chemllmhack 0.1.6

A SDK for computational chemistry LLM hackthon

QDX ChemLLMHack SDK

Welcome to the QDX Computational Chemistry and Large Language Model (LLM) Hackathon! This SDK is tailored specifically for the hackathon and is designed to seamlessly integrate with the most advanced RUSH's computational cloud platform (https://rush.cloud). It enables the community to effortlessly develop and apply cutting-edge LLM and Artificial Intelligence (AI) technologies in computational chemistry.

Installation

To install the QDX ChemLLMHack SDK, simply run the following command:

pip install chemllmhack

Features

• Get help information about the Rex language. Retrieve specific expressions used in RUSH modules from Rex Database.

• Download the paper dataset and Chroma vector database. The Paper Dataset comprises a comprehensive collection of scientific papers sourced from open-access databases including arXiv, bioRxiv, chemRxiv, and medRxiv. Below are the statistics for the dataset:

  Tool	Number of Papers
  MMseqs2	1000
  PLIP	2000
  Gina	3000
  RDock	4000
  Auto3d	5000

• Use MongoDB Atlas cloud vector database to retrieve vectors and query online.

• Submit your Rex expression to the RUSH platform.

• Retrieve the results and stats against benchmark of your submitted Rex expression.

QDX Hackathon Setup Guide

Prerequisites

Before you begin, make sure you have a Google account. You'll need this to register for the QDX Hackathon. You also need a OPENAI_API_KEY set up in your environment. You will be granted a RUSH token, make sure you set it up in your environment.

TENGU_TOKEN=<your-rush-token>

Registration

Register for the QDX Hackathon here.

Getting Help Information for Rex Language

To get help information about the Rex language, use the following command:

chemllmhack --rex-help language

Retrieving Specific Rex Expressions

To retrieve a specific Rex expression associated with a module, use the command below:

chemllmhack --rex-help expression -rex <module_name>

Replace <module_name> with the actual name of the module you're interested in. or you could use python language to query the rex expression:

from chemllmhack import get_rex_expression
get_rex_expression('module_name')

Querying with natural language

The SDK allows a LLM friendly way to query, to query with natural language, use the following command:

from chemllmhack import query
query('your-natural-language-query')

Submitting Rex Expressions to RUSH

To submit a Rex expression to the RUSH platform, use the following command:

from chemllmhack import submit_rex_expression
submit_rex_expression('your-rex-expression')

Downloading Datasets

you can download the necessary datasets:

• Paper Dataset
• Chroma Vector Database

Configuring Google Cloud CLI

To interact with Cloud Storage using the Google Cloud CLI, follow these steps:

1. Run the following command to authenticate:

   sudo gcloud auth login
   

   or

   sudo gcloud auth application-default login
   

2. Provide the path to your credentials file. Typically, it is located at:

   /Users/<your_user_name>/.config/gcloud/application_default_credentials.json
   

Replace <your_user_name> with your actual username on your system. Make sure you grant appropriate permissions to the json file. For more information, refer to the Google Cloud CLI documentation.

Downloading Datasets with the Command Line

Use the following command to initiate the download:

command-to-download-datasets

Downloading Datasets with functions

from chemllmhack import download_vector_db
download_vector_db(credential_path='your-credential-path', destination_file_name='your-destination-file-name')

Your Task

Build an AI experiment system with the provided paper database and RAG Database LLM and RUSH platform to beat the benchmark.

Contributing

We welcome contributions from the community. If you'd like to contribute, please fork the repository and use a feature branch. Pull requests are warmly welcome.

Contact Information

For any questions or comments, please email [e-mail]. Alternatively, you can open an issue in this repository's issue tracker.

Acknowledgments

Thanks to everyone participating in the development and use of this SDK. We hope it serves you well in the QDX Hackathon.