up in the preprint, but I think its something worth thinking about. We don't want making SMIRKS to take significant computing time, it should be the fast step. Its worth thinking about if there is a way to flatten the loops currently required for typing molecules.
This was an issue Daniel and I found really early on. However, I think its possible its a bigger openforcefield question. Basically, the problem is that looping over all molecules and all SMIRKS patterns doesn't scale well when you have hundreds of molecules. In testing ChemPer I found that running 5,000 Reducer
steps for torsions on the 20 amino acid polypeptide required 5ish hours on my laptop.
This will be the first of a number of issues that I am migrating form the smarty repo. That is problems around chemical perception searching that we discussed, but chose not to directly address in that code. I'm not actually sure if this will end up being as big of a problem here as it was with smarty/smirky.
Essentially the looping through molecules and smirks patterns was the cause of smirky's slowness. Discussion available at smarty issue#261. Here is the original text: