Package schrodinger :: Package protein :: Module findhets

Module findhets

Classes

GroupByConnectivity
Groups the atoms by molecule connectivity.

AddNeighborGroups
For each untemplated atom that is bound to a templated het, create a list of atoms that it is bound to that are not templated.

Functions

[hide private]

is_metal(atom)
Returns boolean: whether atom is a metal or not

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.

Variables

[hide private]

__doc__ = ...

MAX_ATOM_ITERATIONS = 50

MAX_BRANCH_ITERATIONS = 15

MAX_HET_SIZE = 200

non_het_resnames = ["ALA", "VAL", "PHE", "PRO", "MET", "ILE", ...

metal_charges = {11: [1], 12: [2], 19: [1], 20: [2], 26: [2, 3...

Function Details

[hide private]

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

Variables Details

[hide private]

doc

Value:

"""
Module for finding 'het' groups in a protein structure. These are the 
groups
which would typically be represented by HETATOM records in PDB file an
d
appear as orange when a file is first imported into Maestro. However t
his
module determines whether a residue represents a 'het' group independe
...

non_het_resnames

Value:

["ALA", "VAL", "PHE", "PRO", "MET", "ILE", "LEU", "ASP", "GLU", "LYS",
 "ARG", "SER", "THR", "TYR", "HIS", "CYS", "ASN", "GLN", "TRP", "GLY",
 "2AS", "3AH", "5HP", "ACL", "AIB", "ALM", "ALO", "ALY", "ARM", "ASA",
 "ASB", "ASK", "ASL", "ASQ", "AYA", "BHD", "BMT", "BNN", "BUC", "SPC",
 "BUG", "C5C", "C6C", "CCS", "CEA", "CHG", "CLE", "CME", "CSD", "CSO",
 "CSP", "CSS", "CSW", "CXM", "CY1", "CY3", "CYG", "CYM", "CYQ", "DAH",
 "DAL", "DAR", "DAS", "DCY", "DGL", "DGN", "DHA", "DHI", "DIL", "DIV",
 "DLE", "DLY", "DNP", "DPN", "DPR", "DSN", "DSP", "DTH", "DTR", "DTY",
...

metal_charges

Value:

{11: [1], 12: [2], 19: [1], 20: [2], 26: [2, 3], 27: [2, 3], 28: [2, 3
], 29: [1, 2, 3], 30: [2]}