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
For now, it appears that these capture the desired chemistry based on inspecting the captured molecules, so I’m leaving them as is.
New parameter: Renamed a3 to a41, due to moving it to the end, though it sounds like the numbering is arbitrary so could probably keep the same name.
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. For now, I am trying two approaches:
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:
[*:1]~;!@[*;r4:2]~;!@[*:3]and[*;r4:1]@[*;r4:2]~;!@[*:3].
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.
5-member rings (Lexie)
Currently we don’t have any internal r5-r5-r5 ring angles, so I made one. I just made a generic one: [*;r5:1]@[*;r5:2]@[*;r5:3] but we may want to break it down further. Looking at the MSM parameter distribution, it seemed like the non-aromatic rings were clustered together, but the aromatic rings were all over the place in a way that made it not obvious how to split them.
New parameter: Added a new parameter to the end called a43.
Other parameters I’ve looked at (Lexie)
All parameters:
High-priority parameters: