Welcome to RestraintMaker

RestraintMaker is a tool that allows automatic distance restraint assignment for dual-topology relative free energy calculations. The package can be used either in a scripting mode or with a GUI-based in PyMOL(see [2]).

This repository is heavy under development! It will be nicer soon ;)

Introduction

coming soon

Examples

coming soon

Content

Using

For usage examples, checkout the examples folder.

Development

Restraint make is split two parts.

• RestraintMaker This part is the core of the program. It can be executed as standalone.

  • algorithm: restraint selecting algorithms
  • tools_Rdkit: additional functions for filtering or selecting (see [1])
  • io: writing/importing outputfiles
  • utils

• Interface PyMOL: Allows interfacing to PyMOL and generates the GUI-Expierence (see [2])

Installation

You can retrieve the repository from GitHub: https://github.com/rinikerlab/restraintmaker

• Install via Pymol Plugin Manager

  coming soon

• Install with Anaconda

  #!/usr/bash
  # 1. Retrieve the repository
  git clone https://github.com/rinikerlab/restraintmaker.git
  cd restraintmaker
  
  # 2. activate submodules
  git submodule init
  git submodule update
  
  # 3. generate an Anaconda environment with the environment file and add the repository to its path:       
  conda env create --file devtools/conda-envs/dev_env.yaml -n restraintmaker
  conda develop -n restraintmaker /absolute_path/to/restraintmaker
  
  # 4. Test    
  conda activate restraintmaker
  python examples/example_gui.py
  

GUI Tutorial

GUI Menu

Optimized Distance Restraints

Start by loading

You can checkout the file provided in examples on how to start the GUI.

Select & Filter

Optimize restraints

Export restraints to files

Author

Benjamin Ries (@SchroederB), Salomé R. Rieder (@SalomeRonja), Clemens Rhiner (@ClemensRhiner)

Acknowledgments

The authors want to thank Carmen Esposito and Dominik Sidler for the great discussions. Project based on the Computational Molecular Science Python Cookiecutter version 1.3.

References

[1] RDKit: Cheminformatics and machine learning software (2021) - http://www.rdkit.org

[2] The PyMOL Molecular Graphics System, Version 2.5 Schrödinger, LLC. (Anaconda OpenSource Version)

Copyright

Copyright (c) 2021, Benjamin Ries (@SchroederB), Salomé R. Rieder (@SalomeRonja), Clemens Rhiner (@ClemensRhiner)