Metadata-Version: 2.1
Name: AMDock
Version: 1.6.2
Summary: AMDock: Assisted Molecular Docking with Autodock4 and Autodock Vina
Home-page: https://github.com/Valdes-Tresanco-MS/AMDock
Author: Mario S. Valdes-Tresanco and Mario E. Valdes-Tresanco 
Author-email: mariosergiovaldes145@gmail.com
Maintainer: Mario S. Valdes-Tresanco
Maintainer-email: mariosergiovaldes145@gmail.com
License: GPLv3
Keywords: AMDock,AutoDock Vina,AutoDock4,AutoDock4Zn,Docking
Platform: UNKNOWN
Description-Content-Type: text/markdown
License-File: LICENSE.txt

# AMDock: **A***ssisted* **M***olecular* **Dock***ing with Autodock4 and Autodock Vina*
AMDock (Assisted Molecular Docking) is a user-friendly graphical tool to assist in the docking of protein-ligand 
complexes using Autodock-Vina or AutoDock4. This tool integrates several external programs for processing docking input 
files, define the search space (box) and perform docking under user’s supervision.

**Version 1.6.x for Linux** (**Build 1.6.1-beta**)

**DOCUMENTATION**

Manual, tutorials and test files are located in **Doc** folder. (May be out of date. Please check the wiki)

**Cite us**

Valdes-Tresanco, M.S., Valdes-Tresanco, M.E., Valiente, P.A. and Moreno E. AMDock: a versatile graphical tool for
 assisting molecular docking with Autodock Vina and Autodock4. Biol Direct 15, 12 (2020). https://doi.org/10.1186/s13062-020-00267-2
 
 <a href="https://www.scimagojr.com/journalsearch.php?q=5800173376&amp;tip=sid&amp;exact=no" title="SCImago Journal &amp; Country Rank"><img border="0" src="https://www.scimagojr.com/journal_img.php?id=5800173376" alt="SCImago Journal &amp; Country Rank"  /></a>

**INSTALL**

Installation can be carried out in two ways
1. (For Linux only) Using a conda environment. 

Note: macOS users can use this procedure, however, PyMOL must be compiled using this environment's Python interpreter, 
since there is no working version of PyMOL for mac in the anaconda repositories. 

To do this, proceed as follows:

If you don't have conda installed, please visit the [Miniconda download page](https://docs.conda.io/en/latest/miniconda.html).

Those with an existing conda installation may wish to create a new conda "environment" to avoid conflicts with what 
you already have installed. To do this:

    conda create --name AMDock
    conda activate AMDock

(Note that you would need to perform the "conda activate" step every time you wish to use AMDock in a new terminal; 
  it might be appropriate to add this to your start-up script. Creating a new environment should not be necessary if 
  you only use conda for AMDock.)

Once this is done, type:

    conda install -c conda-forge pymol-open-source openbabel pdb2pqr

and finally: 

    python -m pip install git+https://github.com/Valdes-Tresanco-MS/AutoDockTools_py3
    python -m pip install AMDock

2. Using the OS Python 3 environment. To do this, proceed as follows:

    
    sudo apt install pymol openbabel

(Note that this version of AMDock works with openbabel 3.x)

    python3 -m pip install pdb2pqr
    python3 -m pip install git+https://github.com/Valdes-Tresanco-MS/AutoDockTools_py3
    python3 -m pip install AMDock
    
Before using AMDock, you most install the PyMOL plugin (grid_amdock.py).

If it does not appear please follow the instructions:
- Download the grid_amdock.py file
- Open PyMOL > Plugins > Manager Plugins > Install New Plugin > Choose File and select the grid_amdock.py file
- Restart PyMOL


To open AMDock, type in the terminal:
    
    AMDock

For macOS users, 


To view the update history, please check Changes_History file

**TUTORIALS**

Please, check the wiki https://github.com/Valdes-Tresanco-MS/AMDock-win/wiki

[<img src="./AMDock/AMDock/images/jetbrains-variant-4.png" height="100" align="right" />](https://www.jetbrains.com/?from=https://github.com/Valdes-Tresanco-MS/AMDock)

## Support
This project is possible thanks to the Open Source license of the 
[JetBrains](https://www.jetbrains.com/?from=https://github.com/Valdes-Tresanco-MS/AMDock
) programs.


