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Currently, `pyemma.msm.MSM(P)` does not support a disconnected transition matrix `P` as input. Enabling this feature would be tremendously helpful for the TRAM-related classes where we have multiple t…
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Several questions accompany this issue, @khalifenizar.
How does the quantum description of reality, which includes elements such as the superposition of states and wavefunction collapse or quantum de…
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We currently use numpy.ndarrays with shape=(T, M, M) for dense count matrices. Scipy.sparse unfortunately supports only 2D matrices.
We could replace the 3D structure by a list of sparse 2D matrices …
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The documentation for MBAR strenuously points out the need for uncorrelated input configurations. I am only interested in unbiased estimates of observables for many simulations and do not need to mea…
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--- Proposed Terms ----
response to misfolded protein
misfolded protein binding
--- Proposed Locations ----
Biological_Response
GO:0006950: response to stress
> GO:*******: response to misf…
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I think we _should_ be able to use logging to control the verbosity level without having to pass around `verbose` arguments everywhere.
It might be possible to make this work with MPI as well: https:…
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The Debye model for heat capacity developed by S+LB is great for a lot of simple materials. For others, landau-type transitions lead to spikes in heat capacity (particularly at low temperatures), and …
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General question--how should topology proposals be organized, and how should they be matched with `System` construction?
Currently, under the small molecule scheme, there is:
- `Transformation`
- `…
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We have a decent skeleton of the functions we want from #250, but I have a few questions to check details of how some things should be implemented. In particular, I'm hoping @jchodera and/or @bolhuis …
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Hi, I was able to install python-refprop on my Mac using my purchased copy of RP.
However, when I try to run the example, it fails when executing settest:
import refprop as rp
## rptest.settest('m…