proteinspy 1.1.1

A CLI tool and Python library to analyse protein structures from .cif and .pdb files

Proteinspy

This is a python package based on Poetry.

This repository can be used to find the Resolution, Missing residues, Ligands, and Chains in any Protein sample uploaded. The sample must be in a .cif file format for the package to run properly.

🔋 Installation

pip install proteinspy

Windows note

If proteinspy is not recognized after installation, add the Python Scripts folder to your PATH. Run this once in PowerShell:

$env:PATH += ";$env:APPDATA\Python\Python313\Scripts"
[System.Environment]::SetEnvironmentVariable("PATH", $env:PATH, "User")

Then restart PowerShell and run proteinspy again.

💡 Getting Started

After installation, run this first to see all available commands:

proteinspy

Or use the help flag:

proteinspy --help

📚 Data

A sample protein, has been given, and can also be accessed from the PDB, among many other samples.

🗒️ Requirements

• python poetry and its pre-requisites (Python 3.9+ and pip).
• Dependencies installed automatically: gemmi, rich, click

🚀 To run the pipeline,

Copy these and run them directly for quickest results.

1. For a mode based implementation

proteinspy analyze 10AJ.cif    #replace the protein input name with your own file if you're using a different input or a filename

2. For an argument based implementation

proteinspy resolution 10AJ.cif    #gives the resolution of the protein
proteinspy ligands 10AJ.cif       #gives the ligands in the protein
proteinspy missing 10AJ.cif       #gives the missing residues in the protein
proteinspy chains 10AJ.cif        #gives the chains in the protein

🟥 Note: swap the file name if you are using your own file

💻 Commands

Format: proteinspy <command> <file.cif>

Command	Description
proteinspy analyze	Run all analyses — resolution, chains, ligands, missing residues
proteinspy resolution	Report crystallographic resolution only
proteinspy chains	Report all polymer chains only
proteinspy ligands	Report all ligand molecules only
proteinspy missing	Report all missing residues only

📈 Future Enhancements

• CLI UI/UX
• Containerisation, using docker

⚠️ NOTE

This is an open-source project, and any contributions, even if not mentioned in the future enhancements section, are welcome.

📃 Documentation

Full documentation at https://akhilteja2209.github.io/Proteinspy/

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Version: 1.0.2