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