phenix package

Subpackages

• phenix.protocols package
  • Submodules
    • phenix.protocols.protocol_dock_in_map module
    • phenix.protocols.protocol_emringer module
    • phenix.protocols.protocol_molprobity module
    • phenix.protocols.protocol_real_space_refine module
    • phenix.protocols.protocol_refinement_base module
    • phenix.protocols.protocol_search_fit module
    • phenix.protocols.protocol_superpose_pdbs module
    • phenix.protocols.protocol_validation_cryoem module
  • Module contents
• phenix.viewers package
  • Submodules
    • phenix.viewers.viewer_dock_in_map module
    • phenix.viewers.viewer_emringer module
    • phenix.viewers.viewer_molprobity module
    • phenix.viewers.viewer_real_space_refine module
    • phenix.viewers.viewer_refinement_base module
    • phenix.viewers.viewer_search_fit module
    • phenix.viewers.viewer_superpose_pdbs module
    • phenix.viewers.viewer_validation_cryoem module
  • Module contents

Submodules

• phenix.bibtex module
• phenix.constants module
• phenix.wizards module

Module contents

class phenix.Plugin

Bases: pwem.Plugin

classmethod defineBinaries(env)

Define required binaries in the given Environment.

classmethod getEnviron(first=True)

Setup the environment variables needed to launch programs.

classmethod getPhenixVersion()

Return the program binary that will be used.

classmethod getProgram(progName)

Return the program binary that will be used.

classmethod isVersionActive()

classmethod runPhenixProgram(program, args=None, extraEnvDict=None, cwd=None)

Internal shortcut function to launch a Phenix program.