https://github.com/redesignscience/alphaspace2
Protein surface topographical mapping tool
https://github.com/redesignscience/alphaspace2
jupyter-notebook protein python surface-analysis
Last synced: 12 months 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 (over 8 years ago)
- Default Branch: master
- Last Pushed: 2023-08-17T19:32:20.000Z (almost 3 years ago)
- Last Synced: 2025-04-18T04:55:28.180Z (about 1 year ago)
- Topics: jupyter-notebook, protein, python, surface-analysis
- Language: Jupyter Notebook
- Homepage:
- Size: 22.4 MB
- Stars: 27
- Watchers: 5
- Forks: 7
- Open Issues: 4
-
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 ./
```