pestifer.tasks package

Tasks that can be executed by the Pestifer framework. This package contains various task classes that define the operations to be performed during the execution of a Pestifer run. Each task is responsible for a specific part of the workflow, such as building molecules, running simulations, and processing results.

Each module defines a specific task class that inherits from the base BaseTask class.

Submodules

• pestifer.tasks.basetask module
  • BaseTask
    • BaseTask.do()
    • BaseTask.execute()
    • BaseTask.get_current_artifact()
    • BaseTask.get_current_artifact_data()
    • BaseTask.get_current_artifact_path()
    • BaseTask.get_my_artifactfile_collection()
    • BaseTask.get_scripter()
    • BaseTask.import_artifacts()
    • BaseTask.is_provisioned
    • BaseTask.log_message()
    • BaseTask.next_basename()
    • BaseTask.override_taskname()
    • BaseTask.provision()
    • BaseTask.register()
    • BaseTask.register_if_exists()
    • BaseTask.stash_current_artifact()
  • VMDTask
    • VMDTask.coor_to_pdb()
    • VMDTask.make_constraint_pdb()
    • VMDTask.make_ssrestraints_file()
    • VMDTask.pdb_to_coor()
• pestifer.tasks.cleave module
  • CleaveTask
    • CleaveTask.do()
• pestifer.tasks.continuation module
  • ContinuationTask
    • ContinuationTask.do()
• pestifer.tasks.desolvate module
  • DesolvateTask
    • DesolvateTask.do()
    • DesolvateTask.do_dcd_prune()
    • DesolvateTask.do_idx_psf_gen()
• pestifer.tasks.domainswap module
  • DomainSwapTask
    • DomainSwapTask.do()
    • DomainSwapTask.make_inputs()
• pestifer.tasks.fetch module
  • FetchTask
    • FetchTask.do()
• pestifer.tasks.ligate module
  • LigateTask
    • LigateTask.connect()
    • LigateTask.connect_gaps()
    • LigateTask.do()
    • LigateTask.do_steered_md()
    • LigateTask.measure_distances()
    • LigateTask.write_connect_patches()
    • LigateTask.write_gaps()
• pestifer.tasks.make_membrane_system module
  • MakeMembraneSystemTask
    • MakeMembraneSystemTask.build_patch()
    • MakeMembraneSystemTask.do()
    • MakeMembraneSystemTask.do_psfgen()
    • MakeMembraneSystemTask.embed_protein()
    • MakeMembraneSystemTask.equilibrate_bilayer()
    • MakeMembraneSystemTask.initialize()
    • MakeMembraneSystemTask.make_quilt_from_patch()
    • MakeMembraneSystemTask.orient_protein()
    • MakeMembraneSystemTask.pack_patch()
    • MakeMembraneSystemTask.provision()
    • MakeMembraneSystemTask.register_tmpfiles_from_tcl()
    • MakeMembraneSystemTask.register_tops_streams_from_psfgen()
• pestifer.tasks.manipulate module
  • ManipulateTask
    • ManipulateTask.coormods()
    • ManipulateTask.do()
    • ManipulateTask.provision()
• pestifer.tasks.mdplot module
  • MDPlotTask
    • MDPlotTask.do()
• pestifer.tasks.mdtask module
  • MDTask
    • MDTask.do()
    • MDTask.namdrun()
    • MDTask.provision()
• pestifer.tasks.merge module
  • MergeTask
    • MergeTask.do()
• pestifer.tasks.pdb2pqr module
  • PDB2PQRTask
    • PDB2PQRTask.do()
    • PDB2PQRTask.prep_input()
    • PDB2PQRTask.prep_mods()
    • PDB2PQRTask.run_pdb2pqr()
• pestifer.tasks.psfgen module
  • PsfgenTask
    • PsfgenTask.coormods()
    • PsfgenTask.declash()
    • PsfgenTask.declash_glycans()
    • PsfgenTask.declash_na_loops()
    • PsfgenTask.declash_protein_loops()
    • PsfgenTask.declash_segtype()
    • PsfgenTask.do()
    • PsfgenTask.ingest_molecules()
    • PsfgenTask.patch_topologies()
    • PsfgenTask.provision()
    • PsfgenTask.psfgen()
    • PsfgenTask.resi_topologies()
    • PsfgenTask.strip_remarks()
    • PsfgenTask.update_molecule()
• pestifer.tasks.pytest_buildterminate module
  • Pytest_BuildTerminateTask
    • Pytest_BuildTerminateTask.do()
• pestifer.tasks.ringcheck module
  • RingCheckTask
    • RingCheckTask.do()
• pestifer.tasks.solvate module
  • SolvateTask
    • SolvateTask.do()
• pestifer.tasks.taskcollections module
  • TaskDict
  • TaskList
    • TaskList.from_yaml()
• pestifer.tasks.terminate module
  • TerminateTask
    • TerminateTask.cleanup()
    • TerminateTask.copy_state_to_basename()
    • TerminateTask.do()
    • TerminateTask.generate_minimal_params()
    • TerminateTask.make_package()
    • TerminateTask.print_system_report()
    • TerminateTask.test_standard()
    • TerminateTask.write_chainmaps()
• pestifer.tasks.validate module
  • AttributeTest
    • AttributeTest.name
    • AttributeTest.selection
    • AttributeTest.attribute
    • AttributeTest.value
    • AttributeTest.value_count
    • AttributeTest.write()
  • ConnectionTest
    • ConnectionTest.name
    • ConnectionTest.selection
    • ConnectionTest.connection_type
    • ConnectionTest.connection_count
    • ConnectionTest.connection_type_supported
    • ConnectionTest.write()
  • ResidueTest
    • ResidueTest.write()
  • ValidateTask
    • ValidateTask.do()
    • ValidateTask.provision()