relion.protocols.protocol_base module

class relion.protocols.protocol_base.ProtRelionBase(**args)[source]

Bases: pwem.protocols.protocol.EMProtocol

This class contains the common functions for all Relion protocols. In subclasses there should be little changes about how to create the command line and the files produced.

Most of the Relion protocols, have two modes: NORMAL or CONTINUE. That’s why some of the function have a template pattern approach to define the behaviour depending on the case.

CHANGE_LABELS = ['rlnChangesOptimalOrientations', 'rlnChangesOptimalOffsets', 'rlnOverallAccuracyRotations', 'rlnOverallAccuracyTranslationsAngst', 'rlnChangesOptimalClasses']
CLASS_LABEL = 'rlnClassNumber'
FILE_KEYS = ['data', 'optimiser', 'sampling']
IS_2D = False
IS_3D_INIT = False
IS_CLASSIFY = True
IS_GT30()[source]
OUTPUT_TYPE

alias of pwem.objects.data.SetOfClasses3D

PREFIXES = ['']
addSymmetry(container)[source]
convertInputStep(particlesId, copyAlignment)[source]

Create the input file in STAR format as expected by Relion. If the input particles comes from Relion, just link the file. Params:

particlesId: use this parameters just to force redo of convert if
the input particles are changed.
createDefocusGroups()[source]
createOutputStep()[source]
runRelionStep(params)[source]

Execute the relion steps with the give params.