continuousflex.protocols.protocol_nma_dimred module

class continuousflex.protocols.protocol_nma_dimred.FlexProtDimredNMA(**kwargs)[source]

Bases: pwem.protocols.protocol_3d.ProtAnalysis3D

This protocol will take the images with NMA deformations as points in a N-dimensional space (where N is the number of computed normal modes) and will project them in a reduced spaced (usually with less dimensions).

convertInputStep(deformationFile, inputId)[source]

Iterate through the images and write the plain deformation.txt file that will serve as input for dimensionality reduction.

createOutputStep()[source]
getDeformationFile()[source]
getInputParticles()[source]

Get the output particles of the input NMA protocol.

getInputPdb()[source]
getMethodName()[source]
getOutputMatrixFile()[source]
getProjectorFile()[source]
performDimredStep(deformationsFile, method, extraParams, rows, reducedDim)[source]