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)[source]¶

Bases: object

__init__(**kwargs)[source]¶

update(**kwargs)[source]¶

getStructureSize(st)[source]¶: 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)[source]¶: Returns the vectors representing the box. Origin is the back face bottom left. Returns None on error (after displaying a dialog box)

calculateVolume(st)[source]¶: Will return 0 on error (after showing dialog)

findMinVolume(st)[source]¶

static translateCentroidToOrigin(strucs, skip_solvent=True, solvent_asl=None)[source]¶

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)[source]¶

schrodinger.application.desmond.system_builder_util.truncateProtein(protein_st, ligand_st, retain_ligand=False, truncate_distance=0, restrain_distance=- 1)[source]¶

Parameters: restrain_distance – -1 means no restrain, 0 means restrain all atoms

schrodinger.application.desmond.system_builder_util.truncate_solvate_protein(opt)[source]¶

schrodinger.application.desmond.system_builder_util.find_equivalent_st(my_st, st_list, pname)[source]¶: Find a equivalent st of my_st from iterable st_list Copy the pname values to ‘r_ffio_custom_charge’ of my_st