ranged selection for numerical properties

[mdimura]

Chemfiles selection syntax does not allow for ranged numerical properties. Would it be possible to introduce something like resid 3 to 17 (like VMD)? Similar syntax exists in VMD, pymol, mdtraj, etc., and it is more compact than chemfiles' current alternative: resid >=3 and resid <=17. Possible syntax options are:

1. between(resid, 3, 17)
2. resid 3 to 17
3. 3 <= resid <= 17

My personal favorite is resid 3 to 17. 3 <= resid <= 17 is OK, but less compact and does not exist in any of the other tools I am familiar with (pymol, vmd, mdtraj, cpptraj). I don't know if there are some implementation considerations though.

[Luthaf]

Thank you for opening the issue!

The resid 3-17 syntax would clash with resid == 3 - 17 which is interpreted as resid == -14

resid 3 to 17 is very nice from the user point of view, but might be hard to fit within the current framework. In particular, resid is not a special construct in our selection language, only something that gives us a numerical value that can then be combined and compared with other values. For example, resid + x^2 < y^2, although a bit strange, is a valid selection. resid 3 works by being expanded to resid == 3; and resid 3 4 is expanded to resid == 3 or resid == 4.

My favourite alternatives would be 3 <= resid <= 17, or between(resid, 3, 17). `

• between(resid, 3, 17) is completely unambiguous, although a bit strange and verbose.
• 3 <= resid <= 17 could be the nicest one, and fit pretty well within the current framework. It also works well with mathematical expressions: 3 + x < resid <= 36. Implementing this would require a bit of backtracking in the parser (i.e. when we find 3 <= resid, we have to check if the next token is <= or < before finishing parsing). Not that it is that bad, we already have to backtrack in a few places due to other ambiguities.

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but less compact and does not exist in any of the other tools I am familiar with (pymol, vmd, mdtraj, cpptraj).

What syntax do these tools use?

[mdimura]

Would it be possible to introduce to as a keyword, which expands to >= L and <=R? Here are some examples of ranged selection in other similar tools: vmd: mass 5 to 11.5 pymol: resi 100-200 mdtraj: mass 5.5 to 20 cpptraj: :6-10 mdanalysis (derived from CHARMM’s syntax): resnum 1:5 I guess, options resid 3:17 and resid 3..17 could also be considered.

[Luthaf]

resid 3:17 could work too, or something like resid in 3:17. This would compose nicely with math operations (x + y^2 in cos(z):(3 + sin(z))). I'll have to think a bit more about how a to keyword could work 😃

[Luthaf]

Note for myself: here is a nice explanation of how a <= b > c < e works in Python https://softwareengineering.stackexchange.com/a/316983.