AF3Json

A Python utility that converts FASTA sequence files into structured JSON format for protein structure prediction workflows.

Overview

AF3Json parses FASTA formatted protein sequence files and transforms them into a specialized JSON structure that can be used with protein structure prediction tools. The script preserves sequence names from FASTA headers and organizes the data in a consistent format.

Requirements

• Python 3.6 or higher
• No external dependencies required (uses only standard library)

Installation

No installation required. Simply clone or download this repository:

git clone https://github.com/yourusername/AFSJson.git
cd AFSJson

Usage

Basic Usage

python AF3Json.py input.fasta

This will create a file named protein_jobs.json in the current directory.

Advanced Options

python AF3Json.py input.fasta -o custom_output.json

Command-line Arguments

Argument	Description
fasta_file	Path to the input FASTA file (required)
-o, --output	Custom output filename (default: protein_jobs.json)

Output Format

The script generates a JSON file with the following structure:

[
    {
        "name": "protein_identifier",
        "modelSeeds": [],
        "sequences": [
            {
                "proteinChain": {
                    "sequence": "AMINO_ACID_SEQUENCE",
                    "count": 1
                }
            }
        ]
    },
    ...
]

Each entry in the array represents a protein sequence from the input FASTA file.

Error Handling

The script includes robust error handling for common issues:

• Missing input files
• Permission errors
• Empty or malformed FASTA files

Examples

Example 1: Basic Conversion

python AF3Json.py sequences.fasta

Example 2: Custom Output Name

python AF3Json.py sequences.fasta -o prediction_input.json

License

This project is open source and available under the MIT License.

Contributing

Contributions are welcome! Please feel free to submit a Pull Request.