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_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.app.types.DiscoveryService method) (nanover.essd.servicehub.ServiceHub method) add_simulation() (nanover.omni.omni.OmniRunner method) add_to_frame_data() (nanover.ase.imd_calculator.ImdCalculator method) (nanover.ase.imd_calculator.ImdForceManager method) (nanover.openmm.imd.ImdForceManager method) address (nanover.app.app_server.NanoverApplicationServer property) (nanover.essd.servicehub.ServiceHub 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_next_entry() (nanover.omni.playback.PlaybackSimulation method) advance_to_next_report() (nanover.omni.ase.ASESimulation method) (nanover.omni.openmm.OpenMMSimulation method) advertise() (nanover.websocket.discovery.DiscoveryClient method) advertise_server() (nanover.websocket.discovery.DiscoveryClient class method) app (nanover.testing.servers.ServerClientSetup attribute) app_server (nanover.omni.omni.OmniRunner property) apply_single_interaction_force() (in module nanover.imd.imd_force) AppServer (class in nanover.app.types) AppServerMinimal (class in nanover.app.types) arguments (nanover.app.commands.CommandRegistration attribute) arrays() (in module nanover.testing.strategies) arrays2d() (in module nanover.testing.strategies) 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_frames_synced_soon() (nanover.testing.servers.ServerClientSetup method) assert_in_soon() (in module nanover.testing.asserts) assert_not_in_soon() (in module nanover.testing.asserts) assert_states_synced_soon() (nanover.testing.servers.ServerClientSetup method) assert_true_soon() (in module nanover.testing.asserts) atoms (nanover.ase.trajectory_logger.TrajectoryLogger attribute) (nanover.omni.ase.ASESimulation property) attribute (nanover.mdanalysis.universe.KeyConversion attribute)

B

base_path (nanover.ase.trajectory_logger.TrajectoryLogger attribute) basic_info_string() (in module nanover.app.types) basic_server() (nanover.app.app_server.NanoverApplicationServer class method) (nanover.app.imd_app.NanoverImdApplication class method) (nanover.websocket.server.WebSocketServer class method)

batched() (in module nanover.mdanalysis.universe) 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) cancel() (nanover.utilities.cli.CancellationToken method) CancellationToken (class in nanover.utilities.cli) cell (nanover.omni.ase.InitialState attribute) chain_count (nanover.trajectory.frame_data.FrameData property) chain_names (nanover.trajectory.frame_data.FrameData property) clear_interactions() (nanover.imd.imd_state.ImdStateWrapper method) clear_locks() (nanover.app.app_server.NanoverApplicationServer method) (nanover.app.types.StateService method) (nanover.utilities.state_dictionary.StateDictionary method) clear_particles() (nanover.app.selection.RenderingSelection method) clear_selections() (nanover.websocket.client.selection_client.SelectionClient method) client (nanover.testing.servers.ServerClientSetup attribute) client_current_frame (nanover.testing.servers.ServerClientSetup property) client_current_state (nanover.testing.servers.ServerClientSetup property) close() (nanover.app.app_server.NanoverApplicationServer method) (nanover.app.imd_app.NanoverImdApplication method) (nanover.app.types.Closeable method) (nanover.ase.trajectory_logger.TrajectoryLogger method) (nanover.essd.client.DiscoveryClient method) (nanover.essd.server.DiscoveryServer method) (nanover.omni.omni.OmniRunner method) (nanover.recording.reading.MessageZipReader method) (nanover.recording.writing.NanoverRecordingWriter method) (nanover.trajectory.frame_publisher.FramePublisher method) (nanover.utilities.queues.FrameMergingQueue method) (nanover.websocket.client.base_client.WebsocketClient method) (nanover.websocket.client.interaction_client.InteractionClient method) (nanover.websocket.server.WebSocketServer method)

Closeable (class in nanover.app.types) command_arguments() (in module nanover.testing.strategies) CommandRegistration (class in nanover.app.commands) commands (nanover.app.app_server.NanoverApplicationServer property) (nanover.app.commands.CommandService property) (nanover.app.types.CommandService property) CommandService (class in nanover.app.commands) (class in nanover.app.types) 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_client_to_server() (in module nanover.testing.servers) content_updated (nanover.utilities.state_dictionary.StateDictionary attribute) conversion (nanover.mdanalysis.universe.KeyConversion attribute) convert_dict_state_to_dictionary_change() (in module nanover.trajectory.convert) converter (nanover.mdanalysis.converter.FrameDataFieldConversion attribute) copy() (nanover.trajectory.frame_data.FrameData method) copy_content() (nanover.utilities.change_buffers.DictionaryChangeMultiView method) (nanover.utilities.state_dictionary.StateDictionary method) copy_state() (nanover.app.app_server.NanoverApplicationServer method) (nanover.app.types.StateService method) (nanover.websocket.client.app_client.NanoverImdClient method) create_imd_force() (in module nanover.openmm.imd) create_selection() (nanover.websocket.client.selection_client.SelectionClient method) create_view() (nanover.utilities.change_buffers.DictionaryChangeMultiView method) current_frame (nanover.websocket.client.app_client.NanoverImdClient property) custom_frame_keys() (in module nanover.testing.strategies)

D

DEFAULT_SERVER_NAME (nanover.app.app_server.NanoverApplicationServer attribute) (nanover.app.imd_app.NanoverImdApplication attribute) delete() (nanover.utilities.key_lockable_map.KeyLockableMap method) deserialize_simulation() (in module nanover.openmm.serializer) determine_pbcs() (nanover.omni.openmm.OpenMMSimulation method) dict_frames() (in module nanover.testing.strategies) dict_to_interaction() (in module nanover.imd.imd_state) dictionary_keys() (in module nanover.testing.strategies)

DictionaryChange (class in nanover.utilities.change_buffers) DictionaryChangeBuffer (class in nanover.utilities.change_buffers) DictionaryChangeMultiView (class in nanover.utilities.change_buffers) discovery (nanover.app.app_server.NanoverApplicationServer property) (nanover.app.types.DiscoveryService property) DiscoveryClient (class in nanover.essd.client) (class in nanover.websocket.discovery) DiscoveryServer (class in nanover.essd.server) DiscoveryService (class in nanover.app.types)

E

emit() (nanover.omni.playback.PlaybackSimulation method) empty() (nanover.trajectory.frame_data.FrameData class method)

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

F

fill_empty_fields() (in module nanover.nglview.nglclient) float32s() (in module nanover.testing.strategies) 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_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) (nanover.trajectory.frame_data.FrameData property) frame_interval (nanover.omni.openmm.OpenMMSimulation attribute) frame_publisher (nanover.app.app_server.NanoverApplicationServer property) (nanover.app.types.ImdService property) FrameData (class in nanover.trajectory.frame_data) FrameDataField (class in nanover.mdanalysis.converter) FrameDataFieldConversion (class in nanover.mdanalysis.converter) FrameDataStructure (class in nanover.nglview.nglclient) FrameMergingQueue (class in nanover.utilities.queues) FramePublisher (class in nanover.trajectory.frame_publisher)

FrameRecordingEvent (class in nanover.recording.reading) frames (nanover.websocket.client.app_client.NanoverImdClient property) frames() (in module nanover.testing.strategies) freeze() (nanover.utilities.change_buffers.DictionaryChangeBuffer method) (nanover.utilities.change_buffers.DictionaryChangeMultiView method) (nanover.utilities.state_dictionary.StateDictionary method) from_app_server() (nanover.websocket.client.app_client.NanoverImdClient class method) from_ase_dynamics() (nanover.omni.ase.ASESimulation class method) from_dict() (nanover.trajectory.frame_data.FrameData class method) from_dictionary() (nanover.app.selection.RenderingSelection class method) from_discovery() (nanover.websocket.client.app_client.NanoverImdClient class method) from_io() (nanover.recording.reading.MessageZipReader class method) from_json() (nanover.essd.servicehub.ServiceHub class method) from_path() (nanover.omni.playback.PlaybackSimulation class method) (nanover.recording.reading.MessageZipReader class method) (nanover.recording.writing.NanoverRecordingWriter class method) from_runner() (nanover.websocket.client.app_client.NanoverImdClient class method) from_simulation() (nanover.omni.openmm.OpenMMSimulation class method) from_url() (nanover.websocket.client.base_client.WebsocketClient 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) generate_metadata() (in module nanover.recording.writing) get() (nanover.utilities.key_lockable_map.KeyLockableMap method) (nanover.utilities.queues.LastItemQueue method) get_all() (nanover.utilities.key_lockable_map.KeyLockableMap method) get_all_paths() (in module nanover.omni.cli.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.utilities.state_dictionary.StateDictionary method) get_frame_from_entry() (nanover.recording.reading.NanoverRecordingReader method) get_ipv4_addresses() (in module nanover.essd.utils) get_listing() (nanover.websocket.discovery.DiscoveryClient method)

get_local_ip() (in module nanover.utilities.network) get_message_from_entry() (nanover.recording.reading.MessageZipReader method) get_message_type_from_entry() (nanover.recording.reading.NanoverRecordingReader method) 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_selection() (nanover.websocket.client.selection_client.SelectionClient method) get_service_address() (nanover.essd.servicehub.ServiceHub method) get_shared_value() (nanover.websocket.client.app_client.NanoverImdClient method) get_sparse_forces() (in module nanover.imd.imd_force) get_state_from_entry() (nanover.recording.reading.NanoverRecordingReader method) get_structure_string() (nanover.nglview.nglclient.FrameDataStructure method) get_value() (in module nanover.recording.cli.split_cli) get_websocket_address_from_app_server() (in module nanover.websocket.client.app_client) get_websocket_address_from_hub() (in module nanover.websocket.client.app_client)

H

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

handler (nanover.app.commands.CommandRegistration attribute) 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) (nanover.app.types.ImdService property) ImdCalculator (class in nanover.ase.imd_calculator) ImdForceManager (class in nanover.ase.imd_calculator) (class in nanover.openmm.imd) ImdService (class in nanover.app.types) 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) index2_arrays() (in module nanover.testing.strategies) index_arrays() (in module nanover.testing.strategies) initialise_runner() (in module nanover.omni.cli.omni_cli) initialise_ssl() (in module nanover.omni.cli.omni_cli) InitialState (class in nanover.omni.ase) 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)

InteractionClient (class in nanover.websocket.client.interaction_client) interactions (nanover.ase.imd_calculator.ImdCalculator property) (nanover.websocket.client.interaction_client.InteractionClient property) InternalRunner (class in nanover.omni.omni) interval (nanover.utilities.timing.VariableIntervalGenerator property) InvalidInteractionError invoke() (nanover.utilities.event.Event method) is_broadcasting (nanover.essd.server.DiscoveryServer property) is_cancelled (nanover.utilities.cli.CancellationToken property) is_in_network() (in module nanover.essd.utils) is_paused (nanover.omni.omni.OmniRunner property) is_valid_first_frame() (in module nanover.mdanalysis.universe) iter_frame_updates() (nanover.recording.reading.NanoverRecordingReader method) iter_frames_full() (nanover.recording.reading.NanoverRecordingReader method) iter_full_view() (in module nanover.recording.reading) iter_max() (nanover.recording.reading.NanoverRecordingReader method) iter_message_events() (nanover.recording.reading.NanoverRecordingReader method) iter_recording_file() (in module nanover.recording.reading) iter_state_updates() (nanover.recording.reading.NanoverRecordingReader method) iter_states_full() (nanover.recording.reading.NanoverRecordingReader method)

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) kinetic_energy (nanover.trajectory.frame_data.FrameData property)

L

LastItemQueue (class in nanover.utilities.queues) latest_multiplayer_values (nanover.websocket.client.app_client.NanoverImdClient property) length (nanover.recording.reading.RecordingIndexEntry attribute) list() (nanover.omni.omni.OmniRunner method) 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_content() (nanover.utilities.state_dictionary.StateDictionary method) lock_key() (nanover.utilities.key_lockable_map.KeyLockableMap method) lock_state() (nanover.app.app_server.NanoverApplicationServer method) (nanover.app.types.StateService method) log_addresses() (nanover.essd.server.DiscoveryServer method)

M

main() (in module nanover.essd.list_cli) (in module nanover.omni.cli.omni_cli) (in module nanover.omni.cli.recorder_cli) (in module nanover.recording.cli.dump_cli) (in module nanover.recording.cli.split_cli) make_app_server() (in module nanover.testing.servers) make_bytes_packer() (in module nanover.trajectory.convert) make_connected_server_client_setup() (in module nanover.testing.servers) make_empty() (nanover.recording.reading.FrameRecordingEvent class method) (nanover.recording.reading.StateRecordingEvent class method) make_frame_converter() (nanover.ase.omm_calculator.OpenMMCalculator method) make_key_change_predicate() (in module nanover.recording.cli.split_cli) make_key_name_template() (in module nanover.recording.cli.split_cli) 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) make_websocket_server() (in module nanover.testing.servers) 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) merge_frame_dicts() (in module nanover.trajectory.frame_data) message (nanover.essd.servicehub.ServiceHub property) (nanover.recording.reading.MessageEvent attribute) message_events_from_recording() (in module nanover.recording.reading) message_events_from_websocket() (in module nanover.websocket.record) MessageEvent (class in nanover.recording.reading) MessageZipReader (class in nanover.recording.reading) metadata (nanover.recording.reading.RecordingIndexEntry attribute) MissingDataError modify() (nanover.app.selection.RenderingSelection method) module nanover nanover.app nanover.app.app_server nanover.app.commands nanover.app.imd_app nanover.app.multiuser nanover.app.selection nanover.app.types 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.essd nanover.essd.client nanover.essd.list_cli nanover.essd.server nanover.essd.servicehub nanover.essd.utils nanover.imd nanover.imd.imd_force 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.cli.omni_cli nanover.omni.cli.recorder_cli nanover.omni.omni nanover.omni.openmm nanover.omni.playback nanover.openmm nanover.openmm.converter nanover.openmm.imd nanover.openmm.potentials nanover.openmm.serializer nanover.openmm.thermo nanover.recording nanover.recording.cli nanover.recording.cli.dump_cli nanover.recording.cli.split_cli nanover.recording.reading nanover.recording.writing nanover.testing nanover.testing.asserts nanover.testing.servers nanover.testing.strategies nanover.testing.utilities nanover.trajectory nanover.trajectory.convert nanover.trajectory.frame_data nanover.trajectory.frame_publisher nanover.trajectory.frame_server nanover.trajectory.keys nanover.utilities nanover.utilities.change_buffers nanover.utilities.cli nanover.utilities.event nanover.utilities.key_lockable_map nanover.utilities.network nanover.utilities.queues nanover.utilities.state_dictionary nanover.utilities.timing nanover.websocket nanover.websocket.client nanover.websocket.client.app_client nanover.websocket.client.base_client nanover.websocket.client.interaction_client nanover.websocket.client.playback_client nanover.websocket.client.selection_client nanover.websocket.discovery nanover.websocket.record nanover.websocket.server

N

n_frames (nanover.mdanalysis.universe.NanoverReaderBase property) name (nanover.app.app_server.NanoverApplicationServer property) (nanover.app.commands.CommandRegistration attribute) (nanover.app.types.AppServer property) (nanover.essd.servicehub.ServiceHub property) (nanover.omni.omni.Simulation attribute) name_basic() (in module nanover.recording.cli.split_cli) nanover module nanover.app module nanover.app.app_server module nanover.app.commands module nanover.app.imd_app module nanover.app.multiuser module nanover.app.selection module nanover.app.types 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.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_force 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.cli.omni_cli module nanover.omni.cli.recorder_cli module nanover.omni.omni module nanover.omni.openmm module nanover.omni.playback 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.recording module nanover.recording.cli module nanover.recording.cli.dump_cli module nanover.recording.cli.split_cli module nanover.recording.reading module nanover.recording.writing module nanover.testing module nanover.testing.asserts module nanover.testing.servers module nanover.testing.strategies module nanover.testing.utilities module nanover.trajectory module nanover.trajectory.convert module nanover.trajectory.frame_data module nanover.trajectory.frame_publisher module nanover.trajectory.frame_server module nanover.trajectory.keys module nanover.utilities module nanover.utilities.change_buffers module nanover.utilities.cli module nanover.utilities.event module nanover.utilities.key_lockable_map module nanover.utilities.network module nanover.utilities.queues module nanover.utilities.state_dictionary module nanover.utilities.timing module nanover.websocket module nanover.websocket.client module nanover.websocket.client.app_client module nanover.websocket.client.base_client module nanover.websocket.client.interaction_client module nanover.websocket.client.playback_client module nanover.websocket.client.selection_client module nanover.websocket.discovery module nanover.websocket.record module nanover.websocket.server module NanoverApplicationServer (class in nanover.app.app_server) NanoverImdApplication (class in nanover.app.imd_app) NanoverImdClient (class in nanover.websocket.client.app_client) NanoverParser (class in nanover.mdanalysis.universe) NanoverReader (class in nanover.mdanalysis.universe) NanoverReaderBase (class in nanover.mdanalysis.universe) NanoverRecordingReader (class in nanover.recording.reading) NanoverRecordingWriter (class in nanover.recording.writing) next() (nanover.omni.omni.OmniRunner method) next_frame (nanover.recording.reading.FrameRecordingEvent attribute) (nanover.recording.reading.RecordingEvent property) next_frame_event (nanover.recording.reading.RecordingEvent attribute) next_state (nanover.recording.reading.RecordingEvent property) (nanover.recording.reading.StateRecordingEvent attribute) next_state_event (nanover.recording.reading.RecordingEvent attribute) NGLClient (class in nanover.nglview.nglclient) null_server() (nanover.app.app_server.NanoverApplicationServer class method) nullable_int() (in module nanover.mdanalysis.converter) NullCalculator (class in nanover.ase.null_calculator)

O

ObjectFrozenError offset (nanover.recording.reading.RecordingIndexEntry attribute) OmniRunner (class in nanover.omni.omni)

openmm_to_frame_data() (in module nanover.openmm.converter) OpenMMCalculator (class in nanover.ase.omm_calculator) OpenMMSimulation (class in nanover.omni.openmm)

P

pack (nanover.trajectory.convert.PackingPair attribute) pack_array() (in module nanover.trajectory.convert) pack_dict_frame() (in module nanover.trajectory.convert) packable_primitives() (in module nanover.testing.strategies) packable_structures() (in module nanover.testing.strategies) packed_frame_dicts() (in module nanover.testing.strategies) PackingPair (class in nanover.trajectory.convert) parallel (nanover.ase.trajectory_logger.TrajectoryLogger attribute) parse() (nanover.mdanalysis.universe.NanoverParser method) parse_index() (in module nanover.recording.reading) 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.omni.omni.OmniRunner method) pbc_vectors (nanover.omni.openmm.OpenMMSimulation attribute)

platform_name (nanover.omni.openmm.OpenMMSimulation attribute) play() (nanover.omni.omni.OmniRunner method) play_step_interval (nanover.omni.omni.InternalRunner property) PlaybackClient (class in nanover.websocket.client.playback_client) 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.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) prev_frame (nanover.recording.reading.FrameRecordingEvent attribute) (nanover.recording.reading.RecordingEvent property) prev_frame_event (nanover.recording.reading.RecordingEvent attribute) prev_state (nanover.recording.reading.RecordingEvent property) (nanover.recording.reading.StateRecordingEvent attribute) prev_state_event (nanover.recording.reading.RecordingEvent attribute) print_basic_info() (nanover.omni.omni.OmniRunner method) print_hub() (in module nanover.essd.list_cli) properties (nanover.imd.particle_interaction.ParticleInteraction property) put() (nanover.utilities.queues.FrameMergingQueue method) (nanover.utilities.queues.LastItemQueue method)

Q

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

R

read_from() (nanover.recording.reading.RecordingIndexEntry method) 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_velocity_reset_from_dictionary() (nanover.app.selection.RenderingSelection method) record_from_runner() (in module nanover.websocket.record) record_from_server() (in module nanover.websocket.record) record_messages() (in module nanover.recording.writing) RecordingEvent (class in nanover.recording.reading) RecordingIndexEntry (class in nanover.recording.reading) recv_command() (nanover.websocket.client.base_client.WebsocketClient method) recv_frame() (nanover.nglview.nglclient.NGLClient method) (nanover.websocket.client.app_client.NanoverImdClient method) (nanover.websocket.client.base_client.WebsocketClient method) recv_message() (nanover.websocket.client.base_client.WebsocketClient method) recv_state() (nanover.websocket.client.base_client.WebsocketClient method) register_command() (nanover.app.app_server.NanoverApplicationServer method) (nanover.app.commands.CommandService method) (nanover.app.types.CommandService 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.websocket.client.selection_client.SelectionClient method) remove_shared_value() (nanover.websocket.client.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)

replace_shortcuts() (in module nanover.trajectory.frame_data) required (nanover.mdanalysis.converter.FrameDataField attribute) reset() (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.websocket.client.selection_client.SelectionClient property) run() (nanover.app.commands.CommandRegistration method) (nanover.omni.omni.InternalRunner method) run_command() (nanover.app.app_server.NanoverApplicationServer method) (nanover.app.commands.CommandService method) (nanover.app.types.CommandService method) (nanover.websocket.client.base_client.WebsocketClient method) run_command_blocking() (nanover.websocket.client.base_client.WebsocketClient method) run_list() (nanover.websocket.client.playback_client.PlaybackClient method) run_load() (nanover.websocket.client.playback_client.PlaybackClient method) run_next() (nanover.websocket.client.playback_client.PlaybackClient method) run_pause() (nanover.websocket.client.playback_client.PlaybackClient method) run_play() (nanover.websocket.client.playback_client.PlaybackClient method) run_reset() (nanover.websocket.client.playback_client.PlaybackClient method) run_step() (nanover.websocket.client.playback_client.PlaybackClient 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) SelectionClient (class in nanover.websocket.client.selection_client) selections (nanover.websocket.client.selection_client.SelectionClient property) send_clear() (nanover.trajectory.frame_publisher.FramePublisher method) send_frame() (nanover.trajectory.frame_publisher.FramePublisher method) send_message() (nanover.websocket.client.base_client.WebsocketClient method) serialize_simulation() (in module nanover.openmm.serializer) serve_insecure() (nanover.websocket.server.WebSocketServer method) serve_secure() (nanover.websocket.server.WebSocketServer method) serve_websocket() (nanover.app.imd_app.NanoverImdApplication method) server (nanover.testing.servers.ServerClientSetup attribute) server_current_frame (nanover.testing.servers.ServerClientSetup property) server_current_state (nanover.testing.servers.ServerClientSetup property) server_publish_frame() (nanover.testing.servers.ServerClientSetup method) server_publish_frame_reset() (nanover.testing.servers.ServerClientSetup method) server_timestamp (nanover.trajectory.frame_data.FrameData property) server_update_state() (nanover.testing.servers.ServerClientSetup method) ServerClientSetup (class in nanover.testing.servers) service_hub (nanover.app.app_server.NanoverApplicationServer property) (nanover.app.types.DiscoveryService property) ServiceHub (class in nanover.essd.servicehub) services (nanover.essd.server.DiscoveryServer attribute) (nanover.essd.servicehub.ServiceHub property) set() (nanover.utilities.key_lockable_map.KeyLockableMap 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.websocket.client.app_client.NanoverImdClient method) set_simulation_selections() (nanover.omni.omni.OmniRunner method) simplify_numpy() (in module nanover.testing.utilities) 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_exception (nanover.trajectory.frame_data.FrameData property) simulation_time (nanover.trajectory.frame_data.FrameData property) split_by_simulation_counter() (in module nanover.recording.reading) split_on_frame_reset() (in module nanover.recording.cli.split_cli) split_on_sim_counter_change() (in module nanover.recording.cli.split_cli) split_recording() (in module nanover.recording.cli.split_cli) start() (nanover.essd.server.DiscoveryServer method) start_interaction() (nanover.websocket.client.interaction_client.InteractionClient method) state_dictionary (nanover.app.app_server.NanoverApplicationServer property) (nanover.app.types.StateService property) state_updates() (in module nanover.testing.strategies) StateDictionary (class in nanover.utilities.state_dictionary) StateRecordingEvent (class in nanover.recording.reading) StateService (class in nanover.app.types) step() (nanover.omni.omni.OmniRunner method) stop_all_interactions() (nanover.websocket.client.interaction_client.InteractionClient method) stop_interaction() (nanover.websocket.client.interaction_client.InteractionClient method) subscribe_cancellation() (nanover.utilities.cli.CancellationToken method) subscribe_changes() (nanover.utilities.change_buffers.DictionaryChangeBuffer method) (nanover.utilities.change_buffers.DictionaryChangeMultiView method) subscribe_latest_frames() (nanover.trajectory.frame_publisher.FramePublisher method) suppress_keyboard_interrupt_as_cancellation() (in module nanover.utilities.cli) system_temperature (nanover.trajectory.frame_data.FrameData property)

T

temperature (nanover.ase.imd_calculator.ImdCalculator property) timestamp (nanover.recording.reading.MessageEvent attribute) (nanover.recording.reading.RecordingEvent property) timestamping (nanover.ase.trajectory_logger.TrajectoryLogger property)

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) TYPE_KEY (nanover.imd.particle_interaction.ParticleInteraction attribute)

U

uint32s() (in module nanover.testing.strategies) uint8s() (in module nanover.testing.strategies) units (nanover.mdanalysis.universe.NanoverReaderBase attribute) universe_from_recording() (in module nanover.mdanalysis.universe) universes_from_recording() (in module nanover.mdanalysis.universe) unpack (nanover.trajectory.convert.PackingPair attribute) unpack_array() (in module nanover.trajectory.convert) unpack_dict_frame() (in module nanover.trajectory.convert) unregister_command() (nanover.app.app_server.NanoverApplicationServer method) (nanover.app.commands.CommandService method) (nanover.app.types.CommandService method) unregister_service() (nanover.essd.server.DiscoveryServer method) UnsupportedFormatError update() (nanover.trajectory.frame_data.FrameData method) (nanover.utilities.change_buffers.DictionaryChangeBuffer method) (nanover.utilities.change_buffers.DictionaryChangeMultiView method) update_available_commands() (nanover.websocket.client.app_client.NanoverImdClient method)

update_interaction() (nanover.websocket.client.interaction_client.InteractionClient method) update_interactions() (nanover.ase.imd_calculator.ImdCalculator method) (nanover.ase.imd_calculator.ImdForceManager method) (nanover.openmm.imd.ImdForceManager method) update_locks() (nanover.utilities.state_dictionary.StateDictionary method) update_selection() (nanover.websocket.client.selection_client.SelectionClient method) update_state() (nanover.app.app_server.NanoverApplicationServer method) (nanover.app.types.StateService method) (nanover.utilities.state_dictionary.StateDictionary method) (nanover.websocket.client.base_client.WebsocketClient method) update_universe_from_framedata() (in module nanover.mdanalysis.converter) updated (nanover.app.selection.RenderingSelection property) updates (nanover.utilities.change_buffers.DictionaryChange attribute) use_pbc_wrapping (nanover.omni.openmm.OpenMMSimulation attribute) 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) VariableIntervalGenerator (class in nanover.utilities.timing) vec3_arrays() (in module nanover.testing.strategies) 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_cancellation() (nanover.utilities.cli.CancellationToken method) wait_mixed() (in module nanover.utilities.timing) wait_until_first_frame() (nanover.websocket.client.app_client.NanoverImdClient method) WebsocketClient (class in nanover.websocket.client.base_client)

WebSocketServer (class in nanover.websocket.server) 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_index() (nanover.recording.writing.NanoverRecordingWriter method) write_message_event() (nanover.recording.writing.NanoverRecordingWriter method)

Y

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