relion.convert.convert30 module

class relion.convert.convert30.Reader(**kwargs)[source]

Bases: relion.convert.convert_base.ReaderBase

ALIGNMENT_LABELS = ['rlnOriginX', 'rlnOriginY', 'rlnOriginZ', 'rlnAngleRot', 'rlnAngleTilt', 'rlnAnglePsi']
readSetOfParticles(starFile, partsSet, **kwargs)[source]

Convert a star file into a set of particles.

Params:
starFile: the filename of the star file partsSet: output particles set
Keyword Arguments:
blockName: The name of the data block (default particles) alignType: removeDisabled:
setParticleTransform(particle, row)[source]

Set the transform values from the row.

class relion.convert.convert30.Writer(**kwargs)[source]

Bases: relion.convert.convert_base.WriterBase

Helper class to convert from Scipion SetOfImages subclasses with star file format previous to Relion>3.1, but providing the same

interface as the new Writer class.
writeSetOfMicrographs(micsIterable, starFile)[source]
writeSetOfMovies(moviesIterable, starFile)[source]
writeSetOfParticles(partsSet, starFile, **kwargs)[source]

Convert a set of particles into a star file and maybe binary files.

Params:
partsSet: input particles set starFile: the filename of the star file that will be written.
Keyword Arguments:

blockName: The name of the data block (default particles) fillMagnification: If True set magnification values (default False)

outputStack: A file name to write all particles. If this option is
passed, then the outputDir will be ignored.