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توضیحات

Manipulate molecular DOF and scan PES of aggregates

ویژگی	مقدار
سیستم عامل	POSIX :: Linux
نام فایل	ManipulateAggregates-0.1.3
نام	ManipulateAggregates
نسخه کتابخانه	0.1.3
نگهدارنده	[]
ایمیل نگهدارنده	[]
نویسنده	Torsten Sachse
ایمیل نویسنده	-
آدرس صفحه اصلی	https://github.com/razziel89/ManipulateAggregates
آدرس اینترنتی	https://pypi.org/project/ManipulateAggregates/
مجوز	-

# 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!

نحوه نصب

نصب پکیج whl ManipulateAggregates-0.1.3:

pip install ManipulateAggregates-0.1.3.whl

نصب پکیج tar.gz ManipulateAggregates-0.1.3:

pip install ManipulateAggregates-0.1.3.tar.gz