-
We've taken a few steps toward making `ForceField` more functional for general use cases, but we need to go a bit further to support small molecules and many standard applications.
I'll start by layi…
-
``` python
>>> hmm = msm.coarse_grain(4)
>>> hmm.transition_matrix
array([[ 1., 0., 0., 0.],
[ 0., 1., 0., 0.],
[ 0., 0., 1., 0.],
[ 0., 0., 0., 1.]])
>>> hmm.station…
-
Add a check in coarse_grain() to catch this ? (or maybe do it at higher level to avoid exceptions in highly-repeated code).
-
Analyzing here the dataset as is in the `munged-with-time` right now - some quick notes I made on trajectory lengths:
```
That’s 969 clones active, 3920256 frames total, /4: 980.064 microseconds.
…
-
Discussion of this issue originally began on #385.
`ResidueGroup` and `SegmentGroup` are subclasses of `AtomGroup`, and for properties including `resids`, `resnums`, and `segids` they each yield arra…
-
PyEMMA version: 2.1rc2
bhmm version: 0.6.1
Executed code:
``` python
import pyemma.msm as msm
import numpy as np
dtrajs = np.random.randint(0, 4, 100)
M = msm.estimate_markov_model(dtrajs, 1)
print …
-
https://particle-analytics.gitbooks.io/particle-analytics-documentation/content/manual/post/post_view_coarse_graining.html contains the following ...
> NOTE:
> - Explain something about the Integral …
-
We currently interpolate images by mapping the raw data into RGB, then interpolate that RGB (using any number of algorithms) to produce the final result. This can result in colors that don't actually…
-
https://particle-analytics.gitbooks.io/particle-analytics-documentation/content/manual/post/post_view_coarse_graining.html says
> "The output file can load the particles in the Load post-process fil…
-
We have
> Export current result
> This option exports, in a plain text format, a chosen component of the result currently selected, for
> each node in the coarse-graining mesh, for the current times…