sbmlutils
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sbmlutils
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__author__ (in module sbmlutils)
__isfrozen (sbmlutils.utils.FrozenClass attribute)
__repr__() (sbmlutils.factory.AlgebraicRule method)
(sbmlutils.factory.AssignmentRule method)
(sbmlutils.factory.RateRule method)
(sbmlutils.report.sbmlinfo.SBMLDocumentInfo method)
__setattr__() (sbmlutils.utils.FrozenClass method)
__str__() (sbmlutils.data.interpolation.Interpolator method)
(sbmlutils.factory.Model method)
(sbmlutils.metadata.annotator.ExternalAnnotation method)
(sbmlutils.notes.Notes method)
(sbmlutils.report.sbmlinfo.SBMLDocumentInfo method)
__version__ (in module sbmlutils)
_add_reaction_formula() (sbmlutils.converters.odefac.SBML2ODE method)
_annotate_elements() (sbmlutils.metadata.annotator.ModelAnnotator method)
_annotation_types (sbmlutils.metadata.annotator.ExternalAnnotation attribute)
_assignments_dict() (sbmlutils.factory.Event static method)
_bounds_dict_from_reaction() (sbmlutils.report.sbmlinfo.SBMLDocumentInfo static method)
_bracket_stack() (in module sbmlutils.converters.xpp_helpers)
_check_consistency() (in module sbmlutils.validation)
_create_assignment_map() (sbmlutils.report.sbmlinfo.SBMLDocumentInfo method)
_create_biomodels_testfiles() (in module sbmlutils.biomodels)
_create_curve() (sbmlutils.layout.layout.ReactionGlyph method)
(sbmlutils.layout.ReactionGlyph method)
_create_merged_doc() (in module sbmlutils.manipulation.merge)
_create_odes() (sbmlutils.converters.odefac.SBML2ODE method)
_create_parameter() (in module sbmlutils.distrib.distrib_examples)
_create_port() (in module sbmlutils.comp.comp)
_create_port_map() (sbmlutils.report.sbmlinfo.SBMLDocumentInfo method)
_create_replaced_element() (in module sbmlutils.comp.comp)
_create_sbml() (sbmlutils.data.interpolation.Interpolation method)
_create_unit() (sbmlutils.factory.UnitDefinition static method)
_distrib_doc() (in module sbmlutils.distrib.distrib_examples)
_elements_from_ids() (sbmlutils.metadata.annotator.ModelAnnotator static method)
_equation_from_reaction() (sbmlutils.report.sbmlinfo.SBMLDocumentInfo static method)
_fix_mathit_symbols() (in module sbmlutils.report.mathml)
_formula_constant() (sbmlutils.data.interpolation.Interpolator static method)
_formula_cubic_spline() (sbmlutils.data.interpolation.Interpolator static method)
_formula_linear() (sbmlutils.data.interpolation.Interpolator static method)
_freeze() (sbmlutils.utils.FrozenClass method)
_gene_product_association_from_reaction() (sbmlutils.report.sbmlinfo.SBMLDocumentInfo static method)
_get_eplugin_by_sid() (in module sbmlutils.comp.comp)
_get_ids_from_model() (sbmlutils.metadata.annotator.ModelAnnotator method)
_get_matching_ids() (sbmlutils.metadata.annotator.ModelAnnotator static method)
_get_pk() (sbmlutils.report.sbmlinfo.SBMLDocumentInfo static method)
_get_sbase_attribute() (in module sbmlutils.report.sbmlinfo)
_get_variables() (in module sbmlutils.report.mathml)
_half_equation() (sbmlutils.report.sbmlinfo.SBMLDocumentInfo static method)
_handle_error() (in module sbmlutils.report.api)
_indices() (sbmlutils.converters.odefac.SBML2ODE method)
_init_sbml_model() (sbmlutils.data.interpolation.Interpolation method)
_keys (sbmlutils.factory.Model attribute)
(sbmlutils.metadata.annotator.ExternalAnnotation attribute)
_m (in module sbmlutils.examples.combine_archive.omex_models)
(in module sbmlutils.examples.dallaman.dallaman)
(in module sbmlutils.examples.icg.model_body)
(in module sbmlutils.examples.icg.model_liver)
(in module sbmlutils.examples.parameter)
_modifier_equation() (sbmlutils.report.sbmlinfo.SBMLDocumentInfo static method)
_natural_spline_coeffs() (sbmlutils.data.interpolation.Interpolator static method)
_ordered_yids() (sbmlutils.converters.odefac.SBML2ODE method)
_parse_equation() (sbmlutils.factory.ReactionEquation method)
(sbmlutils.reaction_equation.ReactionEquation method)
_parse_half_equation() (sbmlutils.factory.ReactionEquation method)
(sbmlutils.reaction_equation.ReactionEquation method)
_parse_modifiers() (sbmlutils.factory.ReactionEquation method)
(sbmlutils.reaction_equation.ReactionEquation method)
_parse_qualifier_str() (sbmlutils.metadata.annotator.ExternalAnnotation static method)
_parse_reactant() (sbmlutils.factory.ReactionEquation static method)
(sbmlutils.reaction_equation.ReactionEquation static method)
_pint2sbml (sbmlutils.factory.UnitDefinition attribute)
_prefixes (sbmlutils.factory.UnitDefinition attribute)
_process_equation() (sbmlutils.factory.Reaction static method)
_process_formula() (sbmlutils.factory.Reaction static method)
_render_template() (sbmlutils.converters.odefac.SBML2ODE method)
_rule_variable_to_string() (sbmlutils.report.sbmlinfo.SBMLDocumentInfo static method)
_sbaseref() (sbmlutils.report.sbmlinfo.SBMLDocumentInfo static method)
_sbml_type() (sbmlutils.report.sbmlinfo.SBMLDocumentInfo static method)
_sbml_types (sbmlutils.metadata.annotator.ExternalAnnotation attribute)
_set_fields() (sbmlutils.factory.Compartment method)
(sbmlutils.factory.Constraint method)
(sbmlutils.factory.Deletion method)
(sbmlutils.factory.Event method)
(sbmlutils.factory.ExternalModelDefinition method)
(sbmlutils.factory.Function method)
(sbmlutils.factory.ModelDefinition method)
(sbmlutils.factory.Parameter method)
(sbmlutils.factory.Port method)
(sbmlutils.factory.Reaction method)
(sbmlutils.factory.ReplacedBy method)
(sbmlutils.factory.ReplacedElement method)
(sbmlutils.factory.Species method)
(sbmlutils.factory.Submodel method)
(sbmlutils.factory.UnitDefinition method)
(sbmlutils.layout.Layout method)
(sbmlutils.layout.layout.Layout method)
_set_glyph_fields() (sbmlutils.layout.CompartmentGlyph method)
(sbmlutils.layout.layout.CompartmentGlyph method)
(sbmlutils.layout.layout.ReactionGlyph method)
(sbmlutils.layout.layout.SpeciesGlyph method)
(sbmlutils.layout.ReactionGlyph method)
(sbmlutils.layout.SpeciesGlyph method)
_set_ref() (in module sbmlutils.comp.comp)
_species_reference() (sbmlutils.report.sbmlinfo.SBMLDocumentInfo static method)
_supported_packages (sbmlutils.factory.Model attribute)
_to_string_modifiers() (sbmlutils.factory.ReactionEquation method)
(sbmlutils.reaction_equation.ReactionEquation method)
_to_string_side() (sbmlutils.factory.ReactionEquation static method)
(sbmlutils.reaction_equation.ReactionEquation static method)
_top_bracket_content() (in module sbmlutils.converters.xpp_helpers)
_trigger_from_time() (sbmlutils.factory.Event static method)
_uuid() (sbmlutils.report.sbmlinfo.SBMLDocumentInfo static method)
A
add_compartment_links() (sbmlutils.report.sbmlinfo.SBMLDocumentInfo method)
add_default_flux_bounds() (in module sbmlutils.fbc.fbc)
add_interpolator_to_model() (sbmlutils.data.interpolation.Interpolation static method)
add_species_links() (sbmlutils.report.sbmlinfo.SBMLDocumentInfo method)
add_submodel_from_emd() (in module sbmlutils.comp.comp)
add_uncertainty_example() (in module sbmlutils.distrib.distrib_packages)
algebraic_rules (sbmlutils.factory.Model attribute)
(sbmlutils.factory.ModelDict attribute)
AlgebraicRule (class in sbmlutils.factory)
all_count (sbmlutils.validation.ValidationResult property)
all_distrib_paths() (in module sbmlutils.resources)
ALL_SBML_PATHS (in module sbmlutils.resources)
ampere (sbmlutils.factory.Units attribute)
annotate_model() (sbmlutils.metadata.annotator.ModelAnnotator method)
annotate_sbase() (sbmlutils.metadata.annotator.ModelAnnotator static method)
annotate_sbml() (in module sbmlutils.metadata.annotator)
annotate_sbml_doc() (in module sbmlutils.metadata.annotator)
annotations (sbmlutils.factory.Model attribute)
(sbmlutils.factory.ModelDict attribute)
(sbmlutils.reaction_equation.EquationPart attribute)
antimony_to_model() (in module sbmlutils.parser)
antimony_to_sbml() (in module sbmlutils.parser)
api (in module sbmlutils.report.api)
API_EXAMPLES_MODEL (in module sbmlutils.resources)
API_EXAMPLES_OMEX (in module sbmlutils.resources)
arbitrary_types_allowed (sbmlutils.factory.Model.Config attribute)
(sbmlutils.factory.UnitDefinition.Config attribute)
AssignmentRule (class in sbmlutils.factory)
assignments (sbmlutils.factory.Model attribute)
(sbmlutils.factory.ModelDict attribute)
ast_info() (in module sbmlutils.converters.xpp_helpers)
astnode_to_latex() (in module sbmlutils.report.mathml)
attributes() (sbmlutils.factory.Units class method)
B
BASIC_SBML (in module sbmlutils.resources)
becquerel (sbmlutils.factory.Units attribute)
BIOMODELS_CURATED_PATH (in module sbmlutils.resources)
biomodels_examples() (in module sbmlutils.report.api_examples)
C
c (in module sbmlutils.examples.fbc.fbc_version3)
candela (sbmlutils.factory.Units attribute)
check() (in module sbmlutils.examples.fbc.fbc_version3)
(in module sbmlutils.validation)
(sbmlutils.metadata.annotator.ExternalAnnotation method)
check_mass_balance() (in module sbmlutils.fbc.cobra)
check_packages() (sbmlutils.factory.Model method)
clean_empty() (in module sbmlutils.report.sbmlinfo)
cm (sbmlutils.examples.icg.model_body.U attribute)
(sbmlutils.examples.unit_definitions.U attribute)
cmathml_to_astnode() (in module sbmlutils.report.mathml)
cmathml_to_latex() (in module sbmlutils.report.mathml)
cobra (in module sbmlutils.fbc.cobra)
cobra_reaction_info() (in module sbmlutils.fbc.cobra)
COMP (sbmlutils.factory.Package attribute)
COMP_DEX_BODY (in module sbmlutils.resources)
COMP_DEX_BODY_FLAT (in module sbmlutils.resources)
COMP_DEX_CYP2D6 (in module sbmlutils.resources)
COMP_DEX_INTESTINE (in module sbmlutils.resources)
COMP_DEX_KIDNEY (in module sbmlutils.resources)
COMP_DEX_LIVER (in module sbmlutils.resources)
COMP_ICG_BODY (in module sbmlutils.resources)
COMP_ICG_BODY_FLAT (in module sbmlutils.resources)
COMP_ICG_LIVER (in module sbmlutils.resources)
COMP_V1 (sbmlutils.factory.Package attribute)
Compartment (class in sbmlutils.factory)
CompartmentGlyph (class in sbmlutils.layout)
(class in sbmlutils.layout.layout)
compartments (in module sbmlutils.examples.icg.annotations)
(sbmlutils.factory.Model attribute)
(sbmlutils.factory.ModelDict attribute)
compartments() (sbmlutils.report.sbmlinfo.SBMLDocumentInfo method)
COMPARTMENTS_BODY (in module sbmlutils.examples.icg.model_body)
component (in module sbmlutils.examples.fbc.fbc_version3)
console (in module sbmlutils.console)
constant (sbmlutils.reaction_equation.EquationPart attribute)
Constraint (class in sbmlutils.factory)
constraint (in module sbmlutils.examples.fbc.fbc_version3)
constraints (sbmlutils.factory.Model attribute)
(sbmlutils.factory.ModelDict attribute)
constraints() (sbmlutils.report.sbmlinfo.SBMLDocumentInfo method)
coulomb (sbmlutils.factory.Units attribute)
create() (in module sbmlutils.examples.dallaman.dallaman)
(in module sbmlutils.examples.demo.demo)
(in module sbmlutils.examples.distrib.distrib_comp)
(in module sbmlutils.examples.tiny.tiny)
(in module sbmlutils.examples.tutorial.minimal_model_comp)
(in module sbmlutils.examples.tutorial.model_composition)
create_examples() (in module sbmlutils.distrib.distrib_examples)
create_ExternalModelDefinition() (in module sbmlutils.comp)
(in module sbmlutils.comp.comp)
create_hash_id() (in module sbmlutils.utils)
create_info() (sbmlutils.report.sbmlinfo.SBMLDocumentInfo method)
create_interpolators() (sbmlutils.data.interpolation.Interpolation static method)
create_metaid() (in module sbmlutils.utils)
create_model() (in module sbmlutils.factory)
create_models() (in module sbmlutils.examples.icg.factory)
create_models_metadata() (in module sbmlutils.report.api_examples)
create_omex() (in module sbmlutils.examples.combine_archive.omex_models)
create_omex_metadata() (in module sbmlutils.report.api_examples)
create_online_report() (in module sbmlutils.report.sbmlreport)
create_ports() (in module sbmlutils.comp)
(in module sbmlutils.comp.comp)
create_sbml() (sbmlutils.factory.AlgebraicRule method)
(sbmlutils.factory.AssignmentRule method)
(sbmlutils.factory.Compartment method)
(sbmlutils.factory.Constraint method)
(sbmlutils.factory.Deletion method)
(sbmlutils.factory.Document method)
(sbmlutils.factory.Event method)
(sbmlutils.factory.ExternalModelDefinition method)
(sbmlutils.factory.FluxObjective method)
(sbmlutils.factory.Function method)
(sbmlutils.factory.GeneProduct method)
(sbmlutils.factory.InitialAssignment method)
(sbmlutils.factory.KeyValuePair method)
(sbmlutils.factory.Model method)
(sbmlutils.factory.ModelDefinition method)
(sbmlutils.factory.Objective method)
(sbmlutils.factory.Parameter method)
(sbmlutils.factory.Port method)
(sbmlutils.factory.RateRule method)
(sbmlutils.factory.Reaction method)
(sbmlutils.factory.ReplacedBy method)
(sbmlutils.factory.ReplacedElement method)
(sbmlutils.factory.Species method)
(sbmlutils.factory.Submodel method)
(sbmlutils.factory.Uncertainty method)
(sbmlutils.factory.UnitDefinition method)
(sbmlutils.factory.UserDefinedConstraint method)
(sbmlutils.factory.UserDefinedConstraintComponent method)
(sbmlutils.layout.Layout method)
(sbmlutils.layout.layout.Layout method)
create_unit_definitions() (sbmlutils.factory.Units class method)
creators (in module sbmlutils.examples.icg.templates)
(in module sbmlutils.examples.templates)
(sbmlutils.factory.Model attribute)
(sbmlutils.factory.ModelDict attribute)
custom_theme (in module sbmlutils.console)
cvterms() (sbmlutils.report.sbmlinfo.SBMLDocumentInfo class method)
D
dallaman_model (in module sbmlutils.examples.dallaman.dallaman)
degree_Celsius (sbmlutils.factory.Units attribute)
Deletion (class in sbmlutils.factory)
deletions (sbmlutils.factory.Model attribute)
(sbmlutils.factory.ModelDict attribute)
DEMO_ANNOTATIONS (in module sbmlutils.resources)
DEMO_SBML (in module sbmlutils.resources)
DEMO_SBML_NO_ANNOTATIONS (in module sbmlutils.resources)
dependency_graph() (sbmlutils.converters.odefac.SBML2ODE static method)
deprecated() (in module sbmlutils.utils)
description (sbmlutils.report.api_examples.ExampleMetaData attribute)
dfba_paths (in module sbmlutils.resources)
dimensionless (sbmlutils.factory.Units attribute)
DISTRIB (sbmlutils.factory.Package attribute)
distrib_all() (in module sbmlutils.distrib.distrib_examples)
DISTRIB_COMP_FLAT_SBML (in module sbmlutils.resources)
DISTRIB_COMP_SBML (in module sbmlutils.resources)
DISTRIB_DISTRIBUTIONS_SBML (in module sbmlutils.resources)
distrib_normal() (in module sbmlutils.distrib.distrib_examples)
distrib_paths (in module sbmlutils.resources)
DISTRIB_UNCERTAINTIES_SBML (in module sbmlutils.resources)
DISTRIB_V1 (sbmlutils.factory.Package attribute)
dl_per_kg (sbmlutils.examples.dallaman.dallaman.U attribute)
doc (in module sbmlutils.examples.fbc.fbc_version3)
(in module sbmlutils.examples.tutorial.minimal_model_annotations)
(in module sbmlutils.report.units)
doc2 (in module sbmlutils.examples.fbc.fbc_version3)
doc_fbc (in module sbmlutils.examples.fbc.fbc_version3)
Document (class in sbmlutils.factory)
document() (sbmlutils.report.sbmlinfo.SBMLDocumentInfo method)
download_biomodel_omex() (in module sbmlutils.biomodels)
download_biomodel_sbml() (in module sbmlutils.biomodels)
download_file() (in module sbmlutils.biomodels)
E
EquationPart (class in sbmlutils.reaction_equation)
err_message (in module sbmlutils.examples.fbc.fbc_version3)
error_count (sbmlutils.validation.ValidationResult property)
error_string() (in module sbmlutils.validation)
escape_string() (in module sbmlutils.converters.xpp)
evaluableMathML() (in module sbmlutils.converters.mathml)
evaluateMathML() (in module sbmlutils.converters.mathml)
Event (class in sbmlutils.factory)
events (sbmlutils.factory.Model attribute)
(sbmlutils.factory.ModelDict attribute)
events() (sbmlutils.report.sbmlinfo.SBMLDocumentInfo method)
example() (in module sbmlutils.converters.xpp_examples)
(in module sbmlutils.report.api)
example_ids (in module sbmlutils.resources)
ExampleMetaData (class in sbmlutils.report.api_examples)
examples (in module sbmlutils.reaction_equation)
(in module sbmlutils.report.api_examples)
examples() (in module sbmlutils.report.api)
examples_create (in module sbmlutils.examples)
EXAMPLES_DIR (in module sbmlutils.resources)
examples_info (in module sbmlutils.report.api_examples)
examples_models (in module sbmlutils.examples)
ExchangeReaction (class in sbmlutils.factory)
external_model_definitions (sbmlutils.factory.Model attribute)
(sbmlutils.factory.ModelDict attribute)
ExternalAnnotation (class in sbmlutils.metadata.annotator)
ExternalModelDefinition (class in sbmlutils.factory)
F
fac_result (in module sbmlutils.examples.model)
(in module sbmlutils.examples.tutorial.minimal_model)
(in module sbmlutils.examples.tutorial.model_composition)
(in module sbmlutils.examples.tutorial.random_network)
fac_results (in module sbmlutils.examples.fbc.fbc_userdefinedconstraints)
factory_results (in module sbmlutils.examples.tutorial.linear_chain)
FactoryResult (class in sbmlutils.factory)
farad (sbmlutils.factory.Units attribute)
FBC (sbmlutils.factory.Package attribute)
FBC_DIAUXIC_GROWTH_SBML (in module sbmlutils.resources)
FBC_ECOLI_CORE_SBML (in module sbmlutils.resources)
fbc_reaction (in module sbmlutils.examples.fbc.fbc_version3)
FBC_RECON3D_SBML (in module sbmlutils.resources)
FBC_V2 (sbmlutils.factory.Package attribute)
FBC_V3 (sbmlutils.factory.Package attribute)
fbc_variable_types (sbmlutils.factory.FluxObjective attribute)
file (sbmlutils.report.api_examples.ExampleMetaData attribute)
find_names_in_ast() (in module sbmlutils.converters.xpp_helpers)
flatten_external_model_definitions() (in module sbmlutils.comp.flatten)
flatten_sbml() (in module sbmlutils.comp)
(in module sbmlutils.comp.flatten)
flatten_sbml_doc() (in module sbmlutils.comp)
(in module sbmlutils.comp.flatten)
FLUX_BOUND_GLC_IMPORT (in module sbmlutils.examples.fbc.fbc_v2)
(in module sbmlutils.examples.fbc.fbc_v3)
FLUX_BOUND_MINUS_INF (in module sbmlutils.examples.fbc.fbc_v2)
(in module sbmlutils.examples.fbc.fbc_v3)
FLUX_BOUND_O2_IMPORT (in module sbmlutils.examples.fbc.fbc_v2)
(in module sbmlutils.examples.fbc.fbc_v3)
FLUX_BOUND_PLUS_INF (in module sbmlutils.examples.fbc.fbc_v2)
(in module sbmlutils.examples.fbc.fbc_v3)
FLUX_BOUND_ZERO (in module sbmlutils.examples.fbc.fbc_v2)
(in module sbmlutils.examples.fbc.fbc_v3)
FluxObjective (class in sbmlutils.factory)
formula (in module sbmlutils.converters.xpp_helpers)
Formula (in module sbmlutils.factory)
formula() (sbmlutils.data.interpolation.Interpolator method)
formula_to_astnode() (in module sbmlutils.report.mathml)
formula_to_latex() (in module sbmlutils.report.mathml)
from_csv() (sbmlutils.data.interpolation.Interpolation static method)
from_file() (sbmlutils.converters.odefac.SBML2ODE class method)
from_results() (sbmlutils.validation.ValidationResult static method)
from_sbml() (sbmlutils.report.sbmlinfo.SBMLDocumentInfo static method)
from_str() (sbmlutils.factory.ReactionEquation static method)
(sbmlutils.reaction_equation.ReactionEquation static method)
from_tsv() (sbmlutils.data.interpolation.Interpolation static method)
FrozenClass (class in sbmlutils.utils)
Function (class in sbmlutils.factory)
function_definitions() (sbmlutils.report.sbmlinfo.SBMLDocumentInfo method)
functions (sbmlutils.factory.Model attribute)
(sbmlutils.factory.ModelDict attribute)
G
g_per_mole (sbmlutils.examples.icg.model_body.U attribute)
(sbmlutils.examples.unit_definitions.U attribute)
GALACTOSE_ANNOTATIONS (in module sbmlutils.resources)
GALACTOSE_SINGLECELL_SBML (in module sbmlutils.resources)
GALACTOSE_SINGLECELL_SBML_NO_ANNOTATIONS (in module sbmlutils.resources)
GALACTOSE_TISSUE_SBML (in module sbmlutils.resources)
gene_products (sbmlutils.factory.Model attribute)
(sbmlutils.factory.ModelDict attribute)
gene_products() (sbmlutils.report.sbmlinfo.SBMLDocumentInfo method)
GeneProduct (class in sbmlutils.factory)
general_consistency (sbmlutils.factory.ValidationOptions attribute)
(sbmlutils.validation.ValidationOptions attribute)
get_annotation_resource() (in module sbmlutils.report.api)
get_json() (sbmlutils.factory.Document method)
get_logger() (in module sbmlutils.log)
get_report_from_content() (in module sbmlutils.report.api)
get_sbml() (sbmlutils.factory.Document method)
(sbmlutils.factory.Model method)
get_SBMLQualifier() (sbmlutils.metadata.annotator.ModelAnnotator static method)
get_submodel_frameworks() (in module sbmlutils.comp.comp)
get_uid_for_unit() (sbmlutils.factory.UnitDefinition static method)
GLUCOSE_SBML (in module sbmlutils.resources)
gram (sbmlutils.factory.Units attribute)
gray (sbmlutils.factory.Units attribute)
greek_symbols (in module sbmlutils.report.mathml)
GZ_SBML (in module sbmlutils.resources)
H
help() (sbmlutils.factory.ReactionEquation static method)
(sbmlutils.reaction_equation.ReactionEquation static method)
hertz (sbmlutils.factory.Units attribute)
hr (sbmlutils.examples.algebraic_rule.U attribute)
(sbmlutils.examples.assignment.U attribute)
(sbmlutils.examples.distrib.distrib_comp.U attribute)
(sbmlutils.examples.distrib.distrib_distributions.U attribute)
(sbmlutils.examples.distrib.distrib_uncertainties.U attribute)
(sbmlutils.examples.fbc.fbc_userdefinedconstraints.U attribute)
(sbmlutils.examples.fbc.fbc_v2.U attribute)
(sbmlutils.examples.fbc.fbc_v3.U attribute)
(sbmlutils.examples.icg.model_body.U attribute)
(sbmlutils.examples.parameter.U attribute)
(sbmlutils.examples.unit_definitions.U attribute)
HTML (sbmlutils.notes.NotesFormat attribute)
I
ICG_PATH (in module sbmlutils.examples.icg)
id (sbmlutils.report.api_examples.ExampleMetaData attribute)
identifier_consistency (sbmlutils.factory.ValidationOptions attribute)
(sbmlutils.validation.ValidationOptions attribute)
info() (sbmlutils.converters.odefac.SBML2ODE method)
(sbmlutils.factory.ReactionEquation method)
(sbmlutils.reaction_equation.ReactionEquation method)
initial_assignments() (sbmlutils.report.sbmlinfo.SBMLDocumentInfo method)
InitialAssignment (class in sbmlutils.factory)
INPUT_PORT (sbmlutils.factory.PortType attribute)
internal_consistency (sbmlutils.factory.ValidationOptions attribute)
(sbmlutils.validation.ValidationOptions attribute)
interpolate_data() (in module sbmlutils.data.interpolation_pancreas)
Interpolation (class in sbmlutils.data.interpolation)
INTERPOLATION_CONSTANT (in module sbmlutils.data.interpolation)
INTERPOLATION_CUBIC_SPLINE (in module sbmlutils.data.interpolation)
interpolation_example() (in module sbmlutils.data.interpolation_example)
INTERPOLATION_LINEAR (in module sbmlutils.data.interpolation)
interpolation_paths (in module sbmlutils.resources)
Interpolator (class in sbmlutils.data.interpolation)
IRREVERSIBILITY_PATTERN (in module sbmlutils.reaction_equation)
IRREVERSIBILITY_SEPARATOR (in module sbmlutils.reaction_equation)
is_perfect() (sbmlutils.validation.ValidationResult method)
is_valid() (sbmlutils.validation.ValidationResult method)
item (sbmlutils.factory.Units attribute)
J
json_for_omex() (in module sbmlutils.report.api)
json_for_sbml() (in module sbmlutils.report.api)
K
k_source (in module sbmlutils.examples.tutorial.random_network)
kelvin (sbmlutils.factory.Units attribute)
KeyValuePair (class in sbmlutils.factory)
keyValuePairs (sbmlutils.factory.Model attribute)
(sbmlutils.factory.ModelDict attribute)
(sbmlutils.reaction_equation.EquationPart attribute)
kg (sbmlutils.examples.algebraic_rule.U attribute)
(sbmlutils.examples.annotation.U attribute)
(sbmlutils.examples.assignment.U attribute)
(sbmlutils.examples.dallaman.dallaman.U attribute)
(sbmlutils.examples.icg.model_body.U attribute)
(sbmlutils.examples.multiple_substance_units.U attribute)
(sbmlutils.examples.parameter.U attribute)
(sbmlutils.examples.unit_definitions.U attribute)
kilogram (sbmlutils.factory.Units attribute)
kvp (in module sbmlutils.examples.fbc.fbc_version3)
kvp_list (in module sbmlutils.examples.fbc.fbc_version3)
L
l_per_hr (sbmlutils.examples.algebraic_rule.U attribute)
(sbmlutils.examples.assignment.U attribute)
(sbmlutils.examples.icg.model_body.U attribute)
(sbmlutils.examples.parameter.U attribute)
(sbmlutils.examples.unit_definitions.U attribute)
l_per_kg (sbmlutils.examples.algebraic_rule.U attribute)
(sbmlutils.examples.assignment.U attribute)
(sbmlutils.examples.dallaman.dallaman.U attribute)
(sbmlutils.examples.icg.model_body.U attribute)
(sbmlutils.examples.parameter.U attribute)
(sbmlutils.examples.unit_definitions.U attribute)
l_per_min (sbmlutils.examples.icg.model_body.U attribute)
(sbmlutils.examples.model.U attribute)
(sbmlutils.examples.unit_definitions.U attribute)
l_per_ml (sbmlutils.examples.icg.model_body.U attribute)
(sbmlutils.examples.species.U attribute)
(sbmlutils.examples.unit_definitions.U attribute)
Layout (class in sbmlutils.layout)
(class in sbmlutils.layout.layout)
LAYOUT_ROLE_ACTIVATOR (in module sbmlutils.layout)
(in module sbmlutils.layout.layout)
LAYOUT_ROLE_INHIBITOR (in module sbmlutils.layout)
(in module sbmlutils.layout.layout)
LAYOUT_ROLE_MODIFIER (in module sbmlutils.layout)
(in module sbmlutils.layout.layout)
LAYOUT_ROLE_PRODUCT (in module sbmlutils.layout)
(in module sbmlutils.layout.layout)
LAYOUT_ROLE_SIDEPRODUCT (in module sbmlutils.layout)
(in module sbmlutils.layout.layout)
LAYOUT_ROLE_SIDESUBSTRATE (in module sbmlutils.layout)
(in module sbmlutils.layout.layout)
LAYOUT_ROLE_SUBSTRATE (in module sbmlutils.layout)
(in module sbmlutils.layout.layout)
LAYOUT_ROLE_UNDEFINED (in module sbmlutils.layout)
(in module sbmlutils.layout.layout)
LAYOUT_VERSION (in module sbmlutils.layout)
(in module sbmlutils.layout.layout)
layouts (sbmlutils.factory.Model attribute)
(sbmlutils.factory.ModelDict attribute)
liter (sbmlutils.examples.compartment_species_reaction.U attribute)
(sbmlutils.examples.reaction_with_units.U attribute)
(sbmlutils.factory.Units attribute)
litre (sbmlutils.factory.Units attribute)
liver_id (in module sbmlutils.examples.icg.model_body)
log() (sbmlutils.validation.ValidationResult method)
log_errors (sbmlutils.factory.ValidationOptions attribute)
(sbmlutils.validation.ValidationOptions attribute)
log_sbml_error() (in module sbmlutils.validation)
log_sbml_errors_for_doc() (in module sbmlutils.validation)
logger (in module sbmlutils.biomodels)
(in module sbmlutils.comp.comp)
(in module sbmlutils.comp.flatten)
(in module sbmlutils.converters.odefac)
(in module sbmlutils.cytoscape)
(in module sbmlutils.data.interpolation)
(in module sbmlutils.data.interpolation_example)
(in module sbmlutils.data.interpolation_pancreas)
(in module sbmlutils.distrib.distrib_packages)
(in module sbmlutils.examples.fbc.fbc_version3)
(in module sbmlutils.examples.icg.factory)
(in module sbmlutils.examples.icg.model_body)
(in module sbmlutils.fbc.cobra)
(in module sbmlutils.fbc.fbc)
(in module sbmlutils.io.sbml)
(in module sbmlutils.manipulation.merge)
(in module sbmlutils.metadata.annotator)
(in module sbmlutils.notes)
(in module sbmlutils.parser)
(in module sbmlutils.report.api)
(in module sbmlutils.report.mathml)
(in module sbmlutils.report.sbmlreport)
(in module sbmlutils.validation)
M
m (sbmlutils.examples.compartment_species_reaction.U attribute)
(sbmlutils.examples.icg.model_body.U attribute)
(sbmlutils.examples.reaction_with_units.U attribute)
(sbmlutils.examples.units_namespace.U attribute)
m2 (sbmlutils.examples.algebraic_rule.U attribute)
(sbmlutils.examples.annotation.U attribute)
(sbmlutils.examples.assignment.U attribute)
(sbmlutils.examples.compartment_species_reaction.U attribute)
(sbmlutils.examples.dallaman.dallaman.U attribute)
(sbmlutils.examples.demo.demo.U attribute)
(sbmlutils.examples.distrib.distrib_comp.U attribute)
(sbmlutils.examples.distrib.distrib_distributions.U attribute)
(sbmlutils.examples.distrib.distrib_uncertainties.U attribute)
(sbmlutils.examples.fbc.fbc_mass_charge.U attribute)
(sbmlutils.examples.fbc.fbc_userdefinedconstraints.U attribute)
(sbmlutils.examples.fbc.fbc_v2.U attribute)
(sbmlutils.examples.fbc.fbc_v3.U attribute)
(sbmlutils.examples.icg.model_body.U attribute)
(sbmlutils.examples.icg.model_liver.U attribute)
(sbmlutils.examples.model.U attribute)
(sbmlutils.examples.model_definitions.U attribute)
(sbmlutils.examples.multiple_substance_units.U attribute)
(sbmlutils.examples.parameter.U attribute)
(sbmlutils.examples.reaction_with_units.U attribute)
(sbmlutils.examples.species.U attribute)
(sbmlutils.examples.tiny.tiny.U attribute)
(sbmlutils.examples.unit_definitions.U attribute)
(sbmlutils.examples.units_namespace.U attribute)
m2_per_kg (sbmlutils.examples.icg.model_body.U attribute)
(sbmlutils.examples.unit_definitions.U attribute)
m3 (sbmlutils.examples.annotation.U attribute)
(sbmlutils.examples.dallaman.dallaman.U attribute)
(sbmlutils.examples.demo.demo.U attribute)
(sbmlutils.examples.fbc.fbc_mass_charge.U attribute)
(sbmlutils.examples.multiple_substance_units.U attribute)
(sbmlutils.examples.species.U attribute)
(sbmlutils.examples.units_namespace.U attribute)
MARKDOWN (sbmlutils.notes.NotesFormat attribute)
mathml_consistency (sbmlutils.factory.ValidationOptions attribute)
(sbmlutils.validation.ValidationOptions attribute)
mathmlStr (in module sbmlutils.converters.mathml)
merge_models() (in module sbmlutils.manipulation)
(in module sbmlutils.manipulation.merge)
(sbmlutils.factory.Model static method)
merge_models_example() (in module sbmlutils.examples.merge_models.merge_models)
metaId (sbmlutils.factory.Model attribute)
(sbmlutils.factory.ModelDict attribute)
(sbmlutils.reaction_equation.EquationPart attribute)
meter (sbmlutils.factory.Units attribute)
metre (sbmlutils.factory.Units attribute)
mg (sbmlutils.examples.algebraic_rule.U attribute)
(sbmlutils.examples.assignment.U attribute)
(sbmlutils.examples.icg.model_body.U attribute)
(sbmlutils.examples.parameter.U attribute)
(sbmlutils.examples.unit_definitions.U attribute)
mg_per_day (sbmlutils.examples.unit_definitions.U attribute)
mg_per_dl (sbmlutils.examples.dallaman.dallaman.U attribute)
mg_per_g (sbmlutils.examples.icg.model_body.U attribute)
(sbmlutils.examples.unit_definitions.U attribute)
mg_per_hr (sbmlutils.examples.algebraic_rule.U attribute)
(sbmlutils.examples.assignment.U attribute)
(sbmlutils.examples.icg.model_body.U attribute)
(sbmlutils.examples.parameter.U attribute)
(sbmlutils.examples.unit_definitions.U attribute)
mg_per_kg (sbmlutils.examples.dallaman.dallaman.U attribute)
mg_per_kgmin (sbmlutils.examples.dallaman.dallaman.U attribute)
mg_per_l (sbmlutils.examples.algebraic_rule.U attribute)
(sbmlutils.examples.assignment.U attribute)
(sbmlutils.examples.icg.model_body.U attribute)
(sbmlutils.examples.parameter.U attribute)
(sbmlutils.examples.unit_definitions.U attribute)
mg_per_min (sbmlutils.examples.icg.model_body.U attribute)
(sbmlutils.examples.unit_definitions.U attribute)
mg_per_minpmol (sbmlutils.examples.dallaman.dallaman.U attribute)
mgl_per_kgminpmol (sbmlutils.examples.dallaman.dallaman.U attribute)
min (sbmlutils.examples.compartment_species_reaction.U attribute)
(sbmlutils.examples.dallaman.dallaman.U attribute)
(sbmlutils.examples.icg.model_body.U attribute)
(sbmlutils.examples.icg.model_liver.U attribute)
(sbmlutils.examples.model.U attribute)
(sbmlutils.examples.model_definitions.U attribute)
(sbmlutils.examples.multiple_substance_units.U attribute)
(sbmlutils.examples.unit_definitions.U attribute)
(sbmlutils.examples.units_namespace.U attribute)
min_per_day (sbmlutils.examples.unit_definitions.U attribute)
min_per_hr (sbmlutils.examples.icg.model_body.U attribute)
(sbmlutils.examples.unit_definitions.U attribute)
minkg_per_pmol (sbmlutils.examples.dallaman.dallaman.U attribute)
ml (sbmlutils.examples.icg.model_body.U attribute)
(sbmlutils.examples.unit_definitions.U attribute)
ml_per_l (sbmlutils.examples.icg.model_body.U attribute)
(sbmlutils.examples.species.U attribute)
(sbmlutils.examples.unit_definitions.U attribute)
ml_per_s (sbmlutils.examples.icg.model_body.U attribute)
(sbmlutils.examples.unit_definitions.U attribute)
ml_per_s_kg (sbmlutils.examples.icg.model_body.U attribute)
(sbmlutils.examples.unit_definitions.U attribute)
mM (sbmlutils.examples.annotation.U attribute)
(sbmlutils.examples.compartment_species_reaction.U attribute)
(sbmlutils.examples.demo.demo.U attribute)
(sbmlutils.examples.icg.model_body.U attribute)
(sbmlutils.examples.icg.model_liver.U attribute)
(sbmlutils.examples.model.U attribute)
(sbmlutils.examples.multiple_substance_units.U attribute)
(sbmlutils.examples.reaction_with_units.U attribute)
(sbmlutils.examples.tiny.tiny.U attribute)
(sbmlutils.examples.unit_definitions.U attribute)
mmole (sbmlutils.examples.compartment_species_reaction.U attribute)
(sbmlutils.examples.fbc.fbc_userdefinedconstraints.U attribute)
(sbmlutils.examples.fbc.fbc_v2.U attribute)
(sbmlutils.examples.fbc.fbc_v3.U attribute)
(sbmlutils.examples.icg.model_body.U attribute)
(sbmlutils.examples.icg.model_liver.U attribute)
(sbmlutils.examples.model.U attribute)
(sbmlutils.examples.model_definitions.U attribute)
(sbmlutils.examples.multiple_substance_units.U attribute)
(sbmlutils.examples.reaction_with_units.U attribute)
(sbmlutils.examples.species.U attribute)
(sbmlutils.examples.tiny.tiny.U attribute)
(sbmlutils.examples.unit_definitions.U attribute)
(sbmlutils.examples.units_namespace.U attribute)
mmole_per_hr (sbmlutils.examples.fbc.fbc_userdefinedconstraints.U attribute)
(sbmlutils.examples.fbc.fbc_v2.U attribute)
(sbmlutils.examples.fbc.fbc_v3.U attribute)
(sbmlutils.examples.icg.model_body.U attribute)
(sbmlutils.examples.unit_definitions.U attribute)
mmole_per_hr_ml (sbmlutils.examples.icg.model_body.U attribute)
(sbmlutils.examples.unit_definitions.U attribute)
mmole_per_l (sbmlutils.examples.fbc.fbc_userdefinedconstraints.U attribute)
(sbmlutils.examples.fbc.fbc_v2.U attribute)
(sbmlutils.examples.fbc.fbc_v3.U attribute)
mmole_per_min (sbmlutils.examples.compartment_species_reaction.U attribute)
(sbmlutils.examples.icg.model_body.U attribute)
(sbmlutils.examples.icg.model_liver.U attribute)
(sbmlutils.examples.model.U attribute)
(sbmlutils.examples.multiple_substance_units.U attribute)
(sbmlutils.examples.unit_definitions.U attribute)
mmole_per_min_kg (sbmlutils.examples.icg.model_body.U attribute)
(sbmlutils.examples.unit_definitions.U attribute)
mmole_per_min_l (sbmlutils.examples.icg.model_body.U attribute)
(sbmlutils.examples.icg.model_liver.U attribute)
(sbmlutils.examples.unit_definitions.U attribute)
mmole_per_s (sbmlutils.examples.reaction_with_units.U attribute)
(sbmlutils.examples.species.U attribute)
(sbmlutils.examples.tiny.tiny.U attribute)
Model (class in sbmlutils.factory)
model (in module sbmlutils.examples.algebraic_rule)
(in module sbmlutils.examples.annotation)
(in module sbmlutils.examples.assignment)
(in module sbmlutils.examples.combine_archive.omex_models)
(in module sbmlutils.examples.compartment_species_reaction)
(in module sbmlutils.examples.demo.demo)
(in module sbmlutils.examples.distrib.distrib_comp)
(in module sbmlutils.examples.distrib.distrib_distributions)
(in module sbmlutils.examples.distrib.distrib_uncertainties)
(in module sbmlutils.examples.fbc.fbc_key_value_pair)
(in module sbmlutils.examples.fbc.fbc_mass_charge)
(in module sbmlutils.examples.fbc.fbc_userdefinedconstraints)
(in module sbmlutils.examples.fbc.fbc_v2)
(in module sbmlutils.examples.fbc.fbc_v3)
(in module sbmlutils.examples.fbc.fbc_version3)
(in module sbmlutils.examples.icg.model_liver)
(in module sbmlutils.examples.model)
(in module sbmlutils.examples.model_definitions)
(in module sbmlutils.examples.multiple_substance_units)
(in module sbmlutils.examples.notes)
(in module sbmlutils.examples.parameter)
(in module sbmlutils.examples.reaction)
(in module sbmlutils.examples.reaction_with_units)
(in module sbmlutils.examples.species)
(in module sbmlutils.examples.tiny.tiny)
(in module sbmlutils.examples.tutorial.linear_chain)
(in module sbmlutils.examples.tutorial.minimal_model)
(in module sbmlutils.examples.tutorial.minimal_model_comp)
(in module sbmlutils.examples.tutorial.model_antimony)
(in module sbmlutils.examples.tutorial.model_composition)
(in module sbmlutils.examples.tutorial.random_network)
(in module sbmlutils.examples.unit_definitions)
(in module sbmlutils.examples.units_namespace)
(sbmlutils.factory.FactoryResult attribute)
model() (sbmlutils.report.sbmlinfo.SBMLDocumentInfo method)
Model.Config (class in sbmlutils.factory)
model_antimony (in module sbmlutils.examples.tutorial.model_antimony)
MODEL_BASE_PATH (in module sbmlutils.examples.icg)
model_body (in module sbmlutils.examples.icg.model_body)
model_comp (in module sbmlutils.examples.combine_archive.omex_models)
model_definitions (sbmlutils.factory.Model attribute)
(sbmlutils.factory.ModelDict attribute)
model_definitions() (sbmlutils.report.sbmlinfo.SBMLDocumentInfo method)
model_dict() (sbmlutils.report.sbmlinfo.SBMLDocumentInfo method)
model_fbc (in module sbmlutils.examples.fbc.fbc_version3)
model_history() (sbmlutils.report.sbmlinfo.SBMLDocumentInfo class method)
MODEL_PATH (in module sbmlutils.examples.icg)
model_units (sbmlutils.factory.Model attribute)
(sbmlutils.factory.ModelDict attribute)
ModelAnnotator (class in sbmlutils.metadata.annotator)
ModelDefinition (class in sbmlutils.factory)
ModelDict (class in sbmlutils.factory)
modeling_practice (sbmlutils.factory.ValidationOptions attribute)
(sbmlutils.validation.ValidationOptions attribute)
MODELS_DIR (in module sbmlutils.resources)
ModelUnits (class in sbmlutils.factory)
MODIFIER_PATTERN (in module sbmlutils.reaction_equation)
module
sbmlutils
sbmlutils.biomodels
sbmlutils.comp
sbmlutils.comp.comp
sbmlutils.comp.flatten
sbmlutils.console
sbmlutils.converters
sbmlutils.converters.copasi
sbmlutils.converters.mathml
sbmlutils.converters.odefac
sbmlutils.converters.xpp
sbmlutils.converters.xpp_examples
sbmlutils.converters.xpp_helpers
sbmlutils.cytoscape
sbmlutils.data
sbmlutils.data.interpolation
sbmlutils.data.interpolation_example
sbmlutils.data.interpolation_pancreas
sbmlutils.distrib
sbmlutils.distrib.distrib_examples
sbmlutils.distrib.distrib_packages
sbmlutils.examples
sbmlutils.examples.algebraic_rule
sbmlutils.examples.annotation
sbmlutils.examples.assignment
sbmlutils.examples.combine_archive
sbmlutils.examples.combine_archive.omex_models
sbmlutils.examples.compartment_species_reaction
sbmlutils.examples.dallaman
sbmlutils.examples.dallaman.dallaman
sbmlutils.examples.demo
sbmlutils.examples.demo.demo
sbmlutils.examples.distrib
sbmlutils.examples.distrib.distrib_comp
sbmlutils.examples.distrib.distrib_distributions
sbmlutils.examples.distrib.distrib_uncertainties
sbmlutils.examples.fbc
sbmlutils.examples.fbc.fbc_key_value_pair
sbmlutils.examples.fbc.fbc_mass_charge
sbmlutils.examples.fbc.fbc_userdefinedconstraints
sbmlutils.examples.fbc.fbc_v2
sbmlutils.examples.fbc.fbc_v3
sbmlutils.examples.fbc.fbc_version3
sbmlutils.examples.icg
sbmlutils.examples.icg.annotations
sbmlutils.examples.icg.factory
sbmlutils.examples.icg.model_body
sbmlutils.examples.icg.model_liver
sbmlutils.examples.icg.templates
sbmlutils.examples.merge_models
sbmlutils.examples.merge_models.merge_models
sbmlutils.examples.model
sbmlutils.examples.model_definitions
sbmlutils.examples.multiple_substance_units
sbmlutils.examples.notes
sbmlutils.examples.parameter
sbmlutils.examples.reaction
sbmlutils.examples.reaction_with_units
sbmlutils.examples.species
sbmlutils.examples.templates
sbmlutils.examples.tiny
sbmlutils.examples.tiny.simulation
sbmlutils.examples.tiny.tiny
sbmlutils.examples.tutorial
sbmlutils.examples.tutorial.linear_chain
sbmlutils.examples.tutorial.minimal_model
sbmlutils.examples.tutorial.minimal_model_annotations
sbmlutils.examples.tutorial.minimal_model_comp
sbmlutils.examples.tutorial.model_antimony
sbmlutils.examples.tutorial.model_composition
sbmlutils.examples.tutorial.random_network
sbmlutils.examples.unit_definitions
sbmlutils.examples.units_namespace
sbmlutils.examples.van_der_pol
sbmlutils.factory
sbmlutils.fbc
sbmlutils.fbc.cobra
sbmlutils.fbc.fbc
sbmlutils.io
sbmlutils.io.sbml
sbmlutils.layout
sbmlutils.layout.layout
sbmlutils.log
sbmlutils.manipulation
sbmlutils.manipulation.merge
sbmlutils.metadata
sbmlutils.metadata.annotator
sbmlutils.metadata.miriam
sbmlutils.metadata.sbo
sbmlutils.notes
sbmlutils.parser
sbmlutils.reaction_equation
sbmlutils.report
sbmlutils.report.api
sbmlutils.report.api_examples
sbmlutils.report.mathml
sbmlutils.report.sbmlinfo
sbmlutils.report.sbmlreport
sbmlutils.report.units
sbmlutils.resources
sbmlutils.utils
sbmlutils.validation
mole (sbmlutils.factory.Units attribute)
mole_per_s (sbmlutils.examples.annotation.U attribute)
(sbmlutils.examples.demo.demo.U attribute)
(sbmlutils.examples.fbc.fbc_mass_charge.U attribute)
mul_per_g (sbmlutils.examples.icg.model_body.U attribute)
(sbmlutils.examples.unit_definitions.U attribute)
mul_per_min_mg (sbmlutils.examples.icg.model_body.U attribute)
(sbmlutils.examples.unit_definitions.U attribute)
N
n_cells (in module sbmlutils.examples.combine_archive.omex_models)
(in module sbmlutils.examples.tutorial.minimal_model_comp)
n_chain (in module sbmlutils.examples.tutorial.linear_chain)
n_links (in module sbmlutils.examples.tutorial.random_network)
n_species (in module sbmlutils.examples.tutorial.random_network)
name (sbmlutils.factory.Model attribute)
(sbmlutils.factory.ModelDict attribute)
(sbmlutils.reaction_equation.EquationPart attribute)
(sbmlutils.report.api_examples.ExampleMetaData attribute)
newton (sbmlutils.factory.Units attribute)
normalize_objective_type() (sbmlutils.factory.Objective class method)
normalize_variable_type() (sbmlutils.factory.FluxObjective class method)
Notes (class in sbmlutils.notes)
NOTES (in module sbmlutils.converters.xpp)
notes (in module sbmlutils.data.interpolation)
(in module sbmlutils.notes)
(sbmlutils.factory.Model attribute)
(sbmlutils.factory.ModelDict attribute)
(sbmlutils.reaction_equation.EquationPart attribute)
NotesFormat (class in sbmlutils.notes)
O
Objective (class in sbmlutils.factory)
objective_types (sbmlutils.factory.Objective attribute)
objectives (sbmlutils.factory.Model attribute)
(sbmlutils.factory.ModelDict attribute)
objectives() (sbmlutils.report.sbmlinfo.SBMLDocumentInfo method)
objects (sbmlutils.factory.ModelDict attribute)
ohm (sbmlutils.factory.Units attribute)
OMEX_COMPMODELS (in module sbmlutils.resources)
OMEX_ICGMODEL (in module sbmlutils.resources)
OMEX_OMEPRAZOLEMODEL (in module sbmlutils.resources)
omex_path (in module sbmlutils.parser)
OMEX_SHOWCASE (in module sbmlutils.resources)
origins (in module sbmlutils.report.api)
output_dir (in module sbmlutils.biomodels)
(in module sbmlutils.report.sbmlinfo)
OUTPUT_PORT (sbmlutils.factory.PortType attribute)
overdetermined_model (sbmlutils.factory.ValidationOptions attribute)
(sbmlutils.validation.ValidationOptions attribute)
P
Package (class in sbmlutils.factory)
packages (sbmlutils.factory.Model attribute)
(sbmlutils.factory.ModelDict attribute)
(sbmlutils.report.api_examples.ExampleMetaData attribute)
Parameter (class in sbmlutils.factory)
parameters (sbmlutils.factory.Model attribute)
(sbmlutils.factory.ModelDict attribute)
parameters() (sbmlutils.report.sbmlinfo.SBMLDocumentInfo method)
parse_keyword() (in module sbmlutils.converters.xpp)
parts_from_expression() (in module sbmlutils.converters.xpp)
per_hr (sbmlutils.examples.icg.model_body.U attribute)
(sbmlutils.examples.unit_definitions.U attribute)
per_kg (sbmlutils.examples.unit_definitions.U attribute)
per_min (sbmlutils.examples.dallaman.dallaman.U attribute)
(sbmlutils.examples.icg.model_body.U attribute)
(sbmlutils.examples.icg.model_liver.U attribute)
(sbmlutils.examples.multiple_substance_units.U attribute)
(sbmlutils.examples.unit_definitions.U attribute)
per_mmole (sbmlutils.examples.multiple_substance_units.U attribute)
per_s (sbmlutils.examples.annotation.U attribute)
(sbmlutils.examples.species.U attribute)
piecewise() (in module sbmlutils.converters.mathml)
pmol_per_kg (sbmlutils.examples.dallaman.dallaman.U attribute)
pmol_per_kgmin (sbmlutils.examples.dallaman.dallaman.U attribute)
pmol_per_l (sbmlutils.examples.dallaman.dallaman.U attribute)
pmolmg_per_kgdl (sbmlutils.examples.dallaman.dallaman.U attribute)
pmolmg_per_kgmindl (sbmlutils.examples.dallaman.dallaman.U attribute)
Port (class in sbmlutils.factory)
port (sbmlutils.factory.Model attribute)
PORT (sbmlutils.factory.PortType attribute)
PORT_SUFFIX (in module sbmlutils.factory)
PORT_UNIT_SUFFIX (in module sbmlutils.factory)
ports (sbmlutils.factory.Model attribute)
(sbmlutils.factory.ModelDict attribute)
ports() (sbmlutils.report.sbmlinfo.SBMLDocumentInfo method)
PortType (class in sbmlutils.factory)
PREFIX (sbmlutils.factory.ExchangeReaction attribute)
product (in module sbmlutils.examples.fbc.fbc_version3)
product() (in module sbmlutils.converters.mathml)
program_name (in module sbmlutils)
promote_local_variables() (in module sbmlutils.io.sbml)
Q
Q_ (in module sbmlutils.report.units)
query_curated_biomodels() (in module sbmlutils.biomodels)
R
rate_rules (sbmlutils.factory.Model attribute)
(sbmlutils.factory.ModelDict attribute)
RateRule (class in sbmlutils.factory)
reactant (in module sbmlutils.examples.fbc.fbc_version3)
Reaction (class in sbmlutils.factory)
reaction (in module sbmlutils.examples.fbc.fbc_version3)
ReactionEquation (class in sbmlutils.factory)
(class in sbmlutils.reaction_equation)
ReactionGlyph (class in sbmlutils.layout)
(class in sbmlutils.layout.layout)
reactions (sbmlutils.factory.Model attribute)
(sbmlutils.factory.ModelDict attribute)
reactions() (sbmlutils.report.sbmlinfo.SBMLDocumentInfo method)
read_annotations() (sbmlutils.metadata.annotator.ModelAnnotator static method)
read_annotations_df() (sbmlutils.metadata.annotator.ModelAnnotator static method)
read_cobra_model() (in module sbmlutils.fbc.cobra)
read_sbml() (in module sbmlutils.io)
(in module sbmlutils.io.sbml)
replace_element_in_submodels() (in module sbmlutils.comp.comp)
replace_elements() (in module sbmlutils.comp.comp)
replace_formula() (in module sbmlutils.converters.xpp_helpers)
replaced_by() (in module sbmlutils.comp.comp)
replaced_elements (sbmlutils.factory.Model attribute)
(sbmlutils.factory.ModelDict attribute)
replaced_species (in module sbmlutils.examples.icg.model_body)
ReplacedBy (class in sbmlutils.factory)
ReplacedElement (class in sbmlutils.factory)
report_from_file() (in module sbmlutils.report.api)
report_from_url() (in module sbmlutils.report.api)
REPRESSILATOR_SBML (in module sbmlutils.resources)
RESOURCES_DIR (in module sbmlutils)
(in module sbmlutils.resources)
results (in module sbmlutils.examples.icg.factory)
(in module sbmlutils.examples.icg.model_body)
(in module sbmlutils.examples.icg.model_liver)
REVERSIBILITY_PATTERN (in module sbmlutils.reaction_equation)
REVERSIBILITY_SEPARATOR (in module sbmlutils.reaction_equation)
root() (in module sbmlutils.converters.mathml)
rules (sbmlutils.factory.Model attribute)
(sbmlutils.factory.ModelDict attribute)
rules() (sbmlutils.report.sbmlinfo.SBMLDocumentInfo method)
S
s (sbmlutils.examples.icg.model_body.U attribute)
(sbmlutils.examples.reaction_with_units.U attribute)
(sbmlutils.examples.unit_definitions.U attribute)
s1 (in module sbmlutils.examples.fbc.fbc_version3)
s1_fbc (in module sbmlutils.examples.fbc.fbc_version3)
s2 (in module sbmlutils.examples.fbc.fbc_version3)
s_per_hr (sbmlutils.examples.icg.model_body.U attribute)
(sbmlutils.examples.unit_definitions.U attribute)
s_per_min (sbmlutils.examples.icg.model_body.U attribute)
(sbmlutils.examples.unit_definitions.U attribute)
sbase_dict() (sbmlutils.report.sbmlinfo.SBMLDocumentInfo class method)
SBASE_REF_TYPE_ID (in module sbmlutils.comp.comp)
SBASE_REF_TYPE_METAID (in module sbmlutils.comp.comp)
SBASE_REF_TYPE_PORT (in module sbmlutils.comp.comp)
SBASE_REF_TYPE_UNIT (in module sbmlutils.comp.comp)
sbaseref_dict() (sbmlutils.report.sbmlinfo.SBMLDocumentInfo method)
SBML2ODE (class in sbmlutils.converters.odefac)
SBML_LEVEL (in module sbmlutils.factory)
sbml_path (in module sbmlutils.examples.fbc.fbc_key_value_pair)
(sbmlutils.factory.FactoryResult attribute)
sbml_paths_idfn() (in module sbmlutils.resources)
sbml_str (in module sbmlutils.examples.fbc.fbc_version3)
SBML_TESTSUITE_DIR (in module sbmlutils.resources)
sbml_to_model() (in module sbmlutils.parser)
SBML_VERSION (in module sbmlutils.factory)
SBMLDocumentInfo (class in sbmlutils.report.sbmlinfo)
sbmlns (in module sbmlutils.examples.fbc.fbc_version3)
sbmlutils
module
sbmlutils.biomodels
module
sbmlutils.comp
module
sbmlutils.comp.comp
module
sbmlutils.comp.flatten
module
sbmlutils.console
module
sbmlutils.converters
module
sbmlutils.converters.copasi
module
sbmlutils.converters.mathml
module
sbmlutils.converters.odefac
module
sbmlutils.converters.xpp
module
sbmlutils.converters.xpp_examples
module
sbmlutils.converters.xpp_helpers
module
sbmlutils.cytoscape
module
sbmlutils.data
module
sbmlutils.data.interpolation
module
sbmlutils.data.interpolation_example
module
sbmlutils.data.interpolation_pancreas
module
sbmlutils.distrib
module
sbmlutils.distrib.distrib_examples
module
sbmlutils.distrib.distrib_packages
module
sbmlutils.examples
module
sbmlutils.examples.algebraic_rule
module
sbmlutils.examples.annotation
module
sbmlutils.examples.assignment
module
sbmlutils.examples.combine_archive
module
sbmlutils.examples.combine_archive.omex_models
module
sbmlutils.examples.compartment_species_reaction
module
sbmlutils.examples.dallaman
module
sbmlutils.examples.dallaman.dallaman
module
sbmlutils.examples.demo
module
sbmlutils.examples.demo.demo
module
sbmlutils.examples.distrib
module
sbmlutils.examples.distrib.distrib_comp
module
sbmlutils.examples.distrib.distrib_distributions
module
sbmlutils.examples.distrib.distrib_uncertainties
module
sbmlutils.examples.fbc
module
sbmlutils.examples.fbc.fbc_key_value_pair
module
sbmlutils.examples.fbc.fbc_mass_charge
module
sbmlutils.examples.fbc.fbc_userdefinedconstraints
module
sbmlutils.examples.fbc.fbc_v2
module
sbmlutils.examples.fbc.fbc_v3
module
sbmlutils.examples.fbc.fbc_version3
module
sbmlutils.examples.icg
module
sbmlutils.examples.icg.annotations
module
sbmlutils.examples.icg.factory
module
sbmlutils.examples.icg.model_body
module
sbmlutils.examples.icg.model_liver
module
sbmlutils.examples.icg.templates
module
sbmlutils.examples.merge_models
module
sbmlutils.examples.merge_models.merge_models
module
sbmlutils.examples.model
module
sbmlutils.examples.model_definitions
module
sbmlutils.examples.multiple_substance_units
module
sbmlutils.examples.notes
module
sbmlutils.examples.parameter
module
sbmlutils.examples.reaction
module
sbmlutils.examples.reaction_with_units
module
sbmlutils.examples.species
module
sbmlutils.examples.templates
module
sbmlutils.examples.tiny
module
sbmlutils.examples.tiny.simulation
module
sbmlutils.examples.tiny.tiny
module
sbmlutils.examples.tutorial
module
sbmlutils.examples.tutorial.linear_chain
module
sbmlutils.examples.tutorial.minimal_model
module
sbmlutils.examples.tutorial.minimal_model_annotations
module
sbmlutils.examples.tutorial.minimal_model_comp
module
sbmlutils.examples.tutorial.model_antimony
module
sbmlutils.examples.tutorial.model_composition
module
sbmlutils.examples.tutorial.random_network
module
sbmlutils.examples.unit_definitions
module
sbmlutils.examples.units_namespace
module
sbmlutils.examples.van_der_pol
module
sbmlutils.factory
module
sbmlutils.fbc
module
sbmlutils.fbc.cobra
module
sbmlutils.fbc.fbc
module
sbmlutils.io
module
sbmlutils.io.sbml
module
sbmlutils.layout
module
sbmlutils.layout.layout
module
sbmlutils.log
module
sbmlutils.manipulation
module
sbmlutils.manipulation.merge
module
sbmlutils.metadata
module
sbmlutils.metadata.annotator
module
sbmlutils.metadata.miriam
module
sbmlutils.metadata.sbo
module
sbmlutils.notes
module
sbmlutils.parser
module
sbmlutils.reaction_equation
module
sbmlutils.report
module
sbmlutils.report.api
module
sbmlutils.report.api_examples
module
sbmlutils.report.mathml
module
sbmlutils.report.sbmlinfo
module
sbmlutils.report.sbmlreport
module
sbmlutils.report.units
module
sbmlutils.resources
module
sbmlutils.utils
module
sbmlutils.validation
module
sbo_consistency (sbmlutils.factory.ValidationOptions attribute)
(sbmlutils.validation.ValidationOptions attribute)
sboTerm (sbmlutils.factory.Model attribute)
(sbmlutils.factory.ModelDict attribute)
(sbmlutils.reaction_equation.EquationPart attribute)
second (sbmlutils.factory.Units attribute)
set_boundary_conditions_false() (in module sbmlutils.fbc.fbc)
set_flux_bounds() (in module sbmlutils.fbc.fbc)
set_kinetic_law() (sbmlutils.factory.Reaction static method)
set_level_for_all_loggers() (in module sbmlutils.log)
set_model_units() (sbmlutils.factory.ModelUnits static method)
short_names (in module sbmlutils.report.units)
sid (sbmlutils.factory.Model attribute)
(sbmlutils.factory.ModelDict attribute)
(sbmlutils.reaction_equation.EquationPart attribute)
sid_ex (in module sbmlutils.examples.icg.model_body)
sid_value_from_part() (in module sbmlutils.converters.xpp)
sname (in module sbmlutils.examples.icg.model_body)
,
[1]
Species (class in sbmlutils.factory)
species (in module sbmlutils.examples.icg.annotations)
(sbmlutils.factory.Model attribute)
(sbmlutils.factory.ModelDict attribute)
(sbmlutils.reaction_equation.EquationPart attribute)
species() (sbmlutils.report.sbmlinfo.SBMLDocumentInfo method)
SpeciesGlyph (class in sbmlutils.layout)
(class in sbmlutils.layout.layout)
sqr() (in module sbmlutils.converters.mathml)
start_server() (in module sbmlutils.report.sbmlreport)
stoichiometry (sbmlutils.reaction_equation.EquationPart attribute)
Submodel (class in sbmlutils.factory)
SUBMODEL_SID_DICT (in module sbmlutils.examples.icg.model_body)
submodels (sbmlutils.factory.Model attribute)
(sbmlutils.factory.ModelDict attribute)
submodels() (sbmlutils.report.sbmlinfo.SBMLDocumentInfo method)
SUBSTANCES_BODY (in module sbmlutils.examples.icg.model_body)
symbol_to_latex() (in module sbmlutils.report.mathml)
T
TEMPLATE_DIR (in module sbmlutils.converters.odefac)
terms_of_use (in module sbmlutils.examples.icg.templates)
(in module sbmlutils.examples.templates)
TESTDATA_DIR (in module sbmlutils.resources)
timeit() (in module sbmlutils.utils)
tiny_simulation() (in module sbmlutils.examples.tiny.simulation)
to_json() (sbmlutils.report.sbmlinfo.SBMLDocumentInfo method)
to_markdown() (sbmlutils.converters.odefac.SBML2ODE method)
to_python() (sbmlutils.converters.odefac.SBML2ODE method)
to_R() (sbmlutils.converters.odefac.SBML2ODE method)
to_string() (sbmlutils.factory.ReactionEquation method)
(sbmlutils.reaction_equation.ReactionEquation method)
U
U (class in sbmlutils.examples.algebraic_rule)
(class in sbmlutils.examples.annotation)
(class in sbmlutils.examples.assignment)
(class in sbmlutils.examples.compartment_species_reaction)
(class in sbmlutils.examples.dallaman.dallaman)
(class in sbmlutils.examples.demo.demo)
(class in sbmlutils.examples.distrib.distrib_comp)
(class in sbmlutils.examples.distrib.distrib_distributions)
(class in sbmlutils.examples.distrib.distrib_uncertainties)
(class in sbmlutils.examples.fbc.fbc_mass_charge)
(class in sbmlutils.examples.fbc.fbc_userdefinedconstraints)
(class in sbmlutils.examples.fbc.fbc_v2)
(class in sbmlutils.examples.fbc.fbc_v3)
(class in sbmlutils.examples.icg.model_body)
(class in sbmlutils.examples.icg.model_liver)
(class in sbmlutils.examples.model)
(class in sbmlutils.examples.model_definitions)
(class in sbmlutils.examples.multiple_substance_units)
(class in sbmlutils.examples.parameter)
(class in sbmlutils.examples.reaction_with_units)
(class in sbmlutils.examples.species)
(class in sbmlutils.examples.tiny.tiny)
(class in sbmlutils.examples.unit_definitions)
(class in sbmlutils.examples.units_namespace)
udef_to_string() (in module sbmlutils.report.units)
Uncertainty (class in sbmlutils.factory)
uncertainty() (in module sbmlutils.distrib.distrib_examples)
UncertParameter (class in sbmlutils.factory)
UncertSpan (class in sbmlutils.factory)
unit_definitions() (sbmlutils.report.sbmlinfo.SBMLDocumentInfo method)
UnitDefinition (class in sbmlutils.factory)
UnitDefinition.Config (class in sbmlutils.factory)
Units (class in sbmlutils.factory)
units (sbmlutils.factory.Model attribute)
(sbmlutils.factory.ModelDict attribute)
units_consistency (sbmlutils.factory.ValidationOptions attribute)
(sbmlutils.validation.ValidationOptions attribute)
UnitType (in module sbmlutils.factory)
ureg (in module sbmlutils.report.units)
user_defined_constraints (sbmlutils.factory.Model attribute)
(sbmlutils.factory.ModelDict attribute)
UserDefinedConstraint (class in sbmlutils.factory)
UserDefinedConstraintComponent (class in sbmlutils.factory)
V
validate_data() (sbmlutils.data.interpolation.Interpolation method)
validate_doc() (in module sbmlutils.validation)
validate_sbml() (in module sbmlutils.io)
(in module sbmlutils.io.sbml)
ValidationOptions (class in sbmlutils.factory)
(class in sbmlutils.validation)
ValidationResult (class in sbmlutils.validation)
VDP_SBML (in module sbmlutils.resources)
visualize_antimony() (in module sbmlutils.cytoscape)
visualize_sbml() (in module sbmlutils.cytoscape)
volt (sbmlutils.factory.Units attribute)
W
warning_count (sbmlutils.validation.ValidationResult property)
write_ids_to_names() (in module sbmlutils.converters.copasi)
write_sbml() (in module sbmlutils.io)
(in module sbmlutils.io.sbml)
write_sbml_to_file() (sbmlutils.data.interpolation.Interpolation method)
write_sbml_to_string() (sbmlutils.data.interpolation.Interpolation method)
X
xid (sbmlutils.data.interpolation.Interpolator property)
xor() (in module sbmlutils.converters.mathml)
xpp2sbml() (in module sbmlutils.converters.xpp)
XPP_AUX (in module sbmlutils.converters.xpp)
XPP_COMMENT_CHARS (in module sbmlutils.converters.xpp)
XPP_CONTINUATION_CHAR (in module sbmlutils.converters.xpp)
XPP_DE (in module sbmlutils.converters.xpp)
XPP_END_WORD (in module sbmlutils.converters.xpp)
XPP_FUN (in module sbmlutils.converters.xpp)
XPP_GLO (in module sbmlutils.converters.xpp)
XPP_IE (in module sbmlutils.converters.xpp)
XPP_INIT (in module sbmlutils.converters.xpp)
XPP_MAR (in module sbmlutils.converters.xpp)
XPP_NUM (in module sbmlutils.converters.xpp)
XPP_ODE (in module sbmlutils.converters.xpp)
XPP_PAR (in module sbmlutils.converters.xpp)
XPP_SETTING_CHAR (in module sbmlutils.converters.xpp)
XPP_TAB (in module sbmlutils.converters.xpp)
XPP_TYPE_CHARS (in module sbmlutils.converters.xpp)
XPP_WIE (in module sbmlutils.converters.xpp)
xslt_cmml2pmml (in module sbmlutils.report.mathml)
xslt_pmml2tex (in module sbmlutils.report.mathml)
Y
yid (sbmlutils.data.interpolation.Interpolator property)
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