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)
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)
static translateCentroidToOrigin(strucs, skip_solvent=True, solvent_asl=None)

Re-zeros strucs.

Parameters
  • skip_solvent (bool) – Include solvent positions into centroid.

  • solvent_asl (str or NoneType) – Solvent ASL (relevant for truthy skip_solvent).

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