ecoli.processes.polypeptide_initiation
Polypeptide Initiation
This process models the complementation of 30S and 50S ribosomal subunits into 70S ribosomes on mRNA transcripts. This process is in many ways analogous to the TranscriptInitiation process - the number of initiation events per transcript is determined in a probabilistic manner and dependent on the number of free ribosomal subunits, each mRNA transcript’s translation efficiency, and the counts of each type of transcript.
- class ecoli.processes.polypeptide_initiation.PolypeptideInitiation(parameters=None)[source]
Bases:
PartitionedProcess
Polypeptide Initiation PartitionedProcess
- calculate_activation_prob(fracActiveRibosome, proteinLengths, ribosomeElongationRates, proteinInitProb, timeStepSec)[source]
Calculates the expected ribosome termination rate based on the ribosome elongation rate
- Parameters:
allTranslationTimes – Vector of times required to translate each protein
allTranslationTimestepCounts – Vector of numbers of timesteps required to translate each protein
averageTranslationTimeStepCounts – Average number of timesteps required to translate a protein, weighted by initiation probabilities
expectedTerminationRate – Average number of terminations in one timestep for one protein
-
defaults: Dict[str, Any]
{ 'active_ribosome_footprint_size': 24 [nucleotide], 'active_ribosome_fraction': {}, 'cistron_start_end_pos_in_tu': {}, 'cistron_to_monomer_mapping': {}, 'cistron_tu_mapping_matrix': {}, 'elongation_rates': {}, 'emit_unique': False, 'make_elongation_rates': <function PolypeptideInitiation.<lambda> at 0x7fc270e576a0>, 'monomer_ids': [], 'monomer_index_to_cistron_index': {}, 'monomer_index_to_tu_indexes': {}, 'protein_lengths': [], 'ribosome30S': 'ribosome30S', 'ribosome50S': 'ribosome50S', 'rna_id_to_cistron_indexes': {}, 'seed': 0, 'time_step': 1, 'translation_efficiencies': [], 'tu_ids': [], 'variable_elongation': False}
- name = 'ecoli-polypeptide-initiation'
-
topology
{ 'RNA': ('unique', 'RNA'), 'active_ribosome': ('unique', 'active_ribosome'), 'bulk': ('bulk',), 'environment': ('environment',), 'listeners': ('listeners',), 'timestep': ('timestep',)}