Command Line Interface¶
Our Python package not only provides a powerful Markov state modeling framework for analyzing biomolecular dynamics simulations, but it also includes a command line interface for incorporating key tasks into your bash pipelines. With our CLI, users can easily integrate our package into their workflow, streamlining the analysis process and increasing efficiency.
In addition, our package includes powerful tools for generating publication-ready figures, making it easy for users to create visually stunning and informative data visualizations for their research papers and presentations.
To get an overview over all modules simply run the following command in the shell, or take a look at the reference documentation.
%%bash
python -m msmhelper
Usage: python -m msmhelper [OPTIONS] COMMAND [ARGS]...
msmhelper v1.1.1
Unlock the power of protein dynamics time series with Markov state modeling,
by simplifying scientific analysis.
Copyright (c) 2019-2023, Daniel Nagel
Options:
--help Show this message and exit.
Commands:
ck-test Estimation and visualization of the...
compare-discretization Similarity measure of two different state...
contact-rep Contact representation of states.
dynamical-coring Applying dynamical coring on state trajectory.
gaussian-filtering Applying gaussian filter on time series.
implied-timescales Estimation and visualization of the implied...
waiting-time-dist Estimation and visualization of the waiting...
waiting-times Estimation and visualization of the waiting times.
Further, every submodule gives detailed help, simply run
%%bash
python -m msmhelper ck-test
Usage: python -m msmhelper ck-test [OPTIONS]
Estimation and visualization of the Chapman-Kolmogorov test.
Options:
-f, --filename PATH Path to state trajectory file (single column
ascii file). [required]
--microfilename PATH Path to microstate trajectory file (single
column ascii file) to use Hummer-Szabo
projection.
-c, --concat-limits PATH Path to concatination limit file given the
length of all trajectories, e.g. "3\n3\n5"
-o, --output PATH Output basename of figure. Needs to have a
valid extension (".pdf", ".svg", ".png").
Default format is pdf.
--lagtimes INTEGER RANGE... 5 (!) Lag times given in frames to estimate
Markov state model. [x>=1; required]
--frames-per-unit FLOAT Number of frames per unit. [required]
--unit [fs|ps|ns|us|frames] Unit of data. [required]
--grid INTEGER RANGE... Number of rows and cols. [x>=1]
--max-time INTEGER RANGE Largest time value to evaluate and plot the
test. [x>=1]
--help Show this message and exit.
A simple example of an Chapman-Kolmogorov test produced with a 4 state toy model.