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.imd_app.NanoverImdApplication method) (nanover.core.app_server.DiscoveryService method) (nanover.essd.servicehub.ServiceHub method) add_simulation() (nanover.app.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.imd_app.NanoverImdApplication 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.ase.simulation.ASESimulation method) (nanover.core.simulation.Simulation method) (nanover.mdanalysis.simulation.UniverseSimulation method) (nanover.openmm.simulation.OpenMMSimulation method) (nanover.recording.playback.PlaybackSimulation method)

advance_by_seconds() (nanover.ase.simulation.ASESimulation method) (nanover.core.simulation.Simulation method) (nanover.mdanalysis.simulation.UniverseSimulation method) (nanover.openmm.simulation.OpenMMSimulation method) (nanover.recording.playback.PlaybackSimulation method) advance_to_next_entry() (nanover.recording.playback.PlaybackSimulation method) advance_to_next_report() (nanover.ase.simulation.ASESimulation method) (nanover.openmm.simulation.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.app.omni.OmniRunner property) apply_single_interaction_force() (in module nanover.imd.imd_force) AppServer (class in nanover.core.app_server) AppServerMinimal (class in nanover.core.app_server) arguments (nanover.core.types.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.ase.simulation) ASESimulation (class in nanover.ase.simulation) 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.simulation.ASESimulation property) (nanover.ase.trajectory_logger.TrajectoryLogger attribute) attribute (nanover.mdanalysis.universe.KeyConversion attribute)

B

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

batched() (in module nanover.mdanalysis.universe) bond_orders (nanover.trajectory.frame_wrapper.FrameData property) bond_pairs (nanover.trajectory.frame_wrapper.FrameData property) box_vectors (nanover.trajectory.frame_wrapper.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.ase.simulation.InitialState attribute) chain_count (nanover.trajectory.frame_wrapper.FrameData property) chain_names (nanover.trajectory.frame_wrapper.FrameData property) clear_interactions() (nanover.imd.imd_state.ImdStateWrapper method) clear_locks() (nanover.app.imd_app.NanoverImdApplication method) (nanover.core.app_server.StateService method) (nanover.utilities.state_dictionary.StateDictionary method) (nanover.websocket.client.state_client.StateClient 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.imd_app.NanoverImdApplication method) (nanover.app.omni.OmniRunner method) (nanover.ase.trajectory_logger.TrajectoryLogger method) (nanover.core.app_server.Closeable method) (nanover.essd.client.DiscoveryClient method) (nanover.essd.server.DiscoveryServer method) (nanover.mdanalysis.universe.NanoverReaderBase 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.core.app_server) command_arguments() (in module nanover.testing.strategies) CommandClient (class in nanover.websocket.client.command_client) CommandMessageHandler (class in nanover.core.commands) CommandRegistration (class in nanover.core.types) commands (nanover.app.imd_app.NanoverImdApplication property) (nanover.core.app_server.CommandService property) (nanover.core.commands.CommandService property) (nanover.websocket.client.command_client.CommandClient property) CommandService (class in nanover.core.app_server) (class in nanover.core.commands) 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) converter (nanover.mdanalysis.converter.FrameDataFieldConversion attribute) copy() (nanover.trajectory.frame_wrapper.FrameData method) copy_content() (nanover.utilities.change_buffers.DictionaryChangeMultiView method) (nanover.utilities.state_dictionary.StateDictionary method) copy_state() (nanover.app.imd_app.NanoverImdApplication method) (nanover.core.app_server.StateService method) (nanover.websocket.client.app_client.NanoverImdClient method) (nanover.websocket.client.state_client.StateClient 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.imd_app.NanoverImdApplication attribute) delete() (nanover.utilities.key_lockable_map.KeyLockableMap method) deprecated() (in module nanover.app.cli.server_cli) deserialize_simulation() (in module nanover.openmm.serializer) determine_pbcs() (nanover.openmm.simulation.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.imd_app.NanoverImdApplication property) (nanover.core.app_server.DiscoveryService property) DiscoveryClient (class in nanover.essd.client) (class in nanover.websocket.discovery) DiscoveryServer (class in nanover.essd.server) DiscoveryService (class in nanover.core.app_server)

E

emit() (nanover.recording.playback.PlaybackSimulation method) empty() (nanover.trajectory.frame_wrapper.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.jupyter.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.jupyter.nglclient) frame_data_to_pdb() (in module nanover.jupyter.nglclient) frame_dict (nanover.trajectory.frame_wrapper.FrameData attribute) frame_dict_packer (in module nanover.trajectory.frame_dict) frame_index (nanover.ase.trajectory_logger.TrajectoryLogger attribute) (nanover.trajectory.frame_wrapper.FrameData property) frame_interval (nanover.openmm.simulation.OpenMMSimulation attribute) FRAME_PACKERS (in module nanover.trajectory.frame_dict) frame_publisher (nanover.app.imd_app.NanoverImdApplication property) (nanover.core.app_server.ImdService property) FrameData (class in nanover.trajectory.frame_wrapper) FrameDataField (class in nanover.mdanalysis.converter) FrameDataFieldConversion (class in nanover.mdanalysis.converter) FrameDataStructure (class in nanover.jupyter.nglclient) FrameMergingQueue (class in nanover.utilities.queues) FramePublisher (class in nanover.trajectory.frame_publisher) FramePublisherShim (class in nanover.websocket.client.app_client)

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.ase.simulation.ASESimulation class method) from_client() (nanover.app.omni.OmniRunner class method) from_dict() (nanover.trajectory.frame_wrapper.FrameData class method) (nanover.utilities.change_buffers.DictionaryChange 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.mdanalysis.simulation.UniverseSimulation class method) (nanover.recording.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.openmm.simulation.OpenMMSimulation class method) from_universe() (nanover.mdanalysis.simulation.UniverseSimulation 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.openmm.simulation.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.app.cli.server_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.jupyter.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_message() (nanover.core.commands.CommandMessageHandler method) handle_signals() (nanover.app.omni.InternalRunner method) handle_user_arguments() (in module nanover.app.cli.recorder_cli) (in module nanover.app.cli.server_cli) (in module nanover.essd.list_cli)

handler (nanover.core.types.CommandRegistration attribute) has_minimum_usable_frame (nanover.websocket.client.app_client.NanoverImdClient property) 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.core.app_server.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.core.app_server) ImdStateWrapper (class in nanover.imd.imd_state) implemented_properties (nanover.ase.omm_calculator.OpenMMCalculator attribute) include_forces (nanover.openmm.simulation.OpenMMSimulation attribute) include_velocities (nanover.openmm.simulation.OpenMMSimulation attribute) index2_arrays() (in module nanover.testing.strategies) index_arrays() (in module nanover.testing.strategies) initialise_runner() (in module nanover.app.cli.server_cli) initialise_ssl() (in module nanover.app.cli.server_cli) InitialState (class in nanover.ase.simulation) insert_interaction() (nanover.imd.imd_state.ImdStateWrapper method) interact_button() (in module nanover.jupyter.controls) 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.app.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.app.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_wrapper.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.app.omni.OmniRunner method) load() (nanover.app.omni.OmniRunner method) (nanover.ase.simulation.ASESimulation method) (nanover.core.simulation.Simulation method) (nanover.mdanalysis.simulation.UniverseSimulation method) (nanover.openmm.simulation.OpenMMSimulation method) (nanover.recording.playback.PlaybackSimulation method)

lock_content() (nanover.utilities.state_dictionary.StateDictionary method) lock_key() (nanover.utilities.key_lockable_map.KeyLockableMap method) lock_state() (nanover.app.imd_app.NanoverImdApplication method) (nanover.core.app_server.StateService method) (nanover.websocket.client.state_client.StateClient method) log_addresses() (nanover.essd.server.DiscoveryServer method)

M

main() (in module nanover.app.cli.recorder_cli) (in module nanover.app.cli.server_cli) (in module nanover.essd.list_cli) (in module nanover.recording.cli.dump_cli) (in module nanover.recording.cli.split_cli) make_app_server() (in module nanover.testing.servers) make_button() (in module nanover.jupyter.controls) make_bytes_packer() (in module nanover.utilities.packing) 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.ase.simulation.ASESimulation method) (nanover.openmm.simulation.OpenMMSimulation method) make_toggle() (in module nanover.jupyter.controls) make_topology_frame() (nanover.ase.simulation.ASESimulation method) (nanover.openmm.simulation.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.jupyter.nglclient) mdanalysis_to_frame_data() (in module nanover.mdanalysis.converter) merge_frame_dicts() (in module nanover.trajectory.frame_dict) 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.cli nanover.app.cli.recorder_cli nanover.app.cli.server_cli nanover.app.imd_app nanover.app.multiuser nanover.app.omni nanover.app.selection nanover.ase nanover.ase.converter nanover.ase.imd_calculator nanover.ase.null_calculator nanover.ase.omm_calculator nanover.ase.simulation nanover.ase.thermo nanover.ase.trajectory_logger nanover.ase.wall_constraint nanover.core nanover.core.app_server nanover.core.commands nanover.core.simulation nanover.core.types 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.jupyter nanover.jupyter.controls nanover.jupyter.nglclient nanover.mdanalysis nanover.mdanalysis.converter nanover.mdanalysis.simulation nanover.mdanalysis.universe nanover.nglview nanover.omni nanover.omni.ase nanover.omni.mda 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.simulation nanover.openmm.thermo nanover.recording nanover.recording.cli nanover.recording.cli.dump_cli nanover.recording.cli.split_cli nanover.recording.playback nanover.recording.reading nanover.recording.writing nanover.testing nanover.testing.asserts nanover.testing.servers nanover.testing.strategies nanover.testing.utilities nanover.trajectory nanover.trajectory.frame_dict nanover.trajectory.frame_publisher nanover.trajectory.frame_wrapper 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.packing 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.command_client nanover.websocket.client.interaction_client nanover.websocket.client.playback_client nanover.websocket.client.selection_client nanover.websocket.client.state_client nanover.websocket.discovery nanover.websocket.record nanover.websocket.server

N

n_frames (nanover.mdanalysis.universe.NanoverReaderBase property) name (nanover.app.imd_app.NanoverImdApplication property) (nanover.core.app_server.AppServer property) (nanover.core.simulation.Simulation attribute) (nanover.core.types.CommandRegistration attribute) (nanover.essd.servicehub.ServiceHub property) name_basic() (in module nanover.recording.cli.split_cli) nanover module nanover.app module nanover.app.cli module nanover.app.cli.recorder_cli module nanover.app.cli.server_cli module nanover.app.imd_app module nanover.app.multiuser module nanover.app.omni 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.simulation module nanover.ase.thermo module nanover.ase.trajectory_logger module nanover.ase.wall_constraint module nanover.core module nanover.core.app_server module nanover.core.commands module nanover.core.simulation module nanover.core.types 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.jupyter module nanover.jupyter.controls module nanover.jupyter.nglclient module nanover.mdanalysis module nanover.mdanalysis.converter module nanover.mdanalysis.simulation module nanover.mdanalysis.universe module nanover.nglview module nanover.omni module nanover.omni.ase module nanover.omni.mda 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.simulation 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.playback 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.frame_dict module nanover.trajectory.frame_publisher module nanover.trajectory.frame_wrapper 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.packing 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.command_client module nanover.websocket.client.interaction_client module nanover.websocket.client.playback_client module nanover.websocket.client.selection_client module nanover.websocket.client.state_client module nanover.websocket.discovery module nanover.websocket.record module nanover.websocket.server module 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.app.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.jupyter.nglclient) null_server() (nanover.app.imd_app.NanoverImdApplication 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.app.omni)

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

P

pack (nanover.utilities.packing.PackingPair attribute) pack_array() (in module nanover.utilities.packing) pack_to_dict() (nanover.trajectory.frame_wrapper.FrameData method) 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.utilities.packing) 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_wrapper.FrameData property) particle_elements (nanover.trajectory.frame_wrapper.FrameData property) particle_forces (nanover.trajectory.frame_wrapper.FrameData property) particle_forces_system (nanover.trajectory.frame_wrapper.FrameData property) particle_names (nanover.trajectory.frame_wrapper.FrameData property) particle_positions (nanover.trajectory.frame_wrapper.FrameData property) particle_residues (nanover.trajectory.frame_wrapper.FrameData property) particle_velocities (nanover.trajectory.frame_wrapper.FrameData property) ParticleInteraction (class in nanover.imd.particle_interaction) particles (nanover.imd.particle_interaction.ParticleInteraction property) pause() (nanover.app.omni.OmniRunner method) pbc_vectors (nanover.openmm.simulation.OpenMMSimulation attribute)

platform_name (nanover.openmm.simulation.OpenMMSimulation attribute) play() (nanover.app.omni.OmniRunner method) play_step_interval (nanover.app.omni.InternalRunner property) PlaybackClient (class in nanover.websocket.client.playback_client) PlaybackSimulation (class in nanover.recording.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.ase.simulation.InitialState attribute) potential_energy (nanover.trajectory.frame_wrapper.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.app.omni.OmniRunner method) print_hub() (in module nanover.essd.list_cli) properties (nanover.imd.particle_interaction.ParticleInteraction property) publish_frame() (nanover.websocket.client.app_client.NanoverImdClient method) put() (nanover.utilities.queues.FrameMergingQueue method) (nanover.utilities.queues.LastItemQueue method)

Q

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

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_frame() (nanover.jupyter.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.imd_app.NanoverImdApplication method) (nanover.core.app_server.CommandService method) (nanover.core.commands.CommandMessageHandler method) (nanover.core.commands.CommandService method) (nanover.websocket.client.command_client.CommandClient 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_wrapper) request_command() (nanover.core.commands.CommandMessageHandler method) required (nanover.mdanalysis.converter.FrameDataField attribute) reset() (nanover.app.omni.OmniRunner method) (nanover.ase.simulation.ASESimulation method) (nanover.ase.trajectory_logger.TrajectoryLogger method) (nanover.core.simulation.Simulation method) (nanover.mdanalysis.simulation.UniverseSimulation method) (nanover.openmm.simulation.OpenMMSimulation method) (nanover.recording.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_wrapper.FrameData property) residue_count (nanover.trajectory.frame_wrapper.FrameData property) residue_ids (nanover.trajectory.frame_wrapper.FrameData property) residue_names (nanover.trajectory.frame_wrapper.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.omni.InternalRunner method) (nanover.core.types.CommandRegistration method) run_command() (nanover.app.imd_app.NanoverImdApplication method) (nanover.core.app_server.CommandService method) (nanover.core.commands.CommandService method) (nanover.websocket.client.command_client.CommandClient method) run_command_blocking() (nanover.websocket.client.command_client.CommandClient 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.app.omni.OmniRunner 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) SendMessage (class in nanover.core.commands) serialize_simulation() (in module nanover.openmm.serializer) serve() (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_wrapper.FrameData property) server_update_state() (nanover.testing.servers.ServerClientSetup method) ServerClientSetup (class in nanover.testing.servers) service_hub (nanover.app.imd_app.NanoverImdApplication property) (nanover.core.app_server.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.app.omni.OmniRunner method) show_app_server_controls() (in module nanover.jupyter.controls) show_runner_controls() (in module nanover.jupyter.controls) simplify_numpy() (in module nanover.testing.utilities) Simulation (class in nanover.core.simulation) simulation (nanover.app.omni.OmniRunner property) (nanover.ase.omm_calculator.OpenMMCalculator attribute) simulation_counter (nanover.trajectory.frame_wrapper.FrameData property) simulation_exception (nanover.trajectory.frame_wrapper.FrameData property) simulation_time (nanover.trajectory.frame_wrapper.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.imd_app.NanoverImdApplication property) (nanover.core.app_server.StateService property) (nanover.websocket.client.state_client.StateClient property) state_updates() (in module nanover.testing.strategies) StateClient (class in nanover.websocket.client.state_client) StateDictionary (class in nanover.utilities.state_dictionary) StateRecordingEvent (class in nanover.recording.reading) StateService (class in nanover.core.app_server) step() (nanover.app.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_wrapper.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_dict() (nanover.utilities.change_buffers.DictionaryChange method)

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) UniverseSimulation (class in nanover.mdanalysis.simulation) unpack (nanover.utilities.packing.PackingPair attribute) unpack_array() (in module nanover.utilities.packing) unpack_from_dict() (nanover.trajectory.frame_wrapper.FrameData class method) unregister_command() (nanover.app.imd_app.NanoverImdApplication method) (nanover.core.app_server.CommandService method) (nanover.core.commands.CommandService method) (nanover.websocket.client.command_client.CommandClient method) unregister_service() (nanover.essd.server.DiscoveryServer method) UnsupportedFormatError update() (nanover.trajectory.frame_wrapper.FrameData method) (nanover.utilities.change_buffers.DictionaryChange 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.imd_app.NanoverImdApplication method) (nanover.core.app_server.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.openmm.simulation.OpenMMSimulation attribute) user_energy (nanover.trajectory.frame_wrapper.FrameData property) user_forces_index (nanover.trajectory.frame_wrapper.FrameData property) user_forces_sparse (nanover.trajectory.frame_wrapper.FrameData property) user_ids() (in module nanover.testing.strategies) user_work_done (nanover.trajectory.frame_wrapper.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.ase.simulation.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.jupyter.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) wait_until_minimum_usable_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.app.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)