Metadata-Version: 2.1
Name: alpha_viewer
Version: 0.1.5
Summary: Alphafold Protein model viewer
Author: Severin Dicks
Requires-Python: >=3.8
Description-Content-Type: text/markdown
Requires-Dist: numpy>=1.9.0
Requires-Dist: pandas>=1.3.0
Requires-Dist: py3Dmol>=1.8.0
Requires-Dist: ipywidgets>=7.5.0
Requires-Dist: matplotlib>=3.5.0
Project-URL: Source, https://github.com/Intron7/alpha_viewer

# alpha_viewer
Class to view Alphafold models

alpha_viewer is based on the alphafold2 colab notebook visualization. It automatically chooses the best available prediction. alpha_viewer includes functions to plot PAE (`plot_pae`) and pLDDT (`plot_pLDDT`). It also allows for coloring of the py3Dmol view based on pLDDT with `show_confidence`. alpha_viewer contains `.obs`, a pandas data-frame, that can be used for custom annotations based on aa postion within the chain(s). You can use a key of `.obs` to color the py3Dmol view of your protein(s) based that annotation with `show_annotation`. This can also be used to inspect substructures with `show_substructures`. 

alpha-viewer has been tested to work with `monomer`, `monomer_ptm` and `multimer` models.
So far it's sadly not possible to save the py3Dmol view for exporting.

If you use alpha_viewer in your publication please cite: <a href="https://doi.org/10.5281/zenodo.6548465"><img src="https://zenodo.org/badge/DOI/10.5281/zenodo.6548465.svg" alt="DOI"></a>


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### Install

you can install this repository from pypi with:\
`pip install alpha-viewer`


It's recommended to use alpha_viewer within jupyterlab. Please enable jupyterlab extensions and install `jupyter-widgets/jupyterlab-manager` and `jupyterlab_3dmol`


A tutorial notebook can be found in `https://github.com/Intron7/alpha_viewer/tree/main/tutorials`
