NaviDiv: A Comprehensive Framework for Monitoring Chemical Diversity in Generative Molecular Design

NaviDiv is a comprehensive framework for analyzing chemical diversity in generative molecular design, with a focus on understanding how different diversity metrics evolve during reinforcement learning optimization. The framework introduces multiple complementary metrics that capture different aspects of molecular variation: representation distance-based, string-based, fragment-based, and scaffold-based approaches.

Features

Multiple Diversity Metrics

• Representation Distance-Based: Using molecular fingerprints (Morgan, RDKit) and similarity metrics (Tanimoto coefficient)
• String-Based Analysis: N-gram analysis of SMILES representations for sequence-level diversity assessment
• Fragment-Based Metrics: Systematic molecular decomposition using BRICS fragmentation and frequency analysis
• Scaffold-Based Methods: Bemis-Murcko scaffold analysis for core molecular framework comparison
• Ring System Analysis: Identification and analysis of ring systems and their sizes
• Functional Group Analysis: Detection and diversity assessment of functional groups

Real-Time Monitoring & Visualization

• Interactive Molecular Visualization: 2D structural representations with sorting and filtering options
• Temporal Analysis: Monitor evolution of specific molecular fragments and cluster formation patterns
• Chemical Space Projection: t-SNE and PCA visualization of molecular diversity evolution
• Comparative Analysis: Similarity assessment against user-defined reference sets

Integration Capabilities

• REINVENT4 Compatible: Seamless integration with reinforcement learning workflows
• Real-Time Penalty Functions: Adaptive diversity constraints during generation
• Computational Efficiency: Minimal overhead (~3 seconds per 100 molecules)
• Statistical Analysis: Comprehensive diversity trend reports with significance testing

Installation

To install NaviDiv, follow these steps:

1. Clone the Repository:

   git clone https://github.com/mohammedazzouzi15/NaviDiv.git
   cd NaviDiv

2. Create and Activate Conda Environment:

   conda create -n NaviDiv python==3.12
   conda activate NaviDiv

3. Choose Installation Type:

   • Standard Installation (Core Framework):

     Install the core NaviDiv package with essential dependencies for diversity analysis:

     pip install -e .

   • Full Installation (with REINVENT4 Integration):

     For complete generative molecular design workflows with REINVENT4:

     First, install PyTorch following the official documentation:

     conda install pytorch==2.8.0 torchvision==0.23.0 torchaudio==2.8.0 pytorch-cuda=12.4 -c pytorch -c nvidia

     Then install REINVENT4 and NaviDiv with full dependencies:

     git clone https://github.com/mohammedazzouzi15/REINVENT4_div.git
     cd REINVENT4_div
     pip install --no-deps -e .
     cd ../
     pip install -e .[reinvent]

4. Optional Dependencies:

   For enhanced molecular manipulation capabilities:

   conda install openeye::openeye-toolkits

Quick Start

Interactive Dashboard

Launch the Streamlit dashboard for comprehensive diversity analysis:

streamlit run app.py

Programmatic Usage

from navidiv.diversity.diversity import diversity_all
from rdkit import Chem

# Load SMILES strings
smiles_list = ["CCO", "CCN", "CCC"]  # Your SMILES data

# Calculate various diversity metrics
richness = diversity_all(smiles=smiles_list, mode="Richness")
internal_diversity = diversity_all(smiles=smiles_list, mode="IntDiv")
scaffold_diversity = diversity_all(smiles=smiles_list, mode="BM")

# Analyze functional groups and ring systems
functional_groups = diversity_all(smiles=smiles_list, mode="FG")
ring_systems = diversity_all(smiles=smiles_list, mode="RS")

Integration with REINVENT4

from navidiv.reinvent.run_staged_learning_2 import run_staged_learning
from navidiv.reinvent.InputGenerator import InputGenerator
from omegaconf import DictConfig

# Create configuration
cfg = DictConfig({...})  # Your REINVENT config

# Generate input files with diversity filters
input_generator = InputGenerator(cfg)
input_generator.generate_input()

# Run staged learning with diversity constraints
run_staged_learning(cfg)

Performance

• Real-Time Analysis: <3 seconds per 100 molecules on standard CPU
• Scalable: Complete analysis of 10,000 molecules in ~5 minutes
• Memory Efficient: Optimized for large-scale molecular datasets
• Integration Ready: Minimal computational overhead for existing workflows

Citation

If you use NaviDiv in your research, please cite:

Comming soon

Data Availability: The framework is freely available on GitHub at https://github.com/mohammedazzouzi15/NaviDiv.

Contributing

We welcome contributions! Please see our contribution guidelines for:

• Bug Reports: Issue templates and debugging information
• Feature Requests: Enhancement proposals and use case descriptions
• Code Contributions: Pull request guidelines and coding standards
• Documentation: Help improve examples and tutorials

Development Setup:

git clone https://github.com/mohammedazzouzi15/NaviDiv.git
cd NaviDiv
pip install -e .[dev]
pre-commit install

License

This project is licensed under the MIT License - see the LICENSE file for details.

Acknowledgments

This work was supported by the Swiss National Science Foundation (SNSF).