vivarium.states.chromosome module

class vivarium.states.chromosome.Chromosome(config)

Bases: vivarium.library.datum.Datum

advance_replisomes(distances)

distances is a dictionary of domain ids to tuples of how far each strand advances of the form (lead, lag)

apply_thresholds(thresholds)

bind_rnap(promoter_index, domain)

combine_state(a, b)

copy_number(position, domain_key=None)

defaults = {'domains': {0: {'children': [], 'id': 0, 'lag': 0, 'lead': 0}}, 'genes': {}, 'promoter_order': [], 'promoters': {}, 'rnap_id': 0, 'rnaps': {}, 'root_domain': 0, 'sequence': ''}

divide_chromosome(domain, division=None)

initiate_replication()

next_polymerize(elongation_limit=inf, monomer_limits={})

operons()

polymerize(elongation, monomer_limits)

position_domains(domain_index, position)

product_sequences()

promoter_copy_numbers()

promoter_domains()

promoter_rnaps()

schema = {'domains': <class 'vivarium.states.chromosome.Domain'>, 'promoters': <class 'vivarium.states.chromosome.Promoter'>, 'rnaps': <class 'vivarium.states.chromosome.Rnap'>}

sequences()

terminate_replication()

terminator_distance()

class vivarium.states.chromosome.Domain(config)

Bases: vivarium.library.datum.Datum

contains(position)

defaults = {'children': [], 'id': 0, 'lag': 0, 'lead': 0}

descendants(tree)

random_child()

surpassed(position, lead, lag)

class vivarium.states.chromosome.Operon(config)

Bases: vivarium.library.datum.Datum

defaults = {'direction': 1, 'genes': [], 'id': '', 'length': 0, 'position': 0}

class vivarium.states.chromosome.Promoter(config)

Bases: vivarium.library.polymerize.Template

Promoters are the main unit of expression. They define a direction of polymerization, contain binding sites for transcription factors, and declare some number of terminators, each of which has a strength and corresponds to a particular operon if chosen.

operons(genes)

schema = {'sites': <class 'vivarium.library.polymerize.BindingSite'>, 'terminators': <class 'vivarium.states.chromosome.RnapTerminator'>}

class vivarium.states.chromosome.Rnap(config)

Bases: vivarium.library.polymerize.Polymerase

defaults = {'domain': 0, 'id': 0, 'position': 0, 'state': None, 'template': None, 'template_index': 0, 'terminator': 0}

class vivarium.states.chromosome.RnapTerminator(config)

Bases: vivarium.library.polymerize.Terminator

operon_from(genes, promoter)

vivarium.states.chromosome.frequencies(l)

Return number of times each item appears in the list.

vivarium.states.chromosome.rna_bases(sequence)

vivarium.states.chromosome.sequence_monomers(sequence, begin, end)

vivarium.states.chromosome.test_chromosome()

vivarium.states.chromosome.traverse(tree, key, f, combine)

Traverse the given tree starting using the key node as the root and calling f on each leaf, combining values with combine at each subsequent level to create new leaves for f.