ManipulateAggregates 0.1.3

Description:

ManipulateAggregates 0.1.3

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!