Index A | B | C | D | E | F | G | H | I | K | L | M | N | P | Q | R | S | T | U | V | W A add_to_group() (Branch method) (Cell method) (Compartment method) (Network method) AffineTransform (class in jaxley.optimize.transforms) arrange_in_layers() (Network method) B Branch (class in jaxley) branch() (Branch method) (Cell method) (Compartment method) (Network method) branch_params (Branch attribute) branch_states (Branch attribute) branches (Branch property) (Cell property) (Compartment property) (Network property) build_compartment_graph() (in module jaxley.io.graph) build_dynamic_state_utils() (in module jaxley.utils.dynamics) build_exp_euler_transition_matrix() (Branch method) (Cell method) (Compartment method) (Network method) build_init_and_step_fn() (in module jaxley.integrate) C CaFaradayConcentrationChange (class in jaxley.pumps) CaL (class in jaxley.channels) CaNernstReversal (class in jaxley.pumps) CaPump (class in jaxley.pumps) CaT (class in jaxley.channels) Cell (class in jaxley) cell() (Branch method) (Cell method) (Compartment method) (Network method) cell_params (Cell attribute) cell_states (Cell attribute) cells (Branch property) (Cell property) (Compartment property) (Network property) ChainTransform (class in jaxley.optimize.transforms) change_name() (CaFaradayConcentrationChange method) (CaL method) (CaNernstReversal method) (CaPump method) (CaT method) (Channel method) (Fire method) (HH method) (IonotropicSynapse method) (Izhikevich method) (K method) (Km method) (Leak method) (Na method) (Pump method) (Rate method) (Synapse method) (TanhConductanceSynapse method) (TanhRateSynapse method) Channel (class in jaxley.channels) channel_params (CaFaradayConcentrationChange attribute) (CaL attribute) (CaNernstReversal attribute) (CaPump attribute) (CaT attribute) (Channel attribute) (Fire attribute) (HH attribute) (Izhikevich attribute) (K attribute) (Km attribute) (Leak attribute) (Na attribute) (Pump attribute) (Rate attribute) channel_states (CaFaradayConcentrationChange attribute) (CaL attribute) (CaNernstReversal attribute) (CaPump attribute) (CaT attribute) (Channel attribute) (Fire attribute) (HH attribute) (Izhikevich attribute) (K attribute) (Km attribute) (Leak attribute) (Na attribute) (Pump attribute) (Rate attribute) clamp() (Branch method) (Cell method) (Compartment method) (Network method) comp() (Branch method) (Cell method) (Compartment method) (Network method) Compartment (class in jaxley) compartment_params (Compartment attribute) compartment_states (Compartment attribute) comps (Branch property) (Cell property) (Compartment property) (Network property) compute_compartment_centers() (Branch method) (Cell method) (Compartment method) (Network method) compute_current() (CaFaradayConcentrationChange method) (CaL method) (CaNernstReversal method) (CaPump method) (CaT method) (Channel method) (Fire method) (HH method) (IonotropicSynapse method) (Izhikevich method) (K method) (Km method) (Leak method) (Na method) (Pump method) (Rate method) (Synapse method) (TanhConductanceSynapse method) (TanhRateSynapse method) compute_xyz() (Branch method) (Cell method) (Compartment method) (Network method) connect() (in module jaxley.connect) connectivity_matrix_connect() (in module jaxley.connect) copy() (Branch method) (Cell method) (Compartment method) (Network method) copy_node_property_to_edges() (Branch method) (Cell method) (Compartment method) (Network method) current_name (CaFaradayConcentrationChange attribute) (CaL attribute) (CaNernstReversal attribute) (CaPump attribute) (CaT attribute) (Channel attribute) (Fire attribute) (HH attribute) (Izhikevich attribute) (K attribute) (Km attribute) (Leak attribute) (Na attribute) (Pump attribute) (Rate attribute) customize_solver_exp_euler() (Branch method) (Cell method) (Compartment method) (Network method) CustomTransform (class in jaxley.optimize.transforms) D data_clamp() (Branch method) (Cell method) (Compartment method) (Network method) data_set() (Branch method) (Cell method) (Compartment method) (Network method) data_stimulate() (Branch method) (Cell method) (Compartment method) (Network method) delete() (Branch method) (Cell method) (Compartment method) (Network method) delete_clamps() (Branch method) (Cell method) (Compartment method) (Network method) delete_diffusion() (Branch method) (Cell method) (Compartment method) (Network method) delete_recordings() (Branch method) (Cell method) (Compartment method) (Network method) delete_stimuli() (Branch method) (Cell method) (Compartment method) (Network method) delete_trainables() (Branch method) (Cell method) (Compartment method) (Network method) diffuse() (Branch method) (Cell method) (Compartment method) (Network method) distance_direct() (in module jaxley.morphology) distance_pathwise() (in module jaxley.morphology) E edge() (Branch method) (Cell method) (Compartment method) (Network method) F Fire (class in jaxley.channels) forward() (AffineTransform method) (ChainTransform method) (CustomTransform method) (MaskedTransform method) (NegSoftplusTransform method) (SigmoidTransform method) (SoftplusTransform method) from_graph() (in module jaxley.io.graph) fully_connect() (in module jaxley.connect) G get_parameters() (Branch method) (Cell method) (Compartment method) (Network method) H h_gate() (HH static method) (Na static method) HH (class in jaxley.channels) I init() (TypeOptimizer method) init_state() (CaFaradayConcentrationChange method) (CaL method) (CaNernstReversal method) (CaPump method) (CaT method) (Channel method) (Fire method) (HH method) (Izhikevich method) (K method) (Km method) (Leak method) (Na method) (Pump method) (Rate method) init_states() (Branch method) (Cell method) (Compartment method) (Network method) initialize() (Branch method) (Cell method) (Compartment method) (Network method) initialized (Branch property) (Cell property) (Compartment property) (Network property) insert() (Branch method) (Cell method) (Compartment method) (Network method) integrate() (in module jaxley) inverse() (AffineTransform method) (ChainTransform method) (CustomTransform method) (MaskedTransform method) (NegSoftplusTransform method) (SigmoidTransform method) (SoftplusTransform method) IonotropicSynapse (class in jaxley.synapses) Izhikevich (class in jaxley.channels) K K (class in jaxley.channels) Km (class in jaxley.channels) L Leak (class in jaxley.channels) loc() (Branch method) (Cell method) (Compartment method) (Network method) M m_gate() (HH static method) (Na static method) make_trainable() (Branch method) (Cell method) (Compartment method) (Network method) MaskedTransform (class in jaxley.optimize.transforms) morph_connect() (in module jaxley.morphology) morph_delete() (in module jaxley.morphology) move() (Branch method) (Cell method) (Compartment method) (Network method) move_to() (Branch method) (Cell method) (Compartment method) (Network method) N n_gate() (HH static method) (K static method) Na (class in jaxley.channels) name (CaFaradayConcentrationChange property) (CaL property) (CaNernstReversal property) (CaPump property) (CaT property) (Channel property) (Fire property) (HH property) (IonotropicSynapse property) (Izhikevich property) (K property) (Km property) (Leak property) (Na property) (Pump property) (Rate property) (Synapse property) (TanhConductanceSynapse property) (TanhRateSynapse property) NegSoftplusTransform (class in jaxley.optimize.transforms) Network (class in jaxley) network_params (Network attribute) network_states (Network attribute) P p_gate() (Km static method) Pump (class in jaxley.pumps) Q q_gate() (CaL static method) R r_gate() (CaL static method) Rate (class in jaxley.channels) read_swc() (in module jaxley) record() (Branch method) (Cell method) (Compartment method) (Network method) rotate() (Branch method) (Cell method) (Compartment method) (Network method) S scope() (Branch method) (Cell method) (Compartment method) (Network method) select() (Branch method) (Cell method) (Compartment method) (Network method) set() (Branch method) (Cell method) (Compartment method) (Network method) set_ncomp() (Branch method) (Cell method) (Compartment method) (Network method) set_scope() (Branch method) (Cell method) (Compartment method) (Network method) shape (Branch property) (Cell property) (Compartment property) (Network property) show() (Branch method) (Cell method) (Compartment method) (Network method) SigmoidTransform (class in jaxley.optimize.transforms) SoftplusTransform (class in jaxley.optimize.transforms) sparse_connect() (in module jaxley.connect) step() (Branch method) (Cell method) (Compartment method) (Network method) stimulate() (Branch method) (Cell method) (Compartment method) (Network method) Synapse (class in jaxley.synapses) synapse_params (IonotropicSynapse attribute) (Synapse attribute) (TanhConductanceSynapse attribute) (TanhRateSynapse attribute) synapse_states (IonotropicSynapse attribute) (Synapse attribute) (TanhConductanceSynapse attribute) (TanhRateSynapse attribute) T TanhConductanceSynapse (class in jaxley.synapses) TanhRateSynapse (class in jaxley.synapses) to_graph() (in module jaxley.modules.base) to_jax() (Branch method) (Cell method) (Compartment method) (Network method) to_swc_graph() (in module jaxley.io.graph) TypeOptimizer (class in jaxley.optimize.optimizer) U u_gate() (CaT static method) update() (TypeOptimizer method) update_states() (CaFaradayConcentrationChange method) (CaL method) (CaNernstReversal method) (CaPump method) (CaT method) (Channel method) (Fire method) (HH method) (IonotropicSynapse method) (Izhikevich method) (K method) (Km method) (Leak method) (Na method) (Pump method) (Rate method) (Synapse method) (TanhConductanceSynapse method) (TanhRateSynapse method) V view (Branch property) (Cell property) (Compartment property) (Network property) vis() (Branch method) (Cell method) (Compartment method) (Network method) vis_compartment_graph() (in module jaxley.io.graph) W write_trainables() (Branch method) (Cell method) (Compartment method) (Network method)
