Core

momapy.sbml.core

Classes for SBML maps

Classes:

Name	Description
`BQBiol`	Class for http://biomodels.net/biology-qualifiers/ qualifiers
`BQModel`	Class for http://biomodels.net/model-qualifiers/ qualifiers
`BiomodelQualifier`	Abstract class for http://biomodels.net/ qualifiers
`Compartment`	Compartment(*, id_: str = , name: str \| None = None, sbo_term: momapy.sbml.core.SBOTerm \| None = None, metaid: str \| None = None, outside: Optional[ForwardRef('Compartment', module='momapy.sbml.core')] = None)
`Model`	Model(*, id_: str = , name: str \| None = None, sbo_term: momapy.sbml.core.SBOTerm \| None = None, metaid: str \| None = None, compartments: frozenset[momapy.sbml.core.Compartment] = , species: frozenset[momapy.sbml.core.Species] = , reactions: frozenset[momapy.sbml.core.Reaction] = )
`ModifierSpeciesReference`	ModifierSpeciesReference(*, id_: str = , name: str \| None = None, sbo_term: momapy.sbml.core.SBOTerm \| None = None, metaid: str \| None = None, referred_species: momapy.sbml.core.Species)
`RDFAnnotation`	RDFAnnotation(*, id_: str = , qualifier: momapy.sbml.core.BiomodelQualifier, resources: frozenset[str] = )
`Reaction`	Reaction(*, id_: str = , name: str \| None = None, sbo_term: momapy.sbml.core.SBOTerm \| None = None, metaid: str \| None = None, reversible: bool, compartment: momapy.sbml.core.Compartment \| None = None, reactants: frozenset[momapy.sbml.core.SpeciesReference] = , products: frozenset[momapy.sbml.core.SpeciesReference] = , modifiers: frozenset[momapy.sbml.core.ModifierSpeciesReference] = )
`SBML`	SBML(*, id_: str = , name: str \| None = None, sbo_term: momapy.sbml.core.SBOTerm \| None = None, metaid: str \| None = None, xmlns: str = 'http://www.sbml.org/sbml/level3/version2/core', level: int = 3, version: int = 2, model: momapy.sbml.core.Model \| None = None)
`SBOTerm`	SBOTerm(*, id_: str = )
`SBase`	SBase(*, id_: str = , name: str \| None = None, sbo_term: momapy.sbml.core.SBOTerm \| None = None, metaid: str \| None = None)
`SimpleSpeciesReference`	SimpleSpeciesReference(*, id_: str = , name: str \| None = None, sbo_term: momapy.sbml.core.SBOTerm \| None = None, metaid: str \| None = None, referred_species: momapy.sbml.core.Species)
`Species`	Species(*, id_: str = , name: str \| None = None, sbo_term: momapy.sbml.core.SBOTerm \| None = None, metaid: str \| None = None, compartment: momapy.sbml.core.Compartment \| None = None)
`SpeciesReference`	SpeciesReference(*, id_: str = , name: str \| None = None, sbo_term: momapy.sbml.core.SBOTerm \| None = None, metaid: str \| None = None, referred_species: momapy.sbml.core.Species, stoichiometry: int \| None = None)

BQBiol

Bases: BiomodelQualifier

Class for http://biomodels.net/biology-qualifiers/ qualifiers

BQModel

Bases: BiomodelQualifier

Class for http://biomodels.net/model-qualifiers/ qualifiers

BiomodelQualifier

Bases: Enum

Abstract class for http://biomodels.net/ qualifiers

Compartment `dataclass`

Compartment(
    *,
    id_: str = make_uuid4_as_str(),
    name: str | None = None,
    sbo_term: SBOTerm | None = None,
    metaid: str | None = None,
    outside: Optional[
        ForwardRef(Compartment, module=core)
    ] = None,
)

Bases: SBase

Compartment(*, id_: str = , name: str | None = None, sbo_term: momapy.sbml.core.SBOTerm | None = None, metaid: str | None = None, outside: Optional[ForwardRef('Compartment', module='momapy.sbml.core')] = None)

Parameters:

Name	Type	Description	Default
`id_`	`str`	The id of the map element. This id is purely for the user to keep track of the element, it does not need to be unique and is not part of the identity of the element, i.e., it is not considered when testing for equality between two map elements or when hashing the map element	`'8362e4bd-22e0-4968-8e77-2f91616b974b'`
`name`	`str \| None`		`None`
`sbo_term`	`SBOTerm \| None`		`None`
`metaid`	`str \| None`		`None`
`outside`	`ForwardRef(Compartment, module=core) \| None`		`None`

Model `dataclass`

Model(
    *,
    id_: str = make_uuid4_as_str(),
    name: str | None = None,
    sbo_term: SBOTerm | None = None,
    metaid: str | None = None,
    compartments: frozenset[Compartment] = frozenset(),
    species: frozenset[Species] = frozenset(),
    reactions: frozenset[Reaction] = frozenset(),
)

Bases: SBase, Model

Model(*, id_: str = , name: str | None = None, sbo_term: momapy.sbml.core.SBOTerm | None = None, metaid: str | None = None, compartments: frozenset[momapy.sbml.core.Compartment] = , species: frozenset[momapy.sbml.core.Species] = , reactions: frozenset[momapy.sbml.core.Reaction] = )

Parameters:

Name	Type	Description	Default
`id_`	`str`	The id of the map element. This id is purely for the user to keep track of the element, it does not need to be unique and is not part of the identity of the element, i.e., it is not considered when testing for equality between two map elements or when hashing the map element	`'7af0ea73-488f-4437-a92d-b497bc0ac439'`
`name`	`str \| None`		`None`
`sbo_term`	`SBOTerm \| None`		`None`
`metaid`	`str \| None`		`None`
`compartments`	`frozenset[Compartment]`	frozenset() -> empty frozenset object frozenset(iterable) -> frozenset object Build an immutable unordered collection of unique elements.	`<class 'frozenset'>`
`species`	`frozenset[Species]`	frozenset() -> empty frozenset object frozenset(iterable) -> frozenset object Build an immutable unordered collection of unique elements.	`<class 'frozenset'>`
`reactions`	`frozenset[Reaction]`	frozenset() -> empty frozenset object frozenset(iterable) -> frozenset object Build an immutable unordered collection of unique elements.	`<class 'frozenset'>`

ModifierSpeciesReference `dataclass`

ModifierSpeciesReference(
    *,
    id_: str = make_uuid4_as_str(),
    name: str | None = None,
    sbo_term: SBOTerm | None = None,
    metaid: str | None = None,
    referred_species: Species,
)

Bases: SimpleSpeciesReference

ModifierSpeciesReference(*, id_: str = , name: str | None = None, sbo_term: momapy.sbml.core.SBOTerm | None = None, metaid: str | None = None, referred_species: momapy.sbml.core.Species)

Parameters:

Name	Type	Description	Default
`id_`	`str`	The id of the map element. This id is purely for the user to keep track of the element, it does not need to be unique and is not part of the identity of the element, i.e., it is not considered when testing for equality between two map elements or when hashing the map element	`'8a925aaf-ca1a-4b49-a0bf-685443af201a'`
`name`	`str \| None`		`None`
`sbo_term`	`SBOTerm \| None`		`None`
`metaid`	`str \| None`		`None`
`referred_species`	`Species`		required

RDFAnnotation `dataclass`

RDFAnnotation(
    *,
    id_: str = make_uuid4_as_str(),
    qualifier: BiomodelQualifier,
    resources: frozenset[str] = frozenset(),
)

Bases: ModelElement

RDFAnnotation(*, id_: str = , qualifier: momapy.sbml.core.BiomodelQualifier, resources: frozenset[str] = )

Parameters:

Name	Type	Description	Default
`id_`	`str`	The id of the map element. This id is purely for the user to keep track of the element, it does not need to be unique and is not part of the identity of the element, i.e., it is not considered when testing for equality between two map elements or when hashing the map element	`'3cf168d2-1231-472c-8dcd-7b0fabbfed68'`
`qualifier`	`BiomodelQualifier`		required
`resources`	`frozenset[str]`	frozenset() -> empty frozenset object frozenset(iterable) -> frozenset object Build an immutable unordered collection of unique elements.	`<class 'frozenset'>`

Reaction `dataclass`

Reaction(
    *,
    id_: str = make_uuid4_as_str(),
    name: str | None = None,
    sbo_term: SBOTerm | None = None,
    metaid: str | None = None,
    reversible: bool,
    compartment: Compartment | None = None,
    reactants: frozenset[SpeciesReference] = frozenset(),
    products: frozenset[SpeciesReference] = frozenset(),
    modifiers: frozenset[
        ModifierSpeciesReference
    ] = frozenset(),
)

Bases: SBase

Reaction(*, id_: str = , name: str | None = None, sbo_term: momapy.sbml.core.SBOTerm | None = None, metaid: str | None = None, reversible: bool, compartment: momapy.sbml.core.Compartment | None = None, reactants: frozenset[momapy.sbml.core.SpeciesReference] = , products: frozenset[momapy.sbml.core.SpeciesReference] = , modifiers: frozenset[momapy.sbml.core.ModifierSpeciesReference] = )

Parameters:

Name	Type	Description	Default
`id_`	`str`	The id of the map element. This id is purely for the user to keep track of the element, it does not need to be unique and is not part of the identity of the element, i.e., it is not considered when testing for equality between two map elements or when hashing the map element	`'a8fe1017-287e-4467-b985-8ef266925787'`
`name`	`str \| None`		`None`
`sbo_term`	`SBOTerm \| None`		`None`
`metaid`	`str \| None`		`None`
`reversible`	`bool`		required
`compartment`	`Compartment \| None`		`None`
`reactants`	`frozenset[SpeciesReference]`	frozenset() -> empty frozenset object frozenset(iterable) -> frozenset object Build an immutable unordered collection of unique elements.	`<class 'frozenset'>`
`products`	`frozenset[SpeciesReference]`	frozenset() -> empty frozenset object frozenset(iterable) -> frozenset object Build an immutable unordered collection of unique elements.	`<class 'frozenset'>`
`modifiers`	`frozenset[ModifierSpeciesReference]`	frozenset() -> empty frozenset object frozenset(iterable) -> frozenset object Build an immutable unordered collection of unique elements.	`<class 'frozenset'>`

SBML `dataclass`

SBML(
    *,
    id_: str = make_uuid4_as_str(),
    name: str | None = None,
    sbo_term: SBOTerm | None = None,
    metaid: str | None = None,
    xmlns: str = "http://www.sbml.org/sbml/level3/version2/core",
    level: int = 3,
    version: int = 2,
    model: Model | None = None,
)

Bases: SBase

SBML(*, id_: str = , name: str | None = None, sbo_term: momapy.sbml.core.SBOTerm | None = None, metaid: str | None = None, xmlns: str = 'http://www.sbml.org/sbml/level3/version2/core', level: int = 3, version: int = 2, model: momapy.sbml.core.Model | None = None)

Parameters:

Name	Type	Description	Default
`id_`	`str`	The id of the map element. This id is purely for the user to keep track of the element, it does not need to be unique and is not part of the identity of the element, i.e., it is not considered when testing for equality between two map elements or when hashing the map element	`'9a33dd87-1bc8-488a-8d19-6131f1eb52c9'`
`name`	`str \| None`		`None`
`sbo_term`	`SBOTerm \| None`		`None`
`metaid`	`str \| None`		`None`
`xmlns`	`str`		`'http://www.sbml.org/sbml/level3/version2/core'`
`level`	`int`		`3`
`version`	`int`		`2`
`model`	`Model \| None`		`None`

SBOTerm `dataclass`

SBOTerm(*, id_: str = make_uuid4_as_str())

Bases: ModelElement

SBOTerm(*, id_: str = )

Parameters:

Name	Type	Description	Default
`id_`	`str`	The id of the map element. This id is purely for the user to keep track of the element, it does not need to be unique and is not part of the identity of the element, i.e., it is not considered when testing for equality between two map elements or when hashing the map element	`'8a8751d0-57cf-4281-89ae-ddc70f2107f1'`

SBase `dataclass`

SBase(
    *,
    id_: str = make_uuid4_as_str(),
    name: str | None = None,
    sbo_term: SBOTerm | None = None,
    metaid: str | None = None,
)

Bases: ModelElement

SBase(*, id_: str = , name: str | None = None, sbo_term: momapy.sbml.core.SBOTerm | None = None, metaid: str | None = None)

Parameters:

Name	Type	Description	Default
`id_`	`str`	The id of the map element. This id is purely for the user to keep track of the element, it does not need to be unique and is not part of the identity of the element, i.e., it is not considered when testing for equality between two map elements or when hashing the map element	`'3a9f5651-8d82-48a8-92f2-8840418e8d0a'`
`name`	`str \| None`		`None`
`sbo_term`	`SBOTerm \| None`		`None`
`metaid`	`str \| None`		`None`

SimpleSpeciesReference `dataclass`

SimpleSpeciesReference(
    *,
    id_: str = make_uuid4_as_str(),
    name: str | None = None,
    sbo_term: SBOTerm | None = None,
    metaid: str | None = None,
    referred_species: Species,
)

Bases: SBase

SimpleSpeciesReference(*, id_: str = , name: str | None = None, sbo_term: momapy.sbml.core.SBOTerm | None = None, metaid: str | None = None, referred_species: momapy.sbml.core.Species)

Parameters:

Name	Type	Description	Default
`id_`	`str`	The id of the map element. This id is purely for the user to keep track of the element, it does not need to be unique and is not part of the identity of the element, i.e., it is not considered when testing for equality between two map elements or when hashing the map element	`'f8d0bbfd-fa01-4ac9-bc53-14e7a82aeadc'`
`name`	`str \| None`		`None`
`sbo_term`	`SBOTerm \| None`		`None`
`metaid`	`str \| None`		`None`
`referred_species`	`Species`		required

Species `dataclass`

Species(
    *,
    id_: str = make_uuid4_as_str(),
    name: str | None = None,
    sbo_term: SBOTerm | None = None,
    metaid: str | None = None,
    compartment: Compartment | None = None,
)

Bases: SBase

Species(*, id_: str = , name: str | None = None, sbo_term: momapy.sbml.core.SBOTerm | None = None, metaid: str | None = None, compartment: momapy.sbml.core.Compartment | None = None)

Parameters:

Name	Type	Description	Default
`id_`	`str`	The id of the map element. This id is purely for the user to keep track of the element, it does not need to be unique and is not part of the identity of the element, i.e., it is not considered when testing for equality between two map elements or when hashing the map element	`'70b0db6e-828b-4be3-81a8-19b03817d08e'`
`name`	`str \| None`		`None`
`sbo_term`	`SBOTerm \| None`		`None`
`metaid`	`str \| None`		`None`
`compartment`	`Compartment \| None`		`None`

SpeciesReference `dataclass`

SpeciesReference(
    *,
    id_: str = make_uuid4_as_str(),
    name: str | None = None,
    sbo_term: SBOTerm | None = None,
    metaid: str | None = None,
    referred_species: Species,
    stoichiometry: int | None = None,
)

Bases: SimpleSpeciesReference

SpeciesReference(*, id_: str = , name: str | None = None, sbo_term: momapy.sbml.core.SBOTerm | None = None, metaid: str | None = None, referred_species: momapy.sbml.core.Species, stoichiometry: int | None = None)

Parameters:

Name	Type	Description	Default
`id_`	`str`	The id of the map element. This id is purely for the user to keep track of the element, it does not need to be unique and is not part of the identity of the element, i.e., it is not considered when testing for equality between two map elements or when hashing the map element	`'60868847-7171-48cf-a6c1-4859841c24af'`
`name`	`str \| None`		`None`
`sbo_term`	`SBOTerm \| None`		`None`
`metaid`	`str \| None`		`None`
`referred_species`	`Species`		required
`stoichiometry`	`int \| None`		`None`

Core

momapy.sbml.core

BQBiol

BQModel

BiomodelQualifier

Compartment dataclass

Model dataclass

ModifierSpeciesReference dataclass

RDFAnnotation dataclass

Reaction dataclass

SBML dataclass

SBOTerm dataclass

SBase dataclass

SimpleSpeciesReference dataclass

Species dataclass

SpeciesReference dataclass

Compartment `dataclass`

Model `dataclass`

ModifierSpeciesReference `dataclass`

RDFAnnotation `dataclass`

Reaction `dataclass`

SBML `dataclass`

SBOTerm `dataclass`

SBase `dataclass`

SimpleSpeciesReference `dataclass`

Species `dataclass`

SpeciesReference `dataclass`