EMolCombiner

A fragment-based molecule generation tool for drug discovery

Piggybacking off EMolFrag, EMolCombiner offers a fast way to generate molecules with more control than other similar tools. Written in Python, the code is easy to modify for your purposes, yet fast, due to RDKITs' C++ backend.

Getting Started

These instructions will get you a copy of the project up and running on your local machine for development and testing purposes.

Prerequisites

Only dependencies are numpy, rdkit and networkx, best installed via:

pip install {numpy, networkx} conda install -c rdkit rdkit

Usage

usage: build_mols.py [-h] --input_directory INPUT_DIRECTORY
                     [--output_directory OUTPUT_DIRECTORY]
                     [--num_mols NUM_MOLS] [--draw]

Probabilistically generate new molecules based off fragments.

optional arguments:
  -h, --help            show this help message and exit
  --input_directory INPUT_DIRECTORY
                        emolfrag output dir
  --output_directory OUTPUT_DIRECTORY
                        emolcombiner output dir
  --num_mols NUM_MOLS   number of mols to generated
  --draw                whether to draw output mols

Only required arg is the EMolFrag output directory; everything else has reasonable defaults.

Example outputs:

License

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