continuousflex.protocols.protocol_nma_dimred_vol module

class continuousflex.protocols.protocol_nma_dimred_vol.FlexProtDimredNMAVol(**kwargs)

Bases: pwem.protocols.protocol_3d.ProtAnalysis3D

This protocol will take the volumes with NMA deformations as points in a N-dimensional space (where N is the number of computed normal modes) and will project them onto a reduced space

PDB2List(lines)

convertInputStep(deformationFile, inputId, dataChoice)

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

copyinputPdb(inputFn, localFn)

Copy the input pdb file

createOutputStep()

getDataChoice()

getDeformationFile()

getInputParticles()

Get the output particles of the input NMA protocol.

getInputPdb()

getMethodName()

getOutputMatrixFile()

getParticlesMD()

Get the metadata files that contain the NMA displacement

getProjectorFile()

performDimredStep(deformationsFile, method, extraParams, rows, reducedDim)

readPDB(fnIn)