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. Additional information can be found under the Tutorials section. The Pharmacophore-Toolkit can result in two types:

3D Model

3D conformation of molecules and alignment was performed using RDKit. Spheres were generated based on Serotonin. Blue spheres represent hydrogen donors and gold spheres represent aromatic rings. The 3D images were generated in PyMOL.

2D Model

Similarity map of molecules. All molecules were compared to Serotonin. More information can be seen at RDKit documentation.

Tutorials

Tutorials are written as JupyterNotebooks and 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

Note

Note: The Pharmacophore-Toolkit relies on cairosvg to create images before being converted into .png format. Depending on your workstation/machine, the CairoSVG package will need to be installed manually. Installation instructions can be found here. If it is already installed on your machine globally, on my machine, I used conda to install cairosvg:

conda install conda-forge::cairosvg

This solved the problem on my machine, but may differ from yours.