deeptime
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deeptime-ml
Python library for analysis of time series data including dimensionality reduction, clustering, and Markov model estimation
**Is your feature request related to a problem? Please describe.** The `TICA` and `VAMP` decomposition classes both provide similar interfaces for `.fit_from_timeseries(data)`. However, the `TICA` class allows a `weights` argument....
Probably best through a combination of nox and pipelines.
Hi, I have been exploring the documentation of Deeptime and I haven't found any example for dealing with MD trajectories from common packages like AMBER, GROMACS, NAMD, etc. PyEMMA was...
when I installed deeptime via conda or mamba, my computer shows that: ```shell $ conda install -c conda-forge deeptime Collecting package metadata (current_repodata.json): done Solving environment: failed with initial frozen...
Dear all, I was having a look at the code for VampNets that is in deeptime, and it seems that it is the one from _mardt2018vampnets_, right? Thus, it does...
Hi, I'm currently trying to install the deeptime for the project of investigating conformation kinetics of an ion channel. But I encounter problems when trying to install it. Since I...
`bayesian_hmm.gather_stats('transition_model/mfpt', A=[hmm.prior.metastable_sets[1]], B=hmm.prior.metastable_sets[1]).mean` After executing the above code it gives me error: `ValueError: Chosen set contains states that are not included in the active set.` I don't know how to...
In the original paper, it is stated: "Another advantage of the VAMP-E based validation score is that it does not involve any inverse operation of matrices and can be stably...
We extended the MSM estimator class, such that the transition counts are reweighted according to the reweighting factor trajectory. Joana-Lysiane Schäfer, Bettina G. Keller, Implementation of Girsanov reweighting in OpenMM...
This pull request adds a Jupyter Notebook tutorial (`md_trajectory_tutorial.ipynb`) demonstrating how to analyze molecular dynamics (MD) trajectories using Deeptime library. The tutorial covers loading trajectories, performing Time-lagged Independent Component Analysis...
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Python library for analysis of time series data including dimensionality reduction, clustering, and Markov model estimation