Index

A

active_interactions (nanover.imd.imd_state.ImdStateWrapper property) add_ase_box_vectors_to_frame_data() (in module nanover.ase.converter) add_ase_positions_to_frame_data() (in module nanover.ase.converter) add_ase_state_to_frame_data() (in module nanover.ase.converter) add_ase_topology_to_frame_data() (in module nanover.ase.converter) add_callback() (nanover.utilities.event.Event method) add_CommandServicer_to_server() (in module nanover.protocol.command.command_service_pb2_grpc) add_contribution_to_work() (nanover.omni.openmm.OpenMMSimulation method) add_frame_data_positions_to_ase() (in module nanover.ase.converter) add_frame_data_topology_to_ase() (in module nanover.ase.converter) add_frame_positions_to_mda() (in module nanover.mdanalysis.converter) add_frame_topology_to_mda() (in module nanover.mdanalysis.converter) add_imd_force_to_system() (in module nanover.openmm.imd) add_mda_positions_to_frame_data() (in module nanover.mdanalysis.converter) add_mda_topology_to_frame_data() (in module nanover.mdanalysis.converter) add_multiuser_commands() (in module nanover.app.multiuser) add_openmm_state_to_frame_data() (in module nanover.openmm.converter) add_openmm_topology_to_frame_data() (in module nanover.openmm.converter) add_particles() (nanover.app.selection.RenderingSelection method) add_service() (nanover.app.app_server.NanoverApplicationServer method) (nanover.core.grpc_server.GrpcServer method) (nanover.essd.servicehub.ServiceHub method) add_simulation() (nanover.omni.omni.OmniRunner method) add_StateServicer_to_server() (in module nanover.protocol.state.state_service_pb2_grpc) add_to_frame_data() (nanover.openmm.imd.ImdForceManager method) add_TrajectoryServiceServicer_to_server() (in module nanover.protocol.trajectory.trajectory_service_pb2_grpc) address (nanover.app.app_server.NanoverApplicationServer property) (nanover.app.runner.NanoverRunner property) (nanover.core.grpc_server.GrpcServer property) (nanover.essd.servicehub.ServiceHub property) address_and_port (nanover.core.grpc_server.GrpcServer property) adjust_forces() (nanover.ase.wall_constraint.VelocityWallConstraint method) adjust_momenta() (nanover.ase.wall_constraint.VelocityWallConstraint method) adjust_positions() (nanover.ase.wall_constraint.VelocityWallConstraint method) advance_by_one_step() (nanover.omni.ase.ASESimulation method) (nanover.omni.omni.Simulation method) (nanover.omni.openmm.OpenMMSimulation method) (nanover.omni.playback.PlaybackSimulation method)

advance_by_seconds() (nanover.omni.ase.ASESimulation method) (nanover.omni.omni.Simulation method) (nanover.omni.openmm.OpenMMSimulation method) (nanover.omni.playback.PlaybackSimulation method) advance_to_first_coordinate_frame() (in module nanover.recording.reading) advance_to_first_particle_frame() (in module nanover.recording.reading) advance_to_next_entry() (nanover.omni.playback.PlaybackSimulation method) advance_to_next_report() (nanover.omni.ase.ASESimulation method) (nanover.omni.openmm.OpenMMSimulation method) all_frames (nanover.app.client.NanoverImdClient property) app_server (nanover.app.runner.NanoverRunner property) (nanover.omni.omni.OmniRunner property) apply_single_interaction_force() (in module nanover.imd.imd_force) are_frames_subscribed (nanover.app.client.NanoverImdClient property) arguments (nanover.command.command_info.CommandInfo property) array_keys (nanover.trajectory.frame_data.FrameData property) ArraysView (class in nanover.trajectory.frame_data) ase_atoms_to_frame_data() (in module nanover.ase.converter) ase_to_frame_data() (in module nanover.ase.converter) ASEAtomsToFrameData (class in nanover.omni.ase) ASEOpenMMSimulation (class in nanover.omni.ase_omm) ASESimulation (class in nanover.omni.ase) assert_equal_soon() (in module nanover.testing.asserts) assert_in_soon() (in module nanover.testing.asserts) assert_not_in_soon() (in module nanover.testing.asserts) atoms (nanover.ase.trajectory_logger.TrajectoryLogger attribute) (nanover.omni.ase.ASESimulation property) attempt_update_locks() (nanover.core.nanover_client.NanoverClient method) attempt_update_multiplayer_locks() (nanover.app.client.NanoverImdClient method) attempt_update_multiplayer_state() (nanover.app.client.NanoverImdClient method) attempt_update_state() (nanover.core.nanover_client.NanoverClient method) attribute (nanover.mdanalysis.universe.KeyConversion attribute) autoconnect() (nanover.app.client.NanoverImdClient class method) available_commands (nanover.core.nanover_client.NanoverClient property)

B

base_path (nanover.ase.trajectory_logger.TrajectoryLogger attribute) basic_server() (nanover.app.app_server.NanoverApplicationServer class method) batched() (in module nanover.mdanalysis.universe)

BINDINGS (nanover.omni.rich.OmniTextualApp attribute) bond_orders (nanover.trajectory.frame_data.FrameData property) bond_pairs (nanover.trajectory.frame_data.FrameData property) box_vectors (nanover.trajectory.frame_data.FrameData property)

C

calculate() (nanover.ase.imd_calculator.ImdCalculator method) (nanover.ase.null_calculator.NullCalculator method) (nanover.ase.omm_calculator.OpenMMCalculator method) calculate_constant_force() (in module nanover.imd.imd_force) calculate_gaussian_force() (in module nanover.imd.imd_force) calculate_imd_force() (in module nanover.imd.imd_force) calculate_spring_force() (in module nanover.imd.imd_force) calculator (nanover.ase.imd_calculator.ImdCalculator property) callback (nanover.command.command_service.CommandRegistration attribute) cell (nanover.omni.ase.InitialState attribute) chain_count (nanover.trajectory.frame_data.FrameData property) chain_names (nanover.trajectory.frame_data.FrameData property) channel (nanover.core.grpc_client.GrpcClient attribute) clear_particles() (nanover.app.selection.RenderingSelection method) clear_selections() (nanover.app.client.NanoverImdClient method) close() (nanover.app.app_server.NanoverApplicationServer method) (nanover.app.app_server.SupportsClose method) (nanover.app.client.NanoverImdClient method) (nanover.app.frame_app.NanoverFrameApplication method) (nanover.app.runner.NanoverRunner method) (nanover.ase.trajectory_logger.TrajectoryLogger method) (nanover.core.grpc_client.GrpcClient method) (nanover.core.grpc_server.GrpcServer method) (nanover.core.nanover_client.NanoverClient method) (nanover.core.nanover_server.NanoverServer method) (nanover.essd.client.DiscoveryClient method) (nanover.essd.server.DiscoveryServer method) (nanover.imd.imd_client.ImdClient method) (nanover.omni.omni.OmniRunner method) (nanover.state.state_service.StateService method) (nanover.trajectory.frame_publisher.FramePublisher method) (nanover.trajectory.frame_server.FrameServer method)

Command (class in nanover.protocol.command.command_service_pb2_grpc) CommandInfo (class in nanover.command.command_info) CommandMessage (class in nanover.protocol.command.command_service_pb2) CommandRegistration (class in nanover.command.command_service) CommandReply (class in nanover.protocol.command.command_service_pb2) commands (nanover.command.command_service.CommandService property) (nanover.core.nanover_server.NanoverServer property) CommandService (class in nanover.command.command_service) CommandServicer (class in nanover.protocol.command.command_service_pb2_grpc) CommandStub (class in nanover.protocol.command.command_service_pb2_grpc) compose() (nanover.omni.rich.OmniTextualApp method) configure_reusable_socket() (in module nanover.essd.server) connect() (nanover.app.client.NanoverImdClient method) connect_imd() (nanover.app.client.NanoverImdClient method) connect_multiplayer() (nanover.app.client.NanoverImdClient method) connect_to_single_server() (nanover.app.client.NanoverImdClient class method) connect_to_single_server_multiple_ports() (nanover.app.client.NanoverImdClient class method) connect_trajectory() (nanover.app.client.NanoverImdClient method) content_updated (nanover.state.state_dictionary.StateDictionary attribute) conversion (nanover.mdanalysis.universe.KeyConversion attribute) converter (nanover.mdanalysis.converter.FrameDataFieldConversion attribute) copy() (nanover.trajectory.frame_data.FrameData method) copy_content() (nanover.state.state_dictionary.StateDictionary method) (nanover.utilities.change_buffers.DictionaryChangeMultiView method) copy_state() (nanover.core.nanover_client.NanoverClient method) (nanover.core.nanover_server.NanoverServer method) (nanover.state.state_service.StateService method) create_imd_force() (in module nanover.openmm.imd) create_selection() (nanover.app.client.NanoverImdClient method) create_view() (nanover.utilities.change_buffers.DictionaryChangeMultiView method) CSS_PATH (nanover.omni.rich.OmniTextualApp attribute) current_frame (nanover.app.client.NanoverImdClient property)

D

deep_copy_serializable_dict() (in module nanover.utilities.protobuf_utilities) DEFAULT_CONNECTION_PORT (nanover.core.grpc_client.GrpcClient attribute) DEFAULT_SERVER_NAME (nanover.app.app_server.NanoverApplicationServer attribute) (nanover.app.frame_app.NanoverFrameApplication attribute) (nanover.app.imd_app.NanoverImdApplication attribute) delete() (nanover.trajectory.frame_data.RecordView method) (nanover.utilities.key_lockable_map.KeyLockableMap method) describeNextReport() (nanover.openmm.imd.NanoverImdReporter method) (nanover.openmm.nanoverreporter.NanoverReporter method) DESCRIPTOR (nanover.protocol.array_pb2.FloatArray attribute) (nanover.protocol.array_pb2.IndexArray attribute) (nanover.protocol.array_pb2.StringArray attribute) (nanover.protocol.array_pb2.ValueArray attribute) (nanover.protocol.command.command_service_pb2.CommandMessage attribute) (nanover.protocol.command.command_service_pb2.CommandReply attribute) (nanover.protocol.command.command_service_pb2.GetCommandsReply attribute) (nanover.protocol.command.command_service_pb2.GetCommandsRequest attribute) (nanover.protocol.state.state_service_pb2.StateUpdate attribute) (nanover.protocol.state.state_service_pb2.SubscribeStateUpdatesRequest attribute) (nanover.protocol.state.state_service_pb2.UpdateLocksRequest attribute) (nanover.protocol.state.state_service_pb2.UpdateLocksResponse attribute) (nanover.protocol.state.state_service_pb2.UpdateStateRequest attribute) (nanover.protocol.state.state_service_pb2.UpdateStateResponse attribute) (nanover.protocol.trajectory.frame_pb2.FrameData attribute) (nanover.protocol.trajectory.frame_pb2.FrameData.ArraysEntry attribute) (nanover.protocol.trajectory.frame_pb2.FrameData.ValuesEntry attribute) (nanover.protocol.trajectory.get_frame_pb2.GetFrameRequest attribute) (nanover.protocol.trajectory.get_frame_pb2.GetFrameResponse attribute)

deserialize_simulation() (in module nanover.openmm.serializer) dict_to_interaction() (in module nanover.imd.imd_state) dict_to_struct() (in module nanover.utilities.protobuf_utilities) dictionary_change_to_state_update() (in module nanover.state.state_service) DictionaryChange (class in nanover.utilities.change_buffers) DictionaryChangeBuffer (class in nanover.utilities.change_buffers) DictionaryChangeMultiView (class in nanover.utilities.change_buffers) DictOfQueues (class in nanover.utilities.request_queues) discovery (nanover.app.app_server.NanoverApplicationServer property) DiscoveryClient (class in nanover.essd.client) DiscoveryServer (class in nanover.essd.server)

E

emit() (nanover.omni.playback.PlaybackSimulation method)

Event (class in nanover.utilities.event) explosion_mask() (in module nanover.mdanalysis.universe)

F

fill_empty_fields() (in module nanover.nglview.nglclient) first_frame (nanover.app.client.NanoverImdClient property) FloatArray (class in nanover.protocol.array_pb2) flush_changed_blocking() (nanover.utilities.change_buffers.DictionaryChangeBuffer method) flush_changes() (nanover.app.selection.RenderingSelection method) force_interval (nanover.openmm.imd.NanoverImdReporter attribute) ForceCalculator (class in nanover.imd.imd_force) format (nanover.ase.trajectory_logger.TrajectoryLogger attribute) frame_count (nanover.trajectory.frame_server.FrameServer property) frame_data_to_ase() (in module nanover.ase.converter) frame_data_to_mdanalysis() (in module nanover.mdanalysis.converter) frame_data_to_nglwidget() (in module nanover.nglview.nglclient) frame_data_to_pdb() (in module nanover.nglview.nglclient) frame_index (nanover.ase.trajectory_logger.TrajectoryLogger attribute) frame_interval (nanover.omni.openmm.OpenMMSimulation attribute) (nanover.openmm.imd.NanoverImdReporter attribute) frame_publisher (nanover.app.frame_app.NanoverFrameApplication property) (nanover.openmm.imd.NanoverImdReporter attribute) frame_queues (nanover.trajectory.frame_publisher.FramePublisher attribute) FrameClient (class in nanover.trajectory.frame_client) FrameData (class in nanover.protocol.trajectory.frame_pb2) (class in nanover.trajectory.frame_data)

FrameData.ArraysEntry (class in nanover.protocol.trajectory.frame_pb2) FrameData.ValuesEntry (class in nanover.protocol.trajectory.frame_pb2) FrameDataField (class in nanover.mdanalysis.converter) FrameDataFieldConversion (class in nanover.mdanalysis.converter) FrameDataStructure (class in nanover.nglview.nglclient) FramePublisher (class in nanover.trajectory.frame_publisher) frames (nanover.app.client.NanoverImdClient property) FrameServer (class in nanover.trajectory.frame_server) freeze() (nanover.state.state_dictionary.StateDictionary method) (nanover.utilities.change_buffers.DictionaryChangeBuffer method) (nanover.utilities.change_buffers.DictionaryChangeMultiView method) from_ase_dynamics() (nanover.omni.ase.ASESimulation class method) from_dictionary() (nanover.app.selection.RenderingSelection class method) from_json() (nanover.essd.servicehub.ServiceHub class method) from_paths() (nanover.omni.playback.PlaybackSimulation class method) from_proto() (nanover.command.command_info.CommandInfo class method) from_simulation() (nanover.omni.ase_omm.ASEOpenMMSimulation class method) (nanover.omni.openmm.OpenMMSimulation class method) from_xml() (nanover.ase.omm_calculator.OpenMMCalculator class method) from_xml_path() (nanover.omni.openmm.OpenMMSimulation class method)

G

generate_atoms() (nanover.ase.omm_calculator.OpenMMCalculator method) generate_bonds_from_ase() (in module nanover.ase.converter) get() (nanover.trajectory.frame_data.RecordView method) (nanover.utilities.key_lockable_map.KeyLockableMap method) (nanover.utilities.request_queues.SingleItemQueue method) get_all() (nanover.utilities.key_lockable_map.KeyLockableMap method) get_all_paths() (in module nanover.omni.cli) get_broadcast_addresses() (in module nanover.essd.utils) get_broadcast_addresses_for_service() (nanover.essd.server.DiscoveryServer method) get_broadcastable_ip() (in module nanover.essd.utils) get_center_of_mass_subset() (in module nanover.imd.imd_force) get_change_buffer() (nanover.state.state_dictionary.StateDictionary method) (nanover.state.state_service.StateService method) get_imd_forces_from_system() (in module nanover.openmm.imd) get_ipv4_addresses() (in module nanover.essd.utils) get_nested_or_default() (in module nanover.app.selection) get_periodic_box_lengths() (in module nanover.ase.imd_calculator)

get_radius_of_element() (in module nanover.ase.converter) get_requested_port_or_default() (in module nanover.core.grpc_server) get_selection() (nanover.app.client.NanoverImdClient method) get_service_address() (nanover.essd.servicehub.ServiceHub method) get_shared_value() (nanover.app.client.NanoverImdClient method) get_sparse_forces() (in module nanover.imd.imd_force) get_structure_string() (nanover.nglview.nglclient.FrameDataStructure method) GetCommands() (nanover.command.command_service.CommandService method) (nanover.protocol.command.command_service_pb2_grpc.Command static method) (nanover.protocol.command.command_service_pb2_grpc.CommandServicer method) GetCommandsReply (class in nanover.protocol.command.command_service_pb2) GetCommandsRequest (class in nanover.protocol.command.command_service_pb2) GetFrameRequest (class in nanover.protocol.trajectory.get_frame_pb2) GetFrameResponse (class in nanover.protocol.trajectory.get_frame_pb2) GetFrameResponseAggregatingQueue (class in nanover.utilities.request_queues) GrpcClient (class in nanover.core.grpc_client) GrpcServer (class in nanover.core.grpc_server)

H

handle_signals() (nanover.omni.omni.InternalRunner method) handle_user_arguments() (in module nanover.essd.list_cli) (in module nanover.omni.cli)

has_topology() (in module nanover.mdanalysis.universe) hide (nanover.app.selection.RenderingSelection property)

I

id (nanover.essd.servicehub.ServiceHub property) imd (nanover.app.imd_app.NanoverImdApplication property) imd_force (nanover.openmm.imd.NanoverImdReporter attribute) imd_state (nanover.imd.imd_server.ImdServer property) ImdCalculator (class in nanover.ase.imd_calculator) ImdClient (class in nanover.imd.imd_client) ImdForceManager (class in nanover.openmm.imd) ImdServer (class in nanover.imd.imd_server) ImdStateWrapper (class in nanover.imd.imd_state) implemented_properties (nanover.ase.omm_calculator.OpenMMCalculator attribute) include_energies (nanover.openmm.imd.NextReport attribute) include_forces (nanover.omni.openmm.OpenMMSimulation attribute) (nanover.openmm.imd.NanoverImdReporter attribute) (nanover.openmm.imd.NextReport attribute) include_positions (nanover.openmm.imd.NextReport attribute) include_velocities (nanover.omni.openmm.OpenMMSimulation attribute) (nanover.openmm.imd.NanoverImdReporter attribute) (nanover.openmm.imd.NextReport attribute) IndexArray (class in nanover.protocol.array_pb2) info (nanover.command.command_service.CommandRegistration attribute) initialise_runner() (in module nanover.omni.cli) InitialState (class in nanover.omni.ase) insecure_channel() (nanover.core.grpc_client.GrpcClient class method) insert_interaction() (nanover.imd.imd_state.ImdStateWrapper method)

interaction_method (nanover.app.selection.RenderingSelection property) interaction_to_dict() (in module nanover.imd.imd_state) interaction_type (nanover.imd.particle_interaction.ParticleInteraction property) interactions (nanover.app.client.NanoverImdClient property) (nanover.ase.imd_calculator.ImdCalculator property) (nanover.imd.imd_client.ImdClient property) InternalRunner (class in nanover.omni.omni) interval (nanover.utilities.timing.VariableIntervalGenerator property) InvalidMagicNumber invoke() (nanover.utilities.event.Event method) is_broadcasting (nanover.essd.server.DiscoveryServer property) is_channel_owner (nanover.core.grpc_client.GrpcClient property) is_in_network() (in module nanover.essd.utils) is_paused (nanover.omni.omni.OmniRunner property) is_running (nanover.app.runner.NanoverRunner property) iter_queues() (nanover.utilities.request_queues.DictOfQueues method) iter_queues_items() (nanover.utilities.request_queues.DictOfQueues method) iter_recording_buffers() (in module nanover.recording.reading) iter_recording_entries() (in module nanover.recording.reading) iter_recording_files() (in module nanover.recording.reading) iter_state_file() (in module nanover.recording.reading) iter_state_recording() (in module nanover.recording.reading) iter_trajectory_file() (in module nanover.recording.reading) iter_trajectory_recording() (in module nanover.recording.reading) iter_trajectory_with_elapsed_integrated() (in module nanover.recording.reading)

K

key (nanover.mdanalysis.converter.FrameDataField attribute) (nanover.mdanalysis.converter.FrameDataFieldConversion attribute) KeyConversion (class in nanover.mdanalysis.universe)

KeyLockableMap (class in nanover.utilities.key_lockable_map) keys() (nanover.trajectory.frame_data.RecordView method) kinetic_energy (nanover.trajectory.frame_data.FrameData property)

L

last_frame (nanover.trajectory.frame_publisher.FramePublisher attribute) last_frame_index (nanover.trajectory.frame_publisher.FramePublisher attribute) last_request_id (nanover.trajectory.frame_publisher.FramePublisher attribute) latest_frame (nanover.app.client.NanoverImdClient property) latest_multiplayer_values (nanover.app.client.NanoverImdClient property) list() (nanover.omni.omni.OmniRunner method) list_value_to_list() (in module nanover.utilities.protobuf_utilities) load() (nanover.omni.ase.ASESimulation method) (nanover.omni.ase_omm.ASEOpenMMSimulation method) (nanover.omni.omni.OmniRunner method) (nanover.omni.omni.Simulation method) (nanover.omni.openmm.OpenMMSimulation method) (nanover.omni.playback.PlaybackSimulation method)

lock (nanover.utilities.request_queues.DictOfQueues attribute) lock_content() (nanover.state.state_dictionary.StateDictionary method) lock_key() (nanover.utilities.key_lockable_map.KeyLockableMap method) lock_state() (nanover.core.nanover_client.NanoverClient method) (nanover.core.nanover_server.NanoverServer method) (nanover.state.state_service.StateService method) locks_update_to_acquire_release() (in module nanover.state.state_service) log_addresses() (nanover.essd.server.DiscoveryServer method)

M

main() (in module nanover.essd.list_cli) (in module nanover.omni.cli) (in module nanover.openmm.cli) make_default_ase_omm_dynamics() (in module nanover.omni.ase_omm) make_frame_converter() (nanover.ase.omm_calculator.OpenMMCalculator method) make_regular_frame() (nanover.omni.ase.ASESimulation method) (nanover.omni.openmm.OpenMMSimulation method) (nanover.openmm.imd.NanoverImdReporter method) make_topology_frame() (nanover.omni.ase.ASESimulation method) (nanover.omni.openmm.OpenMMSimulation method) (nanover.openmm.imd.NanoverImdReporter method) mass_weighted (nanover.imd.particle_interaction.ParticleInteraction property) MASS_WEIGHTED_KEY (nanover.imd.particle_interaction.ParticleInteraction attribute) max_force (nanover.imd.particle_interaction.ParticleInteraction property) MAX_FORCE_KEY (nanover.imd.particle_interaction.ParticleInteraction attribute) mda_to_pdb_str() (in module nanover.nglview.nglclient) mdanalysis_to_frame_data() (in module nanover.mdanalysis.converter) message (nanover.essd.servicehub.ServiceHub property) MissingDataError modify() (nanover.app.selection.RenderingSelection method) module nanover nanover.app nanover.app.app_server nanover.app.client nanover.app.frame_app nanover.app.imd_app nanover.app.multiuser nanover.app.runner nanover.app.selection nanover.ase nanover.ase.converter nanover.ase.imd_calculator nanover.ase.null_calculator nanover.ase.omm_calculator nanover.ase.trajectory_logger nanover.ase.wall_constraint nanover.command nanover.command.command_info nanover.command.command_service nanover.core nanover.core.grpc_client nanover.core.grpc_server nanover.core.nanover_client nanover.core.nanover_server nanover.essd nanover.essd.client nanover.essd.list_cli nanover.essd.server nanover.essd.servicehub nanover.essd.utils nanover.imd nanover.imd.imd_client nanover.imd.imd_force nanover.imd.imd_server nanover.imd.imd_state nanover.imd.particle_interaction nanover.mdanalysis nanover.mdanalysis.converter nanover.mdanalysis.universe nanover.nglview nanover.nglview.nglclient nanover.omni nanover.omni.ase nanover.omni.ase_omm nanover.omni.cli nanover.omni.omni nanover.omni.openmm nanover.omni.playback nanover.omni.record nanover.omni.rich nanover.openmm nanover.openmm.cli nanover.openmm.converter nanover.openmm.imd nanover.openmm.nanoverreporter nanover.openmm.potentials nanover.openmm.serializer nanover.protocol nanover.protocol.array_pb2 nanover.protocol.array_pb2_grpc nanover.protocol.command nanover.protocol.command.command_service_pb2 nanover.protocol.command.command_service_pb2_grpc nanover.protocol.state nanover.protocol.state.state_service_pb2 nanover.protocol.state.state_service_pb2_grpc nanover.protocol.trajectory nanover.protocol.trajectory.frame_pb2 nanover.protocol.trajectory.frame_pb2_grpc nanover.protocol.trajectory.get_frame_pb2 nanover.protocol.trajectory.get_frame_pb2_grpc nanover.protocol.trajectory.trajectory_service_pb2 nanover.protocol.trajectory.trajectory_service_pb2_grpc nanover.recording nanover.recording.reading nanover.recording.writing nanover.state nanover.state.state_dictionary nanover.state.state_service nanover.testing nanover.testing.asserts nanover.trajectory nanover.trajectory.frame_client nanover.trajectory.frame_data nanover.trajectory.frame_publisher nanover.trajectory.frame_server nanover.utilities nanover.utilities.change_buffers nanover.utilities.event nanover.utilities.grpc_utilities nanover.utilities.key_lockable_map nanover.utilities.protobuf_utilities nanover.utilities.request_queues nanover.utilities.timing

N

name (nanover.app.app_server.NanoverApplicationServer property) (nanover.app.runner.NanoverRunner property) (nanover.command.command_info.CommandInfo property) (nanover.essd.servicehub.ServiceHub property) (nanover.omni.omni.Simulation attribute) nanover module nanover.app module nanover.app.app_server module nanover.app.client module nanover.app.frame_app module nanover.app.imd_app module nanover.app.multiuser module nanover.app.runner module nanover.app.selection module nanover.ase module nanover.ase.converter module nanover.ase.imd_calculator module nanover.ase.null_calculator module nanover.ase.omm_calculator module nanover.ase.trajectory_logger module nanover.ase.wall_constraint module nanover.command module nanover.command.command_info module nanover.command.command_service module nanover.core module nanover.core.grpc_client module nanover.core.grpc_server module nanover.core.nanover_client module nanover.core.nanover_server module nanover.essd module nanover.essd.client module nanover.essd.list_cli module nanover.essd.server module nanover.essd.servicehub module nanover.essd.utils module nanover.imd module nanover.imd.imd_client module nanover.imd.imd_force module nanover.imd.imd_server module nanover.imd.imd_state module nanover.imd.particle_interaction module nanover.mdanalysis module nanover.mdanalysis.converter module nanover.mdanalysis.universe module nanover.nglview module nanover.nglview.nglclient module nanover.omni module nanover.omni.ase module nanover.omni.ase_omm module nanover.omni.cli module nanover.omni.omni module nanover.omni.openmm module nanover.omni.playback module nanover.omni.record module nanover.omni.rich module nanover.openmm module

nanover.openmm.cli module nanover.openmm.converter module nanover.openmm.imd module nanover.openmm.nanoverreporter module nanover.openmm.potentials module nanover.openmm.serializer module nanover.protocol module nanover.protocol.array_pb2 module nanover.protocol.array_pb2_grpc module nanover.protocol.command module nanover.protocol.command.command_service_pb2 module nanover.protocol.command.command_service_pb2_grpc module nanover.protocol.state module nanover.protocol.state.state_service_pb2 module nanover.protocol.state.state_service_pb2_grpc module nanover.protocol.trajectory module nanover.protocol.trajectory.frame_pb2 module nanover.protocol.trajectory.frame_pb2_grpc module nanover.protocol.trajectory.get_frame_pb2 module nanover.protocol.trajectory.get_frame_pb2_grpc module nanover.protocol.trajectory.trajectory_service_pb2 module nanover.protocol.trajectory.trajectory_service_pb2_grpc module nanover.recording module nanover.recording.reading module nanover.recording.writing module nanover.state module nanover.state.state_dictionary module nanover.state.state_service module nanover.testing module nanover.testing.asserts module nanover.trajectory module nanover.trajectory.frame_client module nanover.trajectory.frame_data module nanover.trajectory.frame_publisher module nanover.trajectory.frame_server module nanover.utilities module nanover.utilities.change_buffers module nanover.utilities.event module nanover.utilities.grpc_utilities module nanover.utilities.key_lockable_map module nanover.utilities.protobuf_utilities module nanover.utilities.request_queues module nanover.utilities.timing module NanoverApplicationServer (class in nanover.app.app_server) NanoverClient (class in nanover.core.nanover_client) NanoverFrameApplication (class in nanover.app.frame_app) NanoverImdApplication (class in nanover.app.imd_app) NanoverImdClient (class in nanover.app.client) NanoverImdReporter (class in nanover.openmm.imd) NanoverParser (class in nanover.mdanalysis.universe) NanoverReader (class in nanover.mdanalysis.universe) NanoverReporter (class in nanover.openmm.nanoverreporter) NanoverRunner (class in nanover.app.runner) NanoverServer (class in nanover.core.nanover_server) NanoverStubClient (class in nanover.core.nanover_client) need_frames() (in module nanover.app.client) need_imd() (in module nanover.app.client) need_multiplayer() (in module nanover.app.client) need_trajectory_joined() (in module nanover.app.client) next() (nanover.omni.omni.OmniRunner method) NextReport (class in nanover.openmm.imd) NGLClient (class in nanover.nglview.nglclient) nullable_int() (in module nanover.mdanalysis.converter) NullCalculator (class in nanover.ase.null_calculator)

O

object_to_value() (in module nanover.utilities.protobuf_utilities) ObjectFrozenError OmniRunner (class in nanover.omni.omni) OmniTextualApp (class in nanover.omni.rich) on_button_pressed() (nanover.omni.rich.OmniTextualApp method)

on_mount() (nanover.omni.rich.OmniTextualApp method) one_queue() (nanover.utilities.request_queues.DictOfQueues method) openmm_to_frame_data() (in module nanover.openmm.converter) OpenMMCalculator (class in nanover.ase.omm_calculator) OpenMMSimulation (class in nanover.omni.openmm)

P

parallel (nanover.ase.trajectory_logger.TrajectoryLogger attribute) parse() (nanover.mdanalysis.universe.NanoverParser method) Parseable (class in nanover.recording.reading) ParseFromString() (nanover.recording.reading.Parseable method) particle_count (nanover.trajectory.frame_data.FrameData property) particle_elements (nanover.trajectory.frame_data.FrameData property) particle_forces (nanover.trajectory.frame_data.FrameData property) particle_forces_system (nanover.trajectory.frame_data.FrameData property) particle_names (nanover.trajectory.frame_data.FrameData property) particle_positions (nanover.trajectory.frame_data.FrameData property) particle_residues (nanover.trajectory.frame_data.FrameData property) particle_velocities (nanover.trajectory.frame_data.FrameData property) ParticleInteraction (class in nanover.imd.particle_interaction) particles (nanover.imd.particle_interaction.ParticleInteraction property) pause() (nanover.app.runner.NanoverRunner method) (nanover.omni.omni.OmniRunner method) platform_name (nanover.omni.openmm.OpenMMSimulation attribute)

play() (nanover.app.runner.NanoverRunner method) (nanover.omni.omni.OmniRunner method) play_step_interval (nanover.omni.omni.InternalRunner property) PlaybackSimulation (class in nanover.omni.playback) player_can_lock_key() (nanover.utilities.key_lockable_map.KeyLockableMap method) populate_imd_force() (in module nanover.openmm.imd) port (nanover.app.app_server.NanoverApplicationServer property) (nanover.app.runner.NanoverRunner property) (nanover.core.grpc_server.GrpcServer property) (nanover.essd.client.DiscoveryClient property) position (nanover.imd.particle_interaction.ParticleInteraction property) positions (nanover.omni.ase.InitialState attribute) potential_energy (nanover.trajectory.frame_data.FrameData property) print_basic_info_and_wait() (nanover.omni.omni.OmniRunner method) print_hub() (in module nanover.essd.list_cli) properties (nanover.imd.particle_interaction.ParticleInteraction property) put() (nanover.utilities.request_queues.GetFrameResponseAggregatingQueue method) (nanover.utilities.request_queues.SingleItemQueue method)

Q

qualified_server_name() (in module nanover.app.app_server)

queue_max_size (nanover.utilities.request_queues.DictOfQueues attribute) queues (nanover.utilities.request_queues.DictOfQueues attribute)

R

raw (nanover.trajectory.frame_data.FrameData property) read() (in module nanover.recording.reading) read_from_dictionary() (nanover.app.selection.RenderingSelection method) read_hide_from_dictionary() (nanover.app.selection.RenderingSelection method) read_interaction_method_from_dictionary() (nanover.app.selection.RenderingSelection method) read_renderer_from_dictionary() (nanover.app.selection.RenderingSelection method) read_selected_particles_from_dictionary() (nanover.app.selection.RenderingSelection method) read_u128() (in module nanover.recording.reading) read_u64() (in module nanover.recording.reading) read_velocity_reset_from_dictionary() (nanover.app.selection.RenderingSelection method) record_entries() (in module nanover.recording.writing) record_from_server() (in module nanover.omni.record) record_messages() (in module nanover.recording.writing) record_messages_to_file() (in module nanover.recording.writing) record_name (nanover.trajectory.frame_data.ArraysView attribute) (nanover.trajectory.frame_data.RecordView attribute) (nanover.trajectory.frame_data.ValuesView attribute) record_state() (in module nanover.omni.record) record_trajectory() (in module nanover.omni.record) RecordView (class in nanover.trajectory.frame_data) register_command() (nanover.command.command_service.CommandService method) (nanover.core.nanover_server.NanoverServer method) register_service() (nanover.essd.server.DiscoveryServer method) release_key() (nanover.utilities.key_lockable_map.KeyLockableMap method) removals (nanover.utilities.change_buffers.DictionaryChange attribute) remove() (nanover.app.selection.RenderingSelection method) remove_callback() (nanover.utilities.event.Event method) remove_interaction() (nanover.imd.imd_state.ImdStateWrapper method) remove_owner() (nanover.utilities.key_lockable_map.KeyLockableMap method) remove_selection() (nanover.app.client.NanoverImdClient method) remove_shared_value() (nanover.app.client.NanoverImdClient method) remove_view() (nanover.utilities.change_buffers.DictionaryChangeMultiView method) removed (nanover.app.selection.RenderingSelection property) renderer (nanover.app.selection.RenderingSelection property) RenderingSelection (class in nanover.app.selection) report() (nanover.openmm.imd.NanoverImdReporter method) (nanover.openmm.nanoverreporter.NanoverReporter method) required (nanover.mdanalysis.converter.FrameDataField attribute)

reset() (nanover.app.runner.NanoverRunner method) (nanover.ase.trajectory_logger.TrajectoryLogger method) (nanover.omni.ase.ASESimulation method) (nanover.omni.omni.OmniRunner method) (nanover.omni.omni.Simulation method) (nanover.omni.openmm.OpenMMSimulation method) (nanover.omni.playback.PlaybackSimulation method) reset_temperature (nanover.ase.imd_calculator.ImdCalculator property) reset_velocities (nanover.imd.particle_interaction.ParticleInteraction property) RESET_VELOCITIES_KEY (nanover.imd.particle_interaction.ParticleInteraction attribute) residue_chains (nanover.trajectory.frame_data.FrameData property) residue_count (nanover.trajectory.frame_data.FrameData property) residue_ids (nanover.trajectory.frame_data.FrameData property) residue_names (nanover.trajectory.frame_data.FrameData property) resolve_host_broadcast_address() (in module nanover.essd.utils) ResourceLockedError restrain_particles() (in module nanover.openmm.potentials) restraint_force() (in module nanover.openmm.potentials) root_selection (nanover.app.client.NanoverImdClient property) RpcAlreadyTerminatedError run() (nanover.app.runner.NanoverRunner method) (nanover.omni.omni.InternalRunner method) run_command() (nanover.app.client.NanoverImdClient method) (nanover.core.nanover_client.NanoverClient method) run_imd_command() (nanover.app.client.NanoverImdClient method) run_list() (nanover.app.client.NanoverImdClient method) run_load() (nanover.app.client.NanoverImdClient method) run_multiplayer_command() (nanover.app.client.NanoverImdClient method) run_next() (nanover.app.client.NanoverImdClient method) run_pause() (nanover.app.client.NanoverImdClient method) run_play() (nanover.app.client.NanoverImdClient method) run_reset() (nanover.app.client.NanoverImdClient method) run_step() (nanover.app.client.NanoverImdClient method) run_trajectory_command() (nanover.app.client.NanoverImdClient method) RunCommand() (nanover.command.command_service.CommandService method) (nanover.protocol.command.command_service_pb2_grpc.Command static method) (nanover.protocol.command.command_service_pb2_grpc.CommandServicer method) runner (nanover.omni.omni.OmniRunner property) running_discovery (nanover.app.app_server.NanoverApplicationServer property)

S

scale (nanover.imd.particle_interaction.ParticleInteraction property) SCALE_KEY (nanover.imd.particle_interaction.ParticleInteraction attribute) search_for_services() (nanover.essd.client.DiscoveryClient method) selected_particle_ids (nanover.app.selection.RenderingSelection property) selection_id (nanover.app.selection.RenderingSelection property) selection_name (nanover.app.selection.RenderingSelection property) selections (nanover.app.client.NanoverImdClient property) send_frame() (nanover.trajectory.frame_publisher.FramePublisher method) (nanover.trajectory.frame_server.FrameServer method) Serializable (class in nanover.recording.writing) serialize_simulation() (in module nanover.openmm.serializer) SerializeToString() (nanover.recording.writing.Serializable method) server (nanover.app.app_server.NanoverApplicationServer property) server_timestamp (nanover.trajectory.frame_data.FrameData property) ServiceHub (class in nanover.essd.servicehub) services (nanover.essd.server.DiscoveryServer attribute) (nanover.essd.servicehub.ServiceHub property) set() (nanover.trajectory.frame_data.ArraysView method) (nanover.trajectory.frame_data.RecordView method) (nanover.trajectory.frame_data.ValuesView method) (nanover.utilities.key_lockable_map.KeyLockableMap method) set_float_array() (nanover.trajectory.frame_data.FrameData method) set_index_array() (nanover.trajectory.frame_data.FrameData method) set_no_replace() (nanover.utilities.key_lockable_map.KeyLockableMap method) set_particles() (nanover.app.selection.RenderingSelection method) set_periodic_bounds() (nanover.ase.omm_calculator.OpenMMCalculator static method) set_shared_value() (nanover.app.client.NanoverImdClient method) set_simulation_selections() (nanover.omni.omni.OmniRunner method) set_string_array() (nanover.trajectory.frame_data.FrameData method) setup_services() (nanover.core.grpc_server.GrpcServer method) (nanover.core.nanover_server.NanoverServer method) (nanover.trajectory.frame_server.FrameServer method) shortcuts (nanover.trajectory.frame_data.FrameData property) Simulation (class in nanover.omni.omni) simulation (nanover.ase.omm_calculator.OpenMMCalculator attribute) (nanover.omni.omni.OmniRunner property) simulation_counter (nanover.trajectory.frame_data.FrameData property) simulation_time (nanover.trajectory.frame_data.FrameData property) SingleItemQueue (class in nanover.utilities.request_queues) singular (nanover.trajectory.frame_data.ArraysView attribute) (nanover.trajectory.frame_data.RecordView attribute) (nanover.trajectory.frame_data.ValuesView attribute) start() (nanover.essd.server.DiscoveryServer method)

start_default_server_and_discovery() (in module nanover.app.app_server) start_interaction() (nanover.app.client.NanoverImdClient method) (nanover.imd.imd_client.ImdClient method) State (class in nanover.protocol.state.state_service_pb2_grpc) state_dictionary (nanover.state.state_service.StateService attribute) state_update_to_dictionary_change() (in module nanover.state.state_service) StateDictionary (class in nanover.state.state_dictionary) StateService (class in nanover.state.state_service) StateServicer (class in nanover.protocol.state.state_service_pb2_grpc) StateStub (class in nanover.protocol.state.state_service_pb2_grpc) StateUpdate (class in nanover.protocol.state.state_service_pb2) step() (nanover.app.runner.NanoverRunner method) (nanover.omni.omni.OmniRunner method) steps (nanover.openmm.imd.NextReport attribute) stop_all_interactions() (nanover.imd.imd_client.ImdClient method) stop_interaction() (nanover.app.client.NanoverImdClient method) (nanover.imd.imd_client.ImdClient method) StringArray (class in nanover.protocol.array_pb2) struct_to_dict() (in module nanover.utilities.protobuf_utilities) subscribe_all_state_updates() (nanover.core.nanover_client.NanoverClient method) subscribe_changes() (nanover.utilities.change_buffers.DictionaryChangeBuffer method) (nanover.utilities.change_buffers.DictionaryChangeMultiView method) subscribe_channel_connectivity_change() (in module nanover.utilities.grpc_utilities) subscribe_frames_async() (nanover.trajectory.frame_client.FrameClient method) subscribe_frames_blocking() (nanover.trajectory.frame_client.FrameClient method) subscribe_frames_iterate() (nanover.trajectory.frame_client.FrameClient method) subscribe_last_frames_async() (nanover.trajectory.frame_client.FrameClient method) subscribe_last_frames_blocking() (nanover.trajectory.frame_client.FrameClient method) subscribe_multiplayer() (nanover.app.client.NanoverImdClient method) subscribe_rpc_termination() (in module nanover.utilities.grpc_utilities) subscribe_to_all_frames() (nanover.app.client.NanoverImdClient method) subscribe_to_frames() (nanover.app.client.NanoverImdClient method) SubscribeFrames() (nanover.protocol.trajectory.trajectory_service_pb2_grpc.TrajectoryService static method) (nanover.protocol.trajectory.trajectory_service_pb2_grpc.TrajectoryServiceServicer method) (nanover.trajectory.frame_publisher.FramePublisher method) SubscribeLatestFrames() (nanover.protocol.trajectory.trajectory_service_pb2_grpc.TrajectoryService static method) (nanover.protocol.trajectory.trajectory_service_pb2_grpc.TrajectoryServiceServicer method) (nanover.trajectory.frame_publisher.FramePublisher method) SubscribeStateUpdates() (nanover.protocol.state.state_service_pb2_grpc.State static method) (nanover.protocol.state.state_service_pb2_grpc.StateServicer method) (nanover.state.state_service.StateService method) SubscribeStateUpdatesRequest (class in nanover.protocol.state.state_service_pb2) SupportsClose (class in nanover.app.app_server)

T

temperature (nanover.ase.imd_calculator.ImdCalculator property) threads (nanover.core.grpc_client.GrpcClient attribute) timestamping (nanover.ase.trajectory_logger.TrajectoryLogger property) TITLE (nanover.omni.rich.OmniTextualApp attribute) to_dictionary() (nanover.app.selection.RenderingSelection method) to_message() (nanover.essd.servicehub.ServiceHub method)

topology (nanover.ase.omm_calculator.OpenMMCalculator property) TrajectoryLogger (class in nanover.ase.trajectory_logger) TrajectoryService (class in nanover.protocol.trajectory.trajectory_service_pb2_grpc) TrajectoryServiceServicer (class in nanover.protocol.trajectory.trajectory_service_pb2_grpc) TrajectoryServiceStub (class in nanover.protocol.trajectory.trajectory_service_pb2_grpc) TYPE_KEY (nanover.imd.particle_interaction.ParticleInteraction attribute)

U

units (nanover.mdanalysis.universe.NanoverReader attribute) unregister_command() (nanover.command.command_service.CommandService method) (nanover.core.nanover_server.NanoverServer method) unregister_service() (nanover.essd.server.DiscoveryServer method) UnsupportedFormatError UnsupportedFormatVersion update() (nanover.omni.rich.OmniTextualApp method) (nanover.utilities.change_buffers.DictionaryChangeBuffer method) (nanover.utilities.change_buffers.DictionaryChangeMultiView method) update_available_commands() (nanover.app.client.NanoverImdClient method) (nanover.core.nanover_client.NanoverClient method) update_interaction() (nanover.app.client.NanoverImdClient method) (nanover.imd.imd_client.ImdClient method) update_interactions() (nanover.openmm.imd.ImdForceManager method) update_locks() (nanover.core.nanover_server.NanoverServer method) (nanover.state.state_dictionary.StateDictionary method) (nanover.state.state_service.StateService method) update_selection() (nanover.app.client.NanoverImdClient method) update_state() (nanover.core.nanover_server.NanoverServer method) (nanover.state.state_dictionary.StateDictionary method) (nanover.state.state_service.StateService method)

updated (nanover.app.selection.RenderingSelection property) UpdateLocks() (nanover.protocol.state.state_service_pb2_grpc.State static method) (nanover.protocol.state.state_service_pb2_grpc.StateServicer method) (nanover.state.state_service.StateService method) UpdateLocksRequest (class in nanover.protocol.state.state_service_pb2) UpdateLocksResponse (class in nanover.protocol.state.state_service_pb2) updates (nanover.utilities.change_buffers.DictionaryChange attribute) UpdateState() (nanover.protocol.state.state_service_pb2_grpc.State static method) (nanover.protocol.state.state_service_pb2_grpc.StateServicer method) (nanover.state.state_service.StateService method) UpdateStateRequest (class in nanover.protocol.state.state_service_pb2) UpdateStateResponse (class in nanover.protocol.state.state_service_pb2) used_shortcuts (nanover.trajectory.frame_data.FrameData property) user_energy (nanover.trajectory.frame_data.FrameData property) user_forces_index (nanover.trajectory.frame_data.FrameData property) user_forces_sparse (nanover.trajectory.frame_data.FrameData property) user_work_done (nanover.trajectory.frame_data.FrameData property)

V

validate_ase_can_append_filename() (in module nanover.ase.trajectory_logger) validate_ase_can_append_format() (in module nanover.ase.trajectory_logger) validate_dict_is_serializable() (in module nanover.state.state_service) value_keys (nanover.trajectory.frame_data.FrameData property) value_to_object() (in module nanover.utilities.protobuf_utilities) ValueArray (class in nanover.protocol.array_pb2) ValuesView (class in nanover.trajectory.frame_data)

VariableIntervalGenerator (class in nanover.utilities.timing) velocities (nanover.omni.ase.InitialState attribute) velocity_reset (nanover.app.selection.RenderingSelection property) velocity_reset_available (nanover.imd.imd_state.ImdStateWrapper property) VelocityWallConstraint (class in nanover.ase.wall_constraint) version (nanover.essd.servicehub.ServiceHub property) view (nanover.nglview.nglclient.NGLClient property)

W

wait_busy() (in module nanover.utilities.timing) wait_mixed() (in module nanover.utilities.timing) wait_until_first_frame() (nanover.app.client.NanoverImdClient method) with_basic_server() (nanover.omni.omni.OmniRunner class method) wrap_pbc() (in module nanover.imd.imd_force)

wrap_positions (nanover.openmm.imd.NextReport attribute) write() (nanover.ase.trajectory_logger.TrajectoryLogger method) write_entry() (in module nanover.recording.writing) write_header() (in module nanover.recording.writing) write_u128() (in module nanover.recording.writing) write_u64() (in module nanover.recording.writing)

Y

yield_interval() (in module nanover.utilities.timing) (nanover.utilities.timing.VariableIntervalGenerator method)