ADCP Refinement Docker Image

This repository contains a Dockerfile for creating a containerized environment to run the Refinment_test_docker.py script. The script is used for protein docking refinement and analysis.

Features

• Miniconda: Provides a Python environment with Conda package management.
• Installed Packages:
  • pandas, biopython, openpyxl (via pip)
  • pymol-bundle (via Conda)
• Environment Variables:
  • PATH: Includes Miniconda and ADFR tools.
• Default Directories:
  • /app/predictions: Input predictions directory.
  • /app/output: Output directory for results.

Usage

Build the Docker Image

To build the Docker image, run:

docker build -t adcp_refinement:v1 .

Run the Docker Container

To run the container with default arguments:

docker run -v /path/to/output:/app/output \
           -v /path/to/predictions:/app/predictions \
           -v /path/to/score_file.xlsx:/app/DockQ/score_file.xlsx \
           adcp_refinement:v1

Explanation of Arguments

• --predictions_dir: Path to the directory containing structure prediction files.
• --output_dir: Path to the directory where output files will be saved (split, docked, and combined).
• --score_file: Path to the Excel file containing DockQ scores of the predicted structures.
• --cutoff: Cutoff category for filtering scores (1, 2, 3, or 4).

The default parameters are defined in the Refinment_test_docker.py. They are:

• --predictions_dir /app/predictions
• --output_dir /app/output
• --score_file /app/DockQ/DockQ_Score.xlsx
• --cutoff 1

Override Default Arguments

You can override the default arguments by passing them to the docker run command. For example:

docker run -v /path/to/output:/app/output \
           -v /path/to/predictions:/app/predictions \
           -v /path/to/score_file.xlsx:/app/DockQ \
           adcp_refinement:v1 --cutoff 2

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Using Docker Compose

You can also use the docker-compose.yml file to simplify running the container. This file defines the necessary volumes and arguments for the container.

Example docker-compose.yml

services:
  adcp_refinement:
    image: refinment:v1
    container_name: adcp_refinement
    volumes:
      - /path/to/predictions:/app/predictions
      - /path/to/output:/app/output
      - /path/to/score_file.xlsx:/app/DockQ/DockQ_Score.xlsx
    command: >
      --score_file /app/DockQ/DockQ_Score.xlsx
      --output_dir /app/output
      --predictions_dir /app/predictions
      --cutoff 1

Run the Container with Docker Compose

To run the container using Docker Compose:

1. Ensure the docker-compose.yml file is in the same directory.
2. Run the following command:

   docker-compose up

Stop the Container

To stop the container, run:

docker-compose down

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Notes

• Ensure that the required input files and directories are correctly mapped using the -v flag or in the docker-compose.yml file.
• Values of cutoff:
  • 1: 0 <= DockQ > 0.230
  • 2: 0.230 <= DockQ > 0.490
  • 3: 0.490 <= DockQ > 0.800
  • 4: 0.800 <= DockQ > 1.000
• If the volume for which the path was defined does not exist on the host machine, the Docker image will create the desired directory upon running.