allow user to specify job name (folder name) for alphafold predict

[phil.cruz@…]

Elaine: paraphrase of conversation with Phil during NIAID zoom meeting...

Phil: Currently files from alphafold get saved in ChimeraX downloads directory, but folders are just named prediction_1, prediction_2. Would like to get a more descriptive folder name so it would be easier to tell which modeling job was which. [shares screen] especially when I click Error Plot and get a dialog asking for the location of the file -- not easy to tell which one will go with the structure. Would be nice if it asked for a job name beforehand, say when you click Predict, and then name the folder with that.

Elaine: something like an option of "alphafold predict" command that allows specifying a job name that would be used as folder name within the ChimeraX download dir (with any necessary character changes), or even the entire output location and folder name. Correspondingly, from the GUI, when the Predict button is clicked, there could be a secondary dialog asking for a job name or output folder name/location.

[Tom Goddard]

This should be easy. But I'm not sure of the best user interface. It is not clear that I should force a user to go through another panel when the press the Predict button. Already the AlphaFold prediction uses 2 panels, and adding another looks really clumsy. I could add to the Options area of the main AlphaFold panel a "Results directory" entry maybe with a browse button and already filled in with the default ~/Downloads/ChimeraX/AlphaFold/prediction_N. What if the user chooses an existing directory? Do I overwrite the previous results? Maybe I need to warn and refuse to run until they choose a new directory. Having the directory choice under Options makes it hard to find.

Ultimately it may be better to have a separate AlphaFold Prediction tool and an AlphaFold Database Search tool with different panels. Or maybe separate tabs. That would be a big job to refine all the details of new GUI interfaces and would reduce the value of a dozen videos I've made with the older GUI. So maybe start with a simple entry field under Options. The Options panel already contains some pretty important options like whether to energy minimize or use PDB templates so the user should really look at Options if they care much about the results.

[Tom Goddard]

Done.

I added a "Results directory" entry field to the AlphaFold GUI under Options. It has a Browse button to choose the directory. The directory does not need to exist and will be created. The default directory is ~/Downloads/ChimeraX/AlphaFold/prediction_[N]. The "[N]" is replaced the smallest positive integer that makes a new directory. This "[N]" can be included in user-specified directories too in order to produce unique directories.

The "alphafold predict" command also has a new option "directory" which takes the results directory with the same rules as the GUI (ie "[N]" can appear in the directory if desired).

If the specified directory exists and contains a results.zip file that indicates that a previous run was already done in that directory because the AlphaFold prediction downloads the results as a zip file of that name. In this case the command and gui will not overwrite the previous results and will instead append "_[N]" to the requested directory to make a new directory. This is a safety feature.