Package schrodinger :: Package application :: Package desmond :: Module simulation_block_data

Module simulation_block_data

Block data calculation script.

For a MD Simulation, calculates properties from log, energy and simbox files Calculates block averages of properties in energy file.

Classes

Array_Prop

Functions

_debug_print(s)
Prints the string 's' if 'is_debugging' is True.

print_usage(text=None)

calc_block_average(ene_fname, prop_list, sba_fname, start_line, time_column=0, start_time=0.0, block_length=10.0)

get_listof_props_ene(ene_fname)
Given a .ene file, parse the ]header and get a list of properties.

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.

get_top_level_props(ene_fname)
Given a .ene file, parse the header and get top level props.

get_log_props(log_fname)
Given a .log file, parse the header and determine if it completed okay.

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.

get_block_summary(inp_content, start_index, stop_index)
From block content get averages, sd, slope and units.

write_sba_file(ene, log, sbafile, simboxfile=None, block_len=10.0)
Write the sba file from specified *.ene and *.log files.

Variables

usage = 'Usage: %prog <-e .ene file> <-l .log file> <-s simbox...

opt = optparse.OptionParser(usage)

is_debugging = True
hash(x)

Function Details

Given a .ene file, parse the header and get top level props. Print those in sba file.

From block content get averages, sd, slope and units. Return them as dictionary.

Variables Details

Value:

'Usage: %prog <-e .ene file> <-l .log file> <-s simbox.dat file> <-c .
sba file> <-n block_length > [options]'