protenix 0.1.0__tar.gz

protenix-0.1.0/LICENSE

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+Implementation of the `LayerNorm` operators (in protenix/model/layer_norm/) referred to [OneFlow]
+(https://github.com/Oneflow-Inc/oneflow) and [FastFold](https://github.com/hpcaitech/FastFold). 
+We used [OpenFold](https://github.com/aqlaboratory/openfold) for some 
+(in protenix/openfold_local/) implementations, except the `LayerNorm` part. the worker OneFlow,  
+FastFold and openfold are licensed under Apache License 2.0.

protenix-0.1.0/PKG-INFO

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+Metadata-Version: 2.1
+Name: protenix
+Version: 0.1.0
+Summary: A trainable PyTorch reproduction of AlphaFold 3.
+Home-page: https://github.com/bytedance/Protenix
+Author: Bytedance Inc.
+Author-email: ai4s-bio@bytedance.com
+License: Attribution-NonCommercial 4.0 International
+Platform: manylinux1
+Requires-Python: >=3.10
+License-File: LICENSE

protenix-0.1.0/README.md

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+# Protenix: Protein + X
+
+A trainable PyTorch reproduction of [AlphaFold 3](https://www.nature.com/articles/s41586-024-07487-w).
+
+For more information on the model's performance and capabilities, see our [technical report](Protenix_Technical_Report.pdf). 
+
+You can follow our [twitter](https://x.com/ai4s_protenix) or join the conversation in the [discord server](https://discord.gg/Utgk4Ykw).
+
+![Protenix predictions](assets/protenix_predictions.gif)
+
+## ⚡ Try it online
+- [Web server link](http://101.126.11.40:8000/) 
+
+## Installation and Preparations
+
+### Installing Protenix
+
+Follow these steps to set up and run Protenix:
+
+#### Run with Docker
+
+1. Install Docker (with GPU Support)
+Ensure that Docker is installed and configured with GPU support. Follow these steps:
+    -  Install [Docker](https://www.docker.com/) if not already installed.
+    *  Install the [NVIDIA Container Toolkit](https://docs.nvidia.com/datacenter/cloud-native/container-toolkit/install-guide.html) to enable GPU support.
+    *  Verify the setup with:
+        ```bash
+        docker run --rm --gpus all nvidia/cuda:12.1.0-base-ubuntu22.04 nvidia-smi
+        ```
+        
+1. Pull the Docker image, which was built based on this [Dockerfile](Dockerfile)
+    ```bash
+    docker pull ai4s-cn-beijing.cr.volces.com/infra/protenix:v0.0.1
+    ```
+
+1. Clone this repository and `cd` into it
+    ```bash
+    git clone https://github.com/bytedance/protenix.git 
+    cd ./protenix
+    pip install -e .
+    ```
+
+1. Run Docker with an interactive shell
+    ```bash
+    docker run --gpus all -it -v $(pwd):/workspace -v /dev/shm:/dev/shm ai4s-cn-beijing.cr.volces.com/infra/protenix:v0.0.1 /bin/bash
+    ```
+  
+  After running above commands, you’ll be inside the container’s environment and can execute commands as you would on a normal Linux terminal.
+
+#### Run directly
+
+```bash
+    # maybe you need to update libxrender1 and libxext6 firstly, run as following for Debian:
+    # apt-get update
+    # apt-get install libxrender1
+    # apt-get install libxext6
+    pip3 install protenix
+```
+
+### Setting up kernels
+
+- **Custom CUDA layernorm kernels** modified from [FastFold](https://github.com/hpcaitech/FastFold) and [Oneflow](https://github.com/Oneflow-Inc/oneflow) accelerate about 30%-50% during different training stages. To use this feature, run the following command:
+  ```bash
+  export LAYERNORM_TYPE=fast_layernorm
+  ```
+  If the environment variable `LAYERNORM_TYPE` is set to `fast_layernorm`, the model will employ the layernorm we have developed; otherwise, the naive PyTorch layernorm will be adopted. The kernels will be compiled when `fast_layernorm` is called for the first time.
+- **[DeepSpeed DS4Sci_EvoformerAttention kernel](https://www.deepspeed.ai/tutorials/ds4sci_evoformerattention/)** is a memory-efficient attention kernel developed as part of a collaboration between OpenFold and the DeepSpeed4Science initiative. To use this feature, simply pass: 
+  ```bash
+  --use_deepspeed_evo_attention true
+  ```
+  into the command line. DS4Sci_EvoformerAttention is implemented based on [CUTLASS](https://github.com/NVIDIA/cutlass). You need to clone the CUTLASS repository and specify the path to it in the environment variable CUTLASS_PATH. The [Dockerfile](Dockerfile) has already include this setting:
+  ```bash
+  RUN git clone -b v3.5.1 https://github.com/NVIDIA/cutlass.git  /opt/cutlass
+  ENV CUTLASS_PATH=/opt/cutlass
+  ```
+  The kernels will be compiled when DS4Sci_EvoformerAttention is called for the first time.
+
+
+### Preparing the datasets
+To download the [wwPDB dataset](https://www.wwpdb.org/) and proprecessed training data, you need at least 1T disk space.
+
+Use the following command to download the preprocessed wwpdb training databases:
+
+```bash
+wget -P /af3-dev/release_data/ https://af3-dev.tos-cn-beijing.volces.com/release_data.tar.gz
+tar -xzvf /af3-dev/release_data/release_data.tar.gz -C /af3-dev/release_data/
+rm /af3-dev/release_data/release_data.tar.gz
+```
+
+
+The data should be placed in the `/af3-dev/release_data/` directory. You can also download it to a different directory, but remember to modify the `DATA_ROOT_DIR` in [configs/configs_data.py](configs/configs_data.py) correspondingly.  Data hierarchy after extraction is as follows:
+
+  ```bash
+  ├── components.v20240608.cif [408M] # ccd source file
+  ├── components.v20240608.cif.rdkit_mol.pkl [121M] # rdkit Mol object generated by ccd source file
+  ├── indices [33M] # chain or interface entries
+  ├── mmcif [283G]  # raw mmcif data
+  ├── mmcif_bioassembly [36G] # preprocessed wwPDB structural data
+  ├── mmcif_msa [450G] # msa files
+  ├── posebusters_bioassembly [42M] # preprocessed posebusters structural data
+  ├── posebusters_mmcif [361M] # raw mmcif data
+  ├── recentPDB_bioassembly [1.5G] # preprocessed recentPDB structural data
+  └── seq_to_pdb_index.json [45M] # sequence to pdb id mapping file
+  ```
+With the above data, you can run the training demo from scratch. `components.v20240608.cif` and `components.v20240608.cif.rdkit_mol.pkl` is also used in inference pipeline for generating [ccd](https://www.wwpdb.org/data/ccd) reference feature. If you only want to run inference, the full released data is not necessary, you can download these two files separately.
+```bash
+wget -P /af3-dev/release_data/ https://af3-dev.tos-cn-beijing.volces.com/release_data/components.v20240608.cif
+wget -P /af3-dev/release_data/ https://af3-dev.tos-cn-beijing.volces.com/release_data/components.v20240608.cif.rdkit_mol.pkl
+```
+Data processing scripts are still being organized and prepared, and distillation data will be released in the future.
+
+## Running your first prediction
+
+### Model checkpoints
+
+Use the following command to download pretrained checkpoint [1.4G]:
+
+```bash
+wget -P /af3-dev/release_model/ https://af3-dev.tos-cn-beijing.volces.com/release_model/model_v1.pt 
+
+```
+the checkpoint should be placed in the `/af3-dev/release_model/` directory.
+
+### Notebook demo
+You can use [notebooks/protenix_inference.ipynb](notebooks/protenix_inference.ipynb)  to run the model inference.
+
+### Inference demo
+You can run the script `inference_demo.sh` to do model inference:
+
+```bash
+bash inference_demo.sh
+```
+
+Arguments in this scripts are explained as follows:
+* `load_checkpoint_path`: path to the model checkpoints.
+* `input_json_path`: path to a JSON file that fully describes the input.
+* `dump_dir`: path to a directory where the results of the inference will be saved. 
+* `dtype`: data type used in inference. Valid options include `"bf16"` and `"fp32"`. 
+* `use_deepspeed_evo_attention`: whether use the EvoformerAttention provided by DeepSpeed.
+* `use_msa`: whether to use the MSA feature, the default is true. If you want to disable the MSA feature, add `--use_msa false` to the [inference_demo.sh](inference_demo.sh) script.
+
+or you can run inference with:
+
+```bash
+# run with examples floder
+protenix_infer --input_json_path examples/example.json --dump_dir  ./output
+```
+
+**Detailed information on the format of the input JSON file and the output files can be found [here](runner/infer_json_format.md)**.
+
+Predicted structures for the posebusters set are available at:  
+```bash
+https://af3-dev.tos-cn-beijing.volces.com/pb_samples_release.tar.gz
+```
+
+## Training and Finetuning
+### Training demo
+After the installation and data preparations, you can run the following command to train the model from scratch:
+
+  ```bash
+  bash train_demo.sh 
+  ```
+Key arguments in this scripts are explained as follows:
+* `dtype`: data type used in training. Valid options include `"bf16"` and `"fp32"`. 
+  * `--dtype fp32`: the model will be trained in full FP32 precision.
+  * `--dtype bf16`: the model will be trained in BF16 Mixed precision, by default, the `SampleDiffusion`,`ConfidenceHead`, `Mini-rollout` and `Loss` part will still be training in FP32 precision. if you want to train and infer the model in full BF16 Mixed precision, pass the following arguments to the [train_demo.sh](train_demo.sh):
+    ```bash
+    --skip_amp.sample_diffusion_training false \
+    --skip_amp.confidence_head false \
+    --skip_amp.sample_diffusion false \
+    --skip_amp.loss false \
+    ```
+* `use_deepspeed_evo_attention`: whether use the EvoformerAttention provided by DeepSpeed as mentioned above.
+* `ema_decay`: the decay rate of the EMA, default is 0.999.
+* `sample_diffusion.N_step`: during evalutaion, the number of steps for the diffusion process is reduced to 20 to improve efficiency.
+* `data.train_sets/data.test_sets`: the datasets used for training and evaluation. If there are multiple datasets, separate them with commas.
+
+* Some settings follow those in the [AlphaFold 3](https://www.nature.com/articles/s41586-024-07487-w) paper, The table below shows the training settings for different fine-tuning stages:
+
+  | Arguments  | Initial training | Fine tuning 1   |  Fine tuning 2  | Fine tuning 3 |
+  |-----------------------------------------|--------|---------|-------|-----|
+  | `train_crop_size`                       | 384    | 640    | 768    | 768 |
+  | `diffusion_batch_size`                  | 48     | 32     | 32     | 32  |
+  | `loss.weight.alpha_pae`                 | 0      | 0      | 0      | 1.0 |
+  | `loss.weight.alpha_bond`                | 0      | 1.0    | 1.0    | 0   | 
+  | `loss.weight.smooth_lddt`               | 1.0    | 0      | 0      | 0   | 
+  | `loss.weight.alpha_confidence`          | 1e-4   | 1e-4   | 1e-4   | 1e-4|
+  | `loss.weight.alpha_diffusion`           | 4.0    | 4.0    | 4.0    | 0   |
+  | `loss.weight.alpha_distogram`           | 0.03   | 0.03   | 0.03   | 0   |
+  | `train_confidence_only`                 | False  | False  | False  | True|
+  | full BF16-mixed speed(A100, s/step)     | ~12    | ~30    | ~44    | ~13 |
+  | full BF16-mixed peak memory (G)         | ~34    | ~35    | ~48    | ~24 |
+  
+  We recommend carrying out the training on A100-80G or H20/H100 GPUs. If utilizing full BF16-Mixed precision training, the initial training stage can also be performed on A800-40G GPUs. GPUs with smaller memory, such as A30, you'll need to reduce the model size, such as decreasing `model.pairformer.nblocks` and `diffusion_batch_size`.
+* In this version, we do not use the template and RNA MSA feature for training. As the default settings in [configs/configs_base.py](configs/configs_base.py) and [configs/configs_data.py](configs/configs_data.py):
+  ```bash
+  --model.template_embedder.n_blocks 0 \
+  --data.msa.enable_rna_msa false \
+  ```
+  This will be considered in our future work.
+
+* The model also supports distributed training with PyTorch’s [`torchrun`](https://pytorch.org/docs/stable/elastic/run.html). For example, if you’re running distributed training on a single node with 4 GPUs, you can use:
+  ```bash
+  torchrun --nproc_per_node=4 runner/train.py
+  ```
+  You can also pass other arguments with `--<ARGS_KEY> <ARGS_VALUE>` as you want.
+
+
+### Finetune demo
+
+If you want to fine-tune the model on a specific subset, such as an antibody dataset, you only need to provide a PDB list file and load the pretrained weights as [finetune_demo.sh](finetune_demo.sh) shows:
+    
+```bash
+checkpoint_path="/af3-dev/release_model/model_v1.pt"
+...
+
+--load_checkpoint_path ${checkpoint_path} \
+--load_checkpoint_ema_path ${checkpoint_path} \
+--data.weightedPDB_before2109_wopb_nometalc_0925.base_info.pdb_list examples/subset.txt \
+```
+
+, where the `subset.txt` is a file containing the PDB IDs like:
+```bash
+6hvq
+5mqc
+5zin
+3ew0
+5akv
+```
+
+## Acknowledgements
+
+Implementation of the layernorm operators referred to [OneFlow](https://github.com/Oneflow-Inc/oneflow) and [FastFold](https://github.com/hpcaitech/FastFold). We used [OpenFold](https://github.com/aqlaboratory/openfold) for some [module](protenix/openfold_local/) implementations, except the [`LayerNorm`](protenix/model/layer_norm/).
+
+
+## Contribution
+
+Please check [Contributing](CONTRIBUTING.md) for more details. If you encounter problems using Protenix, feel free to create an issue! We also welcome pull requests from the community.
+
+## Code of Conduct
+
+Please check [Code of Conduct](CODE_OF_CONDUCT.md) for more details.
+
+## Security
+
+If you discover a potential security issue in this project, or think you may
+have discovered a security issue, we ask that you notify Bytedance Security via our [security center](https://security.bytedance.com/src) or [vulnerability reporting email](sec@bytedance.com).
+
+Please do **not** create a public GitHub issue.
+
+## License
+
+This project, including code and model parameters are made available under the terms of the Creative Commons Attribution-NonCommercial 4.0 International License. You can find details at: https://creativecommons.org/licenses/by-nc/4.0/
+
+For commercial use, please reach out to us at ai4s-bio@bytedance.com for the commercial license. We welcome all types of collaborations.