Dear all,
A question for the community:
Toby Wright submitted a pull request this week that introduces a new,
stricter, rotatable bond definition:
https://github.com/rdkit/rdkit/pull/211/files
The new SMARTS, re-formatted to be somewhat more readable, is:
[!$(*#*)&\
!D1&\
!$(C(F)(F)F)&\
!$(C(Cl)(Cl)Cl)&\
!$(C(Br)(Br)Br)&\
!$(C([CH3])([CH3])[CH3])&\
!$([CD3](=[N,O,S])-!@[#7,O,S!D1])&\
!$([#7,O,S!D1]-!@[CD3]=[N,O,S])&\
!$([CD3](=[N+])-!@[#7!D1])&\
!$([#7!D1]-!@[CD3]=[N+])]\
-!@\
[!$(*#*)&\
!D1&\
!$(C(F)(F)F)&\
!$(C(Cl)(Cl)Cl)&\
!$(C(Br)(Br)Br)&\
!$(C([CH3])([CH3])[CH3])]
Toby was quite careful and added a new descriptor -
NumStrictRotatableBonds() - that uses this SMARTS.
I see a few options to deal with this:
I could add the new descriptor as Toby provided it. People are then free to
pick between NumRotatableBonds() and NumStrictRotatableBonds(). This has
the advantage of maintaining strict backwards compatibility, but I could
imagine it being confusing/irritating to people using the code to have to
choose between them (or, worse, using both).
Another option is to just replace the current NumRotatableBonds() SMARTS
with the new one.
This loses backwards compatibility, but replaces NumRotableBonds() with
something more correct.
Finally, I could take a hybrid approach: replace the default
NumRotatableBonds() with the new one, but add an extra argument that allows
the old one to be used.
I'm leaning towards the second option. I'd normally go with the third, but
I almost view this as a bug fix for the rotatable bonds definition.
Comments? suggestions? Other options?
-greg
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