reliontomo.protocols.protocol_base_tomo module

This module contains the protocol base class for Relion protocols

class reliontomo.protocols.protocol_base_tomo.ProtRelionBaseTomo(**args)[source]

Bases: pwem.protocols.protocol.EMProtocol

This class cointains the common functionalities 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 behaivour depending on the case.

FILE_KEYS = ['data', 'optimiser', 'sampling']
OUTPUT_TYPE

alias of pwem.objects.data.SetOfClasses3D

PREFIXES = ['']
addSymmetry(container)[source]
claasesTable = <emtable.metadata.Table object>
convertInputStep()[source]

Create the input file in STAR format as expected by Relion.

createOutputStep()[source]
dataTable = <emtable.metadata.Table object>
modelTable = <emtable.metadata.Table object>
nClasses = 0
runRelionStep(params)[source]

Execute the relion steps with the give params.