nanover package

Subpackages

• nanover.app package
  • Subpackages
    • nanover.app.cli namespace
      • Submodules
  • Submodules
    • nanover.app.imd_app module
      • NanoverImdApplication
      • add_scene_update_shim()
      • qualified_server_name()
    • nanover.app.multiuser module
      • add_multiuser_commands()
    • nanover.app.omni module
      • InternalRunner
      • OmniRunner
    • nanover.app.selection module
      • RenderingSelection
      • get_nested_or_default()
• nanover.ase package
  • Submodules
    • nanover.ase.converter module
      • add_ase_box_vectors_to_frame_data()
      • add_ase_forces_to_frame_data()
      • add_ase_positions_to_frame_data()
      • add_ase_state_to_frame_data()
      • add_ase_topology_to_frame_data()
      • add_ase_velocities_to_frame_data()
      • add_frame_data_positions_to_ase()
      • add_frame_data_topology_to_ase()
      • ase_atoms_to_frame_data()
      • ase_to_frame_data()
      • frame_data_to_ase()
      • generate_bonds_from_ase()
      • get_radius_of_element()
    • nanover.ase.imd_calculator module
      • ImdCalculator
      • ImdForceManager
      • get_periodic_box_lengths()
    • nanover.ase.null_calculator module
      • NullCalculator
    • nanover.ase.omm_calculator module
      • OpenMMCalculator
    • nanover.ase.simulation module
      • ASEAtomsToFrameData
      • ASESimulation
      • InitialState
    • nanover.ase.thermo module
      • compute_dof()
      • compute_instantaneous_temperature()
    • nanover.ase.trajectory_logger module
      • TrajectoryLogger
      • UnsupportedFormatError
      • validate_ase_can_append_filename()
      • validate_ase_can_append_format()
    • nanover.ase.wall_constraint module
      • VelocityWallConstraint
• nanover.core package
  • Submodules
    • nanover.core.app_server module
      • AppServer
      • AppServerMinimal
      • AppServerMinimalImd
      • Closeable
      • CommandService
      • DiscoveryService
      • ImdService
      • StateService
      • basic_info_string()
    • nanover.core.commands module
      • CommandMessageHandler
      • CommandService
      • SendMessage
    • nanover.core.simulation module
      • Simulation
    • nanover.core.types module
      • CommandRegistration
• nanover.essd package
  • Submodules
    • nanover.essd.client module
      • DiscoveryClient
    • nanover.essd.list_cli module
      • handle_user_arguments()
      • main()
      • print_hub()
    • nanover.essd.server module
      • Example
      • DiscoveryServer
      • configure_reusable_socket()
    • nanover.essd.servicehub module
      • ServiceHub
    • nanover.essd.utils module
      • fix_broadcast_windows()
      • get_broadcast_addresses()
      • get_broadcastable_test_ip()
      • get_ipv4_addresses()
      • is_in_network()
      • resolve_host_broadcast_address()
• nanover.imd package
  • Submodules
    • nanover.imd.imd_force module
      • ForceCalculator
      • InvalidInteractionError
      • apply_single_interaction_force()
      • calculate_constant_force()
      • calculate_contribution_to_work()
      • calculate_gaussian_force()
      • calculate_imd_force()
      • calculate_spring_force()
      • expand_sparse_forces()
      • get_center_of_mass_subset()
      • get_sparse_forces()
      • wrap_pbc()
    • nanover.imd.imd_state module
      • ImdStateWrapper
      • dict_to_interaction()
      • interaction_to_dict()
    • nanover.imd.particle_interaction module
      • ParticleInteraction
• nanover.jupyter package
  • Submodules
    • nanover.jupyter.alignment_transform module
      • AlignmentTransform
    • nanover.jupyter.controls module
      • interact_button()
      • make_button()
      • make_toggle()
      • show_app_server_controls()
      • show_runner_controls()
    • nanover.jupyter.frame_listener module
      • FrameListener
    • nanover.jupyter.ghost_follower module
      • GhostFollowerAgent
    • nanover.jupyter.ghosts module
      • GhostMoleculeData
      • GhostMoleculeObject
      • draw_ghost()
    • nanover.jupyter.imd_agent module
      • ImdAgent
    • nanover.jupyter.modes module
      • Mode
    • nanover.jupyter.nglclient module
      • FrameDataStructure
      • NGLClient
      • fill_empty_fields()
      • frame_data_to_nglwidget()
      • frame_data_to_pdb()
      • mda_to_pdb_str()
    • nanover.jupyter.transform_grabbing module
      • TransformGrabData
      • TransformGrabbingContext
      • constrain_matrix_update()
    • nanover.jupyter.transform_handles module
      • HandleGrabData
      • use_transform_handles()
    • nanover.jupyter.utilities module
      • InteractionsUtility
      • ModesManager
      • NanoverClientUtilities
      • NanoverServerUtilities
      • NanoverSharedUtilities
      • PanelsUtility
      • SceneObjectsUtility
      • SelectionsUtility
      • StateKeysUtility
      • StateTransformEntry
      • TransformHandlesUtility
      • TransformsUtility
      • make_id_generator()
• nanover.mdanalysis package
  • Submodules
    • nanover.mdanalysis.converter module
      • FrameDataField
      • FrameDataFieldConversion
      • add_frame_positions_to_mda()
      • add_frame_topology_to_mda()
      • add_mda_positions_to_frame_data()
      • add_mda_topology_to_frame_data()
      • frame_data_to_mdanalysis()
      • mdanalysis_to_frame_data()
      • nullable_int()
      • update_universe_from_framedata()
    • nanover.mdanalysis.simulation module
      • UniverseSimulation
    • nanover.mdanalysis.universe module
      • KeyConversion
      • NanoverParser
      • NanoverReader
      • NanoverReaderBase
      • batched()
      • explosion_mask()
      • has_topology()
      • universe_from_recording()
      • universes_from_recording()
• nanover.openmm package
  • Submodules
    • nanover.openmm.bundles module
      • bundle_openmm_simulation()
      • unbundle_openmm_simulation()
    • nanover.openmm.converter module
      • add_openmm_state_to_frame_data()
      • add_openmm_topology_to_frame_data()
      • openmm_to_frame_data()
    • nanover.openmm.imd module
      • ImdForceManager
      • add_imd_force_to_system()
      • create_imd_force()
      • populate_imd_force()
    • nanover.openmm.potentials module
      • restrain_particles()
      • restraint_force()
    • nanover.openmm.serializer module
      • deserialize_simulation()
      • serialize_simulation()
    • nanover.openmm.simulation module
      • OpenMMSimulation
    • nanover.openmm.thermo module
      • compute_dof()
      • compute_instantaneous_temperature()
• nanover.recording package
  • Subpackages
    • nanover.recording.cli namespace
      • Submodules
  • Submodules
    • nanover.recording.playback module
      • PlaybackSimulation
    • nanover.recording.reading module
      • FrameRecordingEvent
      • MessageEvent
      • MessageZipReader
      • NanoverRecordingReader
      • RecordingEvent
      • RecordingIndexEntry
      • StateRecordingEvent
      • iter_full_view()
      • iter_recording_file()
      • message_events_from_recording()
      • parse_index()
      • split_by_simulation_counter()
    • nanover.recording.trajectory module
      • NanoverTrajectory
      • is_valid_first_frame()
      • trajectories_from_reader()
      • trajectories_from_recording()
    • nanover.recording.writing module
      • NanoverRecordingWriter
      • generate_metadata()
      • record_messages()
• nanover.testing package
  • Submodules
    • nanover.testing.asserts module
      • assert_equal_soon()
      • assert_in_soon()
      • assert_not_in_soon()
      • assert_true_soon()
    • nanover.testing.servers module
      • ServerClientSetup
      • connect_client_to_server()
      • make_app_server()
      • make_connected_server_client_setup()
      • make_websocket_server()
    • nanover.testing.strategies module
      • arrays()
      • arrays2d()
      • command_arguments()
      • coords()
      • custom_frame_keys()
      • dict_frames()
      • dictionary_keys()
      • enum_arrays()
      • float32s()
      • frames()
      • index2_arrays()
      • index_arrays()
      • packable_primitives()
      • packable_structures()
      • packed_frame_dicts()
      • state_updates()
      • transformation()
      • uint32s()
      • uint8s()
      • user_ids()
      • vec3_arrays()
      • vec3s()
    • nanover.testing.utilities module
      • simplify_numpy()
• nanover.trajectory package
  • Submodules
    • nanover.trajectory.frame_dict module
      • FRAME_PACKERS
      • frame_dict_packer
      • merge_frame_dicts()
    • nanover.trajectory.frame_publisher module
      • FramePublisher
    • nanover.trajectory.frame_queue module
      • FrameMergingQueue
    • nanover.trajectory.frame_wrapper module
      • FrameData
      • MissingDataError
      • replace_shortcuts()
    • nanover.trajectory.keys module
• nanover.utilities package
  • Submodules
    • nanover.utilities.change_buffers module
      • DictionaryChange
      • DictionaryChangeBuffer
      • DictionaryChangeMultiView
      • ObjectFrozenError
    • nanover.utilities.cli module
      • CancellationToken
      • suppress_keyboard_interrupt_as_cancellation()
    • nanover.utilities.event module
      • Event
    • nanover.utilities.intersection module
      • ClosestPointResult
      • closest_point_on_polyline()
    • nanover.utilities.key_lockable_map module
      • KeyLockableMap
      • ResourceLockedError
    • nanover.utilities.network module
      • get_local_ip()
    • nanover.utilities.packing module
      • PackingPair
      • fallback_encoder()
      • make_bytes_packer()
      • pack_array()
      • unpack_array()
    • nanover.utilities.queues module
      • LastItemQueue
    • nanover.utilities.state_dictionary module
      • StateDictionary
    • nanover.utilities.timing module
      • VariableIntervalGenerator
      • wait_busy()
      • wait_mixed()
      • yield_interval()
    • nanover.utilities.transforms module
      • StructureAlignment
      • Transform
      • find_transformation_between_point_patterns()
      • matrix_from_state_transform()
      • state_transform_from_matrix()
      • unpack_partial_state_transform()
• nanover.websocket package
  • Subpackages
    • nanover.websocket.client namespace
      • Submodules
  • Submodules
    • nanover.websocket.discovery module
      • DiscoveryClient
    • nanover.websocket.landing module
      • StaticHTTPRequestHandler
      • make_landing_page_server()
    • nanover.websocket.record module
      • BackgroundRecordingContext
      • message_events_from_websocket()
      • record_from_runner()
    • nanover.websocket.server module
      • ServerLike
      • WebSocketServer