[tutorial] update fastfold tutorial (#2565)

* update readme

* update

* update
This commit is contained in:
oahzxl
2023-02-03 16:54:28 +08:00
committed by GitHub
parent 79079a9d0c
commit 4f5ef73a43
5 changed files with 22 additions and 179 deletions

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@@ -2,23 +2,21 @@
## Table of contents
- [Overview](#📚-overview)
- [Quick Start](#🚀-quick-start)
- [Dive into FastFold](#🔍-dive-into-fastfold)
- [FastFold Inference](#fastfold-inference)
- [Table of contents](#table-of-contents)
- [📚 Overview](#-overview)
- [🚀 Quick Start](#-quick-start)
- [🔍 Dive into FastFold](#-dive-into-fastfold)
## 📚 Overview
This example lets you to quickly try out the inference of FastFold.
**NOTE: We use random data and random parameters in this example.**
This example lets you to try out the inference of FastFold.
## 🚀 Quick Start
1. Install FastFold
We highly recommend installing an Anaconda or Miniconda environment and install PyTorch with conda.
We highly recommend you to install FastFold with conda.
```
git clone https://github.com/hpcaitech/FastFold
cd FastFold
@@ -27,15 +25,19 @@ conda activate fastfold
python setup.py install
```
2. Run the inference scripts.
2. Download datasets.
```bash
python inference.py --gpus=1 --n_res=256 --chunk_size=None --inplace
It may take ~900GB space to keep datasets.
```
+ `gpus` means the DAP size
+ `n_res` means the length of residue sequence
+ `chunk_size` introduces a memory-saving technology at the cost of speed, None means not using, 16 may be a good trade off for long sequences.
+ `inplace` introduces another memory-saving technology with zero cost, drop `--inplace` if you do not want it.
./scripts/download_all_data.sh data/
```
3. Run the inference scripts.
```
bash inference.sh
```
You can find predictions under the `outputs` dir.
## 🔍 Dive into FastFold