Make chirality command return pairs of atom and 'R' or 'S' for chiral centers

[Tom Goddard]

The chirality command currently just returns a list of "R" or "S". It would be useful in Python scripts to know the atoms too. Maybe return [(chiral_atom1, "R"), (chiral_atom2, "S"), ...]. Or a dictionary mapping the atom to the chirality.

[Eric Pettersen]

Command now returns atom→chirality dictionary.

Change: ​https://github.com/RBVI/ChimeraX/commit/08785290b0187a73cfe3a81cf386f4816c601458

[Tom Goddard]

Always returns an empty dictionary. Iterating through the ch_info=zip() iterator to print results reaches the end so dict(ch_info) produces an empty dictionary.

[Tom Goddard]

Also when I fix that it is a bit surprising that the dictionary contains atoms that are not chiral centers. I'd expect it to have only atoms which are chiral centers, or maybe all atoms. But apparently it includes atoms that have 4 bonded atoms which is surprising.

[Tom Goddard]

Would also be nice if the chirality command did not raise UserError when there are no centers but instead just logged an info message. This makes it easier to use in Python scripts.

I think as a user command a common use would be "chirality #1" where you are just asking which atoms are chiral centers. The Log output I think would just include chiral centers, not atoms with 4 substituents that are not chiral.

[Eric Pettersen]

Did you commit/push your fix? I'm not seeing it...

[Tom Goddard]

I did not push any fix. I only made a fix in my local ChimeraX since I am studying AlphaFold/Boltz/OpenFold chirality violations with Tristan.

[Eric Pettersen]

Okay, I changed it so that in the Python layer it no longer always returns an empty dictionary. I also added a "verbose" option to the command, defaulting to false. If verbose is true, it reports the same info as before, which includes the non-chiral 4-substituent atoms. Verbose false will omit those.

Having no 4-substituent atoms in the spec at all has been downgraded from an error to a warning.

Change: ​https://github.com/RBVI/ChimeraX/commit/0ba4395590ed3d61691bd8ca877b7e7f8b8c6fab