https://github.com/moldyn/hp35-benchmark
Benchmarking dimensionality reduction methods and clustering on HP35-DESRES
https://github.com/moldyn/hp35-benchmark
Last synced: over 1 year ago
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Benchmarking dimensionality reduction methods and clustering on HP35-DESRES
- Host: GitHub
- URL: https://github.com/moldyn/hp35-benchmark
- Owner: moldyn
- License: bsd-3-clause
- Created: 2020-02-18T10:04:23.000Z (over 6 years ago)
- Default Branch: master
- Last Pushed: 2022-08-05T06:50:12.000Z (almost 4 years ago)
- Last Synced: 2025-02-12T19:45:47.799Z (over 1 year ago)
- Language: Shell
- Size: 29.3 KB
- Stars: 1
- Watchers: 2
- Forks: 0
- Open Issues: 0
-
Metadata Files:
- Readme: README.md
- License: LICENSE
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# HP35-Benchmark
Benchmarking dimensionality reduction methods and clustering on [HP35-DESRES](https://github.com/moldyn/HP35-DESRES).
This is package automatizes the comparison of different clustring and dimensionality reduction methods and its effects on the resulting Markov state models. So far, only the result of Nagel et al. 19 are reproduced. Comparison methods will follow soon.
If the provided scripts are used, please cite:
- D. Nagel, A. Weber, B. Lickert and G. Stock, *Dynamical coring of Markov state models*, J. Chem. Phys., 150, 094111, 2019; DOI: [10.1063/1.5081767](https://aip.scitation.org/doi/10.1063/1.5081767)
## Getting ready
Simply clone this repository with
```bash
git clone --recurse-submodules git://github.com/moldyn/HP35-Benchmark.git
cd HP35-Benchmark
```
Reproducing the published state trajectory can be achieved with
```bash
cd clustering && bash robust_clustering
```
Until our python package [msmhelper](https://moldyn.github.io/msmhelper) is available, the states are not renamed by their population.
## Add Own Routine
For an example take a look at [robust_clustering](https://github.com/moldyn/HP35-Benchmark/blob/master/clustering/robust_clustering)