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keep a8 and a9, but replace the central atom with a wildcard so it can be any 4-membered ring atom.
Remove a8 and a9, and add two new parameters to the end: a44(
[*;!r4:1]~;!@[*;r4:2]~[*;!@[*r4:3]) and a45 ([*;r4:1]@[*;r4:2]~;!@[*:3]). I specified!r4instead of!@in a44 because specifiying!@led to it not picking up fused rings. I left a45 with!@because specifying!r4led to it missing two attached (e.g. connected by a single, non-ring bond) 4-membered rings.
New parameter: Renamed a7 to a42, due to moving it to the end. In (2) above, added a44 and a45 for the respective SMIRKs patterns listed.
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New parameter: Added a new parameter to the end called a43.
I’ve also looked into splitting a13, as it currently covers both fused and spiro rings. Splitting them into two separate categories seems clear via the MSM parameters, so I added a13a ([*;r6:1]~;@[*;r5;x4:2]~;@[*;r5;x2:3]), which separates out the spiro rings. However, the split is less clear using Espaloma, as there is a lot of variation even within fused or spiro rings that is not present in the MSM data.
New parameter: Added a new parameter after a13 called a13a.
Issue with fused rings (Lexie)
One issue I have noticed with separating the small ring parameters is that there is no way to specify in a SMARTS pattern that a given atom is in a ring of a given size. The primitive r indicates the size of the smallest ring the atom is a part of, but if it is part of a fused or spiro ring, this may lead to issues. The primitive R denotes that an atom is part of a ring, but can only be modified by the number of ring bonds, not the size of the ring.
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After a lot of experimenting I haven’t been able to find a solution that involves a single elegant SMARTS pattern. To get these right, we may have to add a number of very specific parameters, and increase coverage for fused rings.
Other parameters I’ve looked at (Lexie)
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