Index

_ | A | C | D | E | G | I | M | O | P | R | S | U | W

_

__init__ (module)
__main__ (module)

A

amino_acid_spaces (module)
ArdellSellaEvolverAbstractBase (class in evolvers)
ArdellSellaEvolverHomotopy (class in evolvers)
ArdellSellaEvolverNumpy (class in evolvers)
ArdellSellaEvolverNumpyMulticore (class in evolvers)
ArdellSellaEvolverNumpyProcessChild (class in evolvers)
ArdellSellaEvolverPowerCUDA (class in evolvers)
ArdellSellaEvolverPowerMethod (class in evolvers)
ArdellSellaEvolverPowerMethodProcessChild (class in evolvers)
ArdellSellaEvolverPowerMulticore (class in evolvers)

C

calculate() (evolvers.eigensystem_CUDA_implementation method)
codon_spaces (module)
compute_code_fitness_given_messages() (evolvers.ArdellSellaEvolverAbstractBase method)
compute_eigensystem() (evolvers.ArdellSellaEvolverHomotopy method)
(evolvers.ArdellSellaEvolverNumpy method)
(evolvers.ArdellSellaEvolverPowerMethod method)
compute_max_fitness_code_mutation() (evolvers.ArdellSellaEvolverAbstractBase method)

D

done() (evolvers.eigensystem_CUDA_implementation method)

E

eigensystem_CUDA_implementation (class in evolvers)
equilibrate_messages() (evolvers.ArdellSellaEvolverAbstractBase method)
(evolvers.ArdellSellaEvolverHomotopy method)
(evolvers.ArdellSellaEvolverNumpy method)
(evolvers.ArdellSellaEvolverNumpyMulticore method)
(evolvers.ArdellSellaEvolverPowerCUDA method)
(evolvers.ArdellSellaEvolverPowerMethod method)
(evolvers.ArdellSellaEvolverPowerMulticore method)
error_check() (evolvers.eigensystem_CUDA_implementation method)
evolve_code_unless_frozen() (evolvers.ArdellSellaEvolverAbstractBase method)
evolve_one_step() (evolvers.ArdellSellaEvolverAbstractBase method)
evolve_until_frozen() (evolvers.ArdellSellaEvolverAbstractBase method)
evolvers (module)

G

genetic_codes (module)
GeneticCodeMutation (class in genetic_codes)
get_base_mutation_matrix() (codon_spaces.WordCodonSpace method)
get_derivative_matrix() (codon_spaces.RingCodonSpace method)
(codon_spaces.WordCodonSpace method)
get_effective_code_matrix() (genetic_codes.GeneticCodeMutation method)
get_eigenmatrix() (evolvers.eigensystem_CUDA_implementation method)
get_eigenvalue() (evolvers.ArdellSellaEvolverAbstractBase method)
(evolvers.eigensystem_CUDA_implementation method)
get_eigenvalues() (evolvers.eigensystem_CUDA_implementation method)
get_fitness_matrix() (site_type_spaces.MirroringSiteTypeSpace method)
get_mutation_eigensystem() (codon_spaces.RingCodonSpace method)
(codon_spaces.WordCodonSpace method)
get_mutation_selection_matrix() (evolvers.ArdellSellaEvolverAbstractBase method)
get_selection_matrix() (evolvers.ArdellSellaEvolverAbstractBase method)
get_site_type_weights() (site_type_spaces.MirroringSiteTypeSpace method)
growth_rate() (evolvers.ArdellSellaEvolverAbstractBase method)
growth_rate_from_lambda() (evolvers.ArdellSellaEvolverAbstractBase method)

I

in_queue (evolvers.ArdellSellaEvolverPowerMulticore attribute)
initial_equilibrate_messages() (evolvers.ArdellSellaEvolverAbstractBase method)
InitiallyAmbiguousGeneticCode (class in genetic_codes)

M

messages() (evolvers.ArdellSellaEvolverAbstractBase method)
MirroringSiteTypeSpace (class in site_type_spaces)
misreading (module)

O

Observables (class in observables)
observables (module)
out_queue (evolvers.ArdellSellaEvolverPowerMulticore attribute)

P

PositionalMisreading (class in misreading)
post_process_perturbative_solution() (codon_spaces.RingCodonSpace method)
(codon_spaces.WordCodonSpace method)
print_initial_observables() (evolvers.ArdellSellaEvolverAbstractBase method)
print_observables() (evolvers.ArdellSellaEvolverAbstractBase method)
print_observables_header() (evolvers.ArdellSellaEvolverAbstractBase method)

R

RegionAminoAcidSpace (class in amino_acid_spaces)
RingAminoAcidSpace (class in amino_acid_spaces)
RingCodonSpace (class in codon_spaces)
RingMisreading (class in misreading)
run() (evolvers.ArdellSellaEvolverNumpyProcessChild method)
(evolvers.ArdellSellaEvolverPowerMethodProcessChild method)

S

site_type_spaces (module)

U

UserInitializedGeneticCode (class in genetic_codes)

W

WordCodonSpace (class in codon_spaces)