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

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.

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
...