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Make sure the generic ews workflow is documented the following functions should have their respective roxygen comments:
- [x] generic_spews (main function)
- [x] plot methods
- [x] indictest.generic…
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## System
* Pymatgen version: 2017.06.08
* Python version: 3.6.1
* OS version: macOS 10.12.5
## Summary
Reading a CHGCAR and then writing that same CHGCAR results in a CHGCAR that can not b…
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I have sequenced 66 samples.
Running breseq on each sample against the same reference genome.
On 50 samples it works. On 16 samples it fails at the same step.
Heres the output from terminal for 1 of …
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Having chromosome names which are longer than 32 characters leads to hard to detect problems in downstream analysis. When running `cooler coarsegrain`, the chromosome names that are obtained from the…
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I am working on the fusion and integration of polymer melts, where thermal diffusion closely couples with molecular dynamics. Coarse-grain (CG) molecular dynamics simulations are useful to get insight…
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There seems to be typo error in API.py here right?
import Markov_Models
File "C:\Users\Allan\Anaconda2\lib\site-packages\markov_models-0.1-py2.7-win-amd64.egg\Markov_Models\api.py", line 11
def M…
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Implement the coarse graining procedure. Allow the user to specify the partitioning.
```
f = GaloisField(2, 4, [1, 1, 0, 1])
mt = MUBs(f)
coarse_mt = CGMUBs(mt, 4, 2) # Go from F16 down to F4 x F4
`…
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If I ask for lots of macrostates (7 in this case) from PCCA I sometimes get less macrostates back which is ok.
```python
In [40]: set(model.msm.metastable_assignments)
Out[40]: {0, 1, 5, 6}
```
…
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With so many changes to the game since the last major overhaul, research choices and priorities need to be checked and adapted.
If you notice weird behaviour or have general ideas on how to improve t…
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My aim is to probe the rates of folding and unfolding for a given protein. In order to do that, I have a set of trajectories which are not necessarily equilibrated, and run at different temperatures. …