relion.protocols.protocol_base module

class relion.protocols.protocol_base.ProtRelionBase(**args)

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

OUTPUT_TYPE

alias of pwem.objects.data.SetOfClasses3D

PREFIXES = ['']

addSymmetry(container)

convertInputStep(particlesId, copyAlignment)

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()

createOutputStep()

runRelionStep(params)

Execute the relion steps with the give params.

useGpu()

Return True if the protocol has gpu option and it has been selected.