syndirella 4.0.3a0

Synthetically Driven Elaborations

Syndirella (Synthesis Directed Elaborations) is a tool for generating and scoring synthetically practical elaborations of molecules designed from fragment screens. Starting from the retrosynthetic analysis of fragment merged molecules, superstructures of the original reactants are found by catalog search and filtered by selectivity issues. The elaborated final products are defined by reaction SMIRKS patterns and energy minimized in the protein with restraints to experimental data.

Documentation

Full Documentation - Complete user guide, API reference, and examples

Quick Start

Installation

conda create -n syndirella python=3.10
conda activate syndirella
pip install syndirella

Basic Usage

1. Setup AiZynthFinder (required for retrosynthesis):

   syndirella setup-aizynth
   

2. Run the pipeline:

   syndirella run -i input.csv -o output_directory -t templates/ --hits_path fragments.sdf --metadata metadata.csv
   

Example Input

Create a CSV file with your fragment data:

smiles,hit1,hit2,hit3,template,compound_set
O=C(NC1CC(C(F)(F)F)C1)c1cc2ccsc2[nH]1,Ax0556a,Ax0566a,,Ax0310a,my_compound_set
CC(=O)Nc1cc(CC(=O)NCC(NC(=O)CCl)c2cccnc2)c(NC(C)=O)nn1,1346a,,,Ax1346a,my_compound_set

Requirements

• Python 3.10
• RDKit
• AiZynthFinder
• Fragmenstein
• Additional dependencies (see pyproject.toml)

Learn More

• Examples - Jupyter notebooks and sample data
• User Guide - Detailed usage instructions
• Reaction Constants - Advanced reaction settings and options

License

This project is licensed under the MIT License.