Christopher Bayly

Using smirnoff99Frosst-1.0.9.offxml for this case. Found out that the valence angle parameters assigned for the O-S-O valence angle is: `````` which has the right equilibrium angle. Likewise the O-P-O angles...

@jchodera @davidlmobley @bannanc I just realized something important that I want to embody here. It is in the spirit and direction of the ProposalEngine, and it is simply this: choosing...

I agree with the above discussion: with @jchodera on the goal of getting BaFFLE to learn good moves, and with @davidlmobley that I could not wisely undertake this in my...

I will try to think of formalizing higher-level rules as @jchodera suggests.

We want to exclude triple bonds so the form I would suggest is: [#6:1]!#[#6:2] which is asking for a carbon-carbon bond of any order except triple, thus allowing double, single,...

In principle triple bonds would not be ruled out, because they can conjugate too, but I am expecting a lot of finessing needed to map: singleconjugatedSinglearomaticconjugatedDoubledouble correctly, which is where...

Here is an example molecule. DrugBank_2592: c1nc(c2c(n1)n(cn2)[C@H]3[C@@H]([C@H]([C@@H](O3)CO[P@@](=O)(O)OS(=O)(=O)O)OP(=O)(O)O)O)N