Workflow for validation of rings' conformation in ligands

Description

This repository contains the software workflow from the article by Bučeková et al. Analysis of cyclopentane, cyclohexane and benzene conformations in ligands for PDB x-ray structures that has been submitted to the Journal of Cheminformatics.

Prerequisites

• Python 3.12.3 available in the PATH environment
  • a binary installer is available from [here](https://www.python.org/downloads/release/python-3123/
• Mono 6.12.0.200 or newer (non-Windows operating systems only)
  • installation instructions are available [here](https://www.mono-project.com/download/stable
• git (or a compatible alternative) (only if you wish to clone the workflow's repository)
• 1 TB of free space for input and output 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:

      python3 -m venv .venv
     

   • Activate the virtual environment:

      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 Scipy==1.15.2 Numpy==2.1.3 Numba==0.61.0 Biopython==1.85
     

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:

   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:

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.