OpenAD Beta

Open Accelerated Discovery Client
Documentation

OpenAD is an open-source framework developed by IBM Research, aggregating a number of molecular science toolkits into a single API that can be accessed by command line, a Jupyter Notebook and (soon) an API.

The goal of openAD is to provide a common language for scientists to interact with a multitude of of molecular tools to simplify the triage process and drastically accelerate your development timelines.

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Pre-install Note: For updating to 0.2.0 first remove toolkits remove toolkit DS4SD and remove toolkit RXN prior to updating

Whats New ?

• Increased number of Molecules Functions for retrieving from pubchem molecules or creating your own in a working set, including visualisation, tracking of source info
• 3D displaying of molecules in your working set or direct from pubchem
• Attaching Analysis to target Molecules with the enrich command
• Enhanced Help and Tell Me command
• Linking to source documents in DeepSearch
• merging molecules and molsets together
• easy access to dataframes and results sets with the new result command
• smaller install package
• introductory molecule viewer

Note: uninstall all toolkits before installing the new version

Quick Install

Note: This will install OpenAD in your global space. If you wish to use a virtual environment, please see more detailed instructions below.

pip install openad
openad

Get started with Jupyter:

init_magic
init_examples
jupyter lab ~/openad_notebooks/Table_of_Contents.ipynb

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Before You Start

• OpenAD is available for Linux and MacOS
• We support Windows 11 via WSL 2 (ubuntu 22.04) - see Installing on Windows
• When not installing into a virtual environment on MacOS, you may need to use python3 and pip3 instead of python and pip respectively
  

Table of Contents

• OpenAD Beta
• Installation
• Getting Started - CLI
• Getting Started - Jupyter
  • Setting up Jupyter
  • Launching OpenAD in Jupyter
• Interacting with the Toolkits
  • Registration
  • Adding a Toolkit
  • Sample Commands
  • Running Bash Commands (CLI)
• AI Assistant
• For Developers
  • Installation for Development
  • Testing a branch
• Installing on Windows
  • Before you start
  • Installing WSL
• Linux Notes

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Installation

Note: Contributors should skip to Installation for Development
Note: Linux users may want to check the Linux Notes
Note: If you prefer using poetry and you know what you're doing, you can skip the instructions below and run poetry add openad instead.

1. Step 0: Before you start
   Ensure you're running Python 3.10 or 3.11. There's multiple ways of updating Python, we'll use pyenv.

   Note: Due to an issue with one of our dependencies, Python 3.12 is not yet supported.

   git clone https://github.com/pyenv/pyenv.git ~/.pyenv
   pyenv install 3.10
   

2. Step 1: Set up your virtual environment (optional)
   

   python -m venv ~/ad-venv
   source ~/ad-venv/bin/activate
   

   Note: To exit the virtual environment, you can run deactivate

3. Step 2: Installation

   pip install openad
   

Getting Started - CLI

• Enter the virtual environment

  Note: If you just installed OpenAD, you probably already activated the virtual environment.

  source ~/ad-venv/bin/activate
  

• Enter the command shell

  openad
  

• Exit the command shell
  Hit ctrl+c or run:

  exit
  

• Run a single command from outside the command shell

  openad <command>
  

• Exit the virtual environment
  

  deactivate
  

Getting Started - Jupyter

Setting up Jupyter

The following commands only need to be run once after installation:

1. Activate your virtual environment

   Note: If you just installed OpenAD, you probably already activated the virtual environment.

   source ~/ad-venv/bin/activate
   

2. Create an iPython kernel
   This ports your virtual environment to Jupyter.

   python -m ipykernel install --user --name=ad-venv
   

   Note: To list your installed iPython kernels, you can run jupyter kernelspec list, and to remove the kernel you can run jupyter kernelspec uninstall ad-venv

3. Install the magic commands
   This enables OpenAD commands to be run within a Jupyter Notebook.

   init_magic
   

   Alternative: Manually add magic commands

   If you don't want to activate magic commands in all Notebooks, you can instead activate them for individual Notebooks.

   • Run init_examples
   • Copy the file ~/openad_notebooks/openad.ipynb to the same directory as the Notebook you wish to activate.
   • In your Notebook, run this inside a code cell: !run openad.ipynb

4. Install example Notebooks
   This installs our example Notebooks at ~/openad_notebooks.

   init_examples
   

Launching OpenAD in Jupyter

1. Open any Notebook
   The following command will open up the example Notebook:

   jupyter lab ~/openad_notebooks/Table_of_Contents.ipynb
   

2. Select the kernel
   Make sure to select the "ad-venv" iPython kernel. You can do this under Kernel > Change Kernel, or in the latest versions of Jupyter by clicking the kernel name in the top right hand corner. If you don't see your iPython kernel, make sure you followed the Jupyter Setup instructions listed above.

Jupyter Notebook Jupyter Lab

1. Magic Commands
   Magic commands let you run terminal commands from within Jupyter. They are invoked by the %openad prefix. All OpenAD CLI commands can be accessed like this. For example:
   

   %openad list files
   

Interacting with the Toolkits

OpenAD integrates with DS4SD, RXN, and has placeholder support for GT4SD and ST4SD.

⚠ Reminder: when running commands from Jupyter, prepend them with %openad

Registration

Before you can interact with the toolkits, you'll need to register with each individual toolkit.

Register with DS4SD (Deep Search)

1. First, you'll need to generate an API key on the Deep Search website.

   • Visit the Deep Search website and create an account:
     deepsearch-experience.res.ibm.com
     
   • Once logged in, click the Toolkit/API icon in the top right hand corner, then open the HTTP section
   • Click the "Generate new API key" button
     
     

2. Once inside the OpenAD client, you'll be prompted to authenticate when activating the Deep Search (DS4SD) toolkit. When running set context ds4sd :

   • Hostname: https://sds.app.accelerate.science
   • Email: Your email
   • API_key: The DS4SD API key you obtained following the instructions above.

3. You should get a message saying you successfully logged in.

   Note: Your DS4SD auth config file is saved as ~/.openad/deepsearch_api.cred. If you ever want to reset your DS4SD login information you can run set context ds4sd reset, or you can delete this file.
   

Register with RXN

1. First, you'll need to generate an API key on the RXN website.

   • Sign up for an RXN account at rxn.app.accelerate.science
   • Obtain your API key by clicking the user profile icon in the top right hand corner and select "My profile".
     
     

2. When setting the context to RXN using set context rxn you'll be prompted to create a new auth configuration file:

   • Hostname: https://rxn.app.accelerate.science
     
   • API_key: The RXN API key you obtained following the instructions above.

3. You should get a message saying you successfully logged in.
   

   Note: Your RXN auth config file is saved as ~/.openad/rxn_api.cred. If you ever want to reset your RXN login information you can run set context rxn reset, or you can delete this file.
   

Adding a Toolkit

First install the toolkit, then set the context to this toolkit.

add toolkit ds4sd
set context ds4sd

Sample Commands

# DS4SD
display all collections

# RXN
list rxn models

Running Bash Commands (CLI)

To run a command in bash mode, prepend it with openad and make sure to escape quotes.

openad show molecules using file \'base_molecules.sdf\'

AI Assistant

To enable our AI assistant, you'll need an account with OpenAI. There is a one month free trial.

Note: watsonx coming soon

1. Go to platform.openai.com and create an account

2. Click on the profile icon in the top right and choose "View API keys"

3. Create a new key

4. Run tell me to be prompted for your OpenAI API credentials

For Developers

OpenAD is fully open source and we encourage contributions. We plan to provide documentation on how to integrate your own toolkits in the future.

If you have any questions in the meantime, please [reach out]({% link about.md %}).

Installation for Development

Install using the setup wizard (uses poetry)

1. Step 1: Download the repo

   git clone https://github.com/acceleratedscience/open-ad-toolkit.git
   

   Note: To download a specific branch, you can run instead:
   git clone -b <branch_name> https://github.com/acceleratedscience/open-ad-toolkit.git

2. Step 2: Launch the setup wizard

   cd open-ad-toolkit
   ./setup.sh
   

Install using pip

1. Step 0: Before you start
   Ensure you're running Python 3.10.10 or above. There's multiple ways of doing this, we'll use pyenv.

   git clone https://github.com/pyenv/pyenv.git ~/.pyenv
   pyenv install 3.10
   

2. Step 1: Set up your virtual environment (optional)
   

   python -m venv ~/ad-venv
   source ~/ad-venv/bin/activate
   

   Note: To exit the virtual environment, you can run deactivate

3. Step 2: Download the repo

   git clone https://github.com/acceleratedscience/open-ad-toolkit.git
   

   Note: To download a specific branch, you can run instead:
   git clone -b <branch_name> https://github.com/acceleratedscience/open-ad-toolkit.git

4. Step 2: Install the requirements

   cd open-ad-toolkit
   pip install -e .
   

   Note: The -e flag stands for "editable". This means that instead of copying the package's files to the Python site-packages directory as in a regular installation, pip creates a symbolic link (symlink) from your package's source code directory into your Python environment.
   This way you can make changes to the source code of the package, and those changes are immediately reflected in your Python environment. You don't need to reinstall the package every time you make a change.

Testing a branch

To do a regular install from a particular branch, you can run:

pip install git+https://github.com/acceleratedscience/open-ad-toolkit.git@<branch_name>

Installing on Windows

In order to run OpenAD on Windows 11, you will need to install the Ubuntu WSL package ("Windows Subsystem for Linux").

Before you start

• Verify Windows version
  To check if you are running Windows 11 or later, press Win + R, type "winver", and press Enter. A window will open showing your Windows version.

• Verify WSL
  To check if you already have WSL installed, run wsl -l -v into the terminal. To see more information about your current version of Ubuntu, run lsb_release -a

Installing WSL

Install WSL and create a user called 'openad' or one of your choosing.

wsl --install Ubuntu-22.04

Optional: To setup an Ubuntu Python environment from scratch, continue to Linux Notes

Linux Notes

If you wish to setup an Ubuntu Python environment from scratch, run:

sudo add-apt-repository ppa:deadsnakes/ppa
sudo apt update
sudo apt install python3.11-full
sudo apt install python3-pip
sudo update-alternatives --install /usr/bin/python3 python3 /usr/bin/python3.11 100
sudo pip install pip --upgrade

If you get an error when running init_magic, you may first need to setup the default iPython profile for magic commands.

ipython profile create