PyMOL plugin to convert SMILES to molecules

PyMOL is amazingly flexible software to visualize biomolecules. It even comes with a built-in molecular builder that allows you to mold molecules out of thin air. This builder is not really user friendly though, and a better way to introduce (small) molecules to PyMOL is desired if one wants to use it for docking.

Daylight's Simplified Molecular-input Line-Entry Specification, or SMILES, is a decades old 'language' to express a molecular structure (graph) in a single line of quasi-human readable symbols. SMILES for many drugs and other important molecules can be found on Wikipedia or PubChem. Structure sketchers such as ChemDraw and the PubChem Sketcher also allow you to generate SMILES of any structure. Although somewhat human readable (with practice), PyMOL definitely has no clue how to interpret these. This plugin changes this.

The plugin requires the installation of RDKit, an extremely useful Python module. It uses the chemical intelligence of this module to translate SMILES to a mol-block, which can be interpreted by PyMOL. But this isn't all it does. RDKit is also used to generate 1 or more 3D conformers before pushing the data to PyMOL. We live in a 3D world after all. Finally, the plugin also contains functionality (and the code) of Dimorphite-DL, a product of the Durrant lab. This allows the user to specify a pH-range for which the model will predict protonation states. For more information on this, see Ropp PJ, Kaminsky JC, Yablonski S, Durrant JD (2019) J Cheminform 11:14. doi:10.1186/s13321-019-0336-9. Protonation states can also be made explicit in the SMILES, and is thus optional.

As mentioned, we'll need to install RDKit. Depending on how you've installed PyMOL, it either uses the system Python interpreter, or something like conda. For the system interpreter, just launch a terminal. For conda, launch the appropriate prompt on Windows or just a terminal on Linux. Then give the command: pip install rdkit After installation, just download the .zip from GitHub. Use the Plugin manager in PyMOL to install the plugin. Enjoy!