ESM-2 all sizes (#17)

* updated readme

* removing print statements

* formatting

* added user_root variable. Default home

* handle exception

* added different sized esm models

* adding all esm2 model sizes

* adding all esm model sizes

* new release

README.md

@@ -13,30 +13,46 @@ ProteusAI is primarily powered by [PyTorch](https://pytorch.org/get-started/loca
 [scikit-learn](https://scikit-learn.org/stable/), 
 and [ESM](https://github.com/facebookresearch/esm) protein language models. 
 
+Cite our preprint [here](https://www.biorxiv.org/content/10.1101/2024.10.01.616114v1). 
+
 ## Getting started
 
 ----
 The commands used below are tested on Ubuntu 20.04 and IOS. Some tweaks may be needed for other OS.
 We recommend using conda environments to install ProteusAI.
 
 
-Clone the repository and cd to ProteusAI, then:
+Clone the repository and cd to ProteusAI:
+```bash
+git clone https://github.com/jonfunk21/ProteusAI.git
+cd ProteusAI 
+```
 
+Install the latest version of proteusAI in a new environment
 ```bash
-# git clone https://github.com/jonfunk21/ProteusAI.git
-# cd ProteusAI 
-conda env create -n proteusAI # this install the latest version of proteusAI in a new environment
+conda env create -n proteusAI
 conda activate proteusAI
 ```
 
 This uses the `environment.yml` file to install the dependencies.
 
+## GPU support
+By default proteus will install torch-scatter using cpu compatible binaries.
+If you want to take full advantage of GPUs for the Design module consider
+uninstalling the default `torch-scatter`, and replace it with the CUDA 
+compatible version:
+
+```bash
+pip uninstall torch-scatter
+pip install torch-scatter -f https://data.pyg.org/whl/torch-${TORCH_VERSION}+cuda.html
+```
+
 ### Install using pip locally for developement
 
 Install a local version which picks up the latest changes using an editable install:
 
 ```bash
-# conda env create -n proteusAI 
+# conda env create -n proteusAI python=3.8
 # conda activate proteusAI
 pip install -e . --find-links https://data.pyg.org/whl/torch-2.4.1+cpu.html
 ```