imod package

Subpackages

• imod.protocols package
  • Submodules
    • imod.protocols.protocol_applyTransformationMatrix module
    • imod.protocols.protocol_auto3d module
    • imod.protocols.protocol_ctfCorrecion module
    • imod.protocols.protocol_ctfEstimation module
    • imod.protocols.protocol_etomo module
    • imod.protocols.protocol_fiducialAlignment module
    • imod.protocols.protocol_tomoNormalization module
    • imod.protocols.protocol_tomoReconstruction module
    • imod.protocols.protocol_tsNormalization module
    • imod.protocols.protocol_xCorrPrealignment module
    • imod.protocols.script_imod_auto3d module
  • Module contents

Submodules

• imod.bibtex module
• imod.constants module
• imod.utils module
• imod.viewers module

Module contents

class imod.Plugin

Bases: pwem.Plugin

classmethod defineBinaries(env)

Define required binaries in the given Environment.

classmethod getDependencies()

classmethod getEnviron()

Setup the environment variables needed to launch programs.

classmethod getImodCmd(program)

Composes an IMOD command for a given program.

classmethod runImod(protocol, program, args, cwd=None)

Run IMOD command from a given protocol.

classmethod validateInstallation()

Check if imod is in the path