Package schrodinger :: Package application :: Package desmond :: Module system_builder_util
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Module system_builder_util

The script truncates protein beyond truncate_distance from ligand atoms, restrain remaining protein heavy atoms beyond restrain_distance from ligand atoms, and solvate it by solvent_buffer distance. The truncation is done by residue based ASL.

Copyright Schrodinger, LLC. All rights reserved.

Classes [hide private]
  DesmondBoxSize
Functions [hide private]
 
truncateProtein(protein_st, ligand_st, retain_ligand=False, truncate_distance=None, restrain_distance=None)
 
truncate_solvate_protein(opt)
 
find_equivalent_st(my_st, st_list, pname)
Find a equivalent st of my_st from iterable st_list Copy the pname values to 'r_ffio_custom_charge' of my_st
Variables [hide private]
  __doc__ = ...
  usage = ...
  parser = cmdline.SingleDashOptionParser(usage)
  __package__ = 'schrodinger.application.desmond'
Variables Details [hide private]

__doc__

Value:
"""
The script truncates protein beyond truncate_distance from ligand atom\
s, restrain remaining protein heavy atoms beyond restrain_distance fro\
m ligand atoms, and solvate it by solvent_buffer distance. The truncat\
ion is done by residue based ASL.

Copyright Schrodinger, LLC. All rights reserved.

...

usage

Value:
'''
  %prog [options]

Description:
  %prog is a tool to solvate binding site.

Example:
  %prog -protein protein.mae -ligand ligand.mae
...