Index

A

acc() (in module gotranx.templates.python) add_temporal_state() (in module gotranx.ode) AllAtoms (class in gotranx.ode) arguments (gotranx.codegen.base.Func attribute) (gotranx.codegen.Func attribute)

Assignment (class in gotranx.atoms) AssignmentNotFoundInComponent Atom (class in gotranx.atoms) atoms (gotranx.ode_component.BaseComponent property)

B

Backend (class in gotranx.cli.gotran2py) BaseComponent (class in gotranx.ode_component) BaseGotranODECodePrinter (class in gotranx.codegen) (class in gotranx.codegen.ode)

binary_op() (in module gotranx.expressions) build_expression() (in module gotranx.expressions)

C

CCodeGenerator (class in gotranx.codegen) (class in gotranx.codegen.c) cellml_to_gotran() (in module gotranx.myokit) CFormat (in module gotranx.codegen) check_components() (in module gotranx.ode) CodeGenerator (class in gotranx.codegen) (class in gotranx.codegen.base) Comment (class in gotranx.atoms)

comment() (gotranx.transformer.TreeToODE method) (gotranx.TreeToODE method) comments (gotranx.transformer.LarkODE attribute) Component (class in gotranx) (class in gotranx.ode_component) ComponentNotCompleteError components (gotranx.transformer.LarkODE attribute) Conditional() (in module gotranx.sympytools) ContinuousConditional() (in module gotranx.sympytools)

D

dependents() (gotranx.ODE method) (gotranx.ode.ODE method)

DuplicateSymbolError

E

explicit_euler() (in module gotranx.schemes) Expression (class in gotranx.atoms) expressions() (gotranx.transformer.TreeToODE method) (gotranx.TreeToODE method)

extract_nested_variables() (in module gotranx.myokit) extract_unit() (in module gotranx.myokit)

F

find_assignment() (gotranx.ode_component.BaseComponent method) find_assignments() (in module gotranx.transformer) find_components() (in module gotranx.transformer) find_duplicates() (in module gotranx.ode) find_parameter() (gotranx.ode_component.BaseComponent method)

find_state() (gotranx.ode_component.BaseComponent method) Format (class in gotranx.codegen.c) (class in gotranx.codegen.python) fraction_numerator_is_nonzero() (in module gotranx.schemes) Func (class in gotranx.codegen) (class in gotranx.codegen.base)

G

gather_atoms() (in module gotranx.ode) generalized_rush_larsen() (in module gotranx.schemes) get_code() (in module gotranx.cli.gotran2c) (in module gotranx.cli.gotran2py) get_component() (gotranx.ODE method) (gotranx.ode.ODE method) get_scheme() (in module gotranx) (in module gotranx.schemes) get_unit_and_comment_from_assignment() (in module gotranx.transformer) gotran_to_cellml() (in module gotranx.myokit) gotran_to_myokit() (in module gotranx.myokit) GotranCCodePrinter (class in gotranx.codegen) (class in gotranx.codegen.c) GotranODECodePrinter (class in gotranx.codegen) (class in gotranx.codegen.ode) GotranPythonCodePrinter (class in gotranx.codegen) (class in gotranx.codegen.python) gotranx module gotranx.atoms module gotranx.cli module gotranx.cli.cellml2ode module gotranx.cli.gotran2c module gotranx.cli.gotran2py module gotranx.codegen module gotranx.codegen.base module gotranx.codegen.c module

gotranx.codegen.ode module gotranx.codegen.python module gotranx.exceptions module gotranx.expressions module gotranx.load module gotranx.myokit module gotranx.ode module gotranx.ode_component module gotranx.parser module gotranx.save module gotranx.schemes module gotranx.sympytools module gotranx.templates module gotranx.templates.c module gotranx.templates.python module gotranx.transformer module gotranx.units module GotranxError

H

hybrid_rush_larsen() (in module gotranx.schemes)

I

init_parameter_values() (gotranx.templates.Template static method) (in module gotranx.templates.python) init_state_values() (gotranx.templates.Template static method) (in module gotranx.templates.python) initial_parameter_values() (gotranx.codegen.base.CodeGenerator method) (gotranx.codegen.CodeGenerator method) initial_state_values() (gotranx.codegen.base.CodeGenerator method) (gotranx.codegen.CodeGenerator method)

Intermediate (class in gotranx.atoms) intermediates (gotranx.ODE property) (gotranx.ode.ODE property) InvalidODEException InvalidTreeError is_complete() (gotranx.ode_component.BaseComponent method)

J

jacobi_matrix() (in module gotranx.sympytools)

JaxCodeGenerator (class in gotranx.codegen)

L

lark_list_to_parameters() (in module gotranx.transformer) LarkODE (class in gotranx.transformer) license_callback() (in module gotranx.cli) list_schemes() (in module gotranx.schemes)

load_grammar() (in module gotranx.parser) load_ode() (in module gotranx) (in module gotranx.load) lookup (gotranx.ode.AllAtoms attribute)

M

make_ode() (in module gotranx.ode) method() (gotranx.templates.Template static method) (in module gotranx.templates.python) missing_index() (gotranx.templates.Template static method) (in module gotranx.templates.python) missing_variables (gotranx.ODE property) (gotranx.ode.ODE property) MissingSymbolError mmt_to_gotran() (in module gotranx.myokit) module gotranx gotranx.atoms gotranx.cli gotranx.cli.cellml2ode gotranx.cli.gotran2c gotranx.cli.gotran2py gotranx.codegen gotranx.codegen.base gotranx.codegen.c gotranx.codegen.ode gotranx.codegen.python gotranx.exceptions gotranx.expressions gotranx.load gotranx.myokit gotranx.ode gotranx.ode_component gotranx.parser gotranx.save gotranx.schemes gotranx.sympytools gotranx.templates gotranx.templates.c gotranx.templates.python gotranx.transformer gotranx.units

monitor_index() (gotranx.templates.Template static method) (in module gotranx.templates.python) monitor_values() (gotranx.codegen.base.CodeGenerator method) (gotranx.codegen.CodeGenerator method) myokit_to_gotran() (in module gotranx.myokit) MyokitComponent (class in gotranx.ode_component)

N

num_components (gotranx.ODE property) (gotranx.ode.ODE property) num_parameters (gotranx.ODE property) (gotranx.ode.ODE property)

num_return_values (gotranx.codegen.base.Func attribute) (gotranx.codegen.Func attribute) num_states (gotranx.ODE property) (gotranx.ode.ODE property)

O

ODE (class in gotranx) (class in gotranx.ode) ode() (gotranx.transformer.TreeToODE method) (gotranx.TreeToODE method)

ode_from_string() (in module gotranx.load) ODEFileNotFound

P

Parameter (class in gotranx.atoms) parameter_index() (gotranx.templates.Template static method) (in module gotranx.templates.python) ParameterNotFoundInComponent parameters (gotranx.codegen.base.Func attribute) (gotranx.codegen.Func attribute) (gotranx.ODE property) (gotranx.ode.ODE property)

parameters() (gotranx.transformer.TreeToODE method) (gotranx.TreeToODE method) Parser (class in gotranx) (class in gotranx.parser) printer_func (class in gotranx.schemes) PythonCodeGenerator (class in gotranx.codegen) (class in gotranx.codegen.python) PythonFormat (in module gotranx.codegen)

R

relational_to_piecewise() (in module gotranx.expressions) remove_quotes() (in module gotranx.transformer) remove_singularities() (gotranx.atoms.Assignment method) (gotranx.Component method) (gotranx.ode_component.Component method) (in module gotranx.atoms) resolve_expression() (gotranx.atoms.Assignment method) (gotranx.atoms.StateDerivative method)

resolve_expressions() (in module gotranx.ode) ResolveExpressionError return_name (gotranx.codegen.base.Func attribute) (gotranx.codegen.Func attribute) rhs() (gotranx.codegen.base.CodeGenerator method) (gotranx.codegen.CodeGenerator method) rhs_matrix() (in module gotranx.sympytools) RHSArgument (class in gotranx.codegen) (class in gotranx.codegen.base)

S

save() (gotranx.ODE method) (gotranx.ode.ODE method) Scheme (class in gotranx.schemes) scheme() (gotranx.codegen.base.CodeGenerator method) (gotranx.codegen.CodeGenerator method) scheme_func (class in gotranx.schemes) SchemeArgument (class in gotranx.codegen) (class in gotranx.codegen.base) Shape (class in gotranx.codegen.base) simplify() (gotranx.atoms.Assignment method) (gotranx.ODE method) (gotranx.ode.ODE method) (gotranx.ode_component.BaseComponent method) singularities() (gotranx.atoms.Assignment method) sort_assignments() (in module gotranx.ode) sorted_assignments() (gotranx.ODE method) (gotranx.ode.ODE method) sorted_state_derivatives() (gotranx.ODE method) (gotranx.ode.ODE method) sorted_states() (gotranx.ODE method) (gotranx.ode.ODE method)

State (class in gotranx.atoms) state_derivatives (gotranx.ODE property) (gotranx.ode.ODE property) state_index() (gotranx.templates.Template static method) (in module gotranx.templates.python) StateDerivative (class in gotranx.atoms) StateNotFoundInComponent states (gotranx.codegen.base.Func attribute) (gotranx.codegen.Func attribute) (gotranx.ODE property) (gotranx.ode.ODE property) states() (gotranx.transformer.TreeToODE method) (gotranx.TreeToODE method) states_matrix() (in module gotranx.sympytools) states_with_derivatives (gotranx.ode_component.BaseComponent property) states_without_derivatives (gotranx.ode_component.BaseComponent property) symbol_names (gotranx.ode.AllAtoms attribute) symbol_values (gotranx.ode.AllAtoms attribute) symbols (gotranx.ODE property) (gotranx.ode.AllAtoms attribute) (gotranx.ode.ODE property)

T

Template (class in gotranx.templates) TimeDependentState (class in gotranx.atoms) to_intermediate() (gotranx.atoms.Assignment method)

to_state_derivative() (gotranx.atoms.Assignment method) tree2parameter() (in module gotranx.transformer) TreeToODE (class in gotranx) (class in gotranx.transformer)

U

unary_op() (in module gotranx.expressions)

unit_from_string() (in module gotranx.atoms) UnknownTreeTypeError

V

values (gotranx.codegen.base.Func attribute) (gotranx.codegen.Func attribute)

values_type (gotranx.codegen.base.Func attribute) (gotranx.codegen.Func attribute) version_callback() (in module gotranx.cli)

W

write_ODE_to_ode_file() (in module gotranx.save)