relion.protocols.protocol_extract_particles module

class relion.protocols.protocol_extract_particles.ProtRelionExtractParticles(**kwargs)[source]

Bases: pwem.protocols.protocol_particles.ProtExtractParticles, relion.protocols.protocol_base.ProtRelionBase

Protocol to extract particles using a set of coordinates.

convertInputStep(micsId)[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.
createOutputStep()[source]
createParticles(item, row)[source]
getBoxScale()[source]

Computing the sampling factor between input and output. We should take into account the differences in sampling rate between micrographs used for picking and the ones used for extraction. The downsampling factor could also affect the resulting scale.

getCoordSampling()[source]
getCoords()[source]
getInputMicrographs()[source]

Return the micrographs associated to the SetOfCoordinates or Other micrographs.

getNewImgSize()[source]
getOutput()[source]
getScaleFactor()[source]

Returns the scaling factor that needs to be applied to the input coordinates to adapt for the input micrographs.

notOne(value)[source]
readPartsFromMics(micList, outputParts)[source]

Read the particles extract for the given list of micrographs and update the outputParts set with new items.