topaz package

Subpackages

• topaz.protocols package
  • Submodules
    • topaz.protocols.protocol_base module
    • topaz.protocols.protocol_topaz_import module
    • topaz.protocols.protocol_topaz_picking module
    • topaz.protocols.protocol_topaz_training module
  • Module contents

Submodules

• topaz.bibtex module
• topaz.constants module
• topaz.convert module
• topaz.objects module

Module contents

class topaz.Plugin

Bases: pwem.Plugin

classmethod addTopazPackage(env, version, default=False)

classmethod defineBinaries(env)

Define required binaries in the given Environment.

classmethod getDependencies()

classmethod getEnviron()

Setup the environment variables needed to launch topaz.

classmethod getTopazEnvActivation()

Remove the scipion home and activate the conda topaz environment.

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

Run Topaz command from a given protocol.