This is related to ParmEd/ParmEd#209.

I would like to expand the mask parser to be able to select molecules, chain IDs, etc.

Current proposals from @swails

A couple ideas:

Do what Chimera does (see https://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/frameatom_spec.html)
Use :: for chain IDs (in the same way that @% indicates atom type names)
An example of 1:

# Select residues 1-10 in chain A
:1-10.A
# Select residues 1-10 in chains A, B, and C
:1-10.A-C # I *think*; not sure if you can use - for string range, maybe .A,B,C
# etc...

An example of 2:

# Select chain A
::A
# Select residues 1-10 of chains A, B, and C
::A,B,C:1-10
# Select protein backbone atoms of residues 2-20 in chains A and B
::A,B:2-20@CA,C,O,N

Another idea for flexibility is to say that chains are strings, and use the same "chain" syntax to denote molecules when the chain is given a numerical value.

My Thoughts

I do like 2) for chain IDs - I think we could potentially get into trouble with the . syntax. I don't know why but for some reason I feel I've come across atom names with . in them, although nothing is coming to mind now.

For molecule selection, personally I like the idea of having a separate character that can represent molecules, the way there is currently @ for atoms and : for residues. Based on what is currently used in the mask parser, I think that the most likely candidates for "molecule" are ; and %. Both have drawbacks: ; looks enough like : that things could easily get confused (and it's on the same key), while % is already used in a subset of @ to denote "type", so it would have different meanings in different contexts.

Whatever is decided, it should be consistent between ParmEd, Cpptraj, and the rest of Amber.