Index

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__contains__() (cocomico.base.ExchangeNM method) __eq__() (cocomico.base.ExchangeNM method) (sampling.name.Name method) __hash__() (sampling.name.Name method) __iter__() (cocomico.base.ExchangeNM method) __str__() (cocomico.answer.Answer method) (cocomico.base.MetaboliteSet method) (cocomico.base.Seeds method) (cocomico.community.Community method) (cocomico.model.Model method) (cocomico.sbmlreader.SbmlReader method) (sampling.name.Name method)

__version__ (in module cocomico)

A

activated() (cocomico.community.Community method)

Answer (class in cocomico.answer) answers() (cocomico.community.Community method)

B

biomolecule (cocomico.base.Metabolite property) (cocomico.community.Community property)

biomolecules (cocomico.base.MetaboliteSet property)

C

clear_answers() (cocomico.community.Community method) cocomico module cocomico.answer module cocomico.base module cocomico.community module cocomico.constants module cocomico.cwl module cocomico.facts module

cocomico.model module cocomico.report module cocomico.sbmlreader module cocomico.score module Community (class in cocomico.community) community() (in module cocomico.cwl) competition() (in module cocomico.score) consumed_seeds() (cocomico.community.Community method) cooperation() (in module cocomico.score)

D

decode_relations() (cocomico.sbmlreader.SbmlReader static method)

delta() (in module cocomico.score) do_sample() (in module sampling.cwl)

E

entrypoint() (in module cocomico.cwl) ess() (in module sampling) example() (in module cocomico.cwl)

Exchange (class in cocomico.base) exchange() (cocomico.community.Community method) ExchangeNM (class in cocomico.base) expand_source() (in module sampling.cwl)

F

find_specs() (in module cocomico.cwl) from_community() (in module cocomico.report) from_file() (cocomico.base.Seeds class method) (cocomico.sbmlreader.SbmlReader method)

from_specification() (cocomico.community.Community class method) from_string() (cocomico.base.Metabolite class method) (sampling.name.Name class method)

G

gen_added_value() (in module sampling.generate) gen_sample() (in module sampling.generate)

get_coms_from_eco() (in module sampling.cwl) get_eco() (in module sampling.cwl)

K

knowledge_base (cocomico.community.Community property)

L

load_state() (in module sampling)

lookup_serializer() (in module cocomico.report)

M

main() (in module sampling.cwl) Metabolite (class in cocomico.base) MetaboliteSet (class in cocomico.base) mk_id() (sampling.name.Name static method) Model (class in cocomico.model) module cocomico cocomico.answer cocomico.base cocomico.community cocomico.constants cocomico.cwl cocomico.facts cocomico.model cocomico.report cocomico.sbmlreader cocomico.score sampling sampling.cwl sampling.generate sampling.name sampling.types sampling.write

monopsonist() (cocomico.community.Community method)

N

Name (class in sampling.name)

network_facts() (in module cocomico.facts) normalize() (cocomico.sbmlreader.SbmlReader method)

P

polyopsonist() (cocomico.community.Community method) process_communities() (in module cocomico.cwl)

produced_seeds() (cocomico.community.Community method) products (cocomico.community.Community property) provenance (cocomico.base.Metabolite property)

R

reactants (cocomico.community.Community property) Reaction (class in cocomico.base) reactions (cocomico.community.Community property) (cocomico.model.Model property) read_sbml_file() (cocomico.sbmlreader.SbmlReader static method)

read_tabular() (in module cocomico.report) remove_seed_reactions() (cocomico.community.Community method) (cocomico.model.Model method) retrieve_seeds() (in module cocomico.cwl) rho() (in module cocomico.score)

S

sample() (in module sampling.cwl) sample_chain() (in module sampling.cwl) sampling module sampling.cwl module sampling.generate module sampling.name module sampling.types module sampling.write module save_state() (in module sampling) SbmlReader (class in cocomico.sbmlreader) scope() (cocomico.community.Community method)

seed_facts() (in module cocomico.facts) Seeds (class in cocomico.base) seeds() (cocomico.community.Community method) select() (cocomico.base.MetaboliteSet method) serialize() (in module cocomico.report) serialize_community() (in module cocomico.report) serialize_dict() (in module cocomico.report) serialize_exchange() (in module cocomico.report) serialize_iterable() (in module cocomico.report) serialize_metaboliteset() (in module cocomico.report) serialize_model() (in module cocomico.report) serialize_number() (in module cocomico.report) serialize_results() (in module cocomico.report) serialize_seeds() (in module cocomico.report) serialize_str() (in module cocomico.report) serializer() (in module cocomico.report) specification() (in module cocomico.cwl)

T

taxa (cocomico.base.MetaboliteSet property) (cocomico.community.Community property) to_biomolecule() (in module cocomico.facts)

to_exchange() (in module cocomico.facts) to_json() (in module cocomico.report) to_metabolite() (in module cocomico.facts) to_reaction() (in module cocomico.facts)

W

write_json() (in module cocomico.report)

write_specs() (in module sampling.write) write_tabular() (in module cocomico.report)