schrodinger.application.desmond.repair_cms module

Collection of functions to repair structures to be used for desmond simulation

Copyright Schrodinger, LLC. All rights reserved.

schrodinger.application.desmond.repair_cms.create_cms_from_mae(input_fname: str, output_fname: str, membrane_asl: str, solvent_asl: str, cosolvent_asl: str)

This function reads in a structure file which can be either a single full-system CT or a list of component CTs. If the input is a full- system CT, then we woud pass it directly to decompose_to_comp_ct(). However, if the inputs are a list of component CTs, we would generate a full-system CT and then and then pass it to decomopse_to_comp_ct().

schrodinger.application.desmond.repair_cms.create_full_system_from_comp(input_fname, output_fname)
schrodinger.application.desmond.repair_cms.decompose_to_comp_ct(st: schrodinger.structure._structure.Structure, membrane_asl: str = '', solvent_asl: str = '', cosolvent_asl: str = '') List[schrodinger.structure._structure.Structure]

Decompose st to component cts, solute, membrane, cosolvent, solvent (if exists any).


st – Structure object representing a full-system CT


list of non-empty structures that would comprize a CMS: [full_system, membrane_st, …, water_st]

schrodinger.application.desmond.repair_cms.repair_box_vector(st: schrodinger.structure._structure.Structure)

repair box vectors when they are corrupted. create box vectors based on system size