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https://github.com/baaihealth/OpenComplex
Trainable PyTorch framework for developing protein, RNA and complex models.
https://github.com/baaihealth/OpenComplex
alphafold2 protein-structure pytorch rna-structure
Last synced: about 1 month ago
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Trainable PyTorch framework for developing protein, RNA and complex models.
- Host: GitHub
- URL: https://github.com/baaihealth/OpenComplex
- Owner: baaihealth
- License: apache-2.0
- Created: 2023-01-03T10:01:36.000Z (about 2 years ago)
- Default Branch: master
- Last Pushed: 2024-11-13T04:16:27.000Z (about 2 months ago)
- Last Synced: 2024-11-13T05:21:05.446Z (about 2 months ago)
- Topics: alphafold2, protein-structure, pytorch, rna-structure
- Language: Python
- Homepage:
- Size: 14.6 MB
- Stars: 263
- Watchers: 17
- Forks: 33
- Open Issues: 2
-
Metadata Files:
- Readme: README.md
- License: LICENSE
Awesome Lists containing this project
- awesome-biomolfold - code
README
# OpenComplex
OpenComplex is an open-source platform for developing protein and RNA complex models.
Based on DeepMind's [Alphafold 2](https://github.com/deepmind/alphafold) and AQ Laboratory's [OpenFold](https://github.com/aqlaboratory/openfold), OpenComplex support almost all features from Alphafold 2 and OpenFold, and introduces the following new features:
* Reimplemented Alphafold-Multimer models.
* RNA and protein-RNA complex models with high precision.
* Kernel fusion and optimization on >=Ampere GPUs, brings 16%
We will release training results and pretrained parameters soon.
## Installation (Linux)
All Python dependencies are specified in `environment.yml`. For producing sequence
alignments, you'll also need `kalign`, the [HH-suite](https://github.com/soedinglab/hh-suite),
and one of {`jackhmmer`, [MMseqs2](https://github.com/soedinglab/mmseqs2) (nightly build)}
installed on on your system.
Finally, some download scripts require `aria2c` and `aws`.
For convenience, we provide a script that installs Miniconda locally, creates a
`conda` virtual environment, installs all Python dependencies, and downloads
useful resources, including both sets of model parameters. Run:
```bash
scripts/install_third_party_dependencies.sh
```
To activate the environment, run:
```bash
source scripts/activate_conda_env.sh
```
With the environment active, compile CUDA kernels with
```bash
python3 setup.py install
```
To install the HH-suite to `/usr/bin`, run
```bash
scripts/install_hh_suite.sh
```
## Usage
### Data preparation
To run feature generation pipeline from `.fasta` to `feature.pkl` on DeepMind's MSA and template database, run e.g.:
```bash
python ./scripts/extract_pkl_from_fas.py ./example_data/fasta/ ./example_data/features/
```
where `example_data` is the directory containing example fasta . If `jackhmmer`,
`hhblits`, `hhsearch` and `kalign` are available at the default path of
`/usr/bin`, their `binary_path` command-line arguments can be dropped.
If you've already computed alignments for the query, you have the option to
skip the expensive alignment computation here with
`--use_precomputed_alignments`.
### Train and Inference
See example bash scripts in example_data/scripts
## Testing
To run unit tests, use
```bash
scripts/run_unit_tests.sh
```
The script is a thin wrapper around Python's `unittest` suite, and recognizes
`unittest` arguments. E.g., to run a specific test verbosely:
```bash
scripts/run_unit_tests.sh -v tests.test_model
```
Certain tests require that AlphaFold (v2.0.1) be installed in the same Python
environment. These run components of AlphaFold and OpenFold side by side and
ensure that output activations are adequately similar. For most modules, we
target a maximum pointwise difference of `1e-4`.
## Citation
If you find our open-sourced code & models helpful to your research, please also consider star🌟 and cite📑 this repo. Thank you for your support!
```
@misc{OpenComplex_code,
author={Jingcheng, Yu and Zhaoming, Chen and Zhaoqun, Li and Mingliang, Zeng and Wenjun, Lin and He, Huang and Qiwei, Ye},
title={Code of OpenComplex},
year={2022},
howpublished = {\url{https://github.com/baaihealth/OpenComplex}}
}
```
It is recommended to also cite OpenFold and AlphaFold.
## License and Disclaimer
Copyright 2022 BAAI.
Extended from AlphaFold and OpenFold, OpenComplex is licensed under
the permissive Apache Licence, Version 2.0.
## Contributing
If you encounter problems using OpenComplex, feel free to create an issue! We also
welcome pull requests from the community.
## Contact Information
For help or issues using the repos, please submit a GitHub issue.
For other communications, please contact Qiwei Ye ([email protected]).