mini3di 0.2.1
A NumPy port of the foldseek code for encoding structures to 3di.
License: BSD-3-Clause
Requires Python: >=3.7
Keywords: bioinformatics, protein, structure, foldseek, 3di

# 🚀 `mini3di` [![Stars](https://img.shields.io/github/stars/althonos/mini3di.svg?style=social&maxAge=3600&label=Star)](https://github.com/althonos/mini3di/stargazers)

*A [NumPy](https://numpy.org/) port of the [`foldseek`](https://github.com/steineggerlab/foldseek) code for encoding structures to 3di.*

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## 🗺️ Overview

[`foldseek`](https://github.com/steineggerlab/foldseek) is a method developed
by van Kempen *et al.*[\[1\]](#ref1) for the fast and accurate search of
protein structures. In order to search proteins structures at a large scale,
it first encodes the 3D structure into sequences over a structural alphabet,
3di, which captures tertiary amino acid interactions.

`mini3di` is a pure-Python package to encode 3D structures of proteins into
the 3di alphabet, using the trained weights from the `foldseek` VQ-VAE model.

This library only depends on NumPy and is available for all modern Python
versions (3.7+).

<!-- ### 📋 Features -->


## 🔧 Installing

Install the `mini3di` package directly from [PyPi](https://pypi.org/project/mini3di)
which hosts universal wheels that can be installed with `pip`:
```console
$ pip install mini3di
```

<!-- Otherwise, `mini3di` is also available as a [Bioconda](https://bioconda.github.io/)
package:
```console
$ conda install -c bioconda mini3di
``` -->

<!-- ## 📖 Documentation

A complete [API reference](https://mini3di.readthedocs.io/en/stable/api.html)
can be found in the [online documentation](https://mini3di.readthedocs.io/),
or directly from the command line using
[`pydoc`](https://docs.python.org/3/library/pydoc.html):
```console
$ pydoc mini3di
``` -->

## 💡 Example

`mini3di` provides a single `Encoder` class, which expects the 3D coordinates
of the **Cα**, **Cβ**, **N** and **C** atoms from each peptide residue. For
residues without **Cβ** (Gly), simply write the coordinates as `math.nan`.
Call the `encode_atoms` method to get a sequence of 3di states:
```python
from math import nan
import mini3di

encoder = mini3di.Encoder()
states = encoder.encode_atoms(
    ca=[[32.9, 51.9, 28.8], [35.0, 51.9, 26.6], ...],
    cb=[[ nan,  nan,  nan], [35.3, 53.3, 26.4], ...],
    n=[ [32.1, 51.2, 29.8], [35.3, 51.5, 28.1], ...],
    c=[ [34.4, 51.7, 29.1], [36.1, 51.1, 25.8], ...],
)
```

The states returned as output will be a NumPy array of state indices. To turn
it into a sequence, use the `build_sequence` method of the encoder:
```python
sequence = encoder.build_sequence(states)
print(sequence)
```

The encoder can work directly with Biopython objects, if Biopython is available.
A helper method `encode_chain` to extract the atom coordinates from
a [`Bio.PDB.Chain`](https://biopython.org/docs/latest/api/Bio.PDB.Chain.html)
and encoding them directly. For instance, to encode all the chains from a
[PDB file](https://en.wikipedia.org/wiki/Protein_Data_Bank_(file_format)):
```python
import pathlib

import mini3di
from Bio.PDB import PDBParser

encoder = mini3di.Encoder()
parser = PDBParser(QUIET=True)
struct = parser.get_structure("8crb", pathlib.Path("tests", "data", "8crb.pdb"))

for chain in struct.get_chains():
    states = encoder.encode_chain(chain)
    sequence = encoder.build_sequence(states)
    print(chain.get_id(), sequence)
```

## 💭 Feedback

### ⚠️ Issue Tracker

Found a bug? Have an enhancement request? Head over to the [GitHub issue
tracker](https://github.com/althonos/mini3di/issues) if you need to report
or ask something. If you are filing in on a bug, please include as much
information as you can about the issue, and try to recreate the same bug
in a simple, easily reproducible situation.

### 🏗️ Contributing

Contributions are more than welcome! See
[`CONTRIBUTING.md`](https://github.com/althonos/mini3di/blob/main/CONTRIBUTING.md)
for more details.

## 📋 Changelog

This project adheres to [Semantic Versioning](http://semver.org/spec/v2.0.0.html)
and provides a [changelog](https://github.com/althonos/mini3di/blob/master/CHANGELOG.md)
in the [Keep a Changelog](http://keepachangelog.com/en/1.0.0/) format.

## ⚖️ License

This library is provided under the [BSD 3-clause license](https://choosealicense.com/licenses/bsd-3-clause/).
It includes some code ported from `foldseek`, which is licensed under the
[GNU General Public License v3.0](https://choosealicense.com/licenses/gpl-3.0/),
and relicensed with the permission of the authors.

*This project is in no way not affiliated, sponsored, or otherwise endorsed
by the [original `foldseek` authors](https://github.com/steineggerlab).
It was developed by [Martin Larralde](https://github.com/althonos/) during his
PhD project at the [European Molecular Biology Laboratory](https://www.embl.de/)
in the [Zeller team](https://github.com/zellerlab).*


## 📚 References

- <a id="ref1">\[1\]</a> Kempen, Michel van, Stephanie S. Kim, Charlotte Tumescheit, Milot Mirdita, Jeongjae Lee, Cameron L. M. Gilchrist, Johannes Söding, and Martin Steinegger. ‘Fast and Accurate Protein Structure Search with Foldseek’. Nature Biotechnology, 8 May 2023, 1–4. [doi:10.1038/s41587-023-01773-0](https://doi.org/10.1038/s41587-023-01773-0).