API Reference
- Cell
- Chain
ChainChain.nucleotide_seqChain.amino_acid_seqChain.nucleotide_gapsChain.mutability_mapChain.CDR3_lengthChain.junctionChain.cdr_similarityChain.fwr_similarityChain.similarityChain.IS_HEAVYChain.as_AIRR()Chain.calculate_affinity()Chain.copy()Chain.create_mutability_map()Chain.get_functionality()Chain.get_gapped_sequence()Chain.get_observed_mutations()Chain.get_target_from_pair()Chain.is_functionalChain.junctionChain.junction_aaChain.mutate()Chain.mutate_probabilityChain.shm_per_siteChain.update_mutability_map()
EmptyChainHeavyChainLightChain
- Location
- Simble
- Simulation
- Target
TargetAminoAcidTargetAminoAcid.gapped_nucleotide_seqTargetAminoAcid.CDR_POSITIONSTargetAminoAcid.amino_acid_seqTargetAminoAcid.mutation_locationsTargetAminoAcid.all_multipliersTargetAminoAcid.cdr_multipliersTargetAminoAcid.fwr_multipliersTargetAminoAcid.choose_replacement_nucleotide()TargetAminoAcid.max_affinityTargetAminoAcid.mutate()
TargetAminoPair
- Tree
NodeNode.cellNode.parentNode.heavy_mutationsNode.light_mutationsNode.generationNode.clone_idNode.childrenNode.antigenNode.sampled_timeNode.last_migrationNode.add_child()Node.copy()Node.occupancyNode.occupancy_otherNode.prune_subtree()Node.prune_up_tree()Node.time_since_last_splitNode.write_newick()Node.write_newick_node()
simplify_tree()
- Settings
EncodableLocationSettingsSettingsSettings.LOCATIONSSettings.HEAVY_SHM_PER_SITESettings.LIGHT_SHM_PER_SITESettings.TARGET_MUTATIONS_HEAVYSettings.TARGET_MUTATIONS_LIGHTSettings.SELECTIONSettings.UNIFORMSettings.RESULTS_DIRSettings.MULTIPLIERSettings._x_RNGSettings.DEVSettings.FASTASettings.VERBOSESettings.CDR_DISTSettings.CDR_VARSettings.FWR_DISTSettings.FWR_VARSettings.TIME_SWITCHSettings.GENERATIONS_PER_DAYSettings.MEMORY_SAVESettings.KEEP_FULL_TREESettings.QUIETSettings.END_TIMESettings.RNGSettings.SELECTIONSettings.UNIFORMSettings.update_from_dict()
- Helper
- Parsing