MDPath — MD signal transduction calculation and visualization — mdapth.mdpath

MDPath is a Python package for calculating signal transduction paths in molecular dynamics (MD) simulations. The package uses mutual information to identify connections between residue movements. Using a graph shortest paths with the highest mutual information are calculated. Paths are then clustered based on the overlap between them to identify a continuous network throught the analysed protein. The package also includes functionalitys for the visualization of results.

Release under the MIT License. See LICENSE for details.

This is the main script of MDPath. It is used to run MDPath from the command line. MDPath can be called from the comadline using ‘mdapth’ after instalation Use the -h flag to see the available options.

Functions

mdpath.mdpath.main()

Main function for running MDPath from the command line. It can be called using ‘mdpath’ after installation.

Command-line inputs:

-top: Topology file of your MD simulation

-traj: Trajectory file of your MD simulation

-cpu: Amount of cores used in multiprocessing (default: half of available cores)

-lig: Protein ligand interacting residues (default: False)

-bs: How often bootstrapping should be performed (default: False)

-fardist: Default distance for faraway residues (default: 12.0)

-closedist: Default distance for close residues (default: 12.0)

-graphdist: Default distance for residues making up the graph (default: 5.0)

-numpath: Default number of top paths considered for clustering (default: 500)