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Bnp Conf Dyn
Commits
04225908
Commit
04225908
authored
2 years ago
by
Köhs, Lukas
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Extend README
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README.md
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This is the companion code and experimental data to the paper "Nonparametric Bayesian inference for meta-stable conformational dynamics".
The experimental data on switching ion channels is stored in
`/data/ionchannel/input/+160mV_1min.asc`
.
The experimental data on switching ion channels is stored in
`/data/ionchannel/input/`
;
The MD simulation data on alanine dipeptide is stored in
`/data/alanine_dipeptide/input`
.
The code corresponding to the individual figures is found in
`/exp`
; plots are generated by the code in
`/eval`
. The main model is stored in
`/src`
.
To reproduce the figures in the paper,
1.
generate synthetic data by running the respective
`gen_*`
files in
`/src`
:
1.
`gen_3state_gauss_hmm`
: data for figure 2
2.
`gen_SDE_3well_potential`
: data for figure 3
3.
`gen_angular_data`
: data for figure 4
2.
run the inference method in on this data via the scripts in
`/exp`
:
1.
`3state_synNIW`
: inference for figure 2
2.
`3well_SDE`
: inference for figure 3
3.
`3state_synBvM`
: inference for figure 4
4.
`AlaDipeptide_wrapped_NIW`
: inference for figure 5
5.
`ionchannel`
: inference for figure 6
3.
plot the results via methods in
`/eval`
:
1.
`plot_NIW`
: generates figure 2
2.
`plot_NIW_SDE`
: generates figure 3
3.
`plot_wrapped_NIW`
: generates figure 4
4.
`plot_wrapped_NIW_Ala`
: generates figure 5
5.
`plot_NIW_ionchannel`
: generates figure 6
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