Basic Installation

Before you begin, we recommend creating a new environment for Prop3D:

conda create -n Prop3D_env python=3.10
conda activate Prop3D_env

WARNING: Prop3D requires Toil and PyTorch, which must be installed prior to Prop3D to allow for you to install with special options

Prerequisites

#. Install Singularity (preferred) or Docker Follow these steps:** https://docs.sylabs.io/guides/3.5/user-guide/quick_start.html#quick-installation-steps

  1. Install Toil (Allows Building Datasets)

If you plan on building your own datasets, you must you must install Toil first, choosing your preferred Toil extras to install, such as cloud-based cluster choice.

pip install toil #Add specific workflow manager you will be use, e.g. toil[aws]

  1. Install PyTorch (Allows Using Datasets)

If you plan on using the precomputed dataset or one of your own own datasets, it is recommended to install PyTorch. Please follow their install instructions.

An example way to install may be:

#Using conda with GPU support:
conda install pytorch torchvision torchaudio pytorch-cuda=11.7 -c pytorch -c nvidia

#Using conda (no GPU support):
conda install pytorch torchvision torchaudio cpuonly -c pytorch

#Using pip with GPU support:
pip3 install torch torchvision torchaudio

#Using pip (no GPU support):
pip3 install torch torchvision torchaudio --index-url https://download.pytorch.org/whl/cpu

Install Prop3D

Make sure all of the prereuqisites are installed, then run:

git clone https://github.com/bouralab/Prop3D.git
cd Prop3D
git submodule init
git submodule update
python setup.py install

Next, configure HSDS to run with the pre-calculated datasets:

please set the following variables by running hsconfig:

# HDFCloud configuration file
hs_endpoint = http://prop3d-hsds.pods.uvarc.io
hs_username = None
hs_password = None
hs_api_key = None

These values can also be set though the environmental variables, HS_ENDPOINT, HS_USERNAME and HS_PASSWORD.

The path to each pre-computed dataset on our HSDS endpoint is:

Prop3D-20 : /projects/Prop3D/Prop3D-20.h5

In Progress:

PDB : /projects/Prop3D/PDB.h5

Extras

If you are using MinIO underlying HSDS, you should install Prop3D with the s3 extra:

pip install prop3D[s3]