ChopraLab Computational Utilities

Overview

Welcome to the Chopra Lab utilities repository. This repo contains information on commonly used data-parsing, cheminformatic, bioinformatic, machine learning, and other utility scripts. The scripts are generalized and all runtime parameters are specified as runtime arguments unless stated otherwise. Check the List of Utilities section below to see what utilities are available and check the Submission Instructions for instruction on how to submit your own utility to the repo.

List of Utilities

Auto_Mine_PubChem - Automated Mining of PubChem Database using RESTful API (PUG REST)

Auto_Psi4_Energy_Cal - Automated Quantum Mechanical (QM) Calculations Using Psi4

Auto_Mine_Uniprot - Automated Mining of FASTA Information from the UniProt Database

Submission Instructions

1. Clone the repository to your own personal machine
2. If you plan for the utility to be a work in progress, it is suggested that you create a new branch
   • git checkout -b [branch_name]
3. Create a new folder in the base directory
4. Add your scripts to the new folder
5. Create a README in the new folder and describe your scripts and how to use them
6. Create a .gitignore in the new folder if you want to ignore any files
   • Please use this to ignore any testing files/scripts
   • Do Not create a global .gitignore file as this can affect other files in other script folders
7. Update the README in the base directory by adding the appropriate information under the List of Utilities section
8. Regardless of the branch you are working on (master or [branch_name]) you will need to run the following:
   • git add .
   • git commit
   • git push origin [branch_name]
9. If you are working on a seperate branch you will need to run the above commands in addition to the following to merge to master:
   • git checkout master
   • git pull origin master
   • git merge [branch_name]
   • Resolve any conflicts present
   • git push origin master