ligandsplitter 0.0.4

A python package for splitting, creating, and validating ligand files

ligandsplitter

A Python package for creating, splitting, and validating ligand files

Installation

1. Manual

git clone https://github.com/leesch27/ligandsplitter.git

2. PyPi

pip install ligandsplitter

Usage

ligandsplitter contains five main modules that aid in the generation, search and retrieval, isolation, and validation of ligands in the form of MOL2 files.

Ligand Generation

When provided a SMILES string representation of a ligand, MOL2 files of that ligand can be created.

Ligand Search and Retrieval

Using rcsb-api, ligands can be searched using RCSB PDB's Advanced Search feature by user-defined critera.

Ligand Isolation/"Splitting" from Receptor File

Provided a PDB/CIF file of a macromolecule containing at least one ligand, ligands can be extracted and written to individual MOL2 files.

Ligand Validation

From a list of SMILES strings, unique ligands can be determined and are checked to ensure they do not violate any atomic or bonding rules.

Jupyter Notebooks

ligandsplitter was initially made to enhance a series of notebooks that explore molecular docking using Jupyter notebooks. To view this series, known as basil_dock, you can click here.

Copyright

Copyright (c) 2024, Lee Schoneman

Acknowledgements

Project based on the Computational Molecular Science Python Cookiecutter version 1.10.