Index A | B | C | D | E | F | G | H | I | K | L | M | N | P | R | S | T | U | V | W A add_to_group() (Branch method) (Cell method) (Compartment method) (Network method) AffineTransform (class in jaxley.optimize.transforms) AlphaSynapse (class in jaxley.synapses) 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) CaNernstReversal (class in jaxley.pumps) CaPump (class in jaxley.pumps) 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() (AlphaSynapse method) (CaFaradayConcentrationChange method) (CaNernstReversal method) (CaPump method) (Channel method) (ConductanceSynapse method) (CurrentSynapse method) (DynamicSynapse method) (Fire method) (HH method) (IonotropicSynapse method) (Izhikevich method) (K method) (Leak method) (Na method) (Pump method) (Rate method) (SpikeSynapse method) (Synapse method) Channel (class in jaxley.channels) channel_params (CaFaradayConcentrationChange attribute) (CaNernstReversal attribute) (CaPump attribute) (Channel attribute) (Fire attribute) (HH attribute) (Izhikevich attribute) (K attribute) (Leak attribute) (Na attribute) (Pump attribute) (Rate attribute) channel_states (CaFaradayConcentrationChange attribute) (CaNernstReversal attribute) (CaPump attribute) (Channel attribute) (Fire attribute) (HH attribute) (Izhikevich attribute) (K 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() (AlphaSynapse method) (CaFaradayConcentrationChange method) (CaNernstReversal method) (CaPump method) (Channel method) (ConductanceSynapse method) (CurrentSynapse method) (DynamicSynapse method) (Fire method) (HH method) (IonotropicSynapse method) (Izhikevich method) (K method) (Leak method) (Na method) (Pump method) (Rate method) (SpikeSynapse method) (Synapse method) compute_xyz() (Branch method) (Cell method) (Compartment method) (Network method) ConductanceSynapse (class in jaxley.synapses) 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) (CaNernstReversal attribute) (CaPump attribute) (Channel attribute) (Fire attribute) (HH attribute) (Izhikevich attribute) (K attribute) (Leak attribute) (Na attribute) (Pump attribute) (Rate attribute) CurrentSynapse (class in jaxley.synapses) 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) DynamicSynapse (class in jaxley.synapses) E edge() (Branch method) (Cell method) (Compartment method) (Network method) exponential_euler() (in module jaxley.solver_gate) 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 heaviside() (in module jaxley.solver_gate) HH (class in jaxley.channels) I init() (TypeOptimizer method) init_params() (Branch method) (Cell method) (Channel method) (Compartment method) (Fire method) (HH method) (Izhikevich method) (K method) (Leak method) (Na method) (Network method) (Rate method) init_state() (CaFaradayConcentrationChange method) (CaNernstReversal method) (CaPump method) (Channel method) (Fire method) (HH method) (Izhikevich method) (K 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) L Leak (class in jaxley.channels) loc() (Branch method) (Cell method) (Compartment method) (Network method) M 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 Na (class in jaxley.channels) name (AlphaSynapse property) (CaFaradayConcentrationChange property) (CaNernstReversal property) (CaPump property) (Channel property) (ConductanceSynapse property) (CurrentSynapse property) (DynamicSynapse property) (Fire property) (HH property) (IonotropicSynapse property) (Izhikevich property) (K property) (Leak property) (Na property) (Pump property) (Rate property) (SpikeSynapse property) (Synapse property) NegSoftplusTransform (class in jaxley.optimize.transforms) Network (class in jaxley) network_params (Network attribute) network_states (Network attribute) P Pump (class in jaxley.pumps) R Rate (class in jaxley.channels) read_swc() (in module jaxley) record() (Branch method) (Cell method) (Compartment method) (Network method) recording() (Branch method) (Cell method) (Compartment method) (Network method) rotate() (Branch method) (Cell method) (Compartment method) (Network method) S save_exp() (in module jaxley.solver_gate) 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) solve_gate_exponential() (in module jaxley.solver_gate) solve_gate_implicit() (in module jaxley.solver_gate) sparse_connect() (in module jaxley.connect) SpikeSynapse (class in jaxley.synapses) 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 (AlphaSynapse attribute) (ConductanceSynapse attribute) (CurrentSynapse attribute) (DynamicSynapse attribute) (IonotropicSynapse attribute) (SpikeSynapse attribute) (Synapse attribute) synapse_states (AlphaSynapse attribute) (ConductanceSynapse attribute) (CurrentSynapse attribute) (DynamicSynapse attribute) (IonotropicSynapse attribute) (SpikeSynapse attribute) (Synapse attribute) T 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 update() (TypeOptimizer method) update_states() (AlphaSynapse method) (CaFaradayConcentrationChange method) (CaNernstReversal method) (CaPump method) (Channel method) (ConductanceSynapse method) (CurrentSynapse method) (DynamicSynapse method) (Fire method) (HH method) (IonotropicSynapse method) (Izhikevich method) (K method) (Leak method) (Na method) (Pump method) (Rate method) (SpikeSynapse method) (Synapse 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_recordings() (Branch method) (Cell method) (Compartment method) (Network method) write_trainables() (Branch method) (Cell method) (Compartment method) (Network method)
