Tools to visualize pharmacophoric features.
This is a modification of Greg Landrum's original code that control's PyMOL. This version instead takes an SDF or MOL file and outputs a PDB formatted file by taking advantage of the default element colors in PyMOL to indicate different types of pharmacophoric features. It works best using CPK spheres, and set sphere_scale=0.25.
ShowFeatsToPDB.py [optional args] <filenames>
Note: you must use --writeFeatsAsPDB to output a PDB file.
<filenames> can be one or more sd or mol formatted files.
if "-" is provided as a filename, data will be read from stdin (the console)
python ShowFeatsToPDB.py --writeFeatsAsPDB --fdef=$RDBASE/Data/BaseFeatures.fdef input.sdf > output_feats.pdb
When the output_feats.pdb file is loaded into PyMOL and colored by element, the features will have the colors listed in the table "Color Key".
Note that the --fdef=$RDBASE/Data/BaseFeatures.fdef flag is optional, and relies on RDKit's own feature definitions. If RDKit was installed using conda, this may be in $HOME/opt/anaconda3//share/RDKit/Data/BaseFeatures.fdef.
If you give executable permission to ShowFeatsToPDB.py, (using chmod +x ShowFeatsToPDB.py, you can use a simpler command line call:
ShowFeatsToPDB.py --writeFeatsAsPDB my_molecule.sdf > my_molecules_features.pdb
| Pharmacophoric Feature | Element | Color |
|---|---|---|
| Donor | F | light blue |
| Acceptor | B | pink |
| NegIonizable | O | red |
| PosIonizable | N | blue |
| ZnBinder | D | grey |
| Aromatic | P | orange |
| LumpedHydrophobe | Au | gold |
| Hydrophobe | S | yellow |
| Read more about pharmacophores here: https://en.wikipedia.org/wiki/Pharmacophore |