Index

A

add() (simulariumio.data_objects.dimension_data.DimensionData method) add_number_of_agents_plot() (simulariumio.trajectory_converter.TrajectoryConverter method) add_plot() (simulariumio.trajectory_converter.TrajectoryConverter method) AddAgentsFilter (class in simulariumio.filters.add_agents_filter) agent_data (simulariumio.data_objects.trajectory_data.TrajectoryData attribute) AgentData (class in simulariumio.data_objects.agent_data) agents_with_endpoints (simulariumio.medyan.medyan_data.MedyanData attribute) append_agents() (simulariumio.data_objects.trajectory_data.TrajectoryData method) apply() (simulariumio.filters.add_agents_filter.AddAgentsFilter method) (simulariumio.filters.every_nth_agent_filter.EveryNthAgentFilter method) (simulariumio.filters.every_nth_subpoint_filter.EveryNthSubpointFilter method) (simulariumio.filters.every_nth_timestep_filter.EveryNthTimestepFilter method) (simulariumio.filters.filter.Filter method) (simulariumio.filters.multiply_space_filter.MultiplySpaceFilter method) (simulariumio.filters.multiply_time_filter.MultiplyTimeFilter method) (simulariumio.filters.transform_spatial_axes_filter.TransformSpatialAxesFilter method) (simulariumio.filters.translate_filter.TranslateFilter method)

apply_to_plots (simulariumio.filters.multiply_time_filter.MultiplyTimeFilter attribute) authors (simulariumio.data_objects.model_meta_data.ModelMetaData attribute) axes_mapping (simulariumio.filters.transform_spatial_axes_filter.TransformSpatialAxesFilter attribute)

B

BINARY_BLOCK_TYPE (class in simulariumio.constants) BINARY_SETTINGS (class in simulariumio.constants) BinaryBlockInfo (class in simulariumio.readers.binary_info) BinaryChunk (class in simulariumio.writers.binary_chunk) BinaryData (class in simulariumio.data_objects.binary_data) BinaryFileData (class in simulariumio.readers.binary_info) BinaryValues (class in simulariumio.writers.binary_values) BinaryWriter (class in simulariumio.writers.binary_writer)

BLOCK_HEADER_N_VALUES (simulariumio.constants.BINARY_SETTINGS attribute) block_lengths (simulariumio.readers.binary_info.BinaryBlockInfo attribute) BLOCK_OFFSET_BYTE_ALIGNMENT (simulariumio.constants.BINARY_SETTINGS attribute) block_offsets (simulariumio.readers.binary_info.BinaryBlockInfo attribute) block_types (simulariumio.readers.binary_info.BinaryBlockInfo attribute) box_size (simulariumio.data_objects.meta_data.MetaData attribute) byte_view (simulariumio.readers.binary_info.BinaryFileData attribute) BYTES_PER_VALUE (simulariumio.constants.BINARY_SETTINGS attribute)

C

calculate_scale_factor() (simulariumio.trajectory_converter.TrajectoryConverter static method) camera_defaults (simulariumio.data_objects.meta_data.MetaData attribute) CAMERA_POSITION (simulariumio.constants.DEFAULT_CAMERA_SETTINGS attribute) CameraData (class in simulariumio.data_objects.camera_data) CellpackConverter (class in simulariumio.cellpack.cellpack_converter) CellpackData (class in simulariumio.cellpack.cellpack_data) center (simulariumio.medyan.medyan_data.MedyanData attribute) (simulariumio.smoldyn.smoldyn_data.SmoldynData attribute) center_and_scale_agent_data() (simulariumio.trajectory_converter.TrajectoryConverter method)

center_fiber_positions() (simulariumio.trajectory_converter.TrajectoryConverter static method) check_increase_buffer_size() (simulariumio.data_objects.agent_data.AgentData method) check_report_progress() (simulariumio.trajectory_converter.TrajectoryConverter method) color (simulariumio.data_objects.display_data.DisplayData attribute) CURRENT_VERSION (class in simulariumio.constants) cytosim_file (simulariumio.cytosim.cytosim_object_info.CytosimObjectInfo attribute) CytosimConverter (class in simulariumio.cytosim.cytosim_converter) CytosimData (class in simulariumio.cytosim.cytosim_data) CytosimObjectInfo (class in simulariumio.cytosim.cytosim_object_info)

D

DataError DEFAULT (simulariumio.constants.VIZ_TYPE attribute) DEFAULT_BLOCK_TYPES (simulariumio.constants.BINARY_SETTINGS attribute) DEFAULT_CAMERA_SETTINGS (class in simulariumio.constants) default_n (simulariumio.filters.every_nth_agent_filter.EveryNthAgentFilter attribute) (simulariumio.filters.every_nth_subpoint_filter.EveryNthSubpointFilter attribute) default_translation (simulariumio.filters.translate_filter.TranslateFilter attribute) description (simulariumio.data_objects.model_meta_data.ModelMetaData attribute) DimensionData (class in simulariumio.data_objects.dimension_data) display_data (simulariumio.cellpack.cellpack_data.CellpackData attribute) (simulariumio.cytosim.cytosim_object_info.CytosimObjectInfo attribute) (simulariumio.data_objects.agent_data.AgentData attribute) (simulariumio.mcell.mcell_data.McellData attribute) (simulariumio.md.md_data.MdData attribute) (simulariumio.medyan.medyan_data.MedyanData attribute) (simulariumio.nerdss.nerdss_data.NerdssData attribute) (simulariumio.physicell.physicell_data.PhysicellData attribute) (simulariumio.smoldyn.smoldyn_data.SmoldynData attribute) (simulariumio.springsalad.springsalad_data.SpringsaladData attribute)

DISPLAY_TYPE (class in simulariumio.constants) display_type (simulariumio.data_objects.display_data.DisplayData attribute) display_type_for_agent() (simulariumio.data_objects.agent_data.AgentData method) DisplayData (class in simulariumio.data_objects.display_data) doi (simulariumio.data_objects.model_meta_data.ModelMetaData attribute) draw_bonds (simulariumio.md.md_data.MdData attribute) (simulariumio.springsalad.springsalad_data.SpringsaladData attribute) draw_fiber_points (simulariumio.cytosim.cytosim_data.CytosimData attribute) (simulariumio.data_objects.agent_data.AgentData attribute) (simulariumio.medyan.medyan_data.MedyanData attribute)

E

EveryNthAgentFilter (class in simulariumio.filters.every_nth_agent_filter)

EveryNthSubpointFilter (class in simulariumio.filters.every_nth_subpoint_filter) EveryNthTimestepFilter (class in simulariumio.filters.every_nth_timestep_filter)

F

FIBER (simulariumio.constants.DISPLAY_TYPE attribute) (simulariumio.constants.VIZ_TYPE attribute) file_contents (simulariumio.data_objects.input_file_data.InputFileData attribute) FILE_IDENTIFIER (simulariumio.constants.BINARY_SETTINGS attribute) file_path (simulariumio.data_objects.input_file_data.InputFileData attribute) FileConverter (class in simulariumio.file_converter) Filter (class in simulariumio.filters.filter) filter_data() (simulariumio.trajectory_converter.TrajectoryConverter method) first_frame_index (simulariumio.writers.binary_chunk.BinaryChunk attribute) float_view (simulariumio.readers.binary_info.BinaryFileData attribute) format_string (simulariumio.writers.binary_values.BinaryValues attribute) format_trajectory_data() (simulariumio.writers.binary_writer.BinaryWriter static method) (simulariumio.writers.json_writer.JsonWriter static method) (simulariumio.writers.writer.Writer static method) FOV_DEGREES (simulariumio.constants.DEFAULT_CAMERA_SETTINGS attribute)

fov_degrees (simulariumio.data_objects.camera_data.CameraData attribute) FRAME_HEADER_N_VALUES (simulariumio.constants.BINARY_SETTINGS attribute) frame_n_values (simulariumio.writers.binary_chunk.BinaryChunk attribute) FrameData (class in simulariumio.data_objects.frame_data) FrameMetadata (class in simulariumio.data_objects.binary_data) from_buffer_data() (simulariumio.data_objects.agent_data.AgentData class method) (simulariumio.data_objects.trajectory_data.TrajectoryData class method) from_dataframe() (simulariumio.data_objects.agent_data.AgentData class method) from_dict() (simulariumio.data_objects.camera_data.CameraData class method) (simulariumio.data_objects.display_data.DisplayData class method) (simulariumio.data_objects.meta_data.MetaData class method) (simulariumio.data_objects.model_meta_data.ModelMetaData class method) (simulariumio.data_objects.unit_data.UnitData class method) (simulariumio.smoldyn.smoldyn_data.SmoldynData class method) from_dimensions() (simulariumio.data_objects.agent_data.AgentData class method)

G

geometry_type (simulariumio.cellpack.cellpack_data.CellpackData attribute) geometry_url (simulariumio.cellpack.cellpack_data.CellpackData attribute) get_2D_mesh() (simulariumio.physicell.dep.pyMCDS.pyMCDS method) get_cell_df() (simulariumio.physicell.dep.pyMCDS.pyMCDS method) get_cell_df_at() (simulariumio.physicell.dep.pyMCDS.pyMCDS method) get_cell_variables() (simulariumio.physicell.dep.pyMCDS.pyMCDS method) get_concentrations() (simulariumio.physicell.dep.pyMCDS.pyMCDS method) get_concentrations_at() (simulariumio.physicell.dep.pyMCDS.pyMCDS method) get_containing_voxel_ijk() (simulariumio.physicell.dep.pyMCDS.pyMCDS method) get_contents() (simulariumio.data_objects.input_file_data.InputFileData method) get_copy_with_increased_buffer_size() (simulariumio.data_objects.agent_data.AgentData method) get_dimensions() (simulariumio.data_objects.agent_data.AgentData method) get_display_data() (simulariumio.data_objects.agent_data.AgentData static method) get_file_contents() (simulariumio.data_objects.binary_data.BinaryData method) (simulariumio.data_objects.json_data.JsonData method) (simulariumio.data_objects.simularium_file_data.SimulariumFileData method) get_frame_at_index() (simulariumio.data_objects.binary_data.BinaryData method) (simulariumio.data_objects.json_data.JsonData method) (simulariumio.data_objects.simularium_file_data.SimulariumFileData method) get_global_index() (simulariumio.writers.binary_chunk.BinaryChunk method) get_index_for_time() (simulariumio.data_objects.binary_data.BinaryData method) (simulariumio.data_objects.json_data.JsonData method) (simulariumio.data_objects.simularium_file_data.SimulariumFileData method) get_items_from_subpoints() (simulariumio.filters.filter.Filter static method)

get_linear_voxels() (simulariumio.physicell.dep.pyMCDS.pyMCDS method) get_mesh() (simulariumio.physicell.dep.pyMCDS.pyMCDS method) get_mesh_spacing() (simulariumio.physicell.dep.pyMCDS.pyMCDS method) get_min_max_positions() (simulariumio.trajectory_converter.TrajectoryConverter static method) get_num_frames() (simulariumio.data_objects.binary_data.BinaryData method) (simulariumio.data_objects.json_data.JsonData method) (simulariumio.data_objects.simularium_file_data.SimulariumFileData method) get_plot_data() (simulariumio.data_objects.binary_data.BinaryData method) (simulariumio.data_objects.json_data.JsonData method) (simulariumio.data_objects.simularium_file_data.SimulariumFileData method) get_start_end_indices() (simulariumio.data_objects.binary_data.FrameMetadata method) get_subpoints_xyz() (simulariumio.trajectory_converter.TrajectoryConverter static method) get_substrate_names() (simulariumio.physicell.dep.pyMCDS.pyMCDS method) get_time() (simulariumio.physicell.dep.pyMCDS.pyMCDS method) get_trajectory_data_object() (simulariumio.data_objects.binary_data.BinaryData method) (simulariumio.data_objects.json_data.JsonData method) (simulariumio.data_objects.simularium_file_data.SimulariumFileData method) get_trajectory_info() (simulariumio.data_objects.binary_data.BinaryData method) (simulariumio.data_objects.json_data.JsonData method) (simulariumio.data_objects.simularium_file_data.SimulariumFileData method) get_type_ids_and_mapping() (simulariumio.data_objects.agent_data.AgentData method) get_type_names() (simulariumio.data_objects.agent_data.AgentData static method) get_xyz_max() (simulariumio.trajectory_converter.TrajectoryConverter static method) get_xyz_min() (simulariumio.trajectory_converter.TrajectoryConverter static method)

H

HAND_TYPE (class in simulariumio.cellpack.cellpack_data) handedness (simulariumio.cellpack.cellpack_data.CellpackData attribute) HEADER_CONSTANT_N_VALUES (simulariumio.constants.BINARY_SETTINGS attribute)

HEADER_N_INT_VALUES (simulariumio.constants.BINARY_SETTINGS attribute) HEADER_N_VALUES_PER_BLOCK (simulariumio.constants.BINARY_SETTINGS attribute) HistogramPlotData (class in simulariumio.data_objects.histogram_plot_data) HistogramPlotReader (class in simulariumio.plot_readers.histogram_plot_reader)

I

input_data_url (simulariumio.data_objects.model_meta_data.ModelMetaData attribute) InputDataError

InputFileData (class in simulariumio.data_objects.input_file_data) int_view (simulariumio.readers.binary_info.BinaryFileData attribute) is_default() (simulariumio.data_objects.model_meta_data.ModelMetaData method)

J

JMOL_COLORS() (in module simulariumio.constants)

JsonData (class in simulariumio.data_objects.json_data) JsonWriter (class in simulariumio.writers.json_writer)

L

LEFT (simulariumio.cellpack.cellpack_data.HAND_TYPE attribute) load_binary() (simulariumio.readers.simularium_binary_reader.SimulariumBinaryReader static method)

LOOK_AT_POSITION (simulariumio.constants.DEFAULT_CAMERA_SETTINGS attribute) look_at_position (simulariumio.data_objects.camera_data.CameraData attribute)

M

magnitude (simulariumio.data_objects.unit_data.UnitData attribute) MAX (simulariumio.constants.VIEWER_DIMENSION_RANGE attribute) max_agents (simulariumio.data_objects.dimension_data.DimensionData attribute) MAX_BYTES (simulariumio.constants.BINARY_SETTINGS attribute) max_owner_cells (simulariumio.physicell.physicell_data.PhysicellData attribute) max_subpoints (simulariumio.data_objects.dimension_data.DimensionData attribute) McellConverter (class in simulariumio.mcell.mcell_converter) McellData (class in simulariumio.mcell.mcell_data) md_universe (simulariumio.md.md_data.MdData attribute) MdConverter (class in simulariumio.md.md_converter) MdData (class in simulariumio.md.md_data) MedyanConverter (class in simulariumio.medyan.medyan_converter) MedyanData (class in simulariumio.medyan.medyan_data) meta_data (simulariumio.cellpack.cellpack_data.CellpackData attribute) (simulariumio.cytosim.cytosim_data.CytosimData attribute) (simulariumio.data_objects.trajectory_data.TrajectoryData attribute) (simulariumio.mcell.mcell_data.McellData attribute) (simulariumio.md.md_data.MdData attribute) (simulariumio.medyan.medyan_data.MedyanData attribute) (simulariumio.nerdss.nerdss_data.NerdssData attribute) (simulariumio.physicell.physicell_data.PhysicellData attribute) (simulariumio.smoldyn.smoldyn_data.SmoldynData attribute) (simulariumio.springsalad.springsalad_data.SpringsaladData attribute) MetaData (class in simulariumio.data_objects.meta_data) MIN (simulariumio.constants.VIEWER_DIMENSION_RANGE attribute) MIN_VALUES_PER_AGENT (simulariumio.constants.V1_SPATIAL_BUFFER_STRUCT attribute) MissingDataError model_meta_data (simulariumio.data_objects.meta_data.MetaData attribute) ModelMetaData (class in simulariumio.data_objects.model_meta_data) module simulariumio simulariumio.cellpack simulariumio.cellpack.cellpack_converter simulariumio.cellpack.cellpack_data simulariumio.constants simulariumio.cytosim simulariumio.cytosim.cytosim_converter simulariumio.cytosim.cytosim_data simulariumio.cytosim.cytosim_object_info simulariumio.data_objects simulariumio.data_objects.agent_data simulariumio.data_objects.binary_data simulariumio.data_objects.camera_data simulariumio.data_objects.dimension_data simulariumio.data_objects.display_data simulariumio.data_objects.frame_data simulariumio.data_objects.histogram_plot_data simulariumio.data_objects.input_file_data simulariumio.data_objects.json_data simulariumio.data_objects.meta_data simulariumio.data_objects.model_meta_data simulariumio.data_objects.scatter_plot_data simulariumio.data_objects.simularium_file_data simulariumio.data_objects.trajectory_data simulariumio.data_objects.unit_data simulariumio.exceptions simulariumio.file_converter simulariumio.filters simulariumio.filters.add_agents_filter simulariumio.filters.every_nth_agent_filter simulariumio.filters.every_nth_subpoint_filter simulariumio.filters.every_nth_timestep_filter simulariumio.filters.filter simulariumio.filters.multiply_space_filter simulariumio.filters.multiply_time_filter simulariumio.filters.transform_spatial_axes_filter simulariumio.filters.translate_filter simulariumio.mcell simulariumio.mcell.mcell_converter simulariumio.mcell.mcell_data simulariumio.md simulariumio.md.md_converter simulariumio.md.md_data simulariumio.medyan simulariumio.medyan.medyan_converter simulariumio.medyan.medyan_data simulariumio.nerdss simulariumio.nerdss.nerdss_converter simulariumio.nerdss.nerdss_data simulariumio.physicell simulariumio.physicell.dep simulariumio.physicell.dep.pyMCDS simulariumio.physicell.physicell_converter simulariumio.physicell.physicell_data simulariumio.plot_readers simulariumio.plot_readers.histogram_plot_reader simulariumio.plot_readers.plot_reader simulariumio.plot_readers.scatter_plot_reader simulariumio.readers simulariumio.readers.binary_info simulariumio.readers.simularium_binary_reader simulariumio.smoldyn simulariumio.smoldyn.smoldyn_converter simulariumio.smoldyn.smoldyn_data simulariumio.springsalad simulariumio.springsalad.springsalad_converter simulariumio.springsalad.springsalad_data simulariumio.trajectory_converter simulariumio.utils simulariumio.writers simulariumio.writers.binary_chunk simulariumio.writers.binary_values simulariumio.writers.binary_writer simulariumio.writers.json_writer simulariumio.writers.writer

multiplier (simulariumio.filters.multiply_space_filter.MultiplySpaceFilter attribute) (simulariumio.filters.multiply_time_filter.MultiplyTimeFilter attribute) multiply() (simulariumio.data_objects.unit_data.UnitData method) MultiplySpaceFilter (class in simulariumio.filters.multiply_space_filter) MultiplyTimeFilter (class in simulariumio.filters.multiply_time_filter)

N

n (simulariumio.filters.every_nth_timestep_filter.EveryNthTimestepFilter attribute) n_agents (simulariumio.data_objects.agent_data.AgentData attribute) N_BLOCKS (simulariumio.constants.BINARY_SETTINGS attribute) n_blocks (simulariumio.readers.binary_info.BinaryBlockInfo attribute) n_bytes (simulariumio.writers.binary_chunk.BinaryChunk attribute) n_frames (simulariumio.writers.binary_chunk.BinaryChunk attribute) n_per_type (simulariumio.filters.every_nth_agent_filter.EveryNthAgentFilter attribute) (simulariumio.filters.every_nth_subpoint_filter.EveryNthSubpointFilter attribute) n_subpoints (simulariumio.data_objects.agent_data.AgentData attribute) n_timesteps (simulariumio.data_objects.agent_data.AgentData attribute)

n_values (simulariumio.writers.binary_chunk.BinaryChunk attribute) name (simulariumio.data_objects.display_data.DisplayData attribute) (simulariumio.data_objects.unit_data.UnitData attribute) NerdssConverter (class in simulariumio.nerdss.nerdss_converter) NerdssData (class in simulariumio.nerdss.nerdss_data) new_agent_data (simulariumio.filters.add_agents_filter.AddAgentsFilter attribute) NONE (simulariumio.constants.DISPLAY_TYPE attribute) NSP_INDEX (simulariumio.constants.V1_SPATIAL_BUFFER_STRUCT attribute) nth_timestep_to_read (simulariumio.mcell.mcell_data.McellData attribute) (simulariumio.md.md_data.MdData attribute) (simulariumio.physicell.physicell_data.PhysicellData attribute)

O

OBJ (simulariumio.constants.DISPLAY_TYPE attribute)

object_info (simulariumio.cytosim.cytosim_data.CytosimData attribute) owner_cell_display_name (simulariumio.physicell.physicell_data.PhysicellData attribute)

P

path_to_binary_files (simulariumio.mcell.mcell_data.McellData attribute) path_to_data_model_json (simulariumio.mcell.mcell_data.McellData attribute) path_to_output_dir (simulariumio.physicell.physicell_data.PhysicellData attribute) path_to_pdb_files (simulariumio.nerdss.nerdss_data.NerdssData attribute) PDB (simulariumio.constants.DISPLAY_TYPE attribute) phase_names (simulariumio.physicell.physicell_data.PhysicellData attribute) PhysicellConverter (class in simulariumio.physicell.physicell_converter) PhysicellData (class in simulariumio.physicell.physicell_data) PLOT_DATA (simulariumio.constants.CURRENT_VERSION attribute) PLOT_DATA_JSON (simulariumio.constants.BINARY_BLOCK_TYPE attribute) PlotReader (class in simulariumio.plot_readers.plot_reader) plots (simulariumio.cellpack.cellpack_data.CellpackData attribute) (simulariumio.cytosim.cytosim_data.CytosimData attribute) (simulariumio.data_objects.trajectory_data.TrajectoryData attribute) (simulariumio.mcell.mcell_data.McellData attribute) (simulariumio.md.md_data.MdData attribute) (simulariumio.medyan.medyan_data.MedyanData attribute) (simulariumio.nerdss.nerdss_data.NerdssData attribute) (simulariumio.physicell.physicell_data.PhysicellData attribute) (simulariumio.smoldyn.smoldyn_data.SmoldynData attribute) (simulariumio.springsalad.springsalad_data.SpringsaladData attribute)

position (simulariumio.data_objects.camera_data.CameraData attribute) position_indices (simulariumio.cytosim.cytosim_object_info.CytosimObjectInfo attribute) positions (simulariumio.data_objects.agent_data.AgentData attribute) POSX_INDEX (simulariumio.constants.V1_SPATIAL_BUFFER_STRUCT attribute) POSY_INDEX (simulariumio.constants.V1_SPATIAL_BUFFER_STRUCT attribute) POSZ_INDEX (simulariumio.constants.V1_SPATIAL_BUFFER_STRUCT attribute) pyMCDS (class in simulariumio.physicell.dep.pyMCDS)

R

R_INDEX (simulariumio.constants.V1_SPATIAL_BUFFER_STRUCT attribute) radii (simulariumio.data_objects.agent_data.AgentData attribute) radius (simulariumio.data_objects.display_data.DisplayData attribute) raw_output_data_url (simulariumio.data_objects.model_meta_data.ModelMetaData attribute) read() (simulariumio.plot_readers.histogram_plot_reader.HistogramPlotReader method) (simulariumio.plot_readers.plot_reader.PlotReader method) (simulariumio.plot_readers.scatter_plot_reader.ScatterPlotReader method)

recipe_file_path (simulariumio.cellpack.cellpack_data.CellpackData attribute) render_mode (simulariumio.data_objects.scatter_plot_data.ScatterPlotData attribute) results_file (simulariumio.cellpack.cellpack_data.CellpackData attribute) RIGHT (simulariumio.cellpack.cellpack_data.HAND_TYPE attribute) rotations (simulariumio.data_objects.agent_data.AgentData attribute) ROTX_INDEX (simulariumio.constants.V1_SPATIAL_BUFFER_STRUCT attribute) ROTY_INDEX (simulariumio.constants.V1_SPATIAL_BUFFER_STRUCT attribute) ROTZ_INDEX (simulariumio.constants.V1_SPATIAL_BUFFER_STRUCT attribute)

S

save() (simulariumio.trajectory_converter.TrajectoryConverter method) (simulariumio.writers.binary_writer.BinaryWriter static method) (simulariumio.writers.json_writer.JsonWriter static method) (simulariumio.writers.writer.Writer static method) save_plot_data() (simulariumio.trajectory_converter.TrajectoryConverter method) (simulariumio.writers.json_writer.JsonWriter static method) scale_agent_data() (simulariumio.trajectory_converter.TrajectoryConverter static method) scale_factor (simulariumio.data_objects.meta_data.MetaData attribute) ScatterPlotData (class in simulariumio.data_objects.scatter_plot_data) ScatterPlotReader (class in simulariumio.plot_readers.scatter_plot_reader) sim_view_txt_file (simulariumio.springsalad.springsalad_data.SpringsaladData attribute) SimulariumBinaryReader (class in simulariumio.readers.simularium_binary_reader) SimulariumFileData (class in simulariumio.data_objects.simularium_file_data) simulariumio module simulariumio.cellpack module simulariumio.cellpack.cellpack_converter module simulariumio.cellpack.cellpack_data module simulariumio.constants module simulariumio.cytosim module simulariumio.cytosim.cytosim_converter module simulariumio.cytosim.cytosim_data module simulariumio.cytosim.cytosim_object_info module simulariumio.data_objects module simulariumio.data_objects.agent_data module simulariumio.data_objects.binary_data module simulariumio.data_objects.camera_data module simulariumio.data_objects.dimension_data module simulariumio.data_objects.display_data module simulariumio.data_objects.frame_data module simulariumio.data_objects.histogram_plot_data module simulariumio.data_objects.input_file_data module simulariumio.data_objects.json_data module simulariumio.data_objects.meta_data module simulariumio.data_objects.model_meta_data module simulariumio.data_objects.scatter_plot_data module simulariumio.data_objects.simularium_file_data module simulariumio.data_objects.trajectory_data module simulariumio.data_objects.unit_data module simulariumio.exceptions module simulariumio.file_converter module simulariumio.filters module simulariumio.filters.add_agents_filter module simulariumio.filters.every_nth_agent_filter module simulariumio.filters.every_nth_subpoint_filter module simulariumio.filters.every_nth_timestep_filter module simulariumio.filters.filter module simulariumio.filters.multiply_space_filter module simulariumio.filters.multiply_time_filter module simulariumio.filters.transform_spatial_axes_filter module simulariumio.filters.translate_filter module simulariumio.mcell module simulariumio.mcell.mcell_converter module simulariumio.mcell.mcell_data module

simulariumio.md module simulariumio.md.md_converter module simulariumio.md.md_data module simulariumio.medyan module simulariumio.medyan.medyan_converter module simulariumio.medyan.medyan_data module simulariumio.nerdss module simulariumio.nerdss.nerdss_converter module simulariumio.nerdss.nerdss_data module simulariumio.physicell module simulariumio.physicell.dep module simulariumio.physicell.dep.pyMCDS module simulariumio.physicell.physicell_converter module simulariumio.physicell.physicell_data module simulariumio.plot_readers module simulariumio.plot_readers.histogram_plot_reader module simulariumio.plot_readers.plot_reader module simulariumio.plot_readers.scatter_plot_reader module simulariumio.readers module simulariumio.readers.binary_info module simulariumio.readers.simularium_binary_reader module simulariumio.smoldyn module simulariumio.smoldyn.smoldyn_converter module simulariumio.smoldyn.smoldyn_data module simulariumio.springsalad module simulariumio.springsalad.springsalad_converter module simulariumio.springsalad.springsalad_data module simulariumio.trajectory_converter module simulariumio.utils module simulariumio.writers module simulariumio.writers.binary_chunk module simulariumio.writers.binary_values module simulariumio.writers.binary_writer module simulariumio.writers.json_writer module simulariumio.writers.writer module smoldyn_file (simulariumio.smoldyn.smoldyn_data.SmoldynData attribute) SmoldynConverter (class in simulariumio.smoldyn.smoldyn_converter) SmoldynData (class in simulariumio.smoldyn.smoldyn_data) snapshot_file (simulariumio.medyan.medyan_data.MedyanData attribute) source_code_license_url (simulariumio.data_objects.model_meta_data.ModelMetaData attribute) source_code_url (simulariumio.data_objects.model_meta_data.ModelMetaData attribute) SP_INDEX (simulariumio.constants.V1_SPATIAL_BUFFER_STRUCT attribute) SPATIAL_BLOCK_HEADER_CONSTANT_N_VALUES (simulariumio.constants.BINARY_SETTINGS attribute) SPATIAL_BLOCK_HEADER_N_VALUES_PER_FRAME (simulariumio.constants.BINARY_SETTINGS attribute) SPATIAL_DATA (simulariumio.constants.CURRENT_VERSION attribute) SPATIAL_DATA_BINARY (simulariumio.constants.BINARY_BLOCK_TYPE attribute) SPATIAL_DATA_JSON (simulariumio.constants.BINARY_BLOCK_TYPE attribute) spatial_units (simulariumio.cellpack.cellpack_data.CellpackData attribute) (simulariumio.data_objects.trajectory_data.TrajectoryData attribute) (simulariumio.md.md_data.MdData attribute) (simulariumio.nerdss.nerdss_data.NerdssData attribute) (simulariumio.smoldyn.smoldyn_data.SmoldynData attribute) SPHERE (simulariumio.constants.DISPLAY_TYPE attribute) SPHERE_GROUP (simulariumio.constants.DISPLAY_TYPE attribute) SpringsaladConverter (class in simulariumio.springsalad.springsalad_converter) SpringsaladData (class in simulariumio.springsalad.springsalad_data) SUBPOINT_VALUES_PER_ITEM() (in module simulariumio.constants) subpoints (simulariumio.data_objects.agent_data.AgentData attribute) surface_mol_rotation_angle (simulariumio.mcell.mcell_data.McellData attribute)

T

TID_INDEX (simulariumio.constants.V1_SPATIAL_BUFFER_STRUCT attribute) time_step (simulariumio.nerdss.nerdss_data.NerdssData attribute) time_units (simulariumio.cellpack.cellpack_data.CellpackData attribute) (simulariumio.data_objects.trajectory_data.TrajectoryData attribute) (simulariumio.md.md_data.MdData attribute) (simulariumio.nerdss.nerdss_data.NerdssData attribute) (simulariumio.physicell.physicell_data.PhysicellData attribute) (simulariumio.smoldyn.smoldyn_data.SmoldynData attribute) times (simulariumio.data_objects.agent_data.AgentData attribute) timestep (simulariumio.physicell.physicell_data.PhysicellData attribute) title (simulariumio.data_objects.histogram_plot_data.HistogramPlotData attribute) (simulariumio.data_objects.model_meta_data.ModelMetaData attribute) (simulariumio.data_objects.scatter_plot_data.ScatterPlotData attribute)

to_JSON() (simulariumio.trajectory_converter.TrajectoryConverter method) total_steps (simulariumio.data_objects.dimension_data.DimensionData attribute) total_timesteps() (simulariumio.data_objects.agent_data.AgentData method) traces (simulariumio.data_objects.histogram_plot_data.HistogramPlotData attribute) TRAJ_INFO_JSON (simulariumio.constants.BINARY_BLOCK_TYPE attribute) TRAJECTORY_INFO (simulariumio.constants.CURRENT_VERSION attribute) trajectory_title (simulariumio.data_objects.meta_data.MetaData attribute) TrajectoryConverter (class in simulariumio.trajectory_converter) TrajectoryData (class in simulariumio.data_objects.trajectory_data) TransformSpatialAxesFilter (class in simulariumio.filters.transform_spatial_axes_filter) translate_agent_positions() (in module simulariumio.utils) TranslateFilter (class in simulariumio.filters.translate_filter) translation_per_type (simulariumio.filters.translate_filter.TranslateFilter attribute) types (simulariumio.data_objects.agent_data.AgentData attribute)

U

UID_INDEX (simulariumio.constants.V1_SPATIAL_BUFFER_STRUCT attribute) unique_ids (simulariumio.data_objects.agent_data.AgentData attribute) UnitData (class in simulariumio.data_objects.unit_data) unpack_display_data() (in module simulariumio.utils) unpack_position_vector() (in module simulariumio.utils)

UnsupportedPlotTypeError UP_VECTOR (simulariumio.constants.DEFAULT_CAMERA_SETTINGS attribute) up_vector (simulariumio.data_objects.camera_data.CameraData attribute) update_trajectory_info_version() (simulariumio.file_converter.FileConverter static method) url (simulariumio.data_objects.display_data.DisplayData attribute)

V

V1_SPATIAL_BUFFER_STRUCT (class in simulariumio.constants) values (simulariumio.writers.binary_values.BinaryValues attribute) VERSION (simulariumio.constants.BINARY_SETTINGS attribute) version (simulariumio.data_objects.model_meta_data.ModelMetaData attribute)

VIEWER_DIMENSION_RANGE (class in simulariumio.constants) VIZ_TYPE (class in simulariumio.constants) VIZ_TYPE_INDEX (simulariumio.constants.V1_SPATIAL_BUFFER_STRUCT attribute) viz_types (simulariumio.data_objects.agent_data.AgentData attribute)

W

Writer (class in simulariumio.writers.writer)

X

xaxis_title (simulariumio.data_objects.histogram_plot_data.HistogramPlotData attribute) (simulariumio.data_objects.scatter_plot_data.ScatterPlotData attribute)

xtrace (simulariumio.data_objects.histogram_plot_data.HistogramPlotData attribute) (simulariumio.data_objects.scatter_plot_data.ScatterPlotData attribute)

Y

yaxis_title (simulariumio.data_objects.scatter_plot_data.ScatterPlotData attribute)

ytraces (simulariumio.data_objects.scatter_plot_data.ScatterPlotData attribute)