Capitalization of multi-character chain ids in atom specs

[tic20@…]

Begin forwarded message:

From: Tristan Croll
Subject: Bug: chain selection not case sensitive
Date: October 22, 2016 at 7:26:46 AM PDT
To: Tom Goddard

Hi Tom,

Just noticed that if I load a large structure with two-character mixed-case chain names (4v8r) and type:

select /Aa

in the command line, ChimeraX selects both chains Aa and AA (likewise if I use select /AA).

Cheers,

Tristan

[Eric Pettersen]

There is a boolean attribute of Structure (lower_case_chains) that has to be set by the input readers if there are chain IDs with lower-case characters in them. Currently it is only set by the PDB reader. This means it needs to be set by the mmCIF reader, made visible to the Python layer, and used by the atom-spec parser/evaluator.

--Eric

[Greg Couch]

Added code to mmCIF reader to set the lower_case_chains flag if need be.

[Greg Couch]

lower_case_chains is not extruded to python layer yet, so it isn't checked.

[Greg Couch]

Changed mmCIF reader to examine all letters in chain id for lowercase letters.
exposed lower_case_chains attribute to Python layer.
use lower_case_chains attribute in atom spec code to decide whether to use case insensitive test or not.