Nonparametric Bayesian inference for meta-stable conformational dynamics

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/; The MD simulation data on alanine dipeptide is stored in /data/alanine_dipeptide/input.

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