Minimum b-factor value
DocKDE opened this issue · comments
Hi again!
Your fix for the TER statements works fine but I realized that another issue cropped up: I use the occupancy and b-value columns to assign atom to regions in QM/MM calculations. As such, most of the values are necessarily zero. I realize that this is contrary to the intended use of the b-value column but this behavior breaks my use case.
I'm not sure what a good solution might be here. Maybe b-values of 0.00 could be allowed (with warnings shown perhaps) with StrictnessLevel::Loose for open_pdb?
I'm currently in the process of refactoring my code to use this crate and it would be a pity if this excluded the possibility.
I do not remember coding anything anywhere that would prevent B factors or occupancies to be 0.00. I ran some tests and you can totally use atom.set_b_factor() and atom.set_occupancy() to set those properties to 0.0. And the following very minimal PDB file was parsed and saved successfully:
ATOM 2 CA HIS A 465 34.226 -11.294 7.140 1.00 0.00 C
ATOM 3 C HIS A 465 33.549 -10.658 8.347 1.00 0.01 C
ATOM 8 CD2 HIS A 465 35.297 -8.322 5.762 0.00 49.56 C
ATOM 8 CD2 HIS A 465 35.297 -8.322 5.762 0.01 49.56 C
If you have any error messages you could share with me I will dive into it, but otherwise I do not see any problem. Besides that the B factor column is 'misused' quite often for other things then the b factor, so the library should totally support any logical numerical value.
I swear this issue was real... I just ran my code again and it ran through without issue.
Sorry for bothering you about this, I think I should maybe stop for today.