https://github.com/redesignscience/alphaspace2

Protein surface topographical mapping tool
https://github.com/redesignscience/alphaspace2

jupyter-notebook protein python surface-analysis

Last synced: about 1 month ago
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Protein surface topographical mapping tool

• Host: GitHub
• URL: https://github.com/redesignscience/alphaspace2
• Owner: RedesignScience
• License: gpl-3.0
• Created: 2017-09-30T01:35:33.000Z (about 7 years ago)
• Default Branch: master
• Last Pushed: 2023-08-17T19:32:20.000Z (over 1 year ago)
• Last Synced: 2024-11-08T22:03:11.943Z (about 1 month ago)
• Topics: jupyter-notebook, protein, python, surface-analysis
• Language: Jupyter Notebook
• Homepage:
• Size: 22.4 MB
• Stars: 26
• Watchers: 6
• Forks: 6
• Open Issues: 3
• Metadata Files:
  • Readme: README.md
  • License: LICENSE

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README

        
# README

# What is this AlphaSpace2?

AlphaSpace2 is a surface topographical mapping tool.

Based on the algorithm of original AlphaSpace published

[here](http://pubs.acs.org/doi/abs/10.1021/acs.jcim.5b00103),

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 ./

```