autocorrelation Namespace Reference

Functions
def	find_nonmodulo_autocorrelation (x)
def	find_autocorrelation (x)

Variables
	parser = helpers.define_args('torsion', 'plot')
	type
	float
	default
	arguments = parser.parse_args()
	iterations = helpers.load_array(arguments.job, 'iterations')
	torsions = helpers.load_arrays(arguments.job, 'torsions')
def	autocorrelation = find_autocorrelation(torsions[key])
	color = pylab.cm.Dark2(numpy.median(autocorrelation))
	label
	key

Function Documentation

find_autocorrelation()

def autocorrelation.find_autocorrelation

(

x

)

 This homebrew autocorrelation function is specifically written to 
handle modulo variable like dihedral angles.  Think of the cosine function 
as an alternative, and more appropriate, metric for overlap. 

References helpers.connect_to_database(), ObjexxFCL.len(), numeric::conversions.radians(), range, and sum().

find_nonmodulo_autocorrelation()

def autocorrelation.find_nonmodulo_autocorrelation

(

x

)

 The standard correlation function isn't meant for modulo variables, 
like dihedral angles.  I'm sure this version is much faster, but it will 
choke on angles constantly jumping between 180 and -180. 

References ObjexxFCL.len().

Variable Documentation

arguments

autocorrelation.arguments = parser.parse_args()

autocorrelation

autocorrelation.autocorrelation = find_autocorrelation(torsions[key])

color

autocorrelation.color = pylab.cm.Dark2(numpy.median(autocorrelation))

default

autocorrelation.default

float

autocorrelation.float

iterations

autocorrelation.iterations = helpers.load_array(arguments.job, 'iterations')

Referenced by MPDomainAssembly.apply(), SamplingManager.get_iterations(), apps::pilot::KicSandbox.KicSandbox(), main(), my_main(), SamplingManager.SamplingManager(), and NativeEnsemble.write_schema_to_db().

key

autocorrelation.key

label

autocorrelation.label

parser

autocorrelation.parser = helpers.define_args('torsion', 'plot')

torsions

autocorrelation.torsions = helpers.load_arrays(arguments.job, 'torsions')

type

autocorrelation.type