portein.interactions

Protein-ligand interaction detection via peppr.ContactMeasurement.

InteractionSet.find() wraps peppr’s per-interaction-type methods into a single InteractionSet carrying receptor/ligand AtomArray references plus the detected H-bonds, salt bridges, π-cation interactions, and π-stacking interactions.

The InteractionSet can be passed to portein.Pymol via its interactions field to overlay the interactions on a PyMOL render.

Classes

HBond(donor_atom_idx, acceptor_atom_idx, ...)	Hydrogen bond between a donor heavy atom and an acceptor heavy atom.
InteractionSet(receptor, ligand[, hbonds, ...])	Bundle of detected protein-ligand interactions plus the source structures.
PiCation(cation_atom_idx, ring_atom_indices, ...)	π-cation interaction between an aromatic ring and a cationic atom.
PiStacking(receptor_ring_atom_indices, ...)	π-stacking interaction between two aromatic rings.
SaltBridge(receptor_atom_idx, ligand_atom_idx)	Salt bridge between an oppositely-charged receptor and ligand atom.