atomstructutils.protocols.protocol_average_subunits module

class atomstructutils.protocols.protocol_average_subunits.ProtAverageSubunits(**kwargs)[source]

Bases: pwem.protocols.protocol.EMProtocol

Average densities related with the given atomic structures. For example hexons in a unit cell. Alpha carbon are used to compute the transformation matrix

DEBUG = True
DEBUGX = False
computeAveragedSubUnit()[source]

Average the pixel values of the pixels related by symmetry

computeTransformationMatrices(origin, sampling)[source]

compute transformation matrix between reference atom structure (self.atomStructReference) and the other atom structures (self.otherAtomStructs)

read atomic structures identify common AA with first structure compute transformation matrix in PDB system function fills lists

  • listTransformationMatrices
  • listRMS (errors)
  • listObjID (atom structure names)

transform matrix to unitcell system of equations shifts in px

convertAtomicModel2UnitCellMatrix(sampling, origin)[source]

Compute matrix that transform points in atomic structs (A) to unit cell (px) system. p’ = (p - origin ) /sampling

convertUnitCell2AtomicModelMatrix(sampling, origin)[source]

Compute matrix that transform points in unit cell (px) to atom struct (A) system

createOutput()[source]
outputFileName()[source]
trilinearInterpolation(xf, yf, zf, input_array)[source]

Interpolates the value of point “indices” in matrix input_array. return the interpolated value