Ecosyste.ms: Awesome

An open API service indexing awesome lists of open source software.

Awesome Lists | Featured Topics | Projects

https://github.com/lilyminium/atb_api

Last synced: 18 days ago
JSON representation

Host: GitHub
URL: https://github.com/lilyminium/atb_api
Owner: lilyminium
License: mit
Created: 2022-02-17T22:12:07.000Z (almost 3 years ago)
Default Branch: main
Last Pushed: 2022-02-18T14:40:41.000Z (almost 3 years ago)
Last Synced: 2024-11-21T07:17:49.208Z (about 1 month ago)
Language: Python
Size: 183 KB
Stars: 1
Watchers: 2
Forks: 0
Open Issues: 0
Metadata Files:
- Readme: README.md
- Contributing: .github/CONTRIBUTING.md
- License: LICENSE
- Code of conduct: CODE_OF_CONDUCT.md

Awesome Lists containing this project

README

        atb_api

==============================

[//]: # (Badges)

[![GitHub Actions Build Status](https://github.com/lilyminium/atb_api/workflows/CI/badge.svg)](https://github.com/lilyminium/atb_api/actions?query=workflow%3ACI)

[![PyPI version](https://badge.fury.io/py/atb_api.svg)](https://pypi.org/project/atb-api/)

![PyPI - Downloads](https://img.shields.io/pypi/dm/atb_api)

[![codecov](https://codecov.io/gh/lilyminium/atb_api/branch/master/graph/badge.svg)](https://codecov.io/gh/lilyminium/atb_api/branch/master)

This API is a re-write of the [UQ version](https://github.com/ATB-UQ/atb_api_public) in Python 2.7

This is a work in progress. It is for Lily's personal use, so not all features of the old API are supported yet.

Please open an issue on the [Issue tracker](https://github.com/lilyminium/atb_api/issues) if you notice a bug or need a feature.

### Example

You will need a valid ATB token to use this API. Please email the ATB administrators to request a token.

Create an instance by passing an API token, or the filename of one:

```python

    api = ATBApi(api_token="MY_TOKEN")

```

Submit a molecule by passing in a PDB string or filename:

```python

    molid = api.submit_molecule(my_pdb_file.pdb, net_charge=0, molecule_type="heteromolecule")

    assert isinstance(molid, int)

```

Get a molecule with a molecule ID:

```python

    molecule = api.get_molecule(molid=molid)

    print(molecule.atoms)

    print(molecule.bonds[0].code)

```

Download a molecule file with a molecule ID:

```python

    pdb_as_str = api.download_molecule(molid=903922, format="pdb",

                                       resolution="all_atom", optimized=True)

```

### Copyright

Copyright (c) 2022, Lily Wang

#### Acknowledgements

 

Many thanks to the original [ATB API](https://github.com/ATB-UQ/atb_api_public) from Bertrand Caron.

Project based on the 

[Computational Molecular Science Python Cookiecutter](https://github.com/molssi/cookiecutter-cms) version 1.6.