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

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=2, *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_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.

Variables

[hide private]

_version = "$Revision 0.1 $"

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=2, *quantities)

Compares two Desmond ene files.

Checks the units, time, temperature profile and E. Also checks any other quantities requested. Default tolerance is second decimal place.

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_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?