hdbMSM

Contains notebooks used to carry out all the calculations related to the paper Markov state models from hierarchical density based assignment, by Ion Mitxelena, Xabier López and David De Sancho (BioKimika Teorikoa laboratory, UPV-EHU and DIPC).

You can check the preprint for the paper at BioRXiv.

All the trajectories necessary to do the analyses are included here

Requirements to run the notebooks:

1. Python3 (and basic packages: h5py, numpy, matplotlib ...)
2. PyEMMA software package (2.5.7 version)
3. HDBSCAN
4. SKlearn
5. MDTraj