dockposegen-adtgpu 1.0.0

An Automated extraction tool for ligand poses (models) from AutoDock-GPU docking results.

dockposegen

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# [version: 1.0.0]                        |AUTODOCK GPU EDITION|   #
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Automated Ligand Pose Extraction for AutoDock-GPU Results.

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

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dockposegen-adtgpu is the tool specifically re-designed to handle AutoDock-GPU outputs. This version automates the screening of high-throughput docking results, ranking ligands by binding affinity, and extracting optimized coordinates from .dlg and .xml files.

Input Requirements

"Place all .xml and .dlg files into their respective /xml and /dlg directories. If these files are already located in the correctly named folders, no further action is required."

• .xml files

• .dlg files

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

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pip Installation

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

    pip install dockposegen-adtgpu

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Command Line Usage

This edition supports full argument-based execution for automation and pipelines:

    dockposegen-ag --select ALL

Options:

    --select [IDs] : Specific Ligand IDs to extract (space-separated) or ALL.

    -x, --xml : Directory containing .xml files (default: xml).

    -d, --dlg : Directory containing .dlg files (default: dlg).

    -o, --out : Output directory for PDBs (default: ligands).

    -l, --log : Change the default ranking log filename.

    --version : Show current version info.

    --help : Show all available commands.

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Overview

##Step 1: Affinity Screening & Ranking

Input: XML results from the xml/ directory.

Description: The tool parses XML files to find the "Best Run" (lowest binding energy) for every ligand.

Output: A ranked summary file (highest_affinities.log) sorted by kcal/mol.

##Step 2: Selection

Interactive: If run without arguments, the tool displays the Top 10 Candidates and prompts for selection.

Automated: Use the --select flag to process specific hits or the entire library automatically.

##Step 3: Coordinate Extraction

Input: DLG files from the dlg/ directory.

Description: The script extracts the specific coordinates.

Output: Ready-to-use .pdb files in the ligands/ folder.

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#File Structure

xml/: Contains input AutoDock-GPU XML files.

dlg/: Contains input AutoDock-GPU DLG files.

ligands/: Directory where extracted PDB poses are saved.

highest_affinities.log: Ranked list of all processed ligands.

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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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