Note

This repository is no longer being actively maintained. I would be happy for someone else to continue development, please reach out if you are interested and want to have a chat. As it stands, I do not have a concrete use for the code in this repository anymore, which is why it has been archived.

Overview

You are viewing the readme of ManipulateAggregates, a set of tools for computational chemistry. This package comes with two main tools:

• energyscan:

  • Determines geometricaly diverse local energy minima on the potential energy surface of aggregates bound by van-der-Waals or Coulomb forces using empirical force fields.
  • Simply run energyscan --porphin-example or energyscan --urea-example to run the extensive porphin or urea computations published in the following paper in your current directory: "A Program for Automatically Predicting Supramolecular Aggregates and Its Application to Urea and Porphin" by Sachse et al, accessible at https://dx.doi.org/10.1002/jcc.25151
  • You can also run energyscan --anthracene-example for a quick and less demanding scan using the anthracene molecule.
  • Running energyscan --longhelp will output a complete config file including explanations to stdout.
  • If you want to use multiprocessing, set the environment variable OMP_NUM_THREADS to the number of processes you want to use. Happy scanning!

• manipagg:

  • Manipulates internal degrees of freedoms of molecules and aggregates from the command line.
  • Computes the electrostatic potential on van-der-Waals surfaces or isosurfaces of the electron density based on empirical force fields or quantum chemical computations.
  • Simply run manipagg --example-vdw or manipagg --example-iso to run an example visualization of the electrostatic potential on a molecule's van-der-Waals or electrond ensity iso surface, the former as publised in the paper "Introducing double polar heads to highly fluorescent Thiazoles: Influence on supramolecular structures and photonic properties" by Kaufmann et al, accessible at https://doi.org/10.1016/j.jcis.2018.04.105
  • If you want to use multiprocessing, set the environment variable OMP_NUM_THREADS to the number of processes you want to use. Happy rendering and manipulating!

Please see the documentation for a detailed description and a full list of features on https://razziel89.github.io/ManipulateAggregates/ (provided via GitHub pages).

Quick installation

If you are running Ubuntu and use Anaconda to manage your Python environments, you can easily install ManipulateAggregates the following way:

# Install system packages
sudo apt-get install libcgal-dev libmpfr-dev libgmp-dev freeglut3 libglu1-mesa-dev
# If you want to render using PoVRay, run:
sudo apt-get install povray
# Install and activate a new environment like this:
conda create -n manipagg python=3 numpy swig eigen pyopengl
conda activate manipagg
# Install ManipulateAggregates and its dependencies
pip install ManipulateAggregates

Please refer to the documentation on https://razziel89.github.io/ManipulateAggregates/#prerequisites for more information.

Contributing

Contributions are very welcome! Please simply open a pull request. If you would like to make large-ish contributions, it might be prudent to first contact the maintainer to better co-ordinate those efforts.

This project uses the following auto-formatter:

• Python code: black (the uncompromising Python code formatter) https://github.com/psf/black

Please make sure to auto-format your pull request with those options. Furthermore, please document any code you add. Happy contributing!