Package schrodinger :: Package test :: Package stu :: Package outcomes :: Module desmond_workups

Module desmond_workups

Desmond workup techniques, all based on actual numerical results. Intended for import and use as a test workup.

Running directly allows execution of any of the workup methods

Methods for comparing the following Desmond-style information:

Metadynamics FES files
FEP energies from FEP 'result' files
Surface area of membrane systems
.ene files:
- similarity to a reference ene file
log files: Calculation speed (ns/day)
st2 files: comparison of median, mean, and standard deviation to reference values
deltaE.txt files: compare two deltaE.txt files

Classes and helper functions have 'private' names, as only the workup methods are intended to be imported and used as test workups.

$Revision 0.1 $

To Do:

improve speed test to print avg ns/day.
improve speed test to be dependent on cpu^0.8

Classes

[hide private]

_EneFile
Class to find and contain the information in a Desmond .ene file.

Functions

[hide private]

_FES(filename)
Returns a numpy array based on a FES format file.

desmond_compare_FES(file1, file2, tolerance=0.1)
Compare metadynamics FES files.

desmond_FEP_energies(filename, reference, tolerance=0.5)
Compares the deltaF in an FEP result file to a standard.

desmond_FEP_check_html(filename)
Tests the html file written by a Desmond FEP job

desmond_check_surface_area(filename, reference, tolerance=0.5, side1='r_chorus_box_ax', side2='r_chorus_box_bx')
Compares surface area to a standard with optional tolerance and optional choice of box sides.

desmond_tgz_file_list(tgz_fname, *fnames_to_check)

desmond_compare_ene(file1, file2, tolerance, *quantities)
Compares two Desmond ene files.

desmond_speed(filename, reference_rate, tolerance=0.05)
Compares the average rate per step in ns/day against a standard.

desmond_stage_time(log_file, stage_num, max_time)

desmond_st_stats(filename, *options)
Compares the mean, median and/or standard deviation of a desmond st2 file to reference values.

_test_and_print(values, reference, tolerance, function, name)

_normalize_angular_values(array, degree=True)
Centers an array of angles to minimize its standard deviation.

read_dE_file(fname)
Read a dE file and return a dict from time to energy_dict; energy_dict is a dict from (lambda_win, lambda_win) to energy value

desmond_compare_deltaE(file1, file2)
Compares two Desmond deltaE.txt files.

desmond_compare_energy_group(file1, file2, tolerance=0)
Compares two Desmond enegrp.dat files.

Variables

[hide private]

_version = '$Revision 0.1 $'

__package__ = 'schrodinger.test.stu.outcomes'

Function Details

[hide private]

desmond_compare_FES(file1, file2, tolerance=0.1)

Compare metadynamics FES files.

usage: desmond_compare_FES(file1.fes, file2.fes, <0.2>)

Tolerance is optional, and defaults to 0.1

desmond_FEP_energies(filename, reference, tolerance=0.5)

Compares the deltaF in an FEP result file to a standard.

usage: desmond_FEP_energies(filename.log, value, optional tolerance)

desmond_FEP_check_html(filename)

Tests the html file written by a Desmond FEP job

To Do: This does nothing yet.

desmond_check_surface_area(filename, reference, tolerance=0.5, side1=`'r_chorus_box_ax'`, side2=`'r_chorus_box_bx'`)

Compares surface area to a standard with optional tolerance and optional choice of box sides. Default sides are a and b.

usage: desmond_check_surface_area(filename, value, tolerance, side1, side2

desmond_compare_ene(file1, file2, tolerance, *quantities)

Compares two Desmond ene files.

Checks that any quantities requested from the ene file match within some tolerance number of decimal points.

usage desmond_compare_ene(file1.ene, file2.ene, 2, P, E_c)

desmond_speed(filename, reference_rate, tolerance=0.05)

Compares the average rate per step in ns/day against a standard.

usage: desmond_speed(file1.log, reference rate, <tolerance>)

Parameters:

reference_rate - Value to be compared against in ns/day
tolerance - Tolerance. Default is 5%.

desmond_stage_time(log_file, stage_num, max_time)

Parameters:

log_file (str) - Name of log file to be analyzed.
stage_num (int) - Stage number
max_time (float @return : True if the stage completed successfully within max_time seconds, or False if not.
usage: desmond_stage_time(logfile, stage, max_time)
) - Maximum acceptable time for the stage in seconds

desmond_st_stats(filename, *options)

Compares the mean, median and/or standard deviation of a desmond st2 file to reference values.

usage: desmond_st_stats(file.st2, mean=1.2, median=2.3, stddev=1.2, tol=0.2)

_normalize_angular_values(array, degree=True)

Centers an array of angles to minimize its standard deviation.

Parameters:

array (list) - Array to be (possibly) modified.
degree (bool @return : Values, (possibly) offset (by 360 deg) to minimize std dev. @rtype : list) - Are the units of the list degrees?

desmond_compare_deltaE(file1, file2)

Compares two Desmond deltaE.txt files. Checks time and energy. No tolerance (exact sameness).

usage: desmond_compare_deltaE(file1, file2)

desmond_compare_energy_group(file1, file2, tolerance=0)

Compares two Desmond enegrp.dat files. Checks all values upto tolerance value.

usage: desmond_compare_energy_group(file1, file2, tolerance=0)

Module desmond_workups

desmond_compare_FES(file1, file2, tolerance=0.1)

desmond_FEP_energies(filename, reference, tolerance=0.5)

desmond_FEP_check_html(filename)

desmond_check_surface_area(filename, reference, tolerance=0.5, side1='r_chorus_box_ax', side2='r_chorus_box_bx')

desmond_compare_ene(file1, file2, tolerance, *quantities)

desmond_speed(filename, reference_rate, tolerance=0.05)

desmond_stage_time(log_file, stage_num, max_time)

desmond_st_stats(filename, *options)

_normalize_angular_values(array, degree=True)

desmond_compare_deltaE(file1, file2)

desmond_compare_energy_group(file1, file2, tolerance=0)

desmond_check_surface_area(filename, reference, tolerance=0.5, side1=`'r_chorus_box_ax'`, side2=`'r_chorus_box_bx'`)