"like" operator in atomspec

[Conrad Huang]

In an assembly, it would be nice to be able to select chains based on "similarity", which can be either "the same entity" for mmCIF files or sequence similarity if entity data is not available.

A syntax in atom specification would need to be created for selecting items of this type (e.g., chains) that are similar to a concrete example (e.g., chain A)

[Conrad Huang]

Not that urgent (yet).

[Conrad Huang]

This ticket is similar to #480, in that we want the ability to select by entity. The issue is what do we really want to do:

(a) choose chains with the atomspec polymer /A, or
(b) limit chosen atoms to chains with atomspec polymer /A?

The question arises because #480 is inspired by select, which currently implements (b), where

select atomspec polymer polymer_atomspec

means:

• select atomspec
• unselect atoms whose sequence does match any sequences in atoms from polymer_atomspec

Is the select syntax a hack to add polymer-selection functionality, or is that how we want things to work?

[Elaine Meng]

My opinion is that it should really be an atomspec, your option “(a)” and not have this weird automatic intersection behavior.  It’s confusing that it is not exactly an atomspec  but a restrictor in the selection command (and that it can’t be used in other commands), so one reason for asking for the “like” operator is to get rid of this inconsistency.  Then, like all other atomspecs, to intersect one would use ampersand.

[Conrad Huang]

I agree. This means (when this actually gets implemented) that select syntax will change since we probably do not want the polymer keyword anymore.

[pett]

duplicate of #480