From 04225908b20fcc51d3b5ad59d1ac12951c9b765d Mon Sep 17 00:00:00 2001 From: Lukas Koehs <lukas.koehs@bcs.tu-darmstadt.de> Date: Mon, 14 Mar 2022 13:54:47 +0100 Subject: [PATCH] Extend README --- README.md | 22 ++++++++++++++++++++-- 1 file changed, 20 insertions(+), 2 deletions(-) diff --git a/README.md b/README.md index de1037b..0d86327 100644 --- a/README.md +++ b/README.md @@ -2,6 +2,24 @@ 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 -- GitLab