Package schrodinger :: Package application :: Package desmond :: Module repair_cms

Module repair_cms

Functions

create_cms_from_mae(input_fname, output_fname, membrane_asl, solvent_asl)

create_full_system_from_comp(input_fname, output_fname)

decompose_to_comp_ct(in_st, membrane_asl="", solvent_asl="")
decompose in_st to component cts, solute, membrane, solvent, if exists any.

repair_box_vector(st)
repair box vectors when they are corrupted.

_extract_solvent(st, asl="")
extract water molecules

_extract_membrane(st, asl="")
extract membrane assign reference custom charges for lipid molecules found at system_builder/data/lipid_charge.mae

_extract_ion(st)
extract ions

Variables

[hide private]

__doc__ = ...

water_smarts = ["[H]O[H]"]

zob_water_smarts = ["[H]O([H])_[*]", "[H]O[H]_[*]"]

Function Details

[hide private]

decompose_to_comp_ct(in_st, membrane_asl="", solvent_asl="")

decompose in_st to component cts, solute, membrane, solvent, if exists any. return list of component cts return full_system ct also if return_full_system is true

repair_box_vector(st)

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

Variables Details

[hide private]

doc

Value:

"""
Collection of modules to repair structures to be used for desmond simu
lation

Copyright Schrodinger, LLC. All rights reserved.
"""