Index

A

abundances (micom.Community attribute) (micom.community.Community attribute) add_dualized_optcom() (in module micom.optcom) add_linear_obj() (in module micom.media)

add_mip_obj() (in module micom.media) add_moma_optcom() (in module micom.optcom) add_pfba_objective() (in module micom.solution) add_var_from_expression() (in module micom.util) adjust_solver_config() (in module micom.util)

C

check_modification() (in module micom.util) Community (class in micom) (class in micom.community) CommunitySolution (class in micom.solution)

cooperative_tradeoff() (in module micom.problems) (micom.Community method) (micom.community.Community method) crossover() (in module micom.solution)

D

default_excludes (in module micom.media)

download_model() (in module micom.util)

E

elasticities_by_abundance() (in module micom.elasticity) elasticities_by_medium() (in module micom.elasticity) euclidean() (in module micom.algorithms)

exchange_elasticities() (in module micom.elasticity) exchanges (micom.Community attribute) (micom.community.Community attribute)

F

fast_dual() (in module micom.duality) file_logger() (in module micom.logger)

fluxes (micom.solution.CommunitySolution attribute) fluxes_from_primals() (in module micom.util)

G

good (in module micom.solution)

growth_rate (micom.solution.CommunitySolution attribute)

J

jaccard() (in module micom.algorithms)

join_models() (in module micom.util)

K

knockout_species() (in module micom.problems) (micom.Community method) (micom.community.Community method)

L

load_model() (in module micom.util)

load_pickle() (in module micom) (in module micom.community)

M

members (micom.solution.CommunitySolution attribute) metabolic_dist() (in module micom.algorithms) micom (module) micom.algorithms (module) micom.community (module) micom.data (module) micom.duality (module) micom.elasticity (module) micom.logger (module)

micom.media (module) micom.optcom (module) micom.problems (module) micom.solution (module) micom.util (module) micom.workflows (module) minimal_medium() (in module micom.media) model (in module micom.duality) modification (micom.Community attribute) (micom.community.Community attribute)

O

objective_value (micom.solution.CommunitySolution attribute) optcom() (in module micom.optcom) (micom.Community method) (micom.community.Community method) optimize() (micom.Community method) (micom.community.Community method)

optimize_all() (micom.Community method) (micom.community.Community method) optimize_single() (micom.Community method) (micom.community.Community method) optimize_with_fraction() (in module micom.solution) optimize_with_retry() (in module micom.solution)

P

prefix (in module micom.duality)

R

reaction_matrix() (in module micom.algorithms) reduced_costs (micom.solution.CommunitySolution attribute)

regularize_l2_norm() (in module micom.problems) reset_min_community_growth() (in module micom.util) reset_solver() (in module micom.solution)

S

serialize_models() (in module micom.util) set_abundance() (micom.Community method) (micom.community.Community method)

shadow_prices (micom.solution.CommunitySolution attribute) solve() (in module micom.solution) status (micom.solution.CommunitySolution attribute) strategy (micom.solution.CommunitySolution attribute)

T

taxonomy (micom.Community attribute) (micom.community.Community attribute)

test_taxonomy() (in module micom.data) to_pickle() (micom.Community method) (micom.community.Community method)

W

workflow() (in module micom.workflows)