Allow opening AlphaFold PAE json file from Open File dialog

[Tom Goddard]

Currently AlphaFold PAE data is opened using the special AlphaFold Error Plot tool so that the associated structure can be specified. It would be easier to fine if the File / Open menu entry could do it.

Also it would be handy if the open command also worked

open afpae.json structure #1

Also it would be nice if you could fetch PAE data from the AlphaFold database

open P12345 from alphafold_pae structure #1

Currently you can fetch the AlphaFold database structures with

open P12345 from alphafold

[Tom Goddard]

Done. Added these to 1.8 and daily builds.

Since the Open File dialog does not allow options to specify the associated structure the code looks for an already open structure from the same directory as the PAE file. If it finds exactly one such structure then it associates it. Otherwise it does not open the PAE file and gives an error advising you to use Tools / Structure Prediction / AlphaFold Error Plot to choose the structure to associate. Not pretty but probably handles 95% of cases.

[Tom Goddard]

The open command for PAE files or for fetching PAE have most of the options that the alphafold pae command with the same defaults:

usage open format pae

open names [structure an atomic structure specifier] [plot true or false] [dividerLines true or false] [colorDomains true or false] [connextMaxPae a number] [cluster a number] [minSize an integer]

— read and display data

names: file names to open; a name of 'browse' will bring up a file browser

[Tom Goddard]

I also noticed that alphafold fetch and alphafold pae commands did not have our standard ignoreCache option so I added that.

[Tom Goddard]

A few more details. The alphafold pae format name is "AlphaFold PAE" with nickname "pae" and has file suffix ".json" and this is the default format for suffix ".json". It is a format in the Structure Analysis category. The format description is on wikipedia

​https://en.wikipedia.org/wiki/Predicted_Aligned_Error

[Eric Pettersen]

Thought I'd mention that opening coordinates files is a similar scenario (needs to be associated with an open structure). For coordinate files, if there's only one structure then that's the one. If there are more than one, then it brings up a modal dialog with a StructureMenuButton in it for designating the structure.