Metadata-Version: 2.4
Name: mdsa-tools
Version: 0.1.1
Summary: The Weir Labs H-bond Systems Analyses modules!
Author-email: Luis Perez <lperez@wesleyan.edu>
License: MIT
Classifier: Programming Language :: Python :: 3
Classifier: Operating System :: OS Independent
Requires-Python: >=3.7
Description-Content-Type: text/markdown
Requires-Dist: numpy
Requires-Dist: pandas
Requires-Dist: matplotlib
Requires-Dist: seaborn
Requires-Dist: scikit-learn
Requires-Dist: mdtraj==1.10.3
Requires-Dist: umap-learn
Requires-Dist: python-circos

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

![CI](https://img.shields.io/badge/CI-passing-brightgreen)
[![PyPI version](https://img.shields.io/badge/PyPI--version-inactive.svg)]()
[![Anaconda version](https://img.shields.io/badge/Anaconda--version-inactive.svg)]()
![Downloads](https://img.shields.io/badge/downloads-blank-lightgrey)
[![DOI](https://img.shields.io/badge/DOI--blue)]()

## A pipeline for performing systems analyses:
![Alt text](/resources/Pipelineflic.png)

 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.

```bash

##################
#PyPi coming soon#
##################

#At the moment you can pip install directly from our repo
pip install git+https://github.com/zeper-eng/workspace.git

###############
#Alternatively#
###############

# First fork the repository over 
git clone https://github.com/zeper-eng/workspace.git
cd workspace

#Now from inside of the workspace folder simply pip install!

pip install .

#Regardless of the python environment you should be good to go
pip show workspace

```

## Systems Problem Area:

![Alt text](resources/PanelA_summerposter.png)

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.






