Ultra-Fast Contacts Calculation (UFCC)

The Ultra-Fast Contact Calculation (UFCC) tool calculates the distance-based contacts between two references from molecular dynamics simulations. This release of ufcc is done as a concept test covering only the analysis of lipid-protein interactions on the framework of the Canadian Chemistry Conference and Exhibition 2022, but is aimed also to include other types of interactions in the future (i.e. protein-protein, protein-ligand, and membrane-ligand interactions).

Installation

To install ufcc we recommend creating a new conda environment as follows:

   conda create -n ufcc python=3.7 #(or higher)
   conda activate ufcc

Then you can install ufcc via pip:

   pip install ufcc

Basic example:

For serial contacts calculation:

   from ufcc import UFCC

   target_system = UFCC('coordinates.gro', 'trajectory.xtc') 

   target_system.contacts.compute()
   target_system.contacts.count_contacts()
   target_system.contacts.counts

For parallel contacts calculation:

   from ufcc import UFCC

   target_system = UFCC('coordinates.gro', 'trajectory.xtc') 
   target_system.contacts.runner.backend = 'parallel'
   
   target_system.contacts.compute()
   target_system.contacts.count_contacts()
   target_system.contacts.counts

You can find more details on how to use ufcc in the documentation page.

License

Source code included in this project is available under the MIT License.

Copyright

Copyright (c) 2022, Daniel P. Ramirez & Besian I. Sejdiu

Acknowledgements

The respository structure of UFCC is based on the Computational Molecular Science Python Cookiecutter version 1.6.