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.

schrodinger.application.desmond.simulation_block_data.print_usage(text=None)¶

class schrodinger.application.desmond.simulation_block_data.Array_Prop¶

Bases: object

__init__()¶

prop_value = []¶

get_prop_value()¶

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)¶

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.

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.

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.

schrodinger.application.desmond.simulation_block_data.get_ensemble_from_cfg(cfg_fname)¶

Given a cfg filename, get the ensemble class from it.

Parameters: cfg_fname (str) – cfg filename to be parsed.
Returns: The parsed ensemble class
Return type: str

schrodinger.application.desmond.simulation_block_data.get_log_props(log_fname)¶: Given a .log file, parse the header and determine if it completed okay.

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.

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.

schrodinger.application.desmond.simulation_block_data.write_sba_file(ene, log, cfg_fname, sbafile, simboxfile=None, block_len=10.0)¶: Write the sba file from specified *.ene, *.log and *.cfg files.