diff --git a/README.md b/README.md index 84675c0..5c05716 100644 --- a/README.md +++ b/README.md @@ -8,10 +8,29 @@ Identifying transitional states is crucial for understanding protein conformatio ![figure](./docs/figs/fig1.png) +## System requires + +The software package can be installed and runned on Linux, Windows, and MacOS (x86_64) + +Dependency of Python and Python packages: + +(versions that has been previously tested on are also listed below, other versions should work the same) + +```bash +python == 3.9 +numpy == 1.26.1 +scipy == 1.11.4 +torch == 1.13.1 +tqdm == 4.66.1 +``` +The required python packages with the latest versions will be automatically installed if these python packages are not already present in your local Python environment. + ## Installation from sources The source code can be installed with a local clone: +The most time-consuming step is the installation of PyTorch (especially cuda version) and the whole installation procedure takes around 5 mins to complete at a local desktop. + ```bash git clone https://github.com/xuhuihuang/ts-dart.git ``` @@ -19,11 +38,16 @@ git clone https://github.com/xuhuihuang/ts-dart.git ```bash python -m pip install ./ts-dart ``` + ## Quick start ### Start with jupyter notebook -Check this file: +Check these two files for the demo: + +``` +./ts-dart/example/muller-example.ipynb +``` ``` ./ts-dart/example/quadruple-well-example.ipynb @@ -31,6 +55,8 @@ Check this file: ### Start with python script (Linux) +The whole training procedure of the following demo on i9-10900k cpu takes around 30mins to complete at a local desktop. + ```sh python ./ts-dart/scripts/train_tsdart.py \ --seed 1 \