Workflow for validation of rings' conformation in ligands

Description

This repository contains software workflow from the article by Bučeková et al. If you found this workflow, or any of its parts, to be useful, please cite the following article:

BUČEKOVÁ Gabriela, Viktoriia DOSHCHENKO, Aliaksei CHARESHNEU, Jana PORUBSKÁ, Michal PAJTINKA, Michal OLEKSIK, Tomáš SVOBODA, Vladimír HORSKÝ, and Radka SVOBODOVÁ. Rare ring conformations in PDB: Facts or wishful thinking? bioRχiv, 2024. Available from: https://doi.org/10.1101/2024.06.20.598822

Prerequisites

• Python 3.12.3 available in the PATH environment
  • a binary installer is available from here
• .NET 4.0 or newer (Windows only)
• Mono 6.12.0.200 or newer (non-Windows operating systems only)
  • installation instructions are available here
• git (or a compatible alternative) (only if you wish to clone the workflow's repository)
• 600 GB of free space for input data

Getting Started

1. Clone the Project Repository (Recommended):

   • Open a terminal or a command prompt.
   • Navigate to the directory where you want to clone the project.
   • Run:

     git clone https://github.com/sb-ncbr/rings-conformation-validation.git
     

   • Navigate into the cloned project directory:

     cd rings-conformation-validation
     

   Alternative: Download the workflow repository as a ZIP archive:

   • If you're not familiar with Git or GitHub, you can download the whole workflow repository as a ZIP archive from here.
   • Once downloaded, extract the ZIP archive to a directory on your computer.
   • Open a terminal or a command prompt inside the project directory (rings-conformation-validation).

2. Set up Virtual Environment (Optional but Recommended):

   • Create a virtual environment named .venv:
     • Windows Command Prompt:

       python -m venv .venv
       

     • Windows Git Bash / Windows WSL / macOS / Linux:

       python3 -m venv .venv
       

   • Activate the virtual environment:
     • Windows Command Prompt:

       .venv\Scripts\activate
       

     • Windows Git Bash / Windows WSL / macOS / Linux:

       source .venv/bin/activate
       

3. Install Required Packages:

   • Make sure your virtual environment is activated.
   • Run:

     pip install gemmi==0.6.5 pandas==2.2.2 xlsxwriter requests==2.32.3
     
     

Executing the workflow

1. Create or choose a directory where the input data will be downloaded (e.g. user_input_dir).
2. Create or choose a directory where the output of the workflow will be stored (e.g. user_output_dir).
3. Make sure you are in the project root directory (rings-conformation-validation).
4. Execute the workflow:
   • Windows:

      run_workflow.bat user_input_dir user_output_dir
     

   • Linux:

      bash run_workflow.sh user_input_dir user_output_dir
     

Using a small dataset to test the workflow

If you want to test the workflow on a small dataset, execute the workflow in the same way as described earlier, but add the -testing switch in step 4. With the switch, the workflow execution commands are:

• Windows

   run_workflow.bat -testing user_input_dir user_output_dir
  

• Linux:

   bash run_workflow.sh -testing user_input_dir user_output_dir
  

License

This project is licensed under the MIT License - see the LICENSE file for details.