dockposegen 1.0.0

A Tool for Ligands pose extraction and Complex Building Workflow

dockposegen

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(version: 1.0.0)

Ligand Pose Extraction and Complex Assembly Workflow.

For more tools visit: https://github.com/alpha-horizon

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dockposegen is a specialized tool designed to automate the post-processing of molecular docking results. It extracts individual conformations (poses) from AutoDock Vina pdbqt outputs and merges them with a receptor protein to create ready-to-use receptor-ligand complex PDB files.

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Input Requirements

• Receptor: A file named receptor.pdb in the root directory.

• Docking Results: All *_out.pdbqt files should be placed in the out_pdbqt/ folder.

  Note: These are the standard output files generated by AutoDock Vina or AutoDock.

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pip Installation

To install dockposegen, you can use the command mentioned below.

    pip install dockposegen

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Command Line Usage

To run the workflow from the command line, use:

    dockposegen

Options:

    dockposegen --version  
    dockposegen --help

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Overview

This Python script automates the process of generating Ligand poses and ligand-receptor complexes. The workflow involves several steps:

1. PDBQT to PDB Conversion: Extracts individual poses from PDBQT files and saves them as PDB files.
2. Ligands List Generation: Creates a list of ligand IDs from the generated ligand poses.
3. User Ligand Selection: Prompts the user to select ligands based on the generated list.
4. Complex Creation: Combines receptor PDB and selected ligand poses to create ligand-receptor complexes.

Workflow Steps

Step 1: PDBQT to PDB (Pose Extraction)

• Input: Files from out_pdbqt directory (e.g., *_out.pdbqt).
• Output: PDB files for each pose in the ligand_poses directory.
• Description: For each PDBQT file, individual ligand poses are extracted and saved as separate PDB files.

Log: A log file (pose_generation.log) tracks how many poses are generated for each ligand.

Step 2: Ligand ID List Generation

• Input: Ligand pose directories from ligand_poses.
• Output: A text file (ligands_catalog.txt) with one ligand ID per line.
• Description: The script scans the ligand poses directory and creates a list of ligand IDs (from directory names).

Step 3: User Ligand Selection

• Input: ligands_catalog.txt.
• Output: User-selected ligand IDs.
• Description: Prompts the user to enter one or more ligand IDs for processing.

Step 4: Ligand-Receptor Complex Creation

• Input: Receptor PDB (receptor.pdb), selected ligand poses (from the ligand_poses folder).
• Output: PDB files for each ligand-receptor complex in the complexes directory.
• Description: For each selected ligand ID, the script combines each ligand pose with the receptor and writes the resulting complex to a PDB file.

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File Structure

• out_pdbqt/: Contains input PDBQT files. (file name ends with *_out.pdbqt)
• ligand_poses/: Directory where ligand pose PDB files are saved.
• complexes/: Directory where ligand-receptor complexes are saved.
• ligands_catalog.txt: Contains a list of ligand(s) name(s).
• pose_generation.log: Log of the pose extraction process.
• receptor.pdb: Your receptor in .pdb format.

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Contribution

For more tools or to report issues, visit the official GitHub repository:

GitHub: https://github.com/alpha-horizon

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