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.

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, truncation_site_flag: Optional[str] = None)¶

Given a receptor and ligand, truncate the receptor beyond the provided distance from the ligand. Any cut bonds will be replaced with a bond to hydrogen.

Parameters:

restrain_distance – -1 means no restrain, 0 means restrain all atoms
truncation_site_flag – If provided, corresponds to a string for an atom-property that will be set to 1 for the atoms where bonds are removed during truncation.

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