Package schrodinger :: Package protein :: Module remediate

Module remediate


Module for remediating names in PDB structures - converting PDBv2 residue and
atom names to PDBv3 convention.

Used by:
  psp-src/python/modules/PXfiles.py
  mmshare/python/scripts/residue_scanning_backend.py

Copyright Schrodinger, LLC. All rights reserved.

Functions

[hide private]

remediate_ct(ct)

Variables

[hide private]

atom_exch = {" C5A DT": " C7 DT", "2H2* A": "H2'' A", "...

schrod_atom_exch = {"1H ASH": " H1 ASH", "2H ASH": " H2 ...

Variables Details

[hide private]

atom_exch

Value:

{" C5A  DT": " C7   DT", "2H2*   A": "H2''   A", "2H2*   C": "H2''   C
", "2H2*   T": "H2''   T", "2H2*   G": "H2''   G", "2H2*   I": "H2''  
 I", "1H2*   A": " H2'   A", "1H2*   C": " H2'   C", "1H2*   U": " H2'
   U", "1H2*   G": " H2'   G", "1H2*   I": " H2'   I", "5HO*   A": "HO
5'   A", "5HO*   C": "HO5'   C", "5HO*   U": "HO5'   U", "5HO*   G": "
HO5'   G", "5HO*   I": "HO5'   I", "5HO*  DT": "HO5'  DT", "5HO*  DA":
 "HO5'  DA", "5HO*  DC": "HO5'  DC", "5HO*  DG": "HO5'  DG", "5HO*  DI
": "HO5'  DI", "5HO*  DU": "HO5'  DU", "3HO*   A": "HO3'   A", "3HO*  
...

schrod_atom_exch

Value:

{"1H   ASH": " H1  ASH", "2H   ASH": " H2  ASH", "3H   ASH": " H3  ASH
", " HN2 ASH": " H2  ASH", "1HB  ASH": " HB2 ASH", "2HB  ASH": " HB3 A
SH", "1H   GLH": " H1  GLH", "2H   GLH": " H2  GLH", "3H   GLH": " H3 
 GLH", " HN2 GLH": " H2  GLH", "1HB  GLH": " HB2 GLH", "2HB  GLH": " H
B3 GLH", "1HG  GLH": " HG2 GLH", "2HG  GLH": " HG3 GLH", "1H   LYN": "
 H1  LYN", "2H   LYN": " H2  LYN", "3H   LYN": " H3  LYN", " HN2 LYN":
 " H2  LYN", "1HB  LYN": " HB2 LYN", "2HB  LYN": " HB3 LYN", "1HG  LYN
": " HG2 LYN", "2HG  LYN": " HG3 LYN", "1HD  LYN": " HD2 LYN", "2HD  L
...