schrodinger.application.desmond.mdpose.mdpose_average_structure module

Description: A module to generate average structure from watermap trajectory.

Copyright Schrodinger, LLC. All rights reserved.

schrodinger.application.desmond.mdpose.mdpose_average_structure.align_structure(ref_fname, refined_fname, average_fname)
schrodinger.application.desmond.mdpose.mdpose_average_structure.generate_protein_structure(dsim, frame_list=[], superpose=False, avgst_asl_expr='NOT water', fit_asl_expr=None)
schrodinger.application.desmond.mdpose.mdpose_average_structure.generate_water_structure(hs_water_fname)
schrodinger.application.desmond.mdpose.mdpose_average_structure.minimize_structure(raw_average_fname, minimized_fname, forcefield='2.0')

using impref to minimize the average structure

schrodinger.application.desmond.mdpose.mdpose_average_structure.refine_structure(st, do_flips=False, sample_water=True, asl='all', max_com=10000, pH='neutral', minimize=False, quite=False, debug=False)

A function to refine the average structure

Parameters:
  • do_flips (boolean) – sample ASN/GLN/HIS Chi flips (default=False).
  • asl (string) – ASL expression for which residues to sample (default=”all”).
  • sample_water (boolean) – sample water orientations (default=True)
  • max_com (int) – maximum cluster complexity for which full sampling will still be performed (default=10000).
  • pH (string) – pH at which to sample (“very_low”, “low”, “neutral”, or “high”) (default=”neutral”).
  • minimize (boolean) – minimize hydrogens of altered species (default=False).
  • quite (boolean) – suppress output (default=False)