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https://github.com/althonos/mini3di

A NumPy port of the foldseek code for encoding protein structures to 3di.

https://github.com/althonos/mini3di

Science Score: 49.0%

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    CITATION.cff file
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    DOI references
    Found 3 DOI reference(s) in README
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    Academic publication links
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    1 of 2 committers (50.0%) from academic institutions
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    Scientific vocabulary similarity
    Low similarity (11.4%) to scientific vocabulary

Keywords

foldseek numpy-library protein-structure python-library
Last synced: 5 months ago · JSON representation

Repository

A NumPy port of the foldseek code for encoding protein structures to 3di.

Basic Info
  • Host: GitHub
  • Owner: althonos
  • License: bsd-3-clause
  • Language: Python
  • Default Branch: main
  • Homepage:
  • Size: 450 KB
Statistics
  • Stars: 68
  • Watchers: 2
  • Forks: 3
  • Open Issues: 0
  • Releases: 4
Topics
foldseek numpy-library protein-structure python-library
Created about 2 years ago · Last pushed 6 months ago
Metadata Files
Readme Changelog Contributing License

README.md

🚀 mini3di Stars

A NumPy port of the foldseek code for encoding structures to 3di.

Actions Coverage License PyPI Bioconda Wheel Python Versions Python Implementations Source Mirror GitHub issues Docs Changelog Downloads

🗺️ Overview

foldseek is a method developed by van Kempen et al.[1] 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+).

🔧 Installing

Install the mini3di package directly from PyPi which hosts universal wheels that can be installed with pip: console $ pip install 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 is provided to extract the atom coordinates from a Bio.PDB.Chain and encoding them directly. For instance, to encode all the chains from a PDB file: ```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.getchains(): states = encoder.encodechain(chain) sequence = encoder.buildsequence(states) print(chain.getid(), sequence) ```

💭 Feedback

⚠️ Issue Tracker

Found a bug? Have an enhancement request? Head over to the GitHub issue tracker 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 for more details.

📋 Changelog

This project adheres to Semantic Versioning and provides a changelog in the Keep a Changelog format.

⚖️ License

This library is provided under the BSD 3-clause license. It includes some code ported from foldseek, which is licensed under the GNU General Public License v3.0, 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. It was developed by Martin Larralde during his PhD project at the European Molecular Biology Laboratory in the Zeller team.

📚 References

  • [1] 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.

Owner

  • Name: Martin Larralde
  • Login: althonos
  • Kind: user
  • Location: Heidelberg, Germany
  • Company: EMBL / LUMC, @zellerlab

PhD candidate in Bioinformatics, passionate about programming, SIMD-enthusiast, Pythonista, Rustacean. I write poems, and sometimes they are executable.

GitHub Events

Total
  • Issues event: 1
  • Watch event: 39
  • Issue comment event: 1
  • Push event: 10
  • Fork event: 1
Last Year
  • Issues event: 1
  • Watch event: 39
  • Issue comment event: 1
  • Push event: 10
  • Fork event: 1

Committers

Last synced: 9 months ago

All Time
  • Total Commits: 51
  • Total Committers: 2
  • Avg Commits per committer: 25.5
  • Development Distribution Score (DDS): 0.02
Past Year
  • Commits: 13
  • Committers: 2
  • Avg Commits per committer: 6.5
  • Development Distribution Score (DDS): 0.077
Top Committers
Name Email Commits
Martin Larralde m****e@e****e 50
Patrick Kunzmann p****y@g****m 1
Committer Domains (Top 20 + Academic)
embl.de: 1

Issues and Pull Requests

Last synced: 6 months ago

All Time
  • Total issues: 2
  • Total pull requests: 1
  • Average time to close issues: 2 months
  • Average time to close pull requests: about 14 hours
  • Total issue authors: 2
  • Total pull request authors: 1
  • Average comments per issue: 4.0
  • Average comments per pull request: 1.0
  • Merged pull requests: 1
  • Bot issues: 0
  • Bot pull requests: 0
Past Year
  • Issues: 0
  • Pull requests: 1
  • Average time to close issues: N/A
  • Average time to close pull requests: about 14 hours
  • Issue authors: 0
  • Pull request authors: 1
  • Average comments per issue: 0
  • Average comments per pull request: 1.0
  • Merged pull requests: 1
  • Bot issues: 0
  • Bot pull requests: 0
View more stats
Top Authors
Issue Authors
  • kdinashi (1)
  • genomeboy (1)
  • johnlees (1)
Pull Request Authors
  • padix-key (2)
Top Labels
Issue Labels
Pull Request Labels
bug (1)

Packages

  • Total packages: 1
  • Total downloads:
    • pypi 415 last-month
  • Total dependent packages: 0
  • Total dependent repositories: 0
  • Total versions: 4
  • Total maintainers: 1
pypi.org: mini3di

A NumPy port of the foldseek code for encoding structures to 3di.

  • Versions: 4
  • Dependent Packages: 0
  • Dependent Repositories: 0
  • Downloads: 415 Last month
Rankings
Dependent packages count: 9.4%
Average: 35.8%
Dependent repos count: 62.1%
Maintainers (1)
althonos
Last synced: 6 months ago

Dependencies

.github/workflows/test.yml actions
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  • actions/download-artifact v2 composite
  • actions/setup-python v2 composite
  • actions/upload-artifact v2 composite
  • codecov/codecov-action v3 composite
  • pypa/gh-action-pypi-publish master composite
  • rasmus-saks/release-a-changelog-action v1.0.1 composite
.github/workflows/requirements.txt pypi
  • build *
  • coverage *
  • importlib-resources >=1.3
  • setuptools >=46.4
setup.py pypi
tests/requirements.txt pypi
  • biopython * test
  • numpy * test