schrodinger.protein.findhets module¶

Module for finding ‘het’ groups in a protein structure. These are the groups which would typically be represented by HETATOM records in PDB file and appear as orange when a file is first imported into Maestro. However this module determines whether a residue represents a ‘het’ group independently of any information from the PDB file and thus may be used on strucures which do not originate from PDB files.

This module defines a “het” as a group of atoms which are bound to each other and are not in any standard residues. This includes ligands (including covalently bound ones), ions, cofactors, etc.

Usage:

hets = findhets.find_hets(st)
for atoms in hets:
    <do>

schrodinger.protein.findhets.find_hets(st, include_metals=True, include_hydrogens=False, excluded_hets=None)¶

Finds all het groups in the st, and returns them as a list of atom lists. (each atom list is a list of atom indecies)

This module defines a “het” as a group of atoms which are bound to each other and are not in any standard residues. This includes ligands (including covalently bound ones), ions, cofactors, etc.

The list includes heavy atoms only by default

include_metals: whether to consider single metal atoms as het groups include_hydrogens: whether to include het’s hydrogen atoms in the list excluded_hets: a list of residue names to not consider het groups