0.4.3
Site
Getting Started
Flowchart
Test Suite
API Reference
Contributing
Credits
History
Page
Index
A
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B
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C
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D
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F
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G
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H
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M
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N
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P
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R
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S
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T
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V
A
abort_if_false() (in module memote.suite.cli.callbacks)
addargs (memote.suite.cli.config.ConfigSectionSchema.Memote attribute)
B
basic_report() (in module memote.suite.api)
BasicReport (class in memote.suite.reporting.reports.basic_report)
boolean_chart() (in module memote.suite.reporting.plot)
build_index() (memote.suite.reporting.bag.ResultBagWrapper method)
C
check_metabolites_formula_presence() (in module memote.support.basic)
check_stoichiometric_consistency() (in module memote.support.consistency)
collect (memote.suite.cli.config.ConfigSectionSchema.Memote attribute)
config_files (memote.suite.cli.config.ConfigFileProcessor attribute)
config_section_schemas (memote.suite.cli.config.ConfigFileProcessor attribute)
config_sections (memote.suite.cli.config.ConfigFileProcessor attribute)
ConfigFileProcessor (class in memote.suite.cli.config)
ConfigSectionSchema (class in memote.suite.cli.config)
ConfigSectionSchema.Memote (class in memote.suite.cli.config)
D
df2dict() (in module memote.support.helpers)
diff_report() (in module memote.suite.api)
DiffReport (class in memote.suite.reporting.reports.diff_report)
directory (memote.suite.cli.config.ConfigSectionSchema.Memote attribute)
F
find_abc_tag_transporter() (in module memote.support.syntax)
find_atp_adp_converting_reactions() (in module memote.support.helpers)
find_biomass_precursors() (in module memote.support.biomass)
find_biomass_reaction() (in module memote.support.helpers)
find_blocked_biomass_precursors() (in module memote.support.biomass)
find_blocked_reactions() (in module memote.support.consistency)
find_components_without_annotation() (in module memote.support.annotation)
find_demand_reactions() (in module memote.support.helpers)
find_elementary_leakage_modes() (in module memote.support.consistency)
find_exchange_rxns() (in module memote.support.helpers)
find_false_demand_rxns() (in module memote.support.syntax)
find_false_exchange_rxns() (in module memote.support.syntax)
find_false_sink_rxns() (in module memote.support.syntax)
find_functional_units() (in module memote.support.helpers)
find_imbalanced_reactions() (in module memote.support.consistency)
find_inconsistent_min_stoichiometry() (in module memote.support.consistency)
find_reaction_tag_transporter() (in module memote.support.syntax)
find_rxn_id_compartment_suffix() (in module memote.support.syntax)
find_rxn_id_suffix_compartment() (in module memote.support.syntax)
find_sink_reactions() (in module memote.support.helpers)
find_stoichiometrically_balanced_cycles() (in module memote.support.consistency)
find_transport_reactions() (in module memote.support.helpers)
find_transported_elements() (in module memote.support.helpers)
find_unconserved_metabolites() (in module memote.support.consistency)
find_untagged_demand_rxns() (in module memote.support.syntax)
find_untagged_exchange_rxns() (in module memote.support.syntax)
find_untagged_sink_rxns() (in module memote.support.syntax)
find_upper_case_mets() (in module memote.support.syntax)
G
generate_component_annotation_miriam_match() (in module memote.support.annotation)
generate_component_annotation_overview() (in module memote.support.annotation)
generate_component_id_namespace_overview() (in module memote.support.annotation)
get_basic_dataframe() (memote.suite.reporting.bag.ResultBagWrapper method)
get_biomass_dataframe() (memote.suite.reporting.bag.ResultBagWrapper method)
get_consistency_dataframe() (memote.suite.reporting.bag.ResultBagWrapper method)
get_model_ids() (memote.suite.reporting.bag.ResultBagWrapper method)
get_syntax_dataframe() (memote.suite.reporting.bag.ResultBagWrapper method)
git (memote.suite.cli.config.ConfigSectionSchema.Memote attribute)
github_repository (memote.suite.cli.config.ConfigSectionSchema.Memote attribute)
github_username (memote.suite.cli.config.ConfigSectionSchema.Memote attribute)
H
history_report() (in module memote.suite.api)
HistoryReport (class in memote.suite.reporting.reports.history_report)
M
memote (module)
memote.suite (module)
memote.suite.api (module)
memote.suite.cli (module)
memote.suite.cli.callbacks (module)
memote.suite.cli.config (module)
memote.suite.cli.reports (module)
memote.suite.cli.runner (module)
memote.suite.collect (module)
memote.suite.reporting (module)
memote.suite.reporting.bag (module)
memote.suite.reporting.plot (module)
memote.suite.reporting.reports (module)
memote.suite.reporting.reports.basic_report (module)
memote.suite.reporting.reports.diff_report (module)
memote.suite.reporting.reports.history_report (module)
memote.suite.reporting.reports.report (module)
memote.support (module)
memote.support.annotation (module)
memote.support.basic (module)
memote.support.biomass (module)
memote.support.consistency (module)
memote.support.consistency_helpers (module)
memote.support.helpers (module)
memote.support.syntax (module)
memote.version_info (module)
model (memote.suite.cli.config.ConfigSectionSchema.Memote attribute)
model() (memote.suite.collect.ResultCollectionPlugin method)
N
non_cytosolic() (in module test_syntax)
nullspace() (in module memote.support.consistency_helpers)
P
probe_git() (in module memote.suite.cli.callbacks)
produce_atp_closed_exchanges() (in module memote.support.consistency)
R
read_only_model() (memote.suite.collect.ResultCollectionPlugin method)
render_html() (memote.suite.reporting.reports.basic_report.BasicReport method)
(memote.suite.reporting.reports.diff_report.DiffReport method)
(memote.suite.reporting.reports.history_report.HistoryReport method)
(memote.suite.reporting.reports.report.Report method)
Report (class in memote.suite.reporting.reports.report)
ResultBagWrapper (class in memote.suite.reporting.bag)
ResultCollectionPlugin (class in memote.suite.collect)
results (memote.suite.collect.ResultCollectionPlugin attribute)
S
scatter_line_chart() (in module memote.suite.reporting.plot)
section_names (memote.suite.cli.config.ConfigSectionSchema.Memote attribute)
show_versions() (in module memote.version_info)
stoichiometry_matrix() (in module memote.support.consistency_helpers)
store() (memote.suite.collect.ResultCollectionPlugin method)
sum_biomass_weight() (in module memote.support.biomass)
T
test_abc_transp_rxn_tag_match() (in module test_syntax)
test_annotation (module)
test_basic (module)
test_biomass (module)
test_biomass_consistency() (in module test_biomass)
test_biomass_default_production() (in module test_biomass)
test_biomass_precursors_default_production() (in module test_biomass)
test_biomass_precursors_open_production() (in module test_biomass)
test_biomass_presence() (in module test_biomass)
test_blocked_reactions() (in module test_consistency)
test_compartments_presence() (in module test_basic)
test_consistency (module)
test_demand_reaction_tag_match() (in module test_syntax)
test_enzyme_complex_presence() (in module test_basic)
test_exchange_reaction_tag_match() (in module test_syntax)
test_false_demand_reaction() (in module test_syntax)
test_false_exchange_reaction() (in module test_syntax)
test_false_sink_reaction() (in module test_syntax)
test_fast_growth_default() (in module test_biomass)
test_find_pure_metabolic_reactions() (in module test_basic)
test_find_stoichiometrically_balanced_cycles() (in module test_consistency)
test_find_transport_reactions() (in module test_basic)
test_find_unique_metabolites() (in module test_basic)
test_gam_in_biomass() (in module test_biomass)
test_gene_protein_reaction_rule_presence() (in module test_basic)
test_genes_presence() (in module test_basic)
test_imbalanced_reactions() (in module test_consistency)
test_metabolic_coverage() (in module test_basic)
test_metabolite_annotation_overview() (in module test_annotation)
test_metabolite_annotation_presence() (in module test_annotation)
test_metabolite_annotation_wrong_ids() (in module test_annotation)
test_metabolite_id_namespace_consistency() (in module test_annotation)
test_metabolites_charge_presence() (in module test_basic)
test_metabolites_formula_presence() (in module test_basic)
test_metabolites_presence() (in module test_basic)
test_model() (in module memote.suite.api)
test_model_id_presence() (in module test_basic)
test_ngam_presence() (in module test_basic)
test_non_abc_transp_rxn_tag_match() (in module test_syntax)
test_non_transp_rxn_id_compartment_suffix_match() (in module test_syntax)
test_non_transp_rxn_id_suffix_compartment_match() (in module test_syntax)
test_production_of_atp_closed_bounds() (in module test_consistency)
test_reaction_annotation_overview() (in module test_annotation)
test_reaction_annotation_presence() (in module test_annotation)
test_reaction_annotation_wrong_ids() (in module test_annotation)
test_reaction_id_namespace_consistency() (in module test_annotation)
test_reactions_presence() (in module test_basic)
test_sink_reaction_tag_match() (in module test_syntax)
test_stoichiometric_consistency() (in module test_consistency)
test_syntax (module)
test_transport_reaction_presence() (in module test_basic)
test_upper_case_mets() (in module test_syntax)
V
validate_collect() (in module memote.suite.cli.callbacks)
validate_directory() (in module memote.suite.cli.callbacks)
validate_model() (in module memote.suite.cli.callbacks)
validate_pytest_args() (in module memote.suite.cli.callbacks)
validate_repository() (in module memote.suite.cli.callbacks)
validate_username() (in module memote.suite.cli.callbacks)