Post-Simulation Trajectory Analysis
The scripts described below are used to perform all post-simulation analysis
and create the figures in our papers. Short descriptions
of each script are given below. Generally all of the scripts can be run from
the command line by passing arguments. Click on them to learn more about what
they do, the classes and functions that can be borrowed from them, and how to
run them from the command line.
Structural Analysis LLC_Membranes.analysis
| Script Name |
Description |
|---|
| p2p.py |
Calculate the average distance between pore centers |
| rdf.py |
Calculate radial distribution function of a residue with
respect to pore centers |
| correlation_function.py |
Calculate the correlation function of a residue or part
of a residue along an axis |
Non-covalent Interactions LLC_Membranes.analysis
Time Series Analysis LLC_Membranes.timeseries
| Script Name |
Description |
|---|
| msd.py |
Calculate the mean squared displacement and, optionally, the diffusion
coefficient of a residue. |
| coordinate_trace.py |
Track z-coordinate of a residue center of mass along with its radial
position with respect to the pore center |
| ctrwsim.py |
Simulate realizations of a continuous time random walk |
| sfbm_parameters.py |
Fit parameters assuming a solute undergoes subordinated fractional
Brownian motion |
| forecast_ctrw.py |
Fit a correlated continuous time random walk to residue trajectory data |
| fractional_levy_motion.py |
Simulate realizations of fractional Levy motion |
Machine Learning Approaches to Transport Characterization LLC_Membranes.machine_learning