schrodinger.application.desmond.simulation_block_data module¶
Block data calculation script.
For a MD Simulation, calculates properties from log, energy and simbox files Calculates block averages of properties in energy file.
Copyright Schrodinger, LLC. All rights reserved.
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schrodinger.application.desmond.simulation_block_data.
print_usage
(text=None)¶
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class
schrodinger.application.desmond.simulation_block_data.
Array_Prop
¶ Bases:
object
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__init__
()¶
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prop_value
= []¶
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get_prop_value
()¶
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schrodinger.application.desmond.simulation_block_data.
calc_block_average
(ene_fname, prop_list, sba_fname, start_line, time_column=0, start_time=0.0, block_length=10.0)¶
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schrodinger.application.desmond.simulation_block_data.
get_listof_props_ene
(ene_fname)¶ Given a .ene file, parse the ]header and get a list of properties.
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schrodinger.application.desmond.simulation_block_data.
get_print_simbox_data
(simbox_fname, sba_fname)¶ Given a simbox.dat file, parse the file and print simulation box details in the sba file.
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schrodinger.application.desmond.simulation_block_data.
get_top_level_props
(ene_fname)¶ Given a .ene file, parse the header and get top level props. Print those in sba file.
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schrodinger.application.desmond.simulation_block_data.
get_log_props
(log_fname)¶ Given a .log file, parse the header and determine if it completed okay.
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schrodinger.application.desmond.simulation_block_data.
parse_sba
(sba_fname)¶ Given name of a sba file name find all blocks except time and job details and return their average, sd and slope.
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schrodinger.application.desmond.simulation_block_data.
get_block_summary
(inp_content, start_index, stop_index)¶ From block content get averages, sd, slope and units. Return them as dictionary.