README

What is this AlphaSpace2?

AlphaSpace2 is a surface topographical mapping tool. Based on the algorithm of original AlphaSpace published here, the alphaspace2 is a rewritten implementation with multiple new features are added for a more friendly user interface and performance boost.

The documentation can be found at

Key features:

1. Clear and pythonic object based API for manipulation of pockets, alpha atoms, and communities.
2. Integrated trajectory loading and interpretation from mdtraj.
3. Create Chimera script for publication quality visualization
4. Provide new beta score for beta atoms

Getting started

Requirements

python
cython
numpy
scipy
mdtraj

Installation

You can install the package with pip command:

pip install alphaspace2

To install the latest version

git clone https://github.com/lenhsherr/AlphaSpace2.git\
cd AlphaSpace2
pip install -e ./