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 = {' *C2 BIZ': ' C2\' BIZ', ' *C3 BIZ': ' C3\' BIZ',...

schrod_atom_exch = {' C5M DT': ' C7 DT', ' H1 HOH': ' HW1 ...

__package__ = 'schrodinger.protein'

Variables Details

[hide private]

atom_exch

Value:

{' *C2 BIZ': ' C2\' BIZ',
 ' *C3 BIZ': ' C3\' BIZ',
 ' *C4 BIZ': ' C4\' BIZ',
 ' *C5 BIZ': ' C5\' BIZ',
 ' *C6 BIZ': ' C6\' BIZ',
 ' *C7 BIZ': ' C7\' BIZ',
 ' *C9 BIZ': ' C9\' BIZ',
 ' *H3 BIZ': ' H3\' BIZ',
...

schrod_atom_exch

Value:

{' C5M  DT': ' C7   DT',
 ' H1  HOH': ' HW1 HOH',
 ' H2  HOH': ' HW2 HOH',
 ' HN2 ARN': ' H2  ARN',
 ' HN2 ASH': ' H2  ASH',
 ' HN2 GLH': ' H2  GLH',
 ' HN2 HID': ' H2  HID',
 ' HN2 HIE': ' H2  HIE',
...