Skip to content

GitLab

Commit a1c29028 authored by zhangqha's avatar zhangqha
Browse files

update uni-fold

parents
Pipeline #183 canceled with stages
Hide whitespace changes
Inline Side-by-side
Showing with 1234 additions and 0 deletions
CONTRIBUTING.md 0 → 100755
View file @ a1c29028
# How to Contribute
Uni-Fold is an ongoing project. Our target is to develop better protein folding models and to apply them in real scenarios together with the entire community. We welcome all contributions to this repository, including but not limited to 1) reports and fixes of bugs, 2) new features and 3) accuracy and efficiency improvements.
## Developer Certificate of Origin
Contributions to this project must be accompanied by a [Developer Certificate of Origin](DCO.txt). You (or your employer) retain the copyright to your contribution. The certificate only restrict you to use the same license in your contribution.
## Code review
All submissions, including submissions by project members, require review. We use GitHub pull requests for this purpose. Consult [GitHub Help](https://help.github.com/articles/about-pull-requests/) for more information on using pull requests.
DCO.txt 0 → 100755
View file @ a1c29028
Developer Certificate of Origin
By making a contribution to this project, the contributor(“I”) certify that:
(1) The contribution was created in whole or in part by me, and I have the
right to submit it under the open source license indicated in the file; or
(2) The contribution is based upon previous work which is covered under an
appropriate open source license and I have the right under that license to
submit that work with modifications, whether created in whole or in part by
me, which are under the same open source license (unless I am permitted to
submit under a different license); or
(3) The contribution was provided directly to me by some other person who
certified (1), (2) or (3), and I have not modified it.
(4) I understand and agree that this project and the contribution are
public, and that a record of the contribution (including all personal
information I submit with it, including my sign-off) is maintained
indefinitely and may be redistributed consistent with this project or the
open source license(s) involved.
\ No newline at end of file
LICENSE 0 → 100755
View file @ a1c29028
Apache License
Version 2.0, January 2004
http://www.apache.org/licenses/
TERMS AND CONDITIONS FOR USE, REPRODUCTION, AND DISTRIBUTION
1. Definitions.
"License" shall mean the terms and conditions for use, reproduction,
and distribution as defined by Sections 1 through 9 of this document.
"Licensor" shall mean the copyright owner or entity authorized by
the copyright owner that is granting the License.
"Legal Entity" shall mean the union of the acting entity and all
other entities that control, are controlled by, or are under common
control with that entity. For the purposes of this definition,
"control" means (i) the power, direct or indirect, to cause the
direction or management of such entity, whether by contract or
otherwise, or (ii) ownership of fifty percent (50%) or more of the
outstanding shares, or (iii) beneficial ownership of such entity.
"You" (or "Your") shall mean an individual or Legal Entity
exercising permissions granted by this License.
"Source" form shall mean the preferred form for making modifications,
including but not limited to software source code, documentation
source, and configuration files.
"Object" form shall mean any form resulting from mechanical
transformation or translation of a Source form, including but
not limited to compiled object code, generated documentation,
and conversions to other media types.
"Work" shall mean the work of authorship, whether in Source or
Object form, made available under the License, as indicated by a
copyright notice that is included in or attached to the work
(an example is provided in the Appendix below).
"Derivative Works" shall mean any work, whether in Source or Object
form, that is based on (or derived from) the Work and for which the
editorial revisions, annotations, elaborations, or other modifications
represent, as a whole, an original work of authorship. For the purposes
of this License, Derivative Works shall not include works that remain
separable from, or merely link (or bind by name) to the interfaces of,
the Work and Derivative Works thereof.
"Contribution" shall mean any work of authorship, including
the original version of the Work and any modifications or additions
to that Work or Derivative Works thereof, that is intentionally
submitted to Licensor for inclusion in the Work by the copyright owner
or by an individual or Legal Entity authorized to submit on behalf of
the copyright owner. For the purposes of this definition, "submitted"
means any form of electronic, verbal, or written communication sent
to the Licensor or its representatives, including but not limited to
communication on electronic mailing lists, source code control systems,
and issue tracking systems that are managed by, or on behalf of, the
Licensor for the purpose of discussing and improving the Work, but
excluding communication that is conspicuously marked or otherwise
designated in writing by the copyright owner as "Not a Contribution."
"Contributor" shall mean Licensor and any individual or Legal Entity
on behalf of whom a Contribution has been received by Licensor and
subsequently incorporated within the Work.
2. Grant of Copyright License. Subject to the terms and conditions of
this License, each Contributor hereby grants to You a perpetual,
worldwide, non-exclusive, no-charge, royalty-free, irrevocable
copyright license to reproduce, prepare Derivative Works of,
publicly display, publicly perform, sublicense, and distribute the
Work and such Derivative Works in Source or Object form.
3. Grant of Patent License. Subject to the terms and conditions of
this License, each Contributor hereby grants to You a perpetual,
worldwide, non-exclusive, no-charge, royalty-free, irrevocable
(except as stated in this section) patent license to make, have made,
use, offer to sell, sell, import, and otherwise transfer the Work,
where such license applies only to those patent claims licensable
by such Contributor that are necessarily infringed by their
Contribution(s) alone or by combination of their Contribution(s)
with the Work to which such Contribution(s) was submitted. If You
institute patent litigation against any entity (including a
cross-claim or counterclaim in a lawsuit) alleging that the Work
or a Contribution incorporated within the Work constitutes direct
or contributory patent infringement, then any patent licenses
granted to You under this License for that Work shall terminate
as of the date such litigation is filed.
4. Redistribution. You may reproduce and distribute copies of the
Work or Derivative Works thereof in any medium, with or without
modifications, and in Source or Object form, provided that You
meet the following conditions:
(a) You must give any other recipients of the Work or
Derivative Works a copy of this License; and
(b) You must cause any modified files to carry prominent notices
stating that You changed the files; and
(c) You must retain, in the Source form of any Derivative Works
that You distribute, all copyright, patent, trademark, and
attribution notices from the Source form of the Work,
excluding those notices that do not pertain to any part of
the Derivative Works; and
(d) If the Work includes a "NOTICE" text file as part of its
distribution, then any Derivative Works that You distribute must
include a readable copy of the attribution notices contained
within such NOTICE file, excluding those notices that do not
pertain to any part of the Derivative Works, in at least one
of the following places: within a NOTICE text file distributed
as part of the Derivative Works; within the Source form or
documentation, if provided along with the Derivative Works; or,
within a display generated by the Derivative Works, if and
wherever such third-party notices normally appear. The contents
of the NOTICE file are for informational purposes only and
do not modify the License. You may add Your own attribution
notices within Derivative Works that You distribute, alongside
or as an addendum to the NOTICE text from the Work, provided
that such additional attribution notices cannot be construed
as modifying the License.
You may add Your own copyright statement to Your modifications and
may provide additional or different license terms and conditions
for use, reproduction, or distribution of Your modifications, or
for any such Derivative Works as a whole, provided Your use,
reproduction, and distribution of the Work otherwise complies with
the conditions stated in this License.
5. Submission of Contributions. Unless You explicitly state otherwise,
any Contribution intentionally submitted for inclusion in the Work
by You to the Licensor shall be under the terms and conditions of
this License, without any additional terms or conditions.
Notwithstanding the above, nothing herein shall supersede or modify
the terms of any separate license agreement you may have executed
with Licensor regarding such Contributions.
6. Trademarks. This License does not grant permission to use the trade
names, trademarks, service marks, or product names of the Licensor,
except as required for reasonable and customary use in describing the
origin of the Work and reproducing the content of the NOTICE file.
7. Disclaimer of Warranty. Unless required by applicable law or
agreed to in writing, Licensor provides the Work (and each
Contributor provides its Contributions) on an "AS IS" BASIS,
WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or
implied, including, without limitation, any warranties or conditions
of TITLE, NON-INFRINGEMENT, MERCHANTABILITY, or FITNESS FOR A
PARTICULAR PURPOSE. You are solely responsible for determining the
appropriateness of using or redistributing the Work and assume any
risks associated with Your exercise of permissions under this License.
8. Limitation of Liability. In no event and under no legal theory,
whether in tort (including negligence), contract, or otherwise,
unless required by applicable law (such as deliberate and grossly
negligent acts) or agreed to in writing, shall any Contributor be
liable to You for damages, including any direct, indirect, special,
incidental, or consequential damages of any character arising as a
result of this License or out of the use or inability to use the
Work (including but not limited to damages for loss of goodwill,
work stoppage, computer failure or malfunction, or any and all
other commercial damages or losses), even if such Contributor
has been advised of the possibility of such damages.
9. Accepting Warranty or Additional Liability. While redistributing
the Work or Derivative Works thereof, You may choose to offer,
and charge a fee for, acceptance of support, warranty, indemnity,
or other liability obligations and/or rights consistent with this
License. However, in accepting such obligations, You may act only
on Your own behalf and on Your sole responsibility, not on behalf
of any other Contributor, and only if You agree to indemnify,
defend, and hold each Contributor harmless for any liability
incurred by, or claims asserted against, such Contributor by reason
of your accepting any such warranty or additional liability.
END OF TERMS AND CONDITIONS
APPENDIX: How to apply the Apache License to your work.
To apply the Apache License to your work, attach the following
boilerplate notice, with the fields enclosed by brackets "[]"
replaced with your own identifying information. (Don't include
the brackets!) The text should be enclosed in the appropriate
comment syntax for the file format. We also recommend that a
file or class name and description of purpose be included on the
same "printed page" as the copyright notice for easier
identification within third-party archives.
Copyright (c) 2022, DP Technology
Licensed under the Apache License, Version 2.0 (the "License");
you may not use this file except in compliance with the License.
You may obtain a copy of the License at
http://www.apache.org/licenses/LICENSE-2.0
Unless required by applicable law or agreed to in writing, software
distributed under the License is distributed on an "AS IS" BASIS,
WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
See the License for the specific language governing permissions and
limitations under the License.
README.md 0 → 100644
View file @ a1c29028
# Uni-Fold-main
## 模型介绍
深势科技推出的蛋白质结构预测工具Uni-Fold，成功复现曾引起生物学界轰动的 AlphaFold2 的全规模训练，并开源训练代码与推理代码。相应解决方案已集成至深势科技自主研发的药物设计平台 Hermite，供广大用户测试使用。
Uni-Fold 克服了 AlphaFold2 未开源训练代码、硬件支持单一、模型不可商用等局限性，在训练与推理环节进行了 NVIDIA GPU上的适配、性能优化及功能完善等工作，为更多人参与推动领域进一步发展提供了基础。
## 模型结构
Uni-Fold,参考https://github.com/dptech-corp/Uni-Fold
## Uni-Fold代码参考版本
版本：master
原始代码位置：https://github.com/dptech-corp/Uni-Fold.git
## 数据集
示例中验证的数据集来自：
bash scripts/download/download_all_data.sh /path/to/database/directory
## 预训练模型参数
wget https://github.com/dptech-corp/Uni-Fold/releases/download/v2.0.0/unifold_params_2022-08-01.tar.gz
tar -zxf unifold_params_2022-08-01.tar.gz
## 推理
### 环境配置
提供[光源](https://www.sourcefind.cn/#/service-details)拉取的训练的docker镜像：
* 推理镜像：
docker pull image.sourcefind.cn:5000/dcu/admin/base/custom:unifold-latest
cd /root/Uni-Fold-main
* 依赖安装：
安装requirement.txt中的工具，镜像中已经安装好,加载方式
export PATH=/root/software/hmmer/bin${PATH:+:${PATH}}
export PATH=/root/software/hh-suite-master/bin${PATH:+:${PATH}}
export PATH=/root/software/kalign/bin${PATH:+:${PATH}}
export LD_LIBRARY_PATH=/root/software/hh-suite-master/lib${LD_LIBRARY_PATH:+:${LD_LIBRARY_PATH}}
### 安装
#### 安装Uni-Core-main
cd Uni-Core-main
export CUDA_HOME=/opt/dtk-22.04.2
python3 setup.py install
#### 安装Uni-Fold-main
pip install -e .
### 单卡测试
#### 多聚体参考脚本,需要根据实际情况修改路径配置
sh run_multimer.sh
#### 单聚体参考脚本,需要根据实际情况修改路径配置
sh run_monomer.sh
### 性能数据
| 类别 | case | inference time |
| :---- | :---- | ----: |
| 多聚体 |H1036 | 406.94 |
| 单聚体 |T1024| 138.51 |
## 参考
* https://github.com/dptech-corp/Uni-Fold
README_unifold.md 0 → 100755
View file @ a1c29028
# Uni-Fold: an open-source platform for developing protein models beyond AlphaFold.
[[bioRxiv](https://doi.org/10.1101/2022.08.04.502811)], [[Uni-Fold Colab](https://colab.research.google.com/github/dptech-corp/Uni-Fold/blob/main/notebooks/unifold.ipynb)], [[Hermite™](https://hermite.dp.tech/)]
[[UF-Symmetry bioRxiv](https://www.biorxiv.org/content/10.1101/2022.08.30.505833)]
We proudly present Uni-Fold as a thoroughly open-source platform for developing protein models beyond [AlphaFold](https://github.com/deepmind/alphafold/). Uni-Fold introduces the following features:
- Reimplemented AlphaFold and AlphaFold-Multimer models in PyTorch framework. **This is currently the first (if any else) open-source repository that supports training AlphaFold-Multimer.**
- Model correctness proved by successful from-scratch training with equivalent accuracy, both monomer and multimer included.
- Highest efficiency among existing AlphaFold implementations (to our knowledge).
- Easy distributed training based on [Uni-Core](https://github.com/dptech-corp/Uni-Core/), as well as other conveniences including half-precision training (`float16/bfloat16`), per-sample gradient clipping, and fused CUDA kernels.
- Fast prediction of large symmetric complexes with UF-Symmetry.
![case](./img/case.png)
<center>
<small>
Figure 1. Uni-Fold has equivalent or better performances compared with AlphaFold.
</small>
</center>
&nbsp;
We evaluated Uni-Fold on PDB structures release after our training set with less than 40% template identity. The structures for evaluations are included in [`evaluation`](./evaluation). Uni-Fold enjoys similar monomer prediction accuracy and better multimer prediction accuracy compared with AlphaFold(-Multimer). We also benchmarked the efficiency of Uni-Fold. The end-to-end training efficiency is about 2.2 times of the official AlphaFold. More evaluation results and details are included in our [bioRxiv preprint](https://doi.org/10.1101/2022.08.04.502811).
![case](./img/accuracy.png)
<center>
<small>
Figure 2. Uni-Fold has similar performance on monomers and better performance on multimers compared with AlphaFold(-Multimer).
</small>
</center>
&nbsp;
![case](./img/train_time.png)
<center>
<small>
Figure 3. Uni-Fold is to our knowledge the fastest implemetation of AlphaFold.
</small>
</center>
&nbsp;
The name Uni-Fold is inherited from our previous repository, [Uni-Fold-JAX](https://github.com/dptech-corp/Uni-Fold-jax). First released on Dec 8 2021, Uni-Fold-JAX was the first open-source project (with training scripts) that successfully reproduced the from-scratch training of AlphaFold. Until recently, Uni-Fold-JAX is still the only project that supports training of the original AlphaFold implementation in JAX framework. Due to efficiency and collaboration considerations, we moved from JAX to PyTorch on Jan 2022, based on which we further developed the multimer models.
---
## NEWEST in Uni-Fold
[2022-11-15] We released the full dataset used to train Uni-Fold.
[2022-09-06] We released the code of Uni-Fold Symmetry (UF-Symmetry), a fast solution to fold large symmetric protein complexes. The details of UF-Symmetry can be found in [bioRxiv: Uni-Fold Symmetry: Harnessing Symmetry in Folding Large Protein Complexes](https://doi.org/10.1101/2022.08.30.505833). The code of UF-Symmetry is concentrated in the folder [`unifold/symmetry`](./unifold/symmetry/).
![case](./img/uf-symmetry-effect.gif)
<center>
<small>
Figure 4. Prediction of UF-Symmetry. AlphaFold etc. failed due to OOM errors.
</small>
</center>
&nbsp;
## Installation and Preparations
### Installing Uni-Fold
Uni-Fold is implemented on a distributed PyTorch framework, [Uni-Core](https://github.com/dptech-corp/Uni-Core#installation).
As Uni-Core needs to compile CUDA kernels in installation which requires specific CUDA and PyTorch versions, we provide a Docker image to save potential trouble.
To use GPUs within docker you need to [install nvidia-docker-2](https://docs.nvidia.com/datacenter/cloud-native/container-toolkit/install-guide.html#docker) first. Use the following command to pull the docker image:
```bash
docker pull dptechnology/unifold:latest-pytorch1.11.0-cuda11.3
```
Then, you can create and attach into the docker container, and clone & install unifold.
```bash
git clone https://github.com/dptech-corp/Uni-Fold
cd Uni-Fold
pip install -e .
```
### Preparing the datasets
Training and inference with Uni-Fold require homology searches on sequence and structure databases. Use the following command to download these databases:
```bash
bash scripts/download/download_all_data.sh /path/to/database/directory
```
Make sure there is at least 3TB storage space for downloading (~500GB) and uncompressing the databases.
### Downloading the pre-trained model parameters
Inferenece and finetuning with Uni-Fold requires pretrained model parameters. Use the following command to download the parameters:
```bash
wget https://github.com/dptech-corp/Uni-Fold/releases/download/v2.0.0/unifold_params_2022-08-01.tar.gz
tar -zxf unifold_params_2022-08-01.tar.gz
```
It contains 1 **monomer** and 1 **multimer** pretrained model parameters, whose model name are `model_2_ft` and `multimer_ft` respectively.
## Converting the AlphaFold and OpenFold parameters to Uni-Fold
One can convert the pretrained AlphaFold and OpenFold parameters to Uni-Fold format via the following commands.
```bash
model_name=model_2_af2 # specify model name, e.g. model_2_af2, multimer_af2
python scripts/convert_alphafold_to_unifold.py \
/path/to/alphafold_params.npz \ # AlphaFold params *.npz file
/path/to/unifold_format.pt \ # save checkpoint in Uni-Fold format
$model_name
```
```bash
python scripts/convert_openfold_to_unifold.py \
/path/to/openfold_params.pt \ # OpenFold params *.pt file
/path/to/unifold_format.pt \ # save checkpoint in Uni-Fold format
```
## Running Uni-Fold
After properly configurating the environment and databases, run the following command to predict the structure of the target fasta:
```bash
model_name=model_2_ft # specify model name, use `multimer_ft` for multimer prediction
bash run_unifold.sh \
/path/to/the/input.fasta \ # target fasta file
/path/to/the/output/directory/ \ # output directory
/path/to/database/directory/ \ # directory of databases
2020-05-01 \ # use templates before this date
$model_name \
/path/to/model_parameters.pt # model parameters
```
For monomer prediction, each fasta file shall contain only one sequence; for multimer prediction, the input fasta file shall contain all sequences of the target complex including duplicated homologous sequences. That is, **chains with identical sequences shall be duplicated to their number in the complex**.
### Prediction results
The output directory of running Uni-Fold contain the predicted structures in `*.pdb` files, where `best.pdb` contains prediction with the highest confidence. Besides, other outputs are dumped in `*.pkl.gz` files. We summarize the confidence metrics, namely `plddt` and `iptm+ptm` in `*.json` files.
## Training Uni-Fold
Training Uni-Fold relies on pre-calculated features of proteins. We provide a demo dataset in the [example data](example_data) folder. A larger dataset will be released soon.
### Demo case
To start with, we provide a demo script to train the monomer/multimer system of Uni-Fold:
```bash
bash train_monomer_demo.sh .
```
and
```bash
bash train_multimer_demo.sh .
```
This command starts a training process on the [demo data](example_data) included in this repository. Note that this demo script only tests the correctness of package installation and does not reflect any true performances.
### Full training dataset download
We thank [ModelScope](https://modelscope.cn/home) and [Volcengine](https://www.volcengine.com) for providing free hosts of the full training dataset. The downloaded dataset could be directly used to train Uni-Fold from-scratch.
#### Download from ModelScope
Download the dataset from [modelscope](https://modelscope.cn/datasets/DPTech/Uni-Fold-Data/summary) following:
1. install modelscope
```bash
pip3 install https://databot-algo.oss-cn-zhangjiakou.aliyuncs.com/maas/modelscope-1.0.0-py3-none-any.whl
```
2. download the dataset with python
```python
import os
data_path = "your_data_path"
os.environ["CACHE_HOME"] = data_path
from modelscope.msdatasets import MsDataset
ds = MsDataset.load(dataset_name='Uni-Fold-Data', namespace='DPTech', split='train')
# The data will be located at ${your_data_path}/modelscope/hub/datasets/downloads/DPTech/Uni-Fold-Data/master/*
```
#### Download from Volcengine
1. install rclone
```bash
curl https://rclone.org/install.sh | sudo bash
```
2. get the config file path of rclone via
```bash
rclone config file
```
3. update the config file with the following content
```bash
[volces-tos]
type = s3
provider = Other
region = cn-beijing
endpoint = https://tos-s3-cn-beijing.volces.com
force_path_style = false
disable_http2 = true
```
4. download the dataset
```bash
data_path = "your_data_path"
rclone sync volces-tos:bioos-hermite-beijing/unifold_data $data_path
```
### From-scratch Training
Run the following command to train Uni-Fold Monomer/Multimer from-scratch:
```bash
bash train_monomer.sh \ # train_multimer.sh for multimer
/path/to/training/data/directory/ \ # dataset directory
/path/to/output/directory/ \ # output directory where parameters are stored
model_2 # model name
```
Note that:
1. The dataset directory should be configurated in a similar way as the [example data](example_data).
2. The output directory should have enough space to store model parameters (~1.5GB per checkpoint, so empirically 60GB satisfies the default configuration in the shell script).
3. We provide several default model names in [config.py](unifold/config.py), namely `model_1`, `model_2`, `model_2_ft` etc. for monomer models and `multimer`, `multimer_ft` etc. for multimer models. Check `model_config()` function for the differences between model names. You may also personalize your own model by modifying the function (i.e. forking the if-elses).
### Finetuning
Run the following command to finetune the given Uni-Fold Monomer/Multimer parameters:
```bash
bash finetune_monomer.sh \ # finetune_multimer.sh for multimer
/path/to/training/data/directory/ \ # dataset directory
/path/to/output/directory/ \ # output directory where parameters are stored
/path/to/pretrained/parameters.pt \ # pretrained parameters
model_2_ft # model name
```
Besides the notices in the previous section, additionaly note that:
1. The model architecture should be correctly specified by the model name.
2. Checkpoints must be in Uni-Fold format (`*.pt`).
## Run UF-Symmetry
To run UF-Symmetry, please first install the newest version of Uni-Fold, and download the parameters of UF-Symmetry:
```bash
wget https://github.com/dptech-corp/Uni-Fold/releases/download/v2.2.0/uf_symmetry_params_2022-09-06.tar.gz
tar -zxf uf_symmetry_params_2022-09-06.tar.gz
```
Run
```bash
bash run_uf_symmetry.sh \
/path/to/the/input.fasta \ # target fasta file, include AU only
C3 \ # desired symmetry group
/path/to/the/output/directory/ \ # output directory
/path/to/database/directory/ \ # directory of databases
2020-05-01 \ # use templates before this date
/path/to/model_parameters.pt # model parameters
```
to inference with UF-Symmetry. **Note that the input FASTA file should contain the sequences of the asymmetric unit only, and a symmetry group must be specified for the model.**
## Inference on Hermite
We provide covenient structure prediction service on [Hermite™](https://hermite.dp.tech/), a new-generation drug design platform powered by AI, physics, and computing. Users only need to upload sequences of protein monomers and multimers to obtain the predicted structures from Uni-Fold, acompanied by various analyzing tools. [Click here](https://docs.google.com/document/d/1iFdezkKJVuhyqN3WvzsC7-422T-zf18IhP7M9CBj5gs) for more information of how to use Hermite™.
## Features introduced by the community
- **Faster Inference with BladeDISC.** Alibaba PAI team proposed an end-to-end DynamIc Shape Compiler [BladeDISC](https://github.com/alibaba/BladeDISC), which optimized Uni-Fold to achieve faster inference speed and longer sequences inference. For detailed introduction, please see [examples](https://github.com/alibaba/BladeDISC/tree/main/examples/PyTorch/Inference/CUDA/AlphaFold) in BladeDISC.
## Citing this work
If you use the code, the model parameters, the web server at [Hermite™](https://hermite.dp.tech/), or the released data of Uni-Fold as well as [Uni-Fold-JAX](https://github.com/dptech-corp/Uni-Fold-jax), please cite
```bibtex
@article {uni-fold,
author = {Li, Ziyao and Liu, Xuyang and Chen, Weijie and Shen, Fan and Bi, Hangrui and Ke, Guolin and Zhang, Linfeng},
title = {Uni-Fold: An Open-Source Platform for Developing Protein Folding Models beyond AlphaFold},
year = {2022},
doi = {10.1101/2022.08.04.502811},
URL = {https://www.biorxiv.org/content/10.1101/2022.08.04.502811v3},
eprint = {https://www.biorxiv.org/content/10.1101/2022.08.04.502811v3.full.pdf},
journal = {bioRxiv}
}
```
If you use the relative utilities of UF-Symmetry, please cite
```bibtex
@article {uf-symmetry,
author = {Li, Ziyao and Yang, Shuwen and Liu, Xuyang and Chen, Weijie and Wen, Han and Shen, Fan and Ke, Guolin and Zhang, Linfeng},
title = {Uni-Fold Symmetry: Harnessing Symmetry in Folding Large Protein Complexes},
year = {2022},
doi = {10.1101/2022.08.30.505833},
URL = {https://www.biorxiv.org/content/early/2022/08/30/2022.08.30.505833},
eprint = {https://www.biorxiv.org/content/early/2022/08/30/2022.08.30.505833.full.pdf},
journal = {bioRxiv}
}
```
## Acknowledgements
Our training framework is based on [Uni-Core](https://github.com/dptech-corp/Uni-Core/). Implementation of fused operators referred to [fused_ops](https://github.com/guolinke/fused_ops/) and [OneFlow](https://github.com/Oneflow-Inc/oneflow). We partly referred to an early version of [OpenFold](https://github.com/aqlaboratory/openfold) for some of the PyTorch implementations, while mostly followed the original code of [AlphaFold](https://github.com/deepmind/alphafold/). For the data processing part, we followed [AlphaFold](https://github.com/deepmind/alphafold/), and referred to utilities in [Biopython](https://biopython.org/), [HH-suite3](https://github.com/soedinglab/hh-suite/), [HMMER](http://eddylab.org/software/hmmer/), [Kalign](https://msa.sbc.su.se/cgi-bin/msa.cgi), [pandas](https://pandas.pydata.org/), [NumPy](https://numpy.org/), and [SciPy](https://scipy.org/).
## License and Disclaimer
Copyright 2022 DP Technology.
### Code License
Uni-Fold is licensed under permissive Apache Licence, Version 2.0. You may obtain a copy of the License at https://www.apache.org/licenses/LICENSE-2.0.
### Model Parameters License
The Uni-Fold parameters are made available under the terms of the Creative Commons Attribution 4.0 International (CC BY 4.0) license. You can find details at: https://creativecommons.org/licenses/by/4.0/legalcode
### Contributing to Uni-Fold
Uni-Fold is an ongoing project. Our target is to develop better protein folding models and to apply them in real scenarios together with the entire community. We welcome all contributions to this repository, including but not limited to 1) reports and fixes of bugs, 2) new features and 3) accuracy and efficiency improvements. Please refer to [CONTRIBUTING.md](CONTRIBUTING.md) for more information.
### Third-party software
Use of the third-party software, libraries or code referred to in the [Acknowledgements](README.md/#acknowledgements) section above may be governed by separate terms and conditions or license provisions. Your use of the third-party software, libraries or code is subject to any such terms and you should check that you can comply with any applicable restrictions or terms and conditions before use.
Uni-Core-main/.github/workflows/cuda/cu102-Linux-env.sh 0 → 100644
View file @ a1c29028
#!/bin/bash
CUDA_HOME=/usr/local/cuda-10.2
LD_LIBRARY_PATH=${CUDA_HOME}/lib64:${LD_LIBRARY_PATH}
PATH=${CUDA_HOME}/bin:${PATH}
export FORCE_CUDA=1
export TORCH_CUDA_ARCH_LIST="3.5;5.0+PTX;6.0;7.0;7.5"
export CUDA_HOME=/usr/local/cuda-10.2
\ No newline at end of file
Uni-Core-main/.github/workflows/cuda/cu102-Linux.sh 0 → 100644
View file @ a1c29028
#!/bin/bash
OS=ubuntu1804
wget -nv https://developer.download.nvidia.com/compute/cuda/repos/${OS}/x86_64/cuda-${OS}.pin
sudo mv cuda-${OS}.pin /etc/apt/preferences.d/cuda-repository-pin-600
wget -nv https://developer.download.nvidia.com/compute/cuda/10.2/Prod/local_installers/cuda-repo-${OS}-10-2-local-10.2.89-440.33.01_1.0-1_amd64.deb
sudo dpkg -i cuda-repo-${OS}-10-2-local-10.2.89-440.33.01_1.0-1_amd64.deb
sudo apt-key add /var/cuda-repo-10-2-local-10.2.89-440.33.01/7fa2af80.pub
sudo apt-get -qq update
sudo apt install cuda cuda-nvcc-10-2 cuda-libraries-dev-10-2
sudo apt clean
rm -f https://developer.download.nvidia.com/compute/cuda/10.2/Prod/local_installers/cuda-repo-${OS}-10-2-local-10.2.89-440.33.01_1.0-1_amd64.deb
\ No newline at end of file
Uni-Core-main/.github/workflows/cuda/cu113-Linux-env.sh 0 → 100644
View file @ a1c29028
#!/bin/bash
CUDA_HOME=/usr/local/cuda-11.3
LD_LIBRARY_PATH=${CUDA_HOME}/lib64:${LD_LIBRARY_PATH}
PATH=${CUDA_HOME}/bin:${PATH}
export FORCE_CUDA=1
export TORCH_CUDA_ARCH_LIST="3.5;5.0+PTX;6.0;7.0;7.5;8.0;8.6"
export CUDA_HOME=/usr/local/cuda-11.3
\ No newline at end of file
Uni-Core-main/.github/workflows/cuda/cu113-Linux.sh 0 → 100644
View file @ a1c29028
#!/bin/bash
OS=ubuntu1804
wget -nv https://developer.download.nvidia.com/compute/cuda/repos/${OS}/x86_64/cuda-${OS}.pin
sudo mv cuda-${OS}.pin /etc/apt/preferences.d/cuda-repository-pin-600
wget -nv https://developer.download.nvidia.com/compute/cuda/11.3.0/local_installers/cuda-repo-${OS}-11-3-local_11.3.0-465.19.01-1_amd64.deb
sudo dpkg -i cuda-repo-${OS}-11-3-local_11.3.0-465.19.01-1_amd64.deb
sudo apt-key add /var/cuda-repo-${OS}-11-3-local/7fa2af80.pub
sudo apt-get -qq update
sudo apt install cuda cuda-nvcc-11-3 cuda-libraries-dev-11-3
sudo apt clean
rm -f https://developer.download.nvidia.com/compute/cuda/11.3.0/local_installers/cuda-repo-${OS}-11-3-local_11.3.0-465.19.01-1_amd64.deb
\ No newline at end of file
Uni-Core-main/.github/workflows/cuda/cu116-Linux-env.sh 0 → 100644
View file @ a1c29028
#!/bin/bash
CUDA_HOME=/usr/local/cuda-11.6
LD_LIBRARY_PATH=${CUDA_HOME}/lib64:${LD_LIBRARY_PATH}
PATH=${CUDA_HOME}/bin:${PATH}
export FORCE_CUDA=1
export TORCH_CUDA_ARCH_LIST="3.5;5.0+PTX;6.0;7.0;7.5;8.0;8.6"
export CUDA_HOME=/usr/local/cuda-11.6
\ No newline at end of file
Uni-Core-main/.github/workflows/cuda/cu116-Linux.sh 0 → 100644
View file @ a1c29028
#!/bin/bash
OS=ubuntu1804
wget -nv https://developer.download.nvidia.com/compute/cuda/repos/${OS}/x86_64/cuda-${OS}.pin
sudo mv cuda-${OS}.pin /etc/apt/preferences.d/cuda-repository-pin-600
wget -nv https://developer.download.nvidia.com/compute/cuda/11.6.2/local_installers/cuda-repo-${OS}-11-6-local_11.6.2-510.47.03-1_amd64.deb
sudo dpkg -i cuda-repo-${OS}-11-6-local_11.6.2-510.47.03-1_amd64.deb
sudo apt-key add /var/cuda-repo-${OS}-11-6-local/7fa2af80.pub
sudo apt-get -qq update
sudo apt install cuda cuda-nvcc-11-6 cuda-libraries-dev-11-6
sudo apt clean
rm -f https://developer.download.nvidia.com/compute/cuda/11.5.2/local_installers/cuda-repo-${OS}-11-6-local_11.6.2-510.47.03-1_amd64.deb
\ No newline at end of file
Uni-Core-main/.github/workflows/docker.yml 0 → 100644
View file @ a1c29028
name: Build and Publish Docker
on:
create:
tags:
- '**'
jobs:
docker:
runs-on: ubuntu-latest
steps:
-
name: Checkout
uses: actions/checkout@v3
-
name: Set up QEMU
uses: docker/setup-qemu-action@v2
-
name: Set up Docker Buildx
uses: docker/setup-buildx-action@v2
-
name: Login to DockerHub
uses: docker/login-action@v2
with:
username: ${{ secrets.DOCKERHUB_USERNAME }}
password: ${{ secrets.DOCKERHUB_TOKEN }}
-
name: Build and push cu116
uses: docker/build-push-action@v3
with:
context: ./docker/cu116/
push: true
tags: dptechnology/unicore:${{ github.ref_name }}-pytorch1.12.1-cuda11.6
Uni-Core-main/.github/workflows/docker_latest.yml 0 → 100644
View file @ a1c29028
name: Build and Publish Docker
on:
push:
branches:
- main
jobs:
docker:
runs-on: ubuntu-latest
steps:
-
name: Checkout
uses: actions/checkout@v3
-
name: Set up QEMU
uses: docker/setup-qemu-action@v2
-
name: Set up Docker Buildx
uses: docker/setup-buildx-action@v2
-
name: Login to DockerHub
uses: docker/login-action@v2
with:
username: ${{ secrets.DOCKERHUB_USERNAME }}
password: ${{ secrets.DOCKERHUB_TOKEN }}
-
name: Build and push cu116
uses: docker/build-push-action@v3
with:
context: ./docker/cu116/
push: true
tags: dptechnology/unicore:latest-pytorch1.12.1-cuda11.6
Uni-Core-main/.github/workflows/docker_rdma.yml 0 → 100644
View file @ a1c29028
name: Build and Publish Docker
on:
create:
tags:
- '**'
jobs:
docker:
runs-on: ubuntu-latest
steps:
-
name: Checkout
uses: actions/checkout@v3
-
name: Set up QEMU
uses: docker/setup-qemu-action@v2
-
name: Set up Docker Buildx
uses: docker/setup-buildx-action@v2
-
name: Login to DockerHub
uses: docker/login-action@v2
with:
username: ${{ secrets.DOCKERHUB_USERNAME }}
password: ${{ secrets.DOCKERHUB_TOKEN }}
-
name: Build and push cu116 with rdma
uses: docker/build-push-action@v3
with:
context: ./docker/rdma/
push: true
tags: dptechnology/unicore:${{ github.ref_name }}-pytorch1.12.1-cuda11.6-rdma
Uni-Core-main/.github/workflows/docker_rdma_latest.yml 0 → 100644
View file @ a1c29028
name: Build and Publish Docker
on:
push:
branches:
- main
jobs:
docker:
runs-on: ubuntu-latest
steps:
-
name: Checkout
uses: actions/checkout@v3
-
name: Set up QEMU
uses: docker/setup-qemu-action@v2
-
name: Set up Docker Buildx
uses: docker/setup-buildx-action@v2
-
name: Login to DockerHub
uses: docker/login-action@v2
with:
username: ${{ secrets.DOCKERHUB_USERNAME }}
password: ${{ secrets.DOCKERHUB_TOKEN }}
-
name: Build and push cu116 with rdma
uses: docker/build-push-action@v3
with:
context: ./docker/rdma/
push: true
tags: dptechnology/unicore:latest-pytorch1.12.1-cuda11.6-rdma
Uni-Core-main/.github/workflows/env.sh 0 → 100644
View file @ a1c29028
export LANG C.UTF-8
export OFED_VERSION=5.3-1.0.0.1
sudo apt-get update && \
sudo apt-get install -y --no-install-recommends \
software-properties-common \
sudo apt-get install -y --no-install-recommends \
build-essential \
apt-utils \
ca-certificates \
wget \
git \
vim \
libssl-dev \
curl \
unzip \
unrar \
cmake \
net-tools \
sudo \
autotools-dev \
rsync \
jq \
openssh-server \
tmux \
screen \
htop \
pdsh \
openssh-client \
lshw \
dmidecode \
util-linux \
automake \
autoconf \
libtool \
net-tools \
pciutils \
libpci-dev \
libaio-dev \
libcap2 \
libtinfo5 \
fakeroot \
devscripts \
debhelper \
nfs-common
# wget -O ~/miniconda.sh https://repo.continuum.io/miniconda/Miniconda3-latest-Linux-x86_64.sh && \
# chmod +x ~/miniconda.sh && \
# ~/miniconda.sh -b -p /opt/conda && \
# rm ~/miniconda.sh
# export PATH=/opt/conda/bin:$PATH
\ No newline at end of file
Uni-Core-main/.github/workflows/publish.yml 0 → 100644
View file @ a1c29028
# This workflow will upload a Python Package to Release asset
# For more information see: https://help.github.com/en/actions/language-and-framework-guides/using-python-with-github-actions#publishing-to-package-registries
name: Python Package
on:
create:
tags:
- '**'
jobs:
release:
name: Create Release
runs-on: ubuntu-latest
steps:
- name: Get the tag version
id: extract_branch
run: echo ::set-output name=branch::${GITHUB_REF#refs/tags/}
shell: bash
- name: Create Release
id: create_release
uses: actions/create-release@v1
env:
GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
with:
tag_name: ${{ steps.extract_branch.outputs.branch }}
release_name: ${{ steps.extract_branch.outputs.branch }}
wheel:
name: Build Wheel
runs-on: ${{ matrix.os }}
needs: release
strategy:
fail-fast: false
matrix:
# os: [ubuntu-20.04]
os: [ubuntu-18.04]
python-version: ['3.7', '3.8', '3.9', '3.10']
torch-version: [1.11.0, 1.12.0, 1.12.1]
cuda-version: ['113', '116']
exclude:
- torch-version: 1.11.0
cuda-version: '116'
steps:
- name: Checkout
uses: actions/checkout@v3
- name: Set up Python
uses: actions/setup-python@v3
with:
python-version: ${{ matrix.python-version }}
- name: Set up Linux Env
if: ${{ runner.os == 'Linux' }}
run: |
sudo rm -rf /usr/share/dotnet
bash .github/workflows/env.sh
echo ${{ needs.create_release.outputs.upload_url }}
echo ${{ needs.steps.extract_branch.outputs.upload_url }}
shell:
bash
- name: Install CUDA ${{ matrix.cuda-version }}
if: ${{ matrix.cuda-version != 'cpu' }}
run: |
bash .github/workflows/cuda/cu${{ matrix.cuda-version }}-${{ runner.os }}.sh
shell:
bash
- name: Check GPU Env
if: ${{ matrix.cuda-version != 'cpu' }}
run: |
source .github/workflows/cuda/cu${{ matrix.cuda-version }}-${{ runner.os }}-env.sh
nvcc --version
shell:
bash
- name: Install PyTorch ${{ matrix.torch-version }}+cu${{ matrix.cuda-version }}
run: |
pip install numpy pyyaml scipy ipython mkl mkl-include ninja cython typing pandas typing-extensions dataclasses && conda clean -ya
pip install --no-index --no-cache-dir torch==${{ matrix.torch-version }} -f https://download.pytorch.org/whl/cu${{ matrix.cuda-version }}/torch_stable.html
python --version
python -c "import torch; print('PyTorch:', torch.__version__)"
python -c "import torch; print('CUDA:', torch.version.cuda)"
python -c "from torch.utils import cpp_extension; print (cpp_extension.CUDA_HOME)"
shell:
bash
- name: Get the tag version
id: extract_branch
run: echo ::set-output name=branch::${GITHUB_REF#refs/tags/}
- name: Get Release with tag
id: get_current_release
uses: joutvhu/get-release@v1
with:
tag_name: ${{ steps.extract_branch.outputs.branch }}
env:
GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
- name: Build wheel
run: |
export FORCE_CUDA="1"
export PATH=/usr/local/nvidia/bin:/usr/local/nvidia/lib64:$PATH
export LD_LIBRARY_PATH=/usr/local/nvidia/lib64:/usr/local/cuda/lib64:$LD_LIBRARY_PATH
export CUDA_INSTALL_DIR=/usr/local/cuda-11.3$CUDA_INSTALL_DIR
pip install wheel
python setup.py bdist_wheel --dist-dir=dist
tmpname=cu${{ matrix.cuda-version }}torch${{ matrix.torch-version }}
wheel_name=$(ls dist/*whl | xargs -n 1 basename | sed "s/-/+$tmpname-/2")
ls dist/*whl |xargs -I {} mv {} ${wheel_name}
echo "wheel_name=${wheel_name}" >> $GITHUB_ENV
- name: Upload Release Asset
id: upload_release_asset
uses: actions/upload-release-asset@v1
env:
GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
with:
# upload_url: ${{ needs.create_release.outputs.upload_url }}
# why didn't works
upload_url: ${{ steps.get_current_release.outputs.upload_url }}
asset_path: ./${{env.wheel_name}}
asset_name: ${{env.wheel_name}}
asset_content_type: application/*
Uni-Core-main/.gitignore 0 → 100644
View file @ a1c29028
*.pt
*.tfevents.*
# JetBrains PyCharm IDE
.idea/
# Byte-compiled / optimized / DLL files
__pycache__/
*.py[cod]
*$py.class
# C extensions
*.so
# macOS dir files
.DS_Store
# Distribution / packaging
.Python
env/
build/
develop-eggs/
dist/
downloads/
eggs/
.eggs/
lib/
lib64/
parts/
sdist/
var/
wheels/
*.egg-info/
.installed.args
*.egg
# Checkpoints
checkpoints
# PyInstaller
# Usually these files are written by a python script from a template
# before PyInstaller builds the exe, so as to inject date/other infos into it.
*.manifest
*.spec
# Installer logs
pip-log.txt
pip-delete-this-directory.txt
# Unit test / coverage reports
htmlcov/
.tox/
.coverage
.coverage.*
.cache
nosetests.xml
coverage.xml
*.cover
.hypothesis/
# Translations
*.mo
*.pot
# Django stuff:
*.log
local_settings.py
# Flask stuff:
instance/
.webassets-cache
# Scrapy stuff:
.scrapy
# Sphinx documentation
docs/_build/
# PyBuilder
target/
# Jupyter Notebook
.ipynb_checkpoints
# pyenv
.python-version
# celery beat schedule file
celerybeat-schedule
# SageMath parsed files
*.sage.py
# dotenv
.env
# virtualenv
.venv
venv/
ENV/
# Spyder project settings
.spyderproject
.spyproject
# Rope project settings
.ropeproject
# mypy
.mypy_cache/
# VSCODE
.vscode/ftp-sync.json
.vscode/settings.json
# too big to git
*.lmdb
*.sto
*.pt
*.pkl
# pytest
.pytest_cache
test/.pytest_cache
/local*
/_*
\ No newline at end of file
Uni-Core-main/LICENSE 0 → 100644
View file @ a1c29028
The MIT License (MIT)
Copyright (c) 2022 DP Technology
Permission is hereby granted, free of charge, to any person obtaining a copy
of this software and associated documentation files (the "Software"), to deal
in the Software without restriction, including without limitation the rights
to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
copies of the Software, and to permit persons to whom the Software is
furnished to do so, subject to the following conditions:
The above copyright notice and this permission notice shall be included in all
copies or substantial portions of the Software.
THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
SOFTWARE.
\ No newline at end of file
Uni-Core-main/README.md 0 → 100644
View file @ a1c29028
Uni-Core, an efficient distributed PyTorch framework
====================================================
Uni-Core is built for rapidly creating PyTorch models with high performance, especially for Transfromer-based models. It supports the following features:
- Distributed training over multi-GPUs and multi-nodes
- Mixed-precision training with fp16 and bf16
- High-performance fused CUDA kernels
- model checkpoint management
- Friendly logging
- Buffered (GPU-CPU overlapping) data loader
- Gradient accumulation
- Commonly used optimizers and LR schedulers
- Easy to create new models
Installation
------------
**Build from source**
You can use `python setup.py install` or `pip install .` to build Uni-Core from source. The CUDA version in the build environment should be the same as the one in PyTorch.
**Use pre-compiled python wheels**
We also pre-compiled wheels by GitHub Actions. You can download them from the [Release](https://github.com/dptech-corp/Uni-Core/releases). And you should check the pyhon version, PyTorch version and CUDA version. For example, for PyToch 1.12.1, python 3.7, and CUDA 11.3, you can install [unicore-0.0.1+cu113torch1.12.1-cp37-cp37m-linux_x86_64.whl](https://github.com/dptech-corp/Uni-Core/releases/download/0.0.1/unicore-0.0.1+cu113torch1.12.1-cp37-cp37m-linux_x86_64.whl).
**Docker image**
We also provide the docker image. you can pull it by `docker pull dptechnology/unicore:0.0.1-pytorch1.11.0-cuda11.3`. To use GPUs within docker, you need to [install nvidia-docker-2](https://docs.nvidia.com/datacenter/cloud-native/container-toolkit/install-guide.html#docker) first.
Example
-------
To build a model, you can refer to [example/bert](https://github.com/dptech-corp/Uni-Core/tree/main/examples/bert).
Related projects
----------------
- [Uni-Mol](https://github.com/dptech-corp/Uni-Mol)
- [Uni-Fold](https://github.com/dptech-corp/Uni-Fold)
Acknowledgement
---------------
The main framework is from [facebookresearch/fairseq](https://github.com/facebookresearch/fairseq).
The fused kernels are from [guolinke/fused_ops](https://github.com/guolinke/fused_ops).
Dockerfile is from [guolinke/pytorch-docker](https://github.com/guolinke/pytorch-docker).
License
-------
This project is licensed under the terms of the MIT license. See [LICENSE](https://github.com/dptech-corp/Uni-Core/blob/main/LICENSE) for additional details.
Markdown is supported
0% or .
You are about to add 0 people to the discussion. Proceed with caution.
Finish editing this message first!
Please register or to comment