sphire package

Subpackages

• sphire.protocols package
  • Submodules
    • sphire.protocols.protocol_cryolo_import module
    • sphire.protocols.protocol_cryolo_picking module
    • sphire.protocols.protocol_cryolo_tomo_picking module
    • sphire.protocols.protocol_cryolo_training module
    • sphire.protocols.protocol_janni_denoise module
  • Module contents

Submodules

• sphire.bibtex module
• sphire.constants module
• sphire.convert module
• sphire.objects module

Module contents

This package contains the protocols and data for crYOLO

class sphire.Plugin

Bases: pwem.Plugin

classmethod addCryoloPackage(env, version, default=False, useCpu=False, pythonVersion='3.6')

classmethod defineBinaries(env)

Define required binaries in the given Environment.

classmethod getCryoloEnvActivation(useCpu=False)

classmethod getCryoloGeneralModel()

classmethod getCryoloGeneralNNModel()

classmethod getCryoloGeneralNSModel()

classmethod getDependencies()

classmethod getEnviron()

Setup the environment variables needed to launch sphire.

classmethod getJanniGeneralModel()

classmethod runCryolo(protocol, program, args, cwd=None, useCpu=False)

Run crYOLO command from a given protocol.