I have a large number of protein-protein docking results (pdb files) that I am trying to filter according to known constraints. Is BioPython capable of sequentially checking multiple (already aligned) structures with a reference structure and remove all which do not meet my constraints (distance to a set residue etc.)
The key issues I'm running into are comparing distances etc between different pdb files and the aforementioned sequential checking/deletion.
I think I will need to handle this with two or more scripts, a script for the checking and deletion, which calls a separate script for checking my constraints.
I hope this is clear and I am not completely off track
I think there are some methods for this in biopython (or can be coded from hand using biopythons object model to help), but its not really where it excels. This is probably a task for pymol or similar.