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!

License

For personal and professional use. You cannot resell or redistribute these repositories in their original state.

Share

• Share on Facebook
• Share on Twitter