3-membered rings (Lexie)
Moving a3 ([*;r3:1]1~;@[*;r3:2]~;@[*;r3:3]1) to the end so that it also picks up the epoxy C-O-C angle (which was previously covered by a28). Instead of adding to the end, could also change a28 to be not-3 (or 4-) membered ring atoms.
Chris Bayly also suggested the following generic parameters be added for 3-membered rings, to cover situations where you have r3-r3-not r3 and not r3 - r3 - not r3:
[*;r3:1]-[*;r3:2]-[*;!r3:3][*;!r3:1]-[*;r3:2]-[*;!r3:3]
Some of these are already covered with existing parameters, need to figure out how they interact with the suggested ones:
a4: [*;r3:1]~;@[*;r3:2]~;!@[*:3] r3 atom - r3 atom - not in (same) ring
a5: [*:1]~;!@[*;r3:2]~;!@[*:3]not in (same) ring - r3 atom - not in (same) ring
a6: [#1:1]-[*;r3:2]~;!@[*:3] H - r3 atom - not in (same) ring
4-membered rings (Lexie)
Moving a7 ([#6r4:1]-;@[#6r4:2]-;@[#6r4:3]) to the end, and changing the SMIRKS pattern to [*;r4:1]-;@[*;r4:2]-;@[*;r4:3] so that it also catches heteroatoms which were previously included under a1, a18a, and a28. Instead of adding to the end, could also keep SMIRKS change but change a28 to be not-4 (or 3-) membered ring atoms and remove a18a (or make it specific to 5-membered rings).
Chris Bayly also suggested the following generic parameters be added for 3-membered rings, to cover situations where you have r4-r4-not r4 and not r4 - r4 - not r4:
[*;r4:1]-[*;r4:2]-[*;!r4:3][*;!r4:1]-[*;r4:2]-[*;!r4:3]
Our existing parameters are:
a8: [!#1:1]-[#6r4:2]-;!@[!#1:3]a9: [!#1:1]-[#6r4:2]-;!@[#1:3]
Which are both too specific (central atom must be C) and too broad (first atom could be in-ring or out of ring). Need to figure out how to work these together for the right coverage.
Other parameters I’ve looked at (Lexie)
All parameters:
High-priority parameters: