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pierrepo / PBxplore

A suite of tools to explore protein structures with Protein Blocks :snake:
https://pbxplore.readthedocs.org/en/latest/
MIT License
28 stars 17 forks source link

Add a progress bar during PB assignment of a trajectory (#150) #151

Closed HubLot closed 7 years ago

HubLot commented 7 years ago

This progress bar will always print the first frame and one every 100. One every 100 frames seems a good ratio between number of print statements (to avoid a lot unnecessary prints) and time between 2 of them (to avoid a too long time of wait). It is better than one every 50 ;)

The print statements is on stderr.

pierrepo commented 7 years ago

Nice work. Could you also print the total frame number at the end? Do you think we could also move the printing of chains read for PDB/PDBX files into loader.py?

HubLot commented 7 years ago

Could you also print the total frame number at the end?

What do you mean ? The total frame number is already print each time (Frame 100/1000 where 1000 is the number of frames). You mean print the last frame like (Frame 1000/1000) ?

Do you think we could also move the printing of chains read for PDB/PDBX files into loader.py?

Yes, we could. It will be more consistent (instead of a print inside a method)

pierrepo commented 7 years ago 
Could you also print the total frame number at the end?

What do you mean ? The total frame number is already print each time (Frame 100/1000 where 1000 is the number of frames). You mean print the last frame like (Frame 1000/1000) ?

Yes, the very last frame like frame 1000/1000 whether or not the total number of frame is a multiple of 100. For instance, frame 250/250 or frame 153/153 should work too.

Do you think we could also move the printing of chains read for PDB/PDBX files into loader.py?

Yes, we could. It will be more consistent (instead of a print inside a method)

Awesome. Could you do it within the same PR? As an extra bonus, it will also allow to get the number of chains for PDBx structure files (not implemented in the current version).

HubLot commented 7 years ago

Okay I'll look into those!

HubLot commented 7 years ago

For the trajectory, I re-arrange a little bit the progress bar to print the first frame, one every 100 and the last one.

For PDB/PDBx, I create a property to get the number of chains and move the print statement into the chains_from_files function

pierrepo commented 7 years ago

Cool. Thanks @HubLot !