Index

A

active_interactions (nanover.imd.imd_state.ImdStateWrapper property) add_ase_box_vectors_to_frame_data() (in module nanover.ase.converter) add_ase_forces_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_ase_velocities_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_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.ase.imd_calculator.ImdCalculator method) (nanover.ase.imd_calculator.ImdForceManager method) (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) 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_contribution_to_work() (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_locks() (nanover.core.nanover_server.NanoverServer method) (nanover.state.state_dictionary.StateDictionary method) (nanover.state.state_service.StateService method) 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) compute_dof() (in module nanover.ase.thermo) (in module nanover.openmm.thermo) compute_instantaneous_temperature() (in module nanover.ase.thermo) (in module nanover.openmm.thermo) 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) 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) 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) frame_publisher (nanover.app.frame_app.NanoverFrameApplication property) 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.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_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) (in module nanover.omni.recorder_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_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.ase.imd_calculator) (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_forces (nanover.omni.openmm.OpenMMSimulation attribute) include_velocities (nanover.omni.openmm.OpenMMSimulation 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.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.omni.recorder_cli) make_frame_converter() (nanover.ase.omm_calculator.OpenMMCalculator method) make_regular_frame() (nanover.omni.ase.ASESimulation method) (nanover.omni.openmm.OpenMMSimulation method) make_topology_frame() (nanover.omni.ase.ASESimulation method) (nanover.omni.openmm.OpenMMSimulation 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.thermo 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.cli nanover.omni.omni nanover.omni.openmm nanover.omni.playback nanover.omni.record nanover.omni.recorder_cli nanover.omni.rich nanover.openmm nanover.openmm.converter nanover.openmm.imd nanover.openmm.potentials nanover.openmm.serializer nanover.openmm.thermo 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.thermo 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.cli module nanover.omni.omni module nanover.omni.openmm module nanover.omni.playback module nanover.omni.record module nanover.omni.recorder_cli module

nanover.omni.rich module nanover.openmm module nanover.openmm.converter module nanover.openmm.imd module nanover.openmm.potentials module nanover.openmm.serializer module nanover.openmm.thermo 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) NanoverParser (class in nanover.mdanalysis.universe) NanoverReader (class in nanover.mdanalysis.universe) 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) 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_all_keys() (nanover.utilities.key_lockable_map.KeyLockableMap 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) 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) 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) system_temperature (nanover.trajectory.frame_data.FrameData property)

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.ase.imd_calculator.ImdCalculator method) (nanover.ase.imd_calculator.ImdForceManager method) (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)

write() (nanover.ase.trajectory_logger.TrajectoryLogger method) write_entry() (in module nanover.recording.writing) write_header() (in module nanover.recording.writing) write_messages_ignore_disconnect() (in module nanover.omni.record) 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)