Initial Tasks Layout

[AnirudhG07]

The issue contains the overall layout(with future edits) about the CLI for IMPROVISeD.

General Task overview

• [x] name (name BEPT)
• [x] protein analysis
• [x] cross platform testing
• [x] docs
• [x] publish

Protein analysis

• [x] pdb cleanup code (TBD for all cases)

interactive gen

• [x] pdb2pqr
• [x] apbs

automation

• [x] pdb2pqr
• [x] apbs
• [x] potential gen
• [x] gradient gen

Outputs

• [x] main csv file
• [x] .bept main file

  different file gens

• [x] cube
• [x] xyz

Documentation

• [x] explanation of how we utilise apbs, pdb2pqr
• [x] bio explanation
• [x] guide to use the tool
• [x] cool docs on terminal(optional)

Protein Building

Not to be done

Publish

• [x] Pypi
• [x] homebrew
• [x] Docker
• [x] Source build docs

Further Exploration and Inclusions

• [x] generation of surface maps ( we generated surface residues and potential)

[AnirudhG07]

A brief idea about each of the tasks.

General Overview

These tasks will be ticked when all the sub section tasks mentioned below will be done and tested. Name will be given soon since all code will be around it. Cross-Platform Testing will be done on MacOS, Linux & WSL and probably Windows. Publishing will be done on - Pypi, Homebrew(on my Tap), hopefully Docker image.

Protein Analysis

For interactive, just like the webserver we will let the user make the command and optionally execute, same for apbs. The docs will contain everything about the input file so user can read and easily edit on his own.

the automation part is main part, running the commands with subprocess and generation of potentials, fields and gradients.

The output files will be done by pandas, a main csv and metadata file containing ALL data will be made and different files mentioned above will be made based on how they exist.

Documentation

The documentation will be written in markdown formats, explaining what is the motive, bio, engineering behind our tool. Why this was made and not use pre existing ones. Explanation of various factors like fields, force fields, dilectrics, other metrices, etc. will be explained. Docs on apbs, pdb2pqr usages and examples will be added. Detailed docs on usage and examples of this tool will also be added. Docs on protein building will also be added(if this will be done). And more docs wherever required.

Publishing

Pypi publishing with be done through pyproject.toml and requirements will be updated. Homebrew addition is a piece of cake once Pypi is done. Docker image will look good if made. so anyone can have docker daemon running and run command like one would expect.

[AnirudhG07]

Changes to be done in CLI commands + Additions -

• [x] OUT
  • [x] input PQR and dx with 2 flags, its confusing
  • [x] fix xyz X Y Z data, mistakenly used lattice coords instead of actual
  • [x] add cube
  • [x] fix the potential values you are generating
  • [x] add gradients math documentation
• [x] Gen pdb2pqr in textual
• [x] BioPython works
  • [x] look into surface pdb extraction(naccess has LICENSE issues to directly put)
  • [x] more possible additions
• [x] PyMol Extension
  • [x] give PyMol draft codes for common operations in GitHub
  • [x] Generate them with CLI(optional) - again beginner friendly
• [x] Documentation updates for all of the ABOVE
• [x] add docs in readthedocs.io
• [x] make a cool fun logo? maybe just the text in a colorful way, based on our team logo.

To be done before 2nd October.

[AnirudhG07]

Woohhoo! Done great