mdsa-tools 1.0.0

The Weir Labs H-bond Systems Analyses modules!

mdsa-tools: A set of tools for performing systems analyses of Molecular Dynamics (MD) simulations.

A pipeline for performing systems analyses:

Pictured is a directed graph describing the pipeline for our MD trajectory analysis. From left to right, we begin with a trajectory file, and convert it into a set of networks (one for each trajectory frame), which that can be represented as either graphs or adjacency matrices. Each frame adjacency is flattened into a vector by concatenating the matrix’s rows (vector reduction). The frame vectors are vertically concatenated to create a feature matrix that can be used as input to either K-means clustering or PCA, whose results can then be visualized using graphs, scatter plots, MDCcircos plots, (of residue H-bonding), or MD replicate maps of frame measurements of interest.

We also provide an additional module for taking theese various results and using clustering results as input substates for markov state model analyses.

Use pip install to get started:

pip install mdsa-tools

Quickstart example:

from mdsa_tools.Data_gen_hbond import trajectory as traj
import numpy as np
import os

#########################################
#In house test with our own trajectories#
#########################################

#load in and test trajectory
system_one_topology = '/Users/luis/Desktop/workspace/PDBs/5JUP_N2_CGU_nowat.prmtop'
system_one_trajectory = '/Users/luis/Desktop/workspace/PDBs/CCU_CGU_10frames.mdcrd' 

system_two_topology = '/Users/luis/Desktop/workspace/PDBs/5JUP_N2_GCU_nowat.prmtop'
system_two_trajectory = '/Users/luis/Desktop/workspace/PDBs/CCU_GCU_10frames.mdcrd' 

test_trajectory_one = traj(trajectory_path=system_one_trajectory,topology_path=system_one_topology)
test_trajectory_two = traj(trajectory_path=system_two_trajectory,topology_path=system_two_topology)


#now that its loaded in try to make object
test_system_one_ = test_trajectory_one.create_system_representations()
test_system_two_ = test_trajectory_two.create_system_representations()

np.save('/Users/luis/Desktop/workspacetwo/example_systems/test_system_one',test_system_one_)
np.save('/Users/luis/Desktop/workspacetwo/example_systems/test_system_two',test_system_two_)

#########
#
#########

Systems Problem Area:

At the Weir Lab at Wesleyan University, we perform molecular dynamics (MD) simulations of a ribosomal subsystem to study tuning of protein translation by the CAR interaction surface- a ribosomal interface identified by the lab that interacts with the +1 codon (poised to enter the ribosome A site). Our "computational genetics" research focuses on modifying adjacent codon identities at the A-site and the +1 positions to model how changes at these sites influence the behavior of the CAR surface and corellate with translation rate variations.