dockposegen-adtgpu 1.0.0
An Automated extraction tool for ligand poses (models) from AutoDock-GPU docking results.
License: MIT
Requires Python: >=3.7

# dockposegen

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<h1 style="font-weight:800; font-size:1.7em;">
  Automated Ligand Pose Extraction for AutoDock-GPU Results.
</h1>

  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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