schrodinger.application.desmond.mdpose.mdpose_average

Module mdpose_average_structure

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

Functions

generate_protein_structure(dsim, frame_list=[], superpose=False, avgst_asl_expr='NOT water', fit_asl_expr=None)

generate_water_structure(hs_water_fname)

minimize_structure(raw_average_fname, minimized_fname, forcefield='2.0')
using impref to minimize the 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

align_structure(ref_fname, refined_fname, average_fname)

Variables

[hide private]

__doc__ = ...

DEFAULT_ASL = 'NOT water'

RMSF_PROPERTY = 'r_desmod_mdpose_rmsf'

__package__ = 'schrodinger.application.desmond.mdpose'

Function Details

[hide private]

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)
debug (boolean)

Variables Details

[hide private]

doc

Value:

"""

Description: A module to generate average structure from watermap traj
ectory.

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

Module 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)

__doc__

refine_structure(st, do_flips=False, sample_water=True, asl=`'all'`, max_com=10000, pH=`'neutral'`, minimize=False, quite=False, debug=False)

doc