Manipulate molecular DOF and scan PES of aggregates
Project description
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
orenergyscan --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
ormanipagg --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!
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