Metadata-Version: 2.1
Name: ManipulateAggregates
Version: 0.1.3
Summary: Manipulate molecular DOF and scan PES of aggregates
Home-page: https://github.com/razziel89/ManipulateAggregates
Author: Torsten Sachse
License: UNKNOWN
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` 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:
        
        ```bash
        # 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!
        
Platform: UNKNOWN
Classifier: Development Status :: 4 - Beta
Classifier: Environment :: Console
Classifier: Intended Audience :: Developers
Classifier: Intended Audience :: Science/Research
Classifier: License :: OSI Approved :: GNU General Public License v3 or later (GPLv3+)
Classifier: Natural Language :: English
Classifier: Operating System :: POSIX :: Linux
Classifier: Programming Language :: C++
Classifier: Programming Language :: Python :: 3.8
Classifier: Programming Language :: Python :: 3 :: Only
Description-Content-Type: text/markdown
