Index

_

_x_RNG (simble.settings.Settings attribute)

A

add_child() (simble.tree.Node method) Affinity all_multipliers (simble.target.TargetAminoAcid attribute) amino_acid_seq (simble.chain.Chain attribute) (simble.target.TargetAminoAcid attribute) antigen (simble.tree.Node attribute) as_AIRR() (simble.cell.Cell method) (simble.cell.SingleChainCell method) (simble.chain.Chain method) (simble.chain.EmptyChain method)

as_enum() (in module simble.location) as_fasta() (simble.cell.Cell method) (simble.cell.SingleChainCell method) as_fasta_helper() (simble.cell.Cell method)

B

B Cell

B cell receptor BCR

C

calculate_affinity() (simble.cell.Cell method) (simble.cell.SingleChainCell method) (simble.chain.Chain method) (simble.chain.EmptyChain method) cdr3_aa_length (simble.helper.StartChain attribute) CDR3_length (simble.chain.Chain attribute) CDR_DIST (simble.settings.Settings attribute) cdr_multipliers (simble.target.TargetAminoAcid attribute) CDR_POSITIONS (simble.target.TargetAminoAcid attribute) cdr_similarity (simble.chain.Chain attribute) CDR_VAR (simble.settings.Settings attribute) Cell (class in simble.cell) cell (simble.tree.Node attribute) cell_type (simble.cell.Cell attribute) CellType (class in simble.cell)

Chain (class in simble.chain) chain (simble.helper.StartConstants attribute) children (simble.tree.Node attribute) choose_replacement_nucleotide() (simble.target.TargetAminoAcid method) Clone clone_id (simble.tree.Node attribute) codon_to_amino_acid() (in module simble.helper) constants (simble.helper.StartConstants attribute) copy() (simble.chain.Chain method) (simble.chain.EmptyChain method) (simble.tree.Node method) create_mutability_map() (simble.chain.Chain method) created_at (simble.cell.Cell attribute) current_generation (simble.location.Location attribute)

D

DEFAULT (simble.cell.CellType attribute) DEV (simble.settings.Settings attribute) differentiate() (simble.cell.Cell method)

Differentiation do_differentiation() (in module simble.simulation) do_simulation() (in module simble.simble)

E

emit() (simble.simble.TqdmLoggingHandler method) EmptyChain (class in simble.chain) Encodable (class in simble.settings)

encode() (simble.location.LocationName method) (simble.settings.Encodable method) END_TIME (simble.settings.Settings property)

F

FASTA (simble.settings.Settings attribute) finish_migration() (simble.location.Location method) FWR_DIST (simble.settings.Settings attribute)

fwr_multipliers (simble.target.TargetAminoAcid attribute) fwr_similarity (simble.chain.Chain attribute) FWR_VAR (simble.settings.Settings attribute)

G

gapped_nucleotide_seq (simble.target.TargetAminoAcid attribute) gapped_seq (simble.helper.StartChain attribute) GC (simble.location.LocationName attribute) GC B Cell generation (simble.tree.Node attribute) GENERATIONS_PER_DAY (simble.settings.Settings attribute) Germinal Center Germinal Center B Cell get_data() (in module simble.helper) get_functionality() (simble.chain.Chain method)

get_gapped_sequence() (simble.chain.Chain method) get_mutability_of_kmer() (in module simble.helper) get_observed_mutations() (simble.chain.Chain method) (simble.chain.EmptyChain method) get_parser() (in module simble.parsing) get_population_data() (in module simble.simulation) get_random_start_pair() (in module simble.helper) get_substitution_probability() (in module simble.helper) get_target_from_pair() (simble.chain.Chain method) (simble.chain.EmptyChain method) (simble.chain.HeavyChain method) (simble.chain.LightChain method)

H

heavy (simble.target.TargetAminoPair attribute) Heavy Chain heavy_chain (simble.cell.Cell attribute)

heavy_mutations (simble.tree.Node attribute) HEAVY_SHM_PER_SITE (simble.settings.Settings attribute) HeavyChain (class in simble.chain)

I

immigrating_population (simble.location.Location attribute) is_alive (simble.cell.Cell attribute) is_functional (simble.chain.Chain property) IS_HEAVY (simble.chain.Chain property) (simble.chain.EmptyChain property) (simble.chain.HeavyChain attribute) (simble.chain.HeavyChain property) (simble.chain.LightChain attribute) (simble.chain.LightChain property)

J

junction (simble.chain.Chain attribute) (simble.chain.Chain property) (simble.helper.StartChain attribute)

junction_aa (simble.chain.Chain property)

K

KEEP_FULL_TREE (simble.settings.Settings attribute)

kill_cell() (simble.cell.Cell method)

L

last_migration (simble.tree.Node attribute) light (simble.target.TargetAminoPair attribute) Light Chain light_chain (simble.cell.Cell attribute) light_mutations (simble.tree.Node attribute) LIGHT_SHM_PER_SITE (simble.settings.Settings attribute)

LightChain (class in simble.chain) Location (class in simble.location) location (simble.cell.Cell attribute) LocationName (class in simble.location) LOCATIONS (simble.settings.Settings attribute) LocationSettings (class in simble.settings)

M

main() (in module simble.simble) make_all_plots() (in module simble.helper) make_bar_plot() (in module simble.helper) make_plot() (in module simble.helper) max_affinity (simble.target.TargetAminoAcid property) (simble.target.TargetAminoPair property) max_population (simble.settings.LocationSettings attribute) MBC (simble.cell.CellType attribute) Memory B Cell MEMORY_SAVE (simble.settings.Settings attribute) Migration migration_rate (simble.settings.LocationSettings attribute) module simble.cell simble.chain simble.helper simble.location simble.parsing simble.settings simble.simble simble.simulation simble.target simble.tree

MULTIPLIER (simble.settings.Settings attribute) mutability_map (simble.chain.Chain attribute) mutate() (simble.chain.Chain method) (simble.chain.EmptyChain method) (simble.target.TargetAminoAcid method) (simble.target.TargetAminoPair method) mutate_cell() (simble.cell.Cell method) (simble.cell.SingleChainCell method) mutate_probability (simble.chain.Chain property) mutation_locations (simble.target.TargetAminoAcid attribute) mutation_rate (simble.settings.LocationSettings attribute)

N

name (simble.location.Location attribute) (simble.settings.LocationSettings attribute) Neutral Simulation Node (class in simble.tree)

non_gc_population_control() (in module simble.simulation) nucleotide_gaps (simble.chain.Chain attribute) nucleotide_seq (simble.chain.Chain attribute) (simble.helper.StartChain attribute) number_of_children (simble.location.Location attribute)

O

occupancy (simble.tree.Node property)

occupancy_other (simble.tree.Node property) OTHER (simble.location.LocationName attribute)

P

parent (simble.tree.Node attribute) PC (simble.cell.CellType attribute)

Plasma Cell process_results() (in module simble.simble) prune_subtree() (simble.tree.Node method) prune_up_tree() (simble.tree.Node method)

Q

QUIET (simble.settings.Settings attribute)

R

read_from_json() (in module simble.parsing) read_sf5_table() (in module simble.helper) remake_self() (simble.cell.Cell method)

remove_gaps() (in module simble.helper) RESULTS_DIR (simble.settings.Settings attribute) RNG (simble.settings.Settings property) run_simulation() (in module simble.simulation)

S

sample_size (simble.settings.LocationSettings attribute) sample_times (simble.settings.LocationSettings attribute) sampled_time (simble.tree.Node attribute) Selection SELECTION (simble.settings.Settings attribute) (simble.settings.Settings property) set_logger() (in module simble.simble) Settings (class in simble.settings) settings (simble.location.Location attribute) SHM shm_per_site (simble.chain.Chain property) (simble.chain.EmptyChain property) (simble.chain.HeavyChain attribute) (simble.chain.HeavyChain property) (simble.chain.LightChain attribute) (simble.chain.LightChain property) simble.cell module simble.chain module simble.helper module

simble.location module simble.parsing module simble.settings module simble.simble module simble.simulation module simble.target module simble.tree module similarity (simble.chain.Chain attribute) simplify_tree() (in module simble.tree) simulate() (in module simble.simulation) SingleChainCell (class in simble.cell) snake_case_to_normal() (in module simble.helper) Somatic Hypermutation StartChain (class in simble.helper) StartConstants (class in simble.helper)

T

Target sequence TARGET_MUTATIONS_HEAVY (simble.settings.Settings attribute) TARGET_MUTATIONS_LIGHT (simble.settings.Settings attribute) TargetAminoAcid (class in simble.target)

TargetAminoPair (class in simble.target) time_since_last_split (simble.tree.Node property) TIME_SWITCH (simble.settings.Settings attribute) TqdmLoggingHandler (class in simble.simble) translate_to_amino_acid() (in module simble.helper)

U

UNIFORM (simble.settings.Settings attribute) (simble.settings.Settings property) Uniform Neutral Simulation

update_cell() (simble.location.Location method) update_from_dict() (simble.settings.Settings method) update_mutability_map() (simble.chain.Chain method)

V

validate_and_process_args() (in module simble.parsing) validate_json() (in module simble.parsing)

validate_location() (in module simble.parsing) validate_samples() (in module simble.parsing) VERBOSE (simble.settings.Settings attribute)

W

write_newick() (simble.tree.Node method)

write_newick_node() (simble.tree.Node method)