Guillermo Pérez-Hernández
Guillermo Pérez-Hernández
Limit the SASA computation to some atoms of interest via `atom_indices` when calling `md.shrake_rupley` The excluded atoms are still considered as potential surface accessibility blockers, but their own SASA doesn't...
Hi, I've implemented an atom selection option for mdtraj.geometry.sasa here: https://github.com/mdtraj/mdtraj/compare/master...gph82:sasa?expand=1 It allows to include/exclude some atoms from the SASA computation. They excluded atoms are still considered as potential surface...
It would be great to be able to keep adding samples to an object without having to re-compute from scratch. E.g., after having called msm.its with `nsamples=10`, if I want...
Hello! I'm having trouble sorting this one myself, and it might not be even an nglview issue but some jupyter notebook issue. Version report at the bottom of the page....
A little holiday coding for something I had working locally for 3 years and never pushed (#[PR1671](https://github.com/mdtraj/mdtraj/pull/1671) was closed as stale/wontfix). It's been crucial for all my projects all this...
Adds option `scheme="backbone"` for md.compute contacts Adds tests and one test file `backbone.dat` created like this: ``` import mdtraj as md, numpy as np bpti = md.load("tests/data/bpti.pdb") bpti_BB = bpti.atom_slice(bpti.top.select("backbone"))...
Great software! Is there a way to retrieve the alignments as plaintext FASTAs other than retrieving them from the html output? Thanks!