Package schrodinger :: Package protein :: Module pdbname

Module pdbname

Uses MacroModel substructure definitions to set PDB atom and residue names for a structure. Also re-numbers residues, and optionally adds bond orders.

Classes

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Substructure
Holds the information about a substructure

Functions

[hide private]

find_oxt_atom(atoms)
Given a list of atom objects, returns the OXT atom (oxygen of the -COOH) bound to the C-termini atom of the group.

assign_pdb_names(struct, res_names=True, atom_names=True)
Assign PDB residue and/or atom names to struct.

renumber_residues(struct, chains)
Renumber all residues to have a unique residue number and have residue numbers that are contiguous.

process_structure(struct, renumber_chains=None, assign_bond_orders=False)

Variables

[hide private]

__doc__ = ...

_subs_table = [['HN-N0-C3(-H1)(-H1)-C2=O2', 'GLY ', ' H ; N ...

SUBSTRUCTURES = []

__package__ = 'schrodinger.protein'

atom_types = ' CT ; H1 ; H1 ; H1 ; C ; O '

definition = 'C3(-H1)(-H1)(-H1)-C2=O2'

restype = 'ACE '

sub = <schrodinger.protein.pdbname.Substructure object at 0x7f...

Function Details

[hide private]

find_oxt_atom(atoms)

Given a list of atom objects, returns the OXT atom (oxygen of the -COOH) bound to the C-termini atom of the group. If no such atom is found, None is returned.

TODO: Extend to include other termini atoms.

assign_pdb_names(struct, res_names=True, atom_names=True)

Assign PDB residue and/or atom names to struct. This is based on substructure definitions for standard residues. Anything not in the substructure database is left untouched.

Parameters:

struct (schrodinger.structure.Structure) - The structure to operate on. This structure is modified in-place.
res_names (bool) - If True (default), rename matching residues, if False, do not.
atom_names (bool) - If True (default), rename matching atoms to the proper PDB atom type, if False, do not.

renumber_residues(struct, chains)

Renumber all residues to have a unique residue number and have residue numbers that are contiguous.

Parameters:

struct (schrodinger.structure.Structure) - The structure to operate on. This structure is modified in-place.
chains (list or 'all') - A list of chains to renumber, or the string 'all' if all chains should be fixed.

Variables Details

[hide private]

doc

Value:

"""
Uses MacroModel substructure definitions to set PDB atom and residue n
ames for
a structure. Also re-numbers residues, and optionally adds bond orders
.

Copyright Schrodinger, LLC. All rights reserved.
"""

_subs_table

Value:

[['HN-N0-C3(-H1)(-H1)-C2=O2',
  'GLY ',
  ' H  ; N  ; CA ;1HA ;2HA ; C  ; O  '],
 ['HN-N0-C3(-H1)(-CN(-H1)(-H1)-H1)-C2=O2',
  'ALA ',
  ' H  ; N  ; CA ; HA ; CB ;1HB ;2HB ;3HB ; C  ; O  '],
 ['HN-N0-C3(-H1)(-C3(-H1)(-H1)-C2(=O2)-OM)-C2=O2',
  'ASP ',
...

sub

Value:

<schrodinger.protein.pdbname.Substructure object at 0x7f2d46be4a90>