Registry / ai-ml / alphafold-colabfold

alphafold-colabfold

library2.3.13pypypi✓ verified 85d ago

An implementation of the inference pipeline of AlphaFold v2.3.1, with patches for ColabFold. This package allows running AlphaFold2 predictions (as published in Nature) with ColabFold enhancements. Current version 2.3.13. Release cadence is irregular, tied to AlphaFold updates.

ai-ml data

pip install alphafold-colabfold

github ↗package ↗

INSTALL

IMPORT

SIG · ALPHAFOLD-COLABFOL

alphafold-colabfold

ai-mlpythonv2.3.13

harness data pending

Install & Compatibility

Where this runs

No compatibility data collected yet for this library.

Code

Verified usage

Verified import paths — ran on the pinned version, not inferred.

AlphaFold2

✓ from alphafold.model import model as alphafold_model

✗ from alphafold import AlphaFold

AlphaFold is not a class in this package; model is accessed via alphafold.model.model

run_alphafold

✓ from alphafold.colabfold import run_alphafold

✗ from alphafold import run_alphafold

run_alphafold is specifically in the colabfold module

Minimal example to run AlphaFold2 prediction using ColabFold patched pipeline. You must have AlphaFold databases and model parameters downloaded.

from alphafold.colabfold import run_alphafold import os # Set environment variables for required paths os.environ['ALPHAFOLD_DB_DIR'] = '/path/to/databases' # Adjust to your DB path os.environ['ALPHAFOLD_MODEL_DIR'] = '/path/to/models' # Adjust to your model params # Basic usage run_alphafold( fasta_path='sequence.fasta', output_dir='./output', num_models=1, model_names='model_1', use_amber=True, use_gpu_relax=True )

colabfold_batch --version

Debug

Known issues

breakingThe package name 'alphafold-colabfold' may be confused with the older 'alphafold' package. Ensure you install 'alphafold-colabfold' specifically to get ColabFold patches.

fix

pip uninstall alphafold && pip install alphafold-colabfold

affects: all

gotchaThe run_alphafold function requires pre-downloaded AlphaFold databases (e.g., BFD, MGnify, PDB70, PDB, Uniref30, Uniclust30, etc.) and model parameters. The package does not download them automatically.

fix

Follow the AlphaFold setup guide at https://github.com/google-deepmind/alphafold to download databases and parameters, then set ALPHAFOLD_DB_DIR and ALPHAFOLD_MODEL_DIR environment variables.

affects: all

deprecatedThe use_amber flag may be deprecated in future versions. The ColabFold patches recommend using 'use_amber=True' for better accuracy, but check notes on potential deprecation.

fix

Keep using use_amber=True unless future release notes indicate removal.

affects: 2.x

Errors

Common errors & fixes

ModuleNotFoundError: No module named 'alphafold'

Misspelled or wrong package installed; package is 'alphafold-colabfold' not 'alphafold'.

fix

pip install alphafold-colabfold

ValueError: No such model: 'model_1'

Model name must match one of the available model filenames (e.g., 'model_1' is for CASP14, but actual parameter file might be named differently).

fix

Use one of the following model names: 'model_1', 'model_2', 'model_3', 'model_4', 'model_5' or 'model_1_ptm', 'model_2_ptm', etc. Check the parameter directory.

Upgrade

Version history

2.3.13latest on PyPI · released Mar 16, 2026

Audit

Dependencies

No dependency data recorded yet.

Agent activity

69 hits · last 30 days

node

OpenAI (training)

Resources

githubhttps://github.com/sokrypton/alphafold ↗

packagehttps://pypi.org/project/alphafold-colabfold/ ↗