Automate certain processes in FFEA

[Jarvellis Rogers]

Some users of FFEA have said they wish certain processes of FFEA to be automated to reduce the workload of FFEA workflows. These are as follows:

• Automate the initialization of FFEA from atomistic or cryogenic data to a parametrised FFEA surface mesh, i.e. a user inputs a file such as a PDB or EMDB, then inputs a list of parameters they would like either in the command-line interface or a graphical window, and runs the generator to output FFEA input files.
• Automate restarting simulations.
• Automate file and directory management of FFEA, such as naming generated files based on their input files by default and creating new directories for output files.

This proposal was suggested in the evaluation report for FFEA 2.7.2.