gautomatch.protocols.protocol_gautomatch module

class gautomatch.protocols.protocol_gautomatch.ProtGautomatch(**kwargs)[source]

Bases: pwem.protocols.protocol_particles_picking.ProtParticlePickingAuto

Automated particle picker for SPA.

Gautomatch is a GPU accelerated program for accurate, fast, flexible and fully automatic particle picking from cryo-EM micrographs with or without templates.

convertInputStep()[source]

This step will take of the conversions from the inputs. Micrographs: they will be linked if are in ‘.mrc’ format,

converted otherwise.

References: will always be converted to ‘.mrcs’ format

convertReferences(refStack)[source]

Write input references as an .mrcs stack.

createDebugOutput(suffix)[source]
createOutputStep()[source]
getArgs(threshold=True, mindist=True)[source]

Return the Gautomatch parameters for picking one micrograph. The command line will depends on the protocol selected parameters. Params:

micFn: micrograph filename refStack: filename with the references stack (.mrcs)
getMicrographsDir()[source]
getOutputName(fn, key)[source]

Give a key, append the mrc extension and prefix the protocol working dir.

readCoordsFromMics(workingDir, micList, coordSet)[source]

This method should be implemented in subclasses to read the coordinates from a given list of micrographs.

readRejectedCoordsFromMics(micList)[source]