A Simple Pharmacophore-Toolkit

The Pharmacophore-Toolkit is built on RDKit and allows for building simple pharmacophore models. The Pharmacophore-Toolset can generate models from crystal structures, docking poses, or SMILES string. To generate a 3D model, a .pml file will be generated. This files contains scripts to generate spheres with color and XYZ coordinates defined. The final 3D image can be rendered in PyMOL.

Documentation for the project can be found here.

Install

You can install the Pharmacophore-Toolkit using pip:

pip install pharmacophore-toolkit

Alternatively, the environment can be created by cloning the repository and then running the following conda script:

conda env create -f environment.yaml

Tutorials

Tutorials are written as Jupyter Notebooks and can be found here. The 3D drawing tools are also supported in Marimo notebooks, which can be found here. The Pharmacophore-Toolkit can generate several types of images:

Example Images

3D Model

A 3D conformation of molecules and alignment was performed using RDKit. Spheres can be generated for each query molecule to highlight pharmacophore features, such as Hydrogen Bond Donor/Acceptor, Hydrophobic, Aromatic, etc. The molecules can be generated in 3D using two methods:

• py3Dmol

• PyMOL

2D Model

The pharmacophore features can also be depicted as a 2D image, where each atom is highlighted with their respective pharmacophore features.

Similarity Map

For funsies, a method to generate Similarity Maps are also available. Final image generation requires Cairo installation. Additional information on how Similarity Maps work can be found on the RDKit blog.

Citation

If you find this helpful in your work, consider a citation:

@software{lin_pharmacophore_toolkit,
  author  = {Lin, Tony Eight},
  title   = {Pharmacophore-Toolkit: Generate Simple Pharmacophore Models with RDKit},
  year    = {2023},
  version = {X.X.X},
  url     = {https://github.com/tlint101/pharmacophore-toolkit}
}

NOTE: Replace 'X.X.X' with the pharmacophore-toolkit version used.