StrainReliefChat

StrainReliefChat is a naive modular RAG/CAG application for learning more about the StrainRelief drug discovery tool! StrainRelief is a tool developed by Prescient Design to accelerate small molecule drug discovery by using mahcine learning to predict ligand strain energies with quantum mechanical accuracy.

StrainReliefChat is built using a hybrid retrieval and cached augmented generation (RAG/CAG) approach:

1. The full StrainRelief paper is loaded and cached in the context window for all queries.
2. Reference papers cited in StrainRelief are embedded and available for retrieval.
3. The StrainRelief code repository is embedded and available for retrieval.

The chatbot is deployed with streamlit and is available here.

Note: StrainReliefChat runs by default using OpenAI's GPT-4.1-nano model, however for optimal performance using GPT-4.1 you will need to enter your own OpenAI API Key.

PaperQuery

StrainReliefChat™️ is built on the more general PaperQuery framework...

Setup

Installation

mamba env create -f environment.yml
mamba activate paper_query

pre-commit install

API Keys

API keys are stored in ~/.config/my_api_keys. You will need to create and populate this yourself to run the app locally. Example format:

TEMPLATE_API_KEY=some_key

Usage

Both StrainReliefChat and PaperQuery are available through the command line or a streamlit app.

Streamlit App

• StrainReliefChat: locally at src/paper_query/ui/strain_relief_app.py, deployed here.

• PaperQuery: locally at src/paper_query/ui/custom_app.py, deployment coming soon.

streamlit run path/to/app.py

Commandline Chatbots

chatbot

chatbot [model] [provider] is a CLI for a common or garden chatbot.

paper-query

paper-query [model] [provider] [paper] is a CLI for a chatbot querying a single paper. The entire paper is held in context.

code-query

code-query [model] [provider] [paper] [code] is a RAG CLI chatbot for querying a paper and it's code repository. The entire paper is held in context.

paper-query-plus

paper-query-plus [model] [provider] [paper] [references] is a RAG CLI chatbot for querying a paper and all of its references. The paper is held in context, references are stored in embeddings.

hybrid-query

hybrid-query [model] [provider] [paper] [references] [code] is a RAG CLI chatbot for querying both code repositories and literature. The paper is held in context, references are stored in embeddings. StrainReliefChat is an example of this.

Unit Tests

• pytest tests/ - runs all tests (unit, app and integration)
• pytest tests/ -m "app" - runs all streamlit app tests
• pytest tests/ -m "integration" - runs all integration tests