ecoli.library.sim_data
- class ecoli.library.sim_data.LoadSimData(sim_data_path='/home/runner/work/vEcoli/vEcoli/reconstruction/sim_data/kb/simData.cPickle', seed=0, total_time=10, fixed_media=None, media_timeline=((0, 'minimal'),), condition='basal', trna_charging=True, ppgpp_regulation=True, mar_regulon=False, process_configs=None, amp_lysis=False, mass_distribution=True, superhelical_density=False, recycle_stalled_elongation=False, mechanistic_replisome=False, trna_attenuation=True, variable_elongation_transcription=True, variable_elongation_translation=False, mechanistic_translation_supply=True, mechanistic_aa_transport=True, translation_supply=True, aa_supply_in_charging=True, disable_ppgpp_elongation_inhibition=False, adjust_timestep_for_charging=False, time_step_safety_fraction=1.3, update_time_step_freq=5, max_time_step=1, emit_unique=False, **kwargs)[source]
Bases:
object
Loads simulation data generated by the ParCa (
fitSimData_1()
, runscript located atrunscripts.parca
) and extracts parameters for each process. Typically instantiated byEcoli
with keyword arguments given by the config loaded byEcoliSim
.- Parameters:
sim_data_path (str) – Path to simulation data pickle file
seed (int) – Used to deterministically seed all random number generators. Simulations with the same seed will yield the same output.
total_time (int) – Time to simulate (seconds)
media_timeline (tuple[tuple[int, str]]) – Iterable of tuples where the first element of each tuple is the time to start using a certain media and the second element is a string corresponding to one of the media options in
self.sim_data.external_state.saved_media
trna_charging (bool) – Use steady-state charging model (
SteadyStateElongationModel
) inPolypeptideElongation
ppgpp_regulation (bool) – Enable growth rate control using ppGpp in polypeptide elongation and transcript initiation
mar_regulon (bool) – Enable tetracycline-related transcriptional regulation of antibiotic resistance genes by the mar operon
process_configs (dict[str, Any] | None) – Mapping of process names to config dictionaries, currently only used to configure
RnaInterference
amp_lysis (bool) – Enable ampicillin-induced lysis, adds ampicillin and hydrolyzed ampicillin to bulk molecule store
mass_distribution (bool) – If
config['division_variable']
is set to('listeners', 'mass', 'dry_mass')
andconfig['division_threshold']
is set to'mass_distribution'
, enabling this multiplies the division threshold by a Gaussian noise factor. If the simulation is configured to generate an initial state from pickled simulation data (see option 3 ininitial_state()
), enabling this adds Gaussian noise to the generated statesuperhelical_density (bool) – Enables superhelical density calculations on
('unique', 'chromosomal_segment)'
molecules inChromosomeStructure
mechanistic_replisome (bool) – Ensures that there are adequate replisome subunits to initiate each round of chromosome replication in
ChromosomeReplication
recycle_stalled_elongation (bool) – Free up RNAPs and nucleotides for stalled transcripts in
TranscriptElongation
trna_attenuation (bool) – Implements attenuation in
TranscriptInitiation
andTranscriptElongation
variable_elongation_transcription (bool) – Allow different elongation rate for different transcripts (currently increases rates for rRNA, see
make_elongation_rates()
). Usually set this consistently for ParCa and simulation.TranscriptInitiation
Usually set this consistently for ParCa and simulation.variable_elongation_translation (bool) – Allow different polypeptides to have different translation rates (currently increases rates for ribosomal proteins, see
make_elongation_rates()
). Usually set this consistently for ParCa and simulation.mechanistic_translation_supply (bool) – Calculate charged tRNA supply using starting amino acid concentration only based on mechanistic synthesis and supply in
PolypeptideElongation
whentrna_charging
isTrue
mechanistic_aa_transport (bool) – Constrain amino acid uptake based on external concentrations and exchange rates in
Metabolism
translation_supply (bool) – Use
TranslationSupplyElongationModel
inPolypeptideElongation
. Superseded bytrna_charging
aa_supply_in_charging (bool) – Calculate charged tRNA supply from each sub time step while solving the charging steady state in
PolypeptideElongation
whentrna_charging
isTrue
disable_ppgpp_elongation_inhibition (bool) – Turn off ppGpp-mediated inhibition in
PolypeptideElongation
whentrna_charging
isTrue
fixed_media (str | None)
condition (str)
adjust_timestep_for_charging (bool)
time_step_safety_fraction (float)
update_time_step_freq (int)
max_time_step (int)
emit_unique (bool)
- generate_initial_state()[source]
Calculate the initial conditions for a new cell without inherited state from a parent cell.
- get_monomer_counts_indices(names)[source]
Given a list of monomer names without location tags, this returns the indices of those monomers in the monomer_counts listener array. The “id” column of reconstruction/ecoli/flat/proteins.tsv contains nearly all supported monomer names.
- get_mrna_counts_indices(names)[source]
Given a list of mRNA names without location tags, this returns the indices of those mRNAs in the mRNA_counts listener array. The “id” column of reconstruction/ecoli/flat/rnas.tsv contains nearly all supported mRNA names.