Command-line interfaces

[joaomcteixeira]

To our current understanding of the project, which and how many command-line interfaces will be required? @JerryJohnsonLee , you have been using the original code quite intensively, do you foresee the need for several CLIs that would grant fine control to the user on the different tasks that the program will perform? Or is one general CLI enough?

[JerryJohnsonLee]

Currently we have a single CLI interface (the entrance python script) that sets up the calculations and generates structure ensemble. From a design perspective I would say maybe energy calculations and entropy calculations can be two different interfaces that is useful.

[joaomcteixeira]

Do you mean two CLI that would calculate energy and entropy on a battery of PDB files saved in the hardisk? It sounds good to me.

I can prepare the template code to accommodate different CLIs and then you could populate those CLIs with the pertinent options. Btw, which options would you envisage the CLIs having? In general terms, does not need to be a detailed list.

[JerryJohnsonLee]

Yes, or maybe just preparing python functions for these calculations is also enough? So we will create a "protein" class that stores the coordinates of a parsed structure from pdb/mmcif right? We should make the functions support either the string of the source structure file or that "protein" object

[joaomcteixeira]

Yes, that is right. So those are two different things, though. One thing is the functions that we will use internally to build the workflow and another thing is the CLI that is that the user would need to run a battery of energy calculations on a set of PDBs that are stored in a folder. Do you think the latter will be necessary?

[JerryJohnsonLee]

Probably not at highest priority right now