PyCoMo
Basics
Installation
PyCoMo Basics
Tutorials
PyCoMo Maximum Growth-Rate
PyCoMo Loopless FVA
API
PyCoMo Classes
Helper Modules
PyCoMo
Index
Index
A
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C
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D
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E
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F
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G
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H
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I
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L
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M
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P
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R
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S
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T
A
add_boundary_metabolites_to_exchange_compartment() (pycomo.pycomo_models.SingleOrganismModel method)
add_exchange_compartment() (pycomo.pycomo_models.SingleOrganismModel method)
add_exchange_reactions_to_compartment() (pycomo.pycomo_models.SingleOrganismModel method)
add_exchange_reactions_to_metabolites() (pycomo.pycomo_models.SingleOrganismModel method)
add_sink_reactions_to_metabolites() (pycomo.pycomo_models.CommunityModel method)
apply_fixed_abundance() (pycomo.pycomo_models.CommunityModel method)
apply_fixed_growth_rate() (pycomo.pycomo_models.CommunityModel method)
apply_medium() (pycomo.pycomo_models.CommunityModel method)
C
change_reaction_bounds() (pycomo.pycomo_models.CommunityModel method)
check_annotation_overlap_of_metabolites_with_identical_id() (in module pycomo.helper.utils)
check_args() (in module pycomo.helper.cli)
check_mass_balance_fomula_safe() (in module pycomo.helper.utils)
check_mass_balance_of_metabolites_with_identical_id() (in module pycomo.helper.utils)
check_metabolite_equal_mass() (in module pycomo.helper.utils)
close_to_zero() (in module pycomo.helper.utils)
CommunityModel (class in pycomo.pycomo_models)
configure_logger() (in module pycomo.helper.logger)
convert_constraints_to_metabolites() (pycomo.pycomo_models.CommunityModel method)
convert_exchange_to_transfer_reaction() (pycomo.pycomo_models.SingleOrganismModel method)
convert_to_fixed_abundance() (pycomo.pycomo_models.CommunityModel method)
convert_to_fixed_growth_rate() (pycomo.pycomo_models.CommunityModel method)
convert_to_model_without_fraction_metabolites() (pycomo.pycomo_models.CommunityModel method)
create_abundance_parameter() (in module pycomo.helper.utils)
create_arg_parser() (in module pycomo.helper.cli)
create_fraction_reaction() (pycomo.pycomo_models.CommunityModel method)
create_parameter_in_sbml_model() (in module pycomo.helper.utils)
cross_feeding_metabolites_from_fba() (pycomo.pycomo_models.CommunityModel method)
cross_feeding_metabolites_from_fva() (pycomo.pycomo_models.CommunityModel method)
D
doall() (in module pycomo.pycomo_models)
E
ensure_compartment_suffix() (pycomo.pycomo_models.SingleOrganismModel method)
equal_abundance() (pycomo.pycomo_models.CommunityModel method)
F
f_metabolites (pycomo.pycomo_models.CommunityModel property)
f_reactions (pycomo.pycomo_models.CommunityModel property)
fba_solution_flux_vector() (pycomo.pycomo_models.CommunityModel method)
feasible_composition_range() (pycomo.pycomo_models.CommunityModel method)
filter() (pycomo.helper.logger.RegexFilter method)
find_incoherent_bounds() (in module pycomo.helper.utils)
find_loops_in_model() (in module pycomo.helper.utils)
find_matching_annotations() (in module pycomo.helper.utils)
find_metabolites_without_exchange_rxn() (pycomo.pycomo_models.SingleOrganismModel method)
force_add_exchange() (pycomo.pycomo_models.SingleOrganismModel method)
format_exchg_rxns() (pycomo.pycomo_models.CommunityModel method)
fva() (in module pycomo.helper.multiprocess)
fva_solution_flux_vector() (pycomo.pycomo_models.CommunityModel method)
G
generate_community_model() (pycomo.pycomo_models.CommunityModel method)
generate_equal_abundance_dict() (pycomo.pycomo_models.CommunityModel method)
generate_member_name_conversion_dict() (pycomo.pycomo_models.CommunityModel method)
get_abundance_parameters_from_sbml_doc() (in module pycomo.helper.utils)
get_abundance_parameters_from_sbml_file() (in module pycomo.helper.utils)
get_exchange_metabolites() (in module pycomo.helper.utils)
get_f_reactions() (in module pycomo.helper.utils)
get_flags_and_muc_from_sbml_file() (in module pycomo.helper.utils)
get_logger_conf() (in module pycomo.helper.logger)
get_loops() (pycomo.pycomo_models.CommunityModel method)
get_member_name_of_compartment() (pycomo.pycomo_models.CommunityModel method)
get_member_name_of_metabolite() (pycomo.pycomo_models.CommunityModel method)
get_member_name_of_reaction() (pycomo.pycomo_models.CommunityModel method)
get_member_names() (pycomo.pycomo_models.CommunityModel method)
get_metabolite_id_without_compartment() (in module pycomo.helper.utils)
get_model_biomass_compound() (in module pycomo.helper.utils)
get_name_conversion() (pycomo.pycomo_models.SingleOrganismModel method)
get_unbalanced_reactions() (pycomo.pycomo_models.CommunityModel method)
H
handle_boundary_biomass_reaction() (pycomo.pycomo_models.SingleOrganismModel method)
I
is_mass_balanced() (pycomo.pycomo_models.CommunityModel method)
L
list_contains_unique_strings() (in module pycomo.helper.utils)
list_of_strings_is_self_contained() (in module pycomo.helper.utils)
list_without_element() (in module pycomo.helper.utils)
load() (pycomo.pycomo_models.CommunityModel class method)
load_medium_from_file() (pycomo.pycomo_models.CommunityModel method)
load_named_model() (in module pycomo.helper.utils)
load_named_models_from_dir() (in module pycomo.helper.utils)
loopless_fva() (in module pycomo.helper.multiprocess)
M
main() (in module pycomo.pycomo_models)
make_model_ids_sbml_conform() (in module pycomo.helper.utils)
make_string_sbml_id_compatible() (in module pycomo.helper.utils)
max_growth_rate() (pycomo.pycomo_models.CommunityModel method)
medium (pycomo.pycomo_models.CommunityModel property)
merge_fraction_reactions() (pycomo.pycomo_models.CommunityModel method)
model (pycomo.pycomo_models.CommunityModel property)
module
pycomo.helper.cli
pycomo.helper.logger
pycomo.helper.multiprocess
pycomo.helper.spawnprocesspool
pycomo.helper.utils
pycomo.pycomo_models
P
potential_metabolite_exchanges() (pycomo.pycomo_models.CommunityModel method)
prefix_gene_names() (pycomo.pycomo_models.SingleOrganismModel method)
prefix_metabolite_names() (pycomo.pycomo_models.SingleOrganismModel method)
prefix_reaction_names() (pycomo.pycomo_models.SingleOrganismModel method)
prepare_for_merging() (pycomo.pycomo_models.SingleOrganismModel method)
pycomo.helper.cli
module
pycomo.helper.logger
module
pycomo.helper.multiprocess
module
pycomo.helper.spawnprocesspool
module
pycomo.helper.utils
module
pycomo.pycomo_models
module
R
read_abundance_from_file() (in module pycomo.helper.utils)
read_medium_from_file() (in module pycomo.helper.utils)
read_sbml_model_from_file() (in module pycomo.helper.utils)
RegexFilter (class in pycomo.helper.logger)
relax_reaction_constraints_for_zero_flux() (in module pycomo.helper.utils)
remove_ascii_escape_from_string() (in module pycomo.helper.utils)
remove_biomass_exchange_rxn() (pycomo.pycomo_models.SingleOrganismModel method)
remove_dunder_from_ascii_escape() (in module pycomo.helper.utils)
rename_comp_in_met_id() (pycomo.pycomo_models.SingleOrganismModel method)
rename_comp_in_rxn_id() (pycomo.pycomo_models.SingleOrganismModel method)
rename_compartment() (pycomo.pycomo_models.SingleOrganismModel method)
replace_metabolite_stoichiometry() (in module pycomo.helper.utils)
report() (pycomo.pycomo_models.CommunityModel method)
run_fba() (pycomo.pycomo_models.CommunityModel method)
run_fva() (pycomo.pycomo_models.CommunityModel method)
S
save() (pycomo.pycomo_models.CommunityModel method)
set_name_via_annotation() (pycomo.pycomo_models.SingleOrganismModel method)
SingleOrganismModel (class in pycomo.pycomo_models)
SpawnProcessPool (class in pycomo.helper.spawnprocesspool)
summary() (pycomo.pycomo_models.CommunityModel method)
T
transfer_reactions (pycomo.pycomo_models.CommunityModel property)
transport_reactions (pycomo.pycomo_models.CommunityModel property)