Index _ | A | B | C | D | E | F | G | I | K | L | M | N | O | P | R | S | T | U | V | W | X | Y | Z _ _ref (dendrotweaks.morphology.sec_trees.Section attribute) (dendrotweaks.morphology.seg_trees.Segment attribute) _section (dendrotweaks.morphology.seg_trees.Segment attribute) A add_default_mechanisms() (dendrotweaks.model.Model method) add_group() (dendrotweaks.model.Model method) add_iclamp() (dendrotweaks.model.Model method) add_mechanism() (dendrotweaks.model.Model method) add_mechanisms() (dendrotweaks.model.Model method) add_population() (dendrotweaks.model.Model method) add_recording() (dendrotweaks.model.Model method) (dendrotweaks.simulators.NeuronSimulator method) add_section() (dendrotweaks.morphology.domains.Domain method) add_subtree() (dendrotweaks.morphology.point_trees.PointTree method) (dendrotweaks.morphology.sec_trees.SectionTree method) (dendrotweaks.morphology.seg_trees.SegmentTree method) (dendrotweaks.morphology.trees.Tree method) align_apical_dendrite() (dendrotweaks.morphology.point_trees.PointTree method) allocate_synapses() (dendrotweaks.stimuli.populations.Population method) alpha_prime() (dendrotweaks.biophys.mechanisms.StandardIonChannel static method) amp (dendrotweaks.stimuli.iclamps.IClamp property) apical_center (dendrotweaks.morphology.point_trees.PointTree property) area (dendrotweaks.morphology.sec_trees.Section property) ast (dendrotweaks.biophys.io.converter.MODFileConverter property) B beta_prime() (dendrotweaks.biophys.mechanisms.StandardIonChannel static method) bifurcations (dendrotweaks.morphology.point_trees.PointTree property) (dendrotweaks.morphology.sec_trees.SectionTree property) (dendrotweaks.morphology.seg_trees.SegmentTree property) (dendrotweaks.morphology.trees.Tree property) BLOCK_TYPES (dendrotweaks.biophys.io.reader.MODFileReader attribute) blocks (dendrotweaks.biophys.io.converter.MODFileConverter property) (dendrotweaks.biophys.io.reader.MODFileReader attribute) C CaDynamics (class in dendrotweaks.biophys.mechanisms) calculate_cell_statistics() (in module dendrotweaks.analysis.morphometric_analysis) calculate_dendritic_nonlinearity() (in module dendrotweaks.analysis.ephys_analysis) calculate_domain_statistics() (in module dendrotweaks.analysis.morphometric_analysis) calculate_fI_curve() (in module dendrotweaks.analysis.ephys_analysis) calculate_input_resistance() (in module dendrotweaks.analysis.ephys_analysis) calculate_passive_properties() (in module dendrotweaks.analysis.ephys_analysis) calculate_section_statistics() (in module dendrotweaks.analysis.morphometric_analysis) calculate_segment_statistics() (in module dendrotweaks.analysis.morphometric_analysis) calculate_time_constant() (in module dendrotweaks.analysis.ephys_analysis) calculate_voltage_attenuation() (in module dendrotweaks.analysis.ephys_analysis) center (dendrotweaks.morphology.sec_trees.Section property) change_soma_notation() (dendrotweaks.morphology.point_trees.PointTree method) clean() (dendrotweaks.stimuli.populations.Population method) compute_kinetic_variables() (dendrotweaks.biophys.mechanisms.StandardIonChannel method) compute_state() (dendrotweaks.biophys.mechanisms.StandardIonChannel method) conductances (dendrotweaks.model.Model property) connect_to_parent() (dendrotweaks.morphology.point_trees.Point method) (dendrotweaks.morphology.sec_trees.Section method) (dendrotweaks.morphology.seg_trees.Segment method) (dendrotweaks.morphology.trees.Node method) content (dendrotweaks.biophys.io.reader.MODFileReader attribute) convert() (dendrotweaks.biophys.io.converter.MODFileConverter method) copy() (dendrotweaks.morphology.point_trees.Point method) copy_default_mod_files() (dendrotweaks.path_manager.PathManager method) copy_template_files() (dendrotweaks.path_manager.PathManager method) create_and_reference_sections_in_simulator() (dendrotweaks.model.Model method) create_channel() (in module dendrotweaks.biophys.io.factories) create_con() (dendrotweaks.stimuli.populations.Synapse method) create_inputs() (dendrotweaks.stimuli.populations.Population method) create_point_tree() (in module dendrotweaks.morphology.io.factories) create_section_tree() (in module dendrotweaks.morphology.io.factories) create_segment_tree() (in module dendrotweaks.morphology.io.factories) create_standard_channel() (in module dendrotweaks.biophys.io.factories) create_stim() (dendrotweaks.stimuli.populations.Synapse method) D d_lambda (dendrotweaks.model.Model attribute) define_domain() (dendrotweaks.model.Model method) degree (dendrotweaks.biophys.distributions.Distribution property) delay (dendrotweaks.stimuli.iclamps.IClamp property) dendrotweaks.analysis.ephys_analysis module dendrotweaks.analysis.morphometric_analysis module dendrotweaks.biophys.io.factories module dendrotweaks.morphology.io.factories module depth (dendrotweaks.morphology.point_trees.Point property) (dendrotweaks.morphology.sec_trees.Section property) (dendrotweaks.morphology.seg_trees.Segment property) (dendrotweaks.morphology.trees.Node property) detect_somatic_spikes() (in module dendrotweaks.analysis.ephys_analysis) df (dendrotweaks.morphology.point_trees.Point property) (dendrotweaks.morphology.point_trees.PointTree property) (dendrotweaks.morphology.sec_trees.Section property) (dendrotweaks.morphology.sec_trees.SectionTree property) df_params (dendrotweaks.model.Model property) df_points (dendrotweaks.morphology.sec_trees.Section property) diameters (dendrotweaks.morphology.sec_trees.Section property) disconnect_from_parent() (dendrotweaks.morphology.point_trees.Point method) (dendrotweaks.morphology.sec_trees.Section method) (dendrotweaks.morphology.seg_trees.Segment method) (dendrotweaks.morphology.trees.Node method) distance (dendrotweaks.morphology.seg_trees.Segment property) distance_to_parent (dendrotweaks.morphology.point_trees.Point property) distances (dendrotweaks.morphology.sec_trees.Section property) distribute() (dendrotweaks.model.Model method) distribute_all() (dendrotweaks.model.Model method) Distribution (class in dendrotweaks.biophys.distributions) Domain (class in dendrotweaks.morphology.domains) domain (dendrotweaks.morphology.point_trees.Point property) (dendrotweaks.morphology.sec_trees.Section property) (dendrotweaks.morphology.seg_trees.Segment property) domain_distance (dendrotweaks.morphology.seg_trees.Segment property) domains (dendrotweaks.biophys.groups.SegmentGroup attribute) (dendrotweaks.model.Model property) (dendrotweaks.morphology.sec_trees.SectionTree attribute) domains_to_mechs (dendrotweaks.model.Model attribute) downsample() (dendrotweaks.morphology.sec_trees.SectionTree method) dt (dendrotweaks.simulators.NeuronSimulator attribute) dur (dendrotweaks.stimuli.iclamps.IClamp property) E Edge edges (dendrotweaks.morphology.point_trees.PointTree property) (dendrotweaks.morphology.sec_trees.SectionTree property) (dendrotweaks.morphology.seg_trees.SegmentTree property) (dendrotweaks.morphology.trees.Tree property) export_biophys() (dendrotweaks.model.Model method) export_morphology() (dendrotweaks.model.Model method) export_stimuli() (dendrotweaks.model.Model method) export_to_NEURON() (dendrotweaks.model.Model method) extend_sections() (dendrotweaks.morphology.point_trees.PointTree method) F find_in_blocks() (dendrotweaks.biophys.io.parser.MODFileParser method) find_unmatched_content() (dendrotweaks.biophys.io.reader.MODFileReader method) fit() (dendrotweaks.biophys.mechanisms.StandardIonChannel method) fit_distribution() (dendrotweaks.model.Model method) flat_synapses (dendrotweaks.stimuli.populations.Population property) from_dict() (dendrotweaks.biophys.distributions.Distribution static method) (dendrotweaks.biophys.groups.SegmentGroup static method) (dendrotweaks.model.Model method) (dendrotweaks.simulators.NeuronSimulator method) function (dendrotweaks.biophys.distributions.Distribution attribute) function_name (dendrotweaks.biophys.distributions.Distribution property) G generate() (dendrotweaks.biophys.io.code_generators.NMODLCodeGenerator method) (dendrotweaks.biophys.io.code_generators.PythonCodeGenerator method) generator (dendrotweaks.biophys.io.converter.MODFileConverter attribute) get_ast() (dendrotweaks.biophys.io.parser.MODFileParser method) get_blocks() (dendrotweaks.biophys.io.reader.MODFileReader method) get_channel_paths() (dendrotweaks.path_manager.PathManager method) get_data() (dendrotweaks.biophys.mechanisms.IonChannel method) (dendrotweaks.biophys.mechanisms.StandardIonChannel method) get_file_path() (dendrotweaks.path_manager.PathManager method) get_node_data() (in module dendrotweaks.analysis.morphometric_analysis) get_param_value() (dendrotweaks.morphology.sec_trees.Section method) (dendrotweaks.morphology.seg_trees.Segment method) get_path() (dendrotweaks.path_manager.PathManager method) get_sections() (dendrotweaks.model.Model method) get_segments() (dendrotweaks.model.Model method) get_somatic_data() (in module dendrotweaks.analysis.ephys_analysis) get_standard_channel_paths() (dendrotweaks.path_manager.PathManager method) get_traces() (dendrotweaks.model.Model method) get_unit() (dendrotweaks.biophys.mechanisms.StandardIonChannel static method) groups (dendrotweaks.model.Model property) groups_to_parameters (dendrotweaks.model.Model property) I IClamp (class in dendrotweaks.stimuli.iclamps) iclamps (dendrotweaks.model.Model attribute) idx (dendrotweaks.morphology.point_trees.Point attribute) (dendrotweaks.stimuli.populations.Population attribute) independent_var_name (dendrotweaks.biophys.mechanisms.IonChannel attribute) (dendrotweaks.biophys.mechanisms.StandardIonChannel attribute) info() (dendrotweaks.biophys.io.parser.MODFileParser method) (dendrotweaks.model.Model method) (dendrotweaks.morphology.point_trees.Point method) input_params (dendrotweaks.stimuli.populations.Population attribute) insert_mechanism() (dendrotweaks.model.Model method) (dendrotweaks.morphology.sec_trees.Section method) insert_node_after() (dendrotweaks.morphology.point_trees.PointTree method) (dendrotweaks.morphology.sec_trees.SectionTree method) (dendrotweaks.morphology.seg_trees.SegmentTree method) (dendrotweaks.morphology.trees.Tree method) insert_node_before() (dendrotweaks.morphology.point_trees.PointTree method) (dendrotweaks.morphology.sec_trees.SectionTree method) (dendrotweaks.morphology.seg_trees.SegmentTree method) (dendrotweaks.morphology.trees.Tree method) ion (dendrotweaks.biophys.mechanisms.StandardIonChannel attribute) IonChannel (class in dendrotweaks.biophys.mechanisms) is_connected (dendrotweaks.morphology.point_trees.PointTree property) (dendrotweaks.morphology.sec_trees.SectionTree property) (dendrotweaks.morphology.seg_trees.SegmentTree property) (dendrotweaks.morphology.trees.Tree property) is_empty() (dendrotweaks.morphology.domains.Domain method) is_sorted (dendrotweaks.morphology.point_trees.PointTree property) (dendrotweaks.morphology.sec_trees.SectionTree property) (dendrotweaks.morphology.seg_trees.SegmentTree property) (dendrotweaks.morphology.trees.Tree property) K kinetic_params (dendrotweaks.stimuli.populations.Population attribute) L LeakChannel (class in dendrotweaks.biophys.mechanisms) length (dendrotweaks.morphology.sec_trees.Section property) list_biophys() (dendrotweaks.model.Model method) (dendrotweaks.path_manager.PathManager method) list_files() (dendrotweaks.path_manager.PathManager method) list_mechanisms() (dendrotweaks.model.Model method) list_morphologies() (dendrotweaks.model.Model method) (dendrotweaks.path_manager.PathManager method) list_stimuli() (dendrotweaks.model.Model method) (dendrotweaks.path_manager.PathManager method) load_biophys() (dendrotweaks.model.Model method) load_mechanism() (dendrotweaks.biophys.io.loader.MODFileLoader method) (dendrotweaks.model.Model method) load_mechanisms() (dendrotweaks.model.Model method) load_morphology() (dendrotweaks.model.Model method) load_stimuli() (dendrotweaks.model.Model method) loc (dendrotweaks.stimuli.iclamps.IClamp attribute) (dendrotweaks.stimuli.populations.Synapse attribute) M max_value (dendrotweaks.biophys.groups.SegmentGroup attribute) Mechanism (class in dendrotweaks.biophys.mechanisms) mechanisms (dendrotweaks.model.Model attribute) mechs_to_domains (dendrotweaks.model.Model property) mechs_to_params (dendrotweaks.model.Model property) Membrane mechanism merge_domains() (dendrotweaks.model.Model method) min_value (dendrotweaks.biophys.groups.SegmentGroup attribute) MOD file mod_content (dendrotweaks.biophys.io.converter.MODFileConverter property) mod_loader (dendrotweaks.model.Model attribute) Model (class in dendrotweaks.model) MODFileConverter (class in dendrotweaks.biophys.io.converter) MODFileLoader (class in dendrotweaks.biophys.io.loader) MODFileParser (class in dendrotweaks.biophys.io.parser) MODFileReader (class in dendrotweaks.biophys.io.reader) module dendrotweaks.analysis.ephys_analysis dendrotweaks.analysis.morphometric_analysis dendrotweaks.biophys.io.factories dendrotweaks.morphology.io.factories move_group_down() (dendrotweaks.model.Model method) move_group_up() (dendrotweaks.model.Model method) N N (dendrotweaks.stimuli.populations.Population attribute) n_per_seg (dendrotweaks.stimuli.populations.Population property) name (dendrotweaks.biophys.groups.SegmentGroup attribute) (dendrotweaks.biophys.mechanisms.Mechanism attribute) (dendrotweaks.model.Model property) (dendrotweaks.morphology.domains.Domain attribute) (dendrotweaks.stimuli.populations.Population property) nearest_neighbours (dendrotweaks.morphology.point_trees.Point property) (dendrotweaks.morphology.sec_trees.Section property) (dendrotweaks.morphology.seg_trees.Segment property) (dendrotweaks.morphology.trees.Node property) NeuronSimulator (class in dendrotweaks.simulators) NMODLCodeGenerator (class in dendrotweaks.biophys.io.code_generators) Node (class in dendrotweaks.morphology.trees) O overlaps_with() (dendrotweaks.morphology.point_trees.Point method) P Parameter parameters (dendrotweaks.biophys.distributions.Distribution attribute) parameters_to_groups (dendrotweaks.model.Model property) params (dendrotweaks.biophys.mechanisms.CaDynamics attribute) (dendrotweaks.biophys.mechanisms.IonChannel attribute) (dendrotweaks.biophys.mechanisms.LeakChannel attribute) (dendrotweaks.biophys.mechanisms.Mechanism attribute) (dendrotweaks.biophys.mechanisms.StandardIonChannel attribute) (dendrotweaks.model.Model attribute) params_to_mechs (dendrotweaks.model.Model property) params_with_suffix (dendrotweaks.biophys.mechanisms.CaDynamics property) (dendrotweaks.biophys.mechanisms.IonChannel property) (dendrotweaks.biophys.mechanisms.LeakChannel property) (dendrotweaks.biophys.mechanisms.Mechanism property) (dendrotweaks.biophys.mechanisms.StandardIonChannel property) parent (dendrotweaks.morphology.point_trees.Point property) (dendrotweaks.morphology.sec_trees.Section property) (dendrotweaks.morphology.seg_trees.Segment property) (dendrotweaks.morphology.trees.Node property) parent_idx (dendrotweaks.morphology.point_trees.Point attribute) parse() (dendrotweaks.biophys.io.parser.MODFileParser method) parse_block() (dendrotweaks.biophys.io.parser.MODFileParser method) parser (dendrotweaks.biophys.io.converter.MODFileConverter attribute) path_distance() (dendrotweaks.morphology.point_trees.Point method) (dendrotweaks.morphology.sec_trees.Section method) (dendrotweaks.morphology.seg_trees.Segment method) path_distance_to_root (dendrotweaks.morphology.sec_trees.Section property) path_distance_within_domain (dendrotweaks.morphology.sec_trees.Section property) path_manager (dendrotweaks.model.Model attribute) path_to_data (dendrotweaks.path_manager.PathManager property) path_to_model (dendrotweaks.model.Model attribute) (dendrotweaks.path_manager.PathManager attribute) PathManager (class in dendrotweaks.path_manager) paths (dendrotweaks.path_manager.PathManager attribute) plot() (dendrotweaks.model.Model method) (dendrotweaks.morphology.point_trees.PointTree method) (dendrotweaks.morphology.sec_trees.Section method) (dendrotweaks.morphology.sec_trees.SectionTree method) plot_currents() (dendrotweaks.simulators.NeuronSimulator method) plot_dendritic_nonlinearity() (in module dendrotweaks.analysis.ephys_analysis) plot_fI_curve() (in module dendrotweaks.analysis.ephys_analysis) plot_kinetics() (dendrotweaks.biophys.mechanisms.IonChannel method) (dendrotweaks.biophys.mechanisms.StandardIonChannel method) plot_param() (dendrotweaks.model.Model method) plot_passive_properties() (in module dendrotweaks.analysis.ephys_analysis) plot_radii() (dendrotweaks.morphology.sec_trees.Section method) plot_radii_distribution() (dendrotweaks.morphology.point_trees.PointTree method) (dendrotweaks.morphology.sec_trees.SectionTree method) plot_raw_data() (dendrotweaks.morphology.io.reader.SWCReader static method) plot_somatic_spikes() (in module dendrotweaks.analysis.ephys_analysis) plot_var() (dendrotweaks.simulators.NeuronSimulator method) plot_voltage() (dendrotweaks.simulators.NeuronSimulator method) plot_voltage_attenuation() (in module dendrotweaks.analysis.ephys_analysis) Point (class in dendrotweaks.morphology.point_trees) point_tree (dendrotweaks.model.Model attribute) points (dendrotweaks.morphology.point_trees.PointTree property) (dendrotweaks.morphology.sec_trees.Section attribute) PointTree (class in dendrotweaks.morphology.point_trees) Population (class in dendrotweaks.stimuli.populations) populations (dendrotweaks.model.Model attribute) postprocess() (dendrotweaks.biophys.io.parser.MODFileParser method) preprocess() (dendrotweaks.biophys.io.reader.MODFileReader method) print_directory_tree() (dendrotweaks.model.Model method) (dendrotweaks.path_manager.PathManager method) python_content (dendrotweaks.biophys.io.converter.MODFileConverter property) PythonCodeGenerator (class in dendrotweaks.biophys.io.code_generators) R r (dendrotweaks.morphology.point_trees.Point attribute) Ra (dendrotweaks.morphology.seg_trees.Segment property) radii (dendrotweaks.morphology.sec_trees.Section property) range_params (dendrotweaks.biophys.mechanisms.CaDynamics attribute) (dendrotweaks.biophys.mechanisms.IonChannel attribute) (dendrotweaks.biophys.mechanisms.LeakChannel attribute) (dendrotweaks.biophys.mechanisms.Mechanism attribute) (dendrotweaks.biophys.mechanisms.StandardIonChannel attribute) range_params_with_suffix (dendrotweaks.biophys.mechanisms.CaDynamics property) (dendrotweaks.biophys.mechanisms.IonChannel property) (dendrotweaks.biophys.mechanisms.LeakChannel property) (dendrotweaks.biophys.mechanisms.Mechanism property) (dendrotweaks.biophys.mechanisms.StandardIonChannel property) read_file() (dendrotweaks.biophys.io.reader.MODFileReader method) (dendrotweaks.morphology.io.reader.SWCReader static method) reader (dendrotweaks.biophys.io.converter.MODFileConverter attribute) Reconstruction recordings (dendrotweaks.model.Model property) (dendrotweaks.simulators.NeuronSimulator property) reduce_subtree() (dendrotweaks.model.Model method) remove_all_iclamps() (dendrotweaks.model.Model method) remove_all_populations() (dendrotweaks.model.Model method) remove_all_recordings() (dendrotweaks.model.Model method) (dendrotweaks.simulators.NeuronSimulator method) remove_all_stimuli() (dendrotweaks.model.Model method) remove_distribution() (dendrotweaks.model.Model method) remove_group() (dendrotweaks.model.Model method) remove_iclamp() (dendrotweaks.model.Model method) remove_inline_comments() (dendrotweaks.biophys.io.reader.MODFileReader method) remove_node() (dendrotweaks.morphology.point_trees.PointTree method) (dendrotweaks.morphology.sec_trees.SectionTree method) (dendrotweaks.morphology.seg_trees.SegmentTree method) (dendrotweaks.morphology.trees.Tree method) remove_overlaps() (dendrotweaks.morphology.point_trees.PointTree method) remove_population() (dendrotweaks.model.Model method) remove_recording() (dendrotweaks.model.Model method) (dendrotweaks.simulators.NeuronSimulator method) remove_section() (dendrotweaks.morphology.domains.Domain method) remove_subtree() (dendrotweaks.model.Model method) (dendrotweaks.morphology.point_trees.PointTree method) (dendrotweaks.morphology.sec_trees.SectionTree method) (dendrotweaks.morphology.seg_trees.SegmentTree method) (dendrotweaks.morphology.trees.Tree method) remove_suffix_from_gbar() (dendrotweaks.biophys.io.reader.MODFileReader method) remove_unitsoff() (dendrotweaks.biophys.io.reader.MODFileReader method) remove_verbatim() (dendrotweaks.biophys.io.reader.MODFileReader method) remove_zero_length_sections() (dendrotweaks.morphology.sec_trees.SectionTree method) replace_in_blocks() (dendrotweaks.biophys.io.parser.MODFileParser method) replace_suffix_with_name() (dendrotweaks.biophys.io.reader.MODFileReader method) reposition_subtree() (dendrotweaks.morphology.point_trees.PointTree method) (dendrotweaks.morphology.sec_trees.SectionTree method) (dendrotweaks.morphology.seg_trees.SegmentTree method) (dendrotweaks.morphology.trees.Tree method) restore_expressions() (dendrotweaks.biophys.io.parser.MODFileParser method) root (dendrotweaks.morphology.trees.Tree attribute) rotate() (dendrotweaks.morphology.point_trees.PointTree method) round_coordinates() (dendrotweaks.morphology.point_trees.PointTree method) run() (dendrotweaks.model.Model method) (dendrotweaks.simulators.NeuronSimulator method) S sec (dendrotweaks.stimuli.iclamps.IClamp attribute) (dendrotweaks.stimuli.populations.Synapse attribute) sec_tree (dendrotweaks.model.Model attribute) Section (class in dendrotweaks.morphology.sec_trees) sections (dendrotweaks.morphology.domains.Domain property) (dendrotweaks.morphology.sec_trees.SectionTree property) sections_by_depth (dendrotweaks.morphology.sec_trees.SectionTree property) SectionTree (class in dendrotweaks.morphology.sec_trees) seg (dendrotweaks.stimuli.populations.Synapse property) seg_borders (dendrotweaks.morphology.sec_trees.Section property) seg_centers (dendrotweaks.morphology.sec_trees.Section property) seg_tree (dendrotweaks.model.Model attribute) Segment (class in dendrotweaks.morphology.seg_trees) Segment Group Segmentation SegmentGroup (class in dendrotweaks.biophys.groups) segments (dendrotweaks.morphology.sec_trees.Section attribute) (dendrotweaks.morphology.seg_trees.SegmentTree property) (dendrotweaks.stimuli.populations.Population attribute) SegmentTree (class in dendrotweaks.morphology.seg_trees) select_by (dendrotweaks.biophys.groups.SegmentGroup attribute) set_distribution() (dendrotweaks.model.Model method) set_param() (dendrotweaks.model.Model method) set_param_value() (dendrotweaks.morphology.seg_trees.Segment method) set_segmentation() (dendrotweaks.model.Model method) set_tadj() (dendrotweaks.biophys.mechanisms.IonChannel method) (dendrotweaks.biophys.mechanisms.StandardIonChannel method) shift_coordinates_to_soma_center() (dendrotweaks.morphology.point_trees.PointTree method) siblings (dendrotweaks.morphology.point_trees.Point property) (dendrotweaks.morphology.sec_trees.Section property) (dendrotweaks.morphology.seg_trees.Segment property) (dendrotweaks.morphology.trees.Node property) simulator (dendrotweaks.model.Model attribute) simulator_name (dendrotweaks.model.Model attribute) soma (dendrotweaks.morphology.sec_trees.SectionTree property) soma_center (dendrotweaks.morphology.point_trees.PointTree property) soma_notation (dendrotweaks.morphology.point_trees.PointTree property) soma_points (dendrotweaks.morphology.point_trees.PointTree property) sort() (dendrotweaks.morphology.point_trees.PointTree method) (dendrotweaks.morphology.sec_trees.SectionTree method) (dendrotweaks.morphology.seg_trees.SegmentTree method) (dendrotweaks.morphology.trees.Tree method) spike_times (dendrotweaks.stimuli.populations.Population property) (dendrotweaks.stimuli.populations.Synapse property) split_comment_block() (dendrotweaks.biophys.io.parser.MODFileParser method) StandardIonChannel (class in dendrotweaks.biophys.mechanisms) standardize_channel() (dendrotweaks.model.Model method) (in module dendrotweaks.biophys.io.factories) standardize_state_var_names() (dendrotweaks.biophys.io.parser.MODFileParser method) states (dendrotweaks.biophys.mechanisms.StandardIonChannel property) steady_state() (dendrotweaks.biophys.mechanisms.StandardIonChannel static method) stimuli_to_dict() (dendrotweaks.model.Model method) subtree (dendrotweaks.morphology.point_trees.Point property) (dendrotweaks.morphology.sec_trees.Section property) (dendrotweaks.morphology.seg_trees.Segment property) (dendrotweaks.morphology.trees.Node property) subtree_size (dendrotweaks.morphology.point_trees.Point property) (dendrotweaks.morphology.sec_trees.Section property) (dendrotweaks.morphology.seg_trees.Segment property) (dendrotweaks.morphology.trees.Node property) SWC file SWCReader (class in dendrotweaks.morphology.io.reader) syn_type (dendrotweaks.stimuli.populations.Population attribute) Synapse (class in dendrotweaks.stimuli.populations) synapses (dendrotweaks.stimuli.populations.Population attribute) T t (dendrotweaks.simulators.NeuronSimulator property) t_adj() (dendrotweaks.biophys.mechanisms.StandardIonChannel static method) tadj (dendrotweaks.biophys.mechanisms.IonChannel attribute) temperature (dendrotweaks.biophys.mechanisms.IonChannel attribute) (dendrotweaks.biophys.mechanisms.StandardIonChannel attribute) (dendrotweaks.simulators.NeuronSimulator attribute) terminations (dendrotweaks.morphology.point_trees.PointTree property) (dendrotweaks.morphology.sec_trees.SectionTree property) (dendrotweaks.morphology.seg_trees.SegmentTree property) (dendrotweaks.morphology.trees.Tree property) time_constant() (dendrotweaks.biophys.mechanisms.StandardIonChannel method) to_csv() (dendrotweaks.stimuli.populations.Population method) to_dict() (dendrotweaks.biophys.distributions.Distribution method) (dendrotweaks.biophys.groups.SegmentGroup method) (dendrotweaks.biophys.mechanisms.CaDynamics method) (dendrotweaks.biophys.mechanisms.IonChannel method) (dendrotweaks.biophys.mechanisms.LeakChannel method) (dendrotweaks.biophys.mechanisms.Mechanism method) (dendrotweaks.biophys.mechanisms.StandardIonChannel method) (dendrotweaks.model.Model method) (dendrotweaks.simulators.NeuronSimulator method) (dendrotweaks.stimuli.populations.Population method) to_swc() (dendrotweaks.morphology.point_trees.PointTree method) (dendrotweaks.morphology.sec_trees.SectionTree method) topological_type (dendrotweaks.morphology.point_trees.Point property) (dendrotweaks.morphology.sec_trees.Section property) (dendrotweaks.morphology.seg_trees.Segment property) (dendrotweaks.morphology.trees.Node property) topology() (dendrotweaks.morphology.point_trees.PointTree method) (dendrotweaks.morphology.sec_trees.SectionTree method) (dendrotweaks.morphology.seg_trees.SegmentTree method) (dendrotweaks.morphology.trees.Tree method) traverse() (dendrotweaks.morphology.point_trees.PointTree method) (dendrotweaks.morphology.sec_trees.SectionTree method) (dendrotweaks.morphology.seg_trees.SegmentTree method) (dendrotweaks.morphology.trees.Tree method) Tree (class in dendrotweaks.morphology.trees) Tree graph Tree traversal type_idx (dendrotweaks.morphology.point_trees.Point attribute) U uninsert_mechanism() (dendrotweaks.model.Model method) (dendrotweaks.morphology.sec_trees.Section method) unmatched (dendrotweaks.biophys.io.reader.MODFileReader attribute) update_histogram() (in module dendrotweaks.analysis.morphometric_analysis) update_input_params() (dendrotweaks.stimuli.populations.Population method) update_kinetic_params() (dendrotweaks.stimuli.populations.Population method) update_parameters() (dendrotweaks.biophys.distributions.Distribution method) update_population_input_params() (dendrotweaks.model.Model method) update_population_kinetic_params() (dendrotweaks.model.Model method) update_state_vars_with_power() (dendrotweaks.biophys.io.parser.MODFileParser method) V v_init (dendrotweaks.simulators.NeuronSimulator attribute) verbose (dendrotweaks.model.Model property) W write_file() (dendrotweaks.biophys.io.code_generators.NMODLCodeGenerator method) (dendrotweaks.biophys.io.code_generators.PythonCodeGenerator method) X x (dendrotweaks.morphology.point_trees.Point attribute) xs (dendrotweaks.morphology.sec_trees.Section property) Y y (dendrotweaks.morphology.point_trees.Point attribute) ys (dendrotweaks.morphology.sec_trees.Section property) Z z (dendrotweaks.morphology.point_trees.Point attribute) zs (dendrotweaks.morphology.sec_trees.Section property)