schrodinger.application.desmond.mdpose.mdpose_average_structure module¶
Description: A module to generate average structure from watermap trajectory.
Copyright Schrodinger, LLC. All rights reserved.
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schrodinger.application.desmond.mdpose.mdpose_average_structure.
align_structure
(ref_fname, refined_fname, average_fname)¶
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schrodinger.application.desmond.mdpose.mdpose_average_structure.
generate_protein_structure
(dsim, frame_list=[], superpose=False, avgst_asl_expr='NOT water', fit_asl_expr=None)¶
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schrodinger.application.desmond.mdpose.mdpose_average_structure.
generate_water_structure
(hs_water_fname)¶
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schrodinger.application.desmond.mdpose.mdpose_average_structure.
minimize_structure
(raw_average_fname, minimized_fname, forcefield='2.0')¶ using impref to minimize the average structure
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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)