Add simulation extraction and viewing notebook #226
Conversation
|
Check out this pull request on See visual diffs & provide feedback on Jupyter Notebooks. Powered by ReviewNB |
|
|
| @@ -0,0 +1,316 @@ | |||
| { | |||
There was a problem hiding this comment.
We should make it clear here what Protocols this applies to, i.e. this is for HybridTop mostly (i.e. the tempfactor stuff is hybridtop only) but also applies for the most part to ABFEs, AHFEs, and SepTop.
Reply via ReviewNB
| @@ -0,0 +1,316 @@ | |||
| { | |||
There was a problem hiding this comment.
Try adding the -nc or --no-clobber argument to wget? That way you won't double download the file.
Also this is a big nc file but the hybrid system doesn't include water. Would it be worth pulling down one of the smaller NC files? (I think we have newer generated ones?)
Reply via ReviewNB
| @@ -0,0 +1,316 @@ | |||
| { | |||
There was a problem hiding this comment.
I'm not sure that the image will show up in the final html render. Can we embed the image somehow? I know that was done in the MDAnalysis UserGuide.
Reply via ReviewNB
| @@ -0,0 +1,316 @@ | |||
| { | |||
There was a problem hiding this comment.
Line #3. state_atoms = np.array([atom.ix for atom in u_0.atoms if atom.bfactor in (bfactor, 0.5, 0.0)])
Couple of things:
- bfactor is deprecated, use tempfactor
- you can simplify this and the next line (and probably speed things up) by using fancy indexing:
ag = sum([u.atoms[u.atoms.tempfactors == i] for i in (0, 0.25, 0.5)])
Reply via ReviewNB
| @@ -0,0 +1,316 @@ | |||
| { | |||
There was a problem hiding this comment.
I'm thinking, in MDAnalysis, it might be easy enough to align the trajectory to the coordinates of the PDB file and write that out. That's technically "centering" for free.
Also I'd be happy with merging this as-is, but opening a separate issue to try to make an MDAnalysis-only solution work. I'm sure it's doable, just needs the right set of transformations.
Reply via ReviewNB
Co-authored-by: Alyssa Travitz <31974495+atravitz@users.noreply.github.com>
Fixes #223