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:
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
1 maintainer
Metadata
1 maintainer
Release files for alpha-viewer 0.1.5
For a detailed explanation of source distributions (sdists) and built distributions (wheels), please see the package formats documentation.
Source distribution (sdist)
| File | Size | Uploaded | Provenance | Actions |
|---|---|---|---|---|
| alpha_viewer-0.1.5.tar.gz | 6.4 kB | Without provenance | Details for alpha_viewer-0.1.5.tar.gz |
Built distribution (wheel)
| File | Interpreter | ABI | Platform | Actions Reset |
|---|---|---|---|---|
| alpha_viewer-0.1.5-py3-none-any.whl | Python 3 | none | any | Details for alpha_viewer-0.1.5-py3-none-any.whl |
Total release size: 13.4 kB
Release files / alpha_viewer-0.1.5.tar.gz
| Download URL | alpha_viewer-0.1.5.tar.gz |
|---|---|
| Size | 6.4 kB |
| Tags | Source |
|
SHA-256 checksum How to use checksums |
be4acaf9ae93392e9c5394362cff0364b63a4514887fe5192c337f9a7cc570ab
|
|
BLAKE2b-256 checksum How to use checksums |
3c5b99ba348776d36e6dd33637ce7d6f9dbaa10ba8e0a73a0f265d5dc34c9707
|
| Upload date | |
|
Uploaded using Trusted Publishing? What is trusted publishing? |
No |
| Uploaded via |
twine/4.0.2 CPython/3.9.5
|
Release files / alpha_viewer-0.1.5-py3-none-any.whl
| Download URL | alpha_viewer-0.1.5-py3-none-any.whl |
|---|---|
| Size | 7.0 kB |
| Tags | Python 3 |
|
SHA-256 checksum How to use checksums |
a3bfb07c99b3ccd0abc0f57295ea1ac2e4a6fe3493b8c04d94219be9893ec241
|
|
BLAKE2b-256 checksum How to use checksums |
95ac56f6303ffaa449eaec3960d38912cbcc0e3221525588f1708c0bbc71663d
|
| Upload date | |
|
Uploaded using Trusted Publishing? What is trusted publishing? |
No |
| Uploaded via |
twine/4.0.2 CPython/3.9.5
|
Security for alpha-viewer 0.1.5
Provenance
Provenance describes where a file came from. On PyPI, provenance is shared via attestations, which provide a verifiable record of the build or publishing details. View details, limitations and caveats.
No provenance found
None of the files in this release were uploaded with provenance metadata.
A note on package security
PyPI is a repository for distributing packages, not a service for auditing them. While third-party security researchers and our staff do their best to detect and remove malicious packages, PyPI cannot guarantee the quality, security or suitability of any given package.
To learn more about protecting yourself from malicious actors, visit our package security documentation.
