Metadata-Version: 2.4
Name: mdsa-tools
Version: 1.0.0
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: >=3.9
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.

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## A pipeline for performing systems analyses:
![Pipeline](https://raw.githubusercontent.com/zeper-eng/workspace/main/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

pip install mdsa-tools

```

## Quickstart example:
```python
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:

![System panel](https://raw.githubusercontent.com/zeper-eng/workspace/main/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.






