schrodinger.application.desmond.system_builder_util module¶
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.
-
class
schrodinger.application.desmond.system_builder_util.
DesmondBoxSize
(**kwargs)¶ Bases:
object
-
__init__
(**kwargs)¶ Initialize self. See help(type(self)) for accurate signature.
-
update
(**kwargs)¶
-
getStructureSize
(st)¶ Returns the a, b, & c absolute coordinates, even when the user specified buffer distances Returns None if there are no atoms in the Workspace
-
getBoxVectors
(st)¶ Returns the vectors representing the box. Origin is the back face bottom left. Returns None on error (after displaying a dialog box)
-
calculateVolume
(st)¶ Will return 0 on error (after showing dialog)
-
findMinVolume
(st)¶
-
translateCentroidToOrigin
(strucs)¶
-
minimizeVolume
(strucs)¶
-
-
schrodinger.application.desmond.system_builder_util.
truncateProtein
(protein_st, ligand_st, retain_ligand=False, truncate_distance=0, restrain_distance=-1)¶ Parameters: restrain_distance – -1 means no restrain, 0 means restrain all atoms
-
schrodinger.application.desmond.system_builder_util.
truncate_solvate_protein
(opt)¶
-
schrodinger.application.desmond.system_builder_util.
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