Contact Identification

This module defines a routine for contact identification.

prody.apps.prody_apps.prody_contacts.prody_contacts(**kwargs)[source]

Identify contacts of a target structure with one or more ligands. Contacting atoms (or extended subset of atoms, such as residues) are outputted in PDB file format.

Parameters:

  • target – target PDB identifier or filename

  • ligand – ligand PDB identifier(s) or filename(s)

  • select – atom selection string for target structure

  • radius – contact radius (Å), default is 4.0

  • extend – output same 'residue', 'chain', or 'segment' along with contacting atoms

  • prefix – prefix for output file, default is target filename

  • suffix – output filename suffix, default is ligand filename