xmipptomo.protocols.protocol_score_coordinates module

class xmipptomo.protocols.protocol_score_coordinates.XmippProtScoreCoordinates(**kwargs)

Bases: tomo.protocols.protocol_base.ProtTomoPicking

Scoring and (optional) filtering of coordinates based on different scoring functions (carbon distance, neighbour distance)

computeParams(coordinates)

createOutputStep(coordinates)

detectCarbonCloseness(coordinates)

detectOutliers()

generateCoordList(tomo, coordinates)

projectTomo(tomo)

writeTomoCoordinates(tomo, coordList, outputFn, isManual=True, getPosFunc=None)

Write the pos file as expected by Xmipp with the coordinates of a given tomogram. Params:

tomo: input tomogram. coordList: list of (x, y) pairs of the mic coordinates. outputFn: output filename for the pos file . isManual: if the coordinates are ‘Manual’ or ‘Supervised’ getPosFunc: a function to get the positions from the coordinate,

it can be useful for scaling the coordinates if needed.