ModelSEEDpy API

The detailed documentation of all user-operable classes and functions in the ModelSEEDpy library are provided.

core

The core sub-library permits parsing and manipulating metabolic models:

from modelseedpy.core import *

• biology
  • BiologPlate()
    • add_base()
    • get_media()
    • _repr_html_()
    • Accessible content
  • Biolog()
    • add_plate()
    • run_plates()
    • Accessible content
• fbahelper
  • FBAHelper()
    • add_autodrain_reactions_to_community_model()
    • add_drain_from_metabolite_id()
    • test_condition_list()
    • reaction_expansion_test()
    • set_reaction_bounds_from_direction()
    • set_objective_from_target_reaction()
    • compute_flux_values_from_variables()
    • modelseed_id_from_cobra_metabolite()
    • modelseed_id_from_cobra_reaction()
    • metabolite_mw()
    • elemental_mass()
    • get_modelseed_db_api()
    • is_ex() & is_biomass()
    • find_reaction()
    • msid_hash()
    • rxn_hash()
    • rxn_compartment()
    • add_atp_hydrolysis()
    • parse_id()
    • mediaName()
    • validate_dictionary()
• gapfillinghelper
  • GapfillingHelper
    • test_reaction_additions_againt_limits()
    • build_model_extended_for_gapfilling()
    • convert_modelreaction() & convert_modelcompound()
    • binary_check_gapfilling_solution()
    • create_minimal_reaction_objective()
    • convert_cobra_compound_to_kbcompound()
    • convert_cobra_reaction_to_kbreaction()
    • convert_objective_to_constraint()
    • compute_gapfilled_solution()
    • add_gapfilling_solution_to_kbase_model()
    • compute_reaction_scores()
    • replicate_model()
    • test_reaction_additions_againt_limits()
• msatpcorrection
  • MSATPCorrection
    • atp_correction()
• msbuilder
  • MSBuilder
    • get_gpr_from_template_reaction()
    • build_exchanges()
    • build_biomasses()
    • auto_select_template()
    • build_metabolic_reactions()
    • build_non_metabolite_reactions()
    • build()
    • build_full_template_model()
    • build_metabolic_model()
    • gapfill_model()
• mseditor
  • MSEditorAPI
    • remove_reactions()
    • edit_reaction()
    • edit_biomass_compound()
    • compute_molecular_weight()
    • add_custom_reaction()
    • add_ms_reaction()
    • copy_model_reactions()
    • copy_all_model_reactions()
  • MSEquation
    • build_from_palsson_string()
• msgenome
  • MSFeature
    • add_ontology_term()
  • MSGenome
    • from_fasta()
    • from_protein_sequences_hash()
    • alias_hash()
    • search_for_gene()
• msgapfill
  • MSGapfill
    • run_gapfilling()
    • integrate_gapfill_solution()
    • gapfill()
• msgenomeclassifier
  • load_classifier_from_folder()
    • MSGenomeClassifier()
  • extract_features_from_genome()
  • classify()
• msgrowthphenotypes
  • MSGrowthPhenotype
    • build_media()
    • simulate()
    • gapfill_model_for_phenotype()
  • MSGrowthPhenotypes
    • from_compound_hash()
    • from_kbase_object()
    • from_kbase_file()
    • from_ms_file()
    • add_phenotypes()
    • simulate_phenotypes()
• msmedia
  • MediaCompound()
  • MSMedia()
    • from_dict()
    • get_media_constraints()
    • merge()
• msmodel
  • get_reaction_constraints_from_direction()
  • get_direction_from_constraints()
  • get_gpr_string()
  • split_compartment_from_index()
  • get_cmp_token()
  • get_set()
    • MSModel()
  • template() & genome()
• msmodelutils
  • MSModelUtil()
    • find_met()
    • exchange_list()
    • exchange_hash()
    • add_missing_exchanges()
    • add_exchanges_for_metabolites()
    • convert_cobra_compound_to_kbcompound()
    • convert_cobra_reaction_to_kbreaction()
    • add_gapfilling_solution_to_kbase_model()
    • Accessible content
• mstemplate
  • TemplateReactionType
  • MSTemplateMetabolite
    • from_dict()
    • get_data()
    • __repr__() & __str__() & _repr_html_()
  • MSTemplateSpecies
    • to_metabolite()
    • compound(), name(), & formula()
    • name() & formula()
    • from_dict()
    • get_data()
  • MSTemplateReaction
    • gene_reaction_rule()
    • compartment()
    • to_reaction()
    • from_dict()
    • add_complexes() & get_complexes()
    • cstoichiometry()
    • get_roles()
    • get_complex_roles()
    • get_data()
  • NewModelTemplateRole
    • from_dict()
    • get_data()
    • __repr__() & __str__() & _repr_html_()
  • NewModelTemplateComplex
    • from_dict()
    • add_role()
    • get_data()
    • __repr__() & __str__() & _repr_html_()
  • MSTemplateCompartment
    • from_dict()
    • get_data()
  • MSTemplate
    • add_compartments(), add_roles(), add_complexes(), add_compounds(), add_comp_compounds(), & add_reactions()
    • get_complex_from_roles()
    • get_last_id_value()
    • get_complex(), get_reaction(), & get_role()
    • get_data()
    • _repr_html_()
  • MSTemplateBuilder
    • from_dict()
    • from_template()
    • with_role()
    • with_compartment()
    • build()
• rpcclient
  • ServerError()
    • __str__()
    • Accessible content
  • RPCClient()
    • call()
    • Accessible content
• template
  • Template()
    • convert_template_compound()
    • convert_template_reaction()
    • Accessible content

community

The community sub-library compatibilizes transport reactions of individual models for a community model and simulates interactions amongst community members:

from modelseedpy.community import *

• dFBApkg
  • dFBAPkg()
    • simulate()
    • Accessible content
• mssmetana
  • MSSmetana()
    • all_scores()
    • report_generation()
    • mro_score(), mip_score(), mu_score(), mp_score(), sc_score(), smetana_score()
    • Attributes
    • mro()
    • mip()
    • mu()
    • mp()
    • sc()
    • smetana()
• mscommphitting
  • MSCommPhitting()
    • fit()
    • fit_kcat()
  • Un-updated documentation
    • compute()
    • graph()
    • load_model()
    • change_parameters()
    • Accessible content
• mscommunity
  • CommunityModelSpecies()
    • disable_species()
    • compute_max_biomass()
    • compute_max_atp()
    • Accessible content
  • MSCommunity()
    • set_abundance()
    • set_objective()
    • constrain()
    • print_lp()
    • compute_interactions()
    • gapfill()
    • test_individual_species()
    • atp_correction()
    • predict_abundances()
    • run()
    • Accessible content
• mscompatibility
  • MSCompatibility()
    • standardize()
    • align_exchanges()

fbapkg

The fbapkg sub-library constrains and investigates metabolic models through Flux Balance Analysis methods:

from modelseedpy.fbapkg import *

• bilevel
  • BilevelPkg()
    • build_package()
    • Accessible content
• drainfluxpkg
  • DrainFluxPkg()
    • build_package()
    • Accessible content
• elementuptakepkg
  • ElementUptakePkg()
    • build_package()
    • Accessible content
• flexiblebiomass
  • FlexibleBiomassPkg()
    • build_package()
    • Accessible content
• fluxfittingpkg
  • FluxFittingPkg()
    • build_package()
    • Accessible content
• gapfillingpkg
  • GapfillingPkg()
    • build()
    • build_package()
    • extend_model_with_model_for_gapfilling()
    • extend_model_with_template_for_gapfilling()
    • binary_check_gapfilling_solution()
    • run_test_conditions()
    • filter_database_based_on_tests()
    • filter_database_based_on_tests()
    • Accessible content
• KBasemediapkg
  • KBaseMediaPkg()
    • build_package()
    • Accessible content
• metaboFBApkg
  • MetaboFBAPkg()
    • build_package()
    • Accessible content
• proteomefittingpkg
  • ProteomeFittingPkg()
    • build_package()
    • Accessible content
• reactionusepkg
  • ReactionUsePkg()
    • build_package()
    • build_exclusion_constraint()
    • Accessible content
• fullthermopkg
  • FullThermoPkg()
    • build_package()
    • Accessible content

ml

The ml sub-library supports parsing features from genomes, with accessibility to KBase:

from modelseedpy.ml import *

• predict_phenotype functions
  • get_functional_roles()
  • get_list_functional_roles_from_kbase()
  • extract_features_from_genome()
  • classify()