sbmlutils.factory
¶
Factory for creating SBML objects.
This module provides definitions of helper functions for the creation of SBML objects. These are the low level helpers to create models from scratch and are used in the higher level SBML factories.
The general workflow to create new SBML models isto create a lists/iterables of SBMLObjects by using the respective classes in this module, e.g. Compartment, Parameter, Species.
- The actual SBase objects are than created in the SBMLDocument/Model by calling
create_objects(model, objects)
These functions DO NOT take care of the order of the creation, but the order must be correct in the model definition files. To create complete models one should use the modelcreator functionality, which takes care of the order of object creation.
Module Contents¶
Classes¶
Representation of stoichiometric equations with modifiers. |
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Options for SBML validator. |
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Class for storing model units information. |
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KeyValuePair. |
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Unit. |
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Base class for unit definitions. |
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SBML FunctionDefinitions. |
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Parameter. |
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Compartment. |
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Species. |
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InitialAssignments. |
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AssignmentRule. |
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RateRule. |
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AlgebraicRule. |
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Reaction. |
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Event. |
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Constraint. |
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UncertParameter. |
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UncertSpan. |
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Uncertainty. |
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Exchange reactions define substances which can be exchanged. |
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GeneProduct. |
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UserDefinedConstraintComponent. |
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UserDefinedConstraint. |
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FluxObjective. |
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Objective. |
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ModelDefinition. |
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ExternalModelDefinition. |
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Submodel. |
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ReplacedElement. |
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ReplacedBy. |
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Deletion. |
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Supported port types. |
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Port. |
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Supported/tested packages. |
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ModelDict. |
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Model. |
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Document. |
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Data structure for model creation. |
Functions¶
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Create SBML model from models. |
Attributes¶
- class sbmlutils.factory.ReactionEquation(reactants=None, products=None, modifiers=None, reversible=True)[source]¶
Representation of stoichiometric equations with modifiers.
- Parameters
reactants (Optional[List[EquationPart]]) –
products (Optional[List[EquationPart]]) –
modifiers (Optional[List[str]]) –
reversible (bool) –
- static from_str(equation_str)¶
Parse components of equation string.
- Parameters
equation_str (str) –
- Return type
- _parse_equation(equation_str)¶
- Parameters
equation_str (str) –
- Return type
None
- _parse_modifiers(s)¶
- Parameters
s (str) –
- Return type
None
- _parse_half_equation(string)¶
Parse half-equation.
Only ‘+ supported in equation !, do not use negative stoichiometries.
- Parameters
string (str) –
- Return type
List[EquationPart]
- static _parse_reactant(item)¶
Parse stoichiometry, species, sid information.
- Parameters
item (str) –
- Return type
- static _to_string_side(items)¶
- Parameters
items (Iterable[EquationPart]) –
- Return type
str
- _to_string_modifiers()¶
- Return type
str
- to_string(modifiers=False)¶
Get string representation of equation.
- Parameters
modifiers (bool) –
- Return type
str
- info()¶
Print overview of parsed equation.
- Return type
None
- static help()¶
Get help information string.
- Return type
str
- class sbmlutils.factory.ValidationOptions[source]¶
Options for SBML validator.
Controls the consistency checks that are performed when SBMLDocument.checkConsistency() is called.
general_consistency: Correctness and consistency of
specific SBML language constructs. Performing this set of checks is highly recommended. With respect to the SBML specification, these concern failures in applying the validation rules numbered 2xxxx in the Level 2 Versions 2-4 and Level 3 Versions 1-2 specifications.
ìdentifier_consistency: Correctness and consistency of
identifiers used for model entities. An example of inconsistency would be using a species identifier in a reaction rate formula without first having declared the species. With respect to the SBML specification, these concern failures in applying the validation rules numbered 103xx in the Level 2 Versions 2-4 and Level 3 Versions 1-2 specifications.
units_consistency: Consistency of measurement units
associated with quantities in a model. With respect to the SBML specification, these concern failures in applying the validation rules numbered 105xx in the Level 2 Versions 2-4 and Level 3 Versions 1-2 specifications.
mathml_consistency: Syntax of MathML constructs. With
respect to the SBML specification, these concern failures in applying the validation rules numbered 102xx in the Level 2 Versions 2-4 and Level 3 Versions 1-2 specifications.
sbo_consistency: Consistency and validity of SBO
identifiers (if any) used in the model. With respect to the SBML specification, these concern failures in applying the validation rules numbered 107xx in the Level 2 Versions 2-4 and Level 3 Versions 1-2 specifications.
overdetermined_model: Static analysis of whether the
system of equations implied by a model is mathematically overdetermined. With respect to the SBML specification, this is validation rule #10601 in the Level 2 Versions 2-4 and Level 3 Versions 1-2 specifications.
modeling_practise: Additional checks for recommended
good modeling practice. (These are tests performed by libSBML and do not have equivalent SBML validation rules.) By default, all validation checks are applied to the model in an SBMLDocument object unless SBMLDocument.setConsistencyChecks() is called to indicate that only a subset should be applied. Further, this default (i.e., performing all checks) applies separately to each new SBMLDocument object created. In other words, each time a model is read using SBMLReader.readSBML(), SBMLReader.readSBMLFromString(), or the global functions readSBML() and readSBMLFromString(), a new SBMLDocument is created and for that document, a call to SBMLDocument.checkConsistency() will default to applying all possible checks. Calling programs must invoke SBMLDocument.setConsistencyChecks() for each such new model if they wish to change the consistency checks applied.
internal_consistency: Additional checks that model is consistent XML.
log_errors Boolean flag to log errors.
- log_errors :bool = True¶
- internal_consistency :bool = True¶
- general_consistency :bool = True¶
- identifier_consistency :bool = True¶
- mathml_consistency :bool = True¶
- units_consistency :bool = True¶
- sbo_consistency :bool = True¶
- overdetermined_model :bool = True¶
- modeling_practice :bool = True¶
- class sbmlutils.factory.ModelUnits(time=None, extent=None, substance=None, length=None, area=None, volume=None)[source]¶
Class for storing model units information.
The ModelUnits define globally the units for time, extent, substance, length, area and volume.
The following SBML Level 3 base units can be used.
ampere farad joule lux radian volt avogadro gram katal metre second watt becquerel gray kelvin mole siemens weber candela henry kilogram newton sievert coulomb hertz litre ohm steradian dimensionless item lumen pascal tesla
- Parameters
time (UnitType) –
extent (UnitType) –
substance (UnitType) –
length (UnitType) –
area (UnitType) –
volume (UnitType) –
- static set_model_units(model, model_units)[source]¶
Set the main units in model from dictionary.
Setting the model units is important for understanding the model dynamics. Allowed keys are:
time extent substance length area volume
- Parameters
model (libsbml.Model) – SBMLModel
model_units (ModelUnits) – dict of units
- Returns
- Return type
None
- class sbmlutils.factory.KeyValuePair(key, value, uri, sid=None, name=None, sboTerm=None, metaId=None, notes=None, annotations=None, keyValuePairs=None, port=None, uncertainties=None, replacedBy=None)[source]¶
Bases:
Sbase
KeyValuePair.
- Parameters
key (str) –
value (Optional[str]) –
uri (Optional[str]) –
sid (Optional[str]) –
name (Optional[str]) –
sboTerm (Optional[str]) –
metaId (Optional[str]) –
notes (Optional[str]) –
annotations (OptionalAnnotationsType) –
keyValuePairs (Optional[List[KeyValuePair]]) –
port (Any) –
uncertainties (Optional[List[Uncertainty]]) –
replacedBy (Optional[Any]) –
- class sbmlutils.factory.UnitDefinition(sid, definition=None, name=None, sboTerm=None, metaId=None, annotations=None, notes=None, keyValuePairs=None, port=None, replacedBy=None)[source]¶
Bases:
Sbase
Unit.
Corresponds to the information in the libsbml.UnitDefinition.
- Parameters
sid (str) –
definition (Optional[str]) –
name (Optional[str]) –
sboTerm (Optional[str]) –
metaId (Optional[str]) –
annotations (OptionalAnnotationsType) –
notes (Optional[str]) –
keyValuePairs (Optional[List[KeyValuePair]]) –
port (Any) –
replacedBy (Optional[Any]) –
- create_sbml(model)[source]¶
Create libsbml.UnitDefinition.
- Parameters
model (libsbml.Model) –
- Return type
Optional[libsbml.UnitDefinition]
- _set_fields(sbase, model)[source]¶
Set fields on libsbml.UnitDefinition.
- Parameters
sbase (libsbml.UnitDefinition) –
model (libsbml.Model) –
- Return type
None
- static _create_unit(udef, kind, exponent, scale=0, multiplier=1.0)[source]¶
Create libsbml.Unit.
- Parameters
udef (libsbml.UnitDefinition) –
kind (str) –
exponent (float) –
scale (int) –
multiplier (float) –
- Return type
libsbml.Unit
- static get_uid_for_unit(unit)[source]¶
Get unit id for given definition string.
- Parameters
unit (Union[UnitDefinition, str]) –
- Return type
Optional[str]
- class sbmlutils.factory.Units[source]¶
Base class for unit definitions.
- classmethod attributes()[source]¶
Get the attributes list.
- Return type
List[Tuple[str, Union[str, UnitDefinition]]]
- class sbmlutils.factory.Function(sid, value, name=None, sboTerm=None, metaId=None, annotations=None, notes=None, keyValuePairs=None, port=None, uncertainties=None, replacedBy=None)[source]¶
Bases:
Sbase
SBML FunctionDefinitions.
- FunctionDefinitions consist of a lambda expression in the value field, e.g.,
lambda(x,y, piecewise(x,gt(x,y),y) ) # definition of minimum function lambda(x, sin(x) )
- Parameters
sid (str) –
value (str) –
name (Optional[str]) –
sboTerm (Optional[str]) –
metaId (Optional[str]) –
annotations (OptionalAnnotationsType) –
notes (Optional[str]) –
keyValuePairs (Optional[List[KeyValuePair]]) –
port (Any) –
uncertainties (Optional[List[Uncertainty]]) –
replacedBy (Optional[Any]) –
- class sbmlutils.factory.Parameter(sid, value=None, unit=None, constant=True, name=None, sboTerm=None, metaId=None, annotations=None, notes=None, keyValuePairs=None, port=None, uncertainties=None, replacedBy=None)[source]¶
Bases:
ValueWithUnit
Parameter.
- Parameters
sid (str) –
value (Optional[Union[str, float]]) –
unit (UnitType) –
constant (bool) –
name (Optional[str]) –
sboTerm (Optional[str]) –
metaId (Optional[str]) –
annotations (OptionalAnnotationsType) –
notes (Optional[str]) –
keyValuePairs (Optional[List[KeyValuePair]]) –
port (Any) –
uncertainties (Optional[List[Uncertainty]]) –
replacedBy (Optional[Any]) –
- class sbmlutils.factory.Compartment(sid, value, unit=None, constant=True, spatialDimensions=3, name=None, sboTerm=None, metaId=None, annotations=None, notes=None, keyValuePairs=None, port=None, uncertainties=None, replacedBy=None)[source]¶
Bases:
ValueWithUnit
Compartment.
- Parameters
sid (str) –
value (Union[str, float]) –
unit (UnitType) –
constant (bool) –
spatialDimensions (float) –
name (Optional[str]) –
sboTerm (Optional[str]) –
metaId (Optional[str]) –
annotations (OptionalAnnotationsType) –
notes (Optional[str]) –
keyValuePairs (Optional[List[KeyValuePair]]) –
port (Any) –
uncertainties (Optional[List[Uncertainty]]) –
replacedBy (Optional[Any]) –
- class sbmlutils.factory.Species(sid, compartment, initialAmount=None, initialConcentration=None, substanceUnit=None, hasOnlySubstanceUnits=False, constant=False, boundaryCondition=False, charge=None, chemicalFormula=None, conversionFactor=None, name=None, sboTerm=None, metaId=None, annotations=None, notes=None, keyValuePairs=None, port=None, uncertainties=None, replacedBy=None)[source]¶
Bases:
Sbase
Species.
- Parameters
sid (str) –
compartment (str) –
initialAmount (Optional[float]) –
initialConcentration (Optional[float]) –
substanceUnit (UnitType) –
hasOnlySubstanceUnits (bool) –
constant (bool) –
boundaryCondition (bool) –
charge (Optional[float]) –
chemicalFormula (Optional[str]) –
conversionFactor (Optional[str]) –
name (Optional[str]) –
sboTerm (Optional[str]) –
metaId (Optional[str]) –
annotations (OptionalAnnotationsType) –
notes (Optional[str]) –
keyValuePairs (Optional[List[KeyValuePair]]) –
port (Any) –
uncertainties (Optional[List[Uncertainty]]) –
replacedBy (Optional[Any]) –
- class sbmlutils.factory.InitialAssignment(symbol, value, unit=Units.dimensionless, sid=None, name=None, sboTerm=None, metaId=None, annotations=None, notes=None, keyValuePairs=None, port=None, uncertainties=None, replacedBy=None)[source]¶
Bases:
Value
InitialAssignments.
The unit attribute is only for the case where a parameter must be created (which has the unit). In case of an initialAssignment of a value the units have to be defined in the math.
- Parameters
symbol (str) –
value (Union[str, float]) –
unit (UnitType) –
sid (Optional[str]) –
name (Optional[str]) –
sboTerm (Optional[str]) –
metaId (Optional[str]) –
annotations (OptionalAnnotationsType) –
notes (Optional[str]) –
keyValuePairs (Optional[List[KeyValuePair]]) –
port (Any) –
uncertainties (Optional[List[Uncertainty]]) –
replacedBy (Optional[Any]) –
- class sbmlutils.factory.AssignmentRule(variable, value, unit=Units.dimensionless, sid=None, name=None, sboTerm=None, metaId=None, annotations=None, notes=None, keyValuePairs=None, port=None, uncertainties=None, replacedBy=None)[source]¶
Bases:
ValueWithUnit
,RuleWithVariable
AssignmentRule.
The unit attribute is only for the case where a parameter must be created (which has the unit). In case of an initialAssignment of a value the units have to be defined in the math.
- Parameters
variable (str) –
value (Union[str, float]) –
unit (UnitType) –
sid (Optional[str]) –
name (Optional[str]) –
sboTerm (Optional[str]) –
metaId (Optional[str]) –
annotations (OptionalAnnotationsType) –
notes (Optional[str]) –
keyValuePairs (Optional[List[KeyValuePair]]) –
port (Any) –
uncertainties (Optional[List[Uncertainty]]) –
replacedBy (Optional[Any]) –
- class sbmlutils.factory.RateRule(variable, value, unit=Units.dimensionless, sid=None, name=None, sboTerm=None, metaId=None, annotations=None, notes=None, keyValuePairs=None, port=None, uncertainties=None, replacedBy=None)[source]¶
Bases:
ValueWithUnit
,RuleWithVariable
RateRule.
- Parameters
variable (str) –
value (Union[str, float]) –
unit (UnitType) –
sid (Optional[str]) –
name (Optional[str]) –
sboTerm (Optional[str]) –
metaId (Optional[str]) –
annotations (OptionalAnnotationsType) –
notes (Optional[str]) –
keyValuePairs (Optional[List[KeyValuePair]]) –
port (Any) –
uncertainties (Optional[List[Uncertainty]]) –
replacedBy (Optional[Any]) –
- class sbmlutils.factory.AlgebraicRule(sid, value, unit=Units.dimensionless, name=None, sboTerm=None, metaId=None, annotations=None, notes=None, keyValuePairs=None, port=None, uncertainties=None, replacedBy=None)[source]¶
Bases:
ValueWithUnit
,RuleWithVariable
AlgebraicRule.
- Parameters
sid (str) –
value (Union[str, float]) –
unit (UnitType) –
name (Optional[str]) –
sboTerm (Optional[str]) –
metaId (Optional[str]) –
annotations (OptionalAnnotationsType) –
notes (Optional[str]) –
keyValuePairs (Optional[List[KeyValuePair]]) –
port (Any) –
uncertainties (Optional[List[Uncertainty]]) –
replacedBy (Optional[Any]) –
- class sbmlutils.factory.Reaction(sid, equation, formula=None, pars=None, rules=None, compartment=None, fast=False, reversible=None, lowerFluxBound=None, upperFluxBound=None, geneProductAssociation=None, name=None, sboTerm=None, metaId=None, annotations=None, notes=None, keyValuePairs=None, port=None, uncertainties=None, replacedBy=None)[source]¶
Bases:
Sbase
Reaction.
Class for creating libsbml.Reaction.
Equations are of the form ‘1.0 S1 + 2 S2 => 2.0 P1 + 2 P2 [M1, M2]’
The equation consists of - substrates concatenated via ‘+’ on the left side
(with optional stoichiometric coefficients)
separation characters separating the left and right equation sides: ‘<=>’ or ‘<->’ for reversible reactions, ‘=>’ or ‘->’ for irreversible reactions (irreversible reactions are written from left to right)
products concatenated via ‘+’ on the right side (with optional stoichiometric coefficients)
optional list of modifiers within brackets [] separated by ‘,’
- Examples of valid equations are:
‘1.0 S1 + 2 S2 => 2.0 P1 + 2 P2 [M1, M2]’, ‘c__gal1p => c__gal + c__phos’, ‘e__h2oM <-> c__h2oM’, ‘3 atp + 2.0 phos + ki <-> 16.98 tet’, ‘c__gal1p => c__gal + c__phos [c__udp, c__utp]’, ‘A_ext => A []’, ‘=> cit’, ‘acoa =>’,
- Parameters
sid (str) –
equation (Union[sbmlutils.reaction_equation.ReactionEquation, str]) –
formula (Optional[Union[Formula, Tuple[str, UnitType], str]]) –
pars (Optional[List[Parameter]]) –
rules (Optional[List[AssignmentRule]]) –
compartment (Optional[str]) –
fast (bool) –
reversible (Optional[bool]) –
lowerFluxBound (Optional[str]) –
upperFluxBound (Optional[str]) –
geneProductAssociation (Optional[str]) –
name (Optional[str]) –
sboTerm (Optional[str]) –
metaId (Optional[str]) –
annotations (OptionalAnnotationsType) –
notes (Optional[str]) –
keyValuePairs (Optional[List[KeyValuePair]]) –
port (Any) –
uncertainties (Optional[List[Uncertainty]]) –
replacedBy (Optional[Any]) –
- static _process_equation(equation)[source]¶
Process reaction equation.
- Parameters
equation (Union[sbmlutils.reaction_equation.ReactionEquation, str]) –
- Return type
- static _process_formula(formula)[source]¶
Process reaction formula (kinetic law).
- Parameters
formula (Optional[Union[Formula, Tuple[str, UnitType], str]]) –
- Return type
Optional[Formula]
- create_sbml(model)[source]¶
Create Reaction SBML in model.
- Parameters
model (libsbml.Model) –
- Return type
libsbml.Reaction
- class sbmlutils.factory.Event(sid, trigger, assignments=None, trigger_persistent=True, trigger_initialValue=False, useValuesFromTriggerTime=True, priority=None, delay=None, name=None, sboTerm=None, metaId=None, annotations=None, notes=None, keyValuePairs=None, port=None, uncertainties=None, replacedBy=None)[source]¶
Bases:
Sbase
Event.
- Trigger have the format of a logical expression:
time%200 == 0
- Assignments have the format
sid = value
- Parameters
sid (str) –
trigger (str) –
assignments (Optional[Dict[str, Union[str, float]]]) –
trigger_persistent (bool) –
trigger_initialValue (bool) –
useValuesFromTriggerTime (bool) –
priority (Optional[str]) –
delay (Optional[str]) –
name (Optional[str]) –
sboTerm (Optional[str]) –
metaId (Optional[str]) –
annotations (OptionalAnnotationsType) –
notes (Optional[str]) –
keyValuePairs (Optional[List[KeyValuePair]]) –
port (Any) –
uncertainties (Optional[List[Uncertainty]]) –
replacedBy (Optional[Any]) –
- create_sbml(model)[source]¶
Create Event SBML in model.
- Parameters
model (libsbml.Model) –
- Return type
libsbml.Event
- _set_fields(sbase, model)[source]¶
Set fields in libsbml.Event.
- Parameters
sbase (libsbml.Event) –
model (libsbml.Model) –
- Return type
None
- class sbmlutils.factory.Constraint(sid, math, message=None, name=None, sboTerm=None, metaId=None, annotations=None, notes=None, keyValuePairs=None, port=None, uncertainties=None, replacedBy=None)[source]¶
Bases:
Sbase
Constraint.
The Constraint object is a mechanism for stating the assumptions under which a model is designed to operate. The constraints are statements about permissible values of different quantities in a model.
- The message must be well formated XHTML, e.g.,
message=’<body xmlns=”http://www.w3.org/1999/xhtml”>ATP must be non-negative</body>’
- Parameters
sid (str) –
math (str) –
message (Optional[str]) –
name (Optional[str]) –
sboTerm (Optional[str]) –
metaId (Optional[str]) –
annotations (OptionalAnnotationsType) –
notes (Optional[str]) –
keyValuePairs (Optional[List[KeyValuePair]]) –
port (Any) –
uncertainties (Optional[List[Uncertainty]]) –
replacedBy (Optional[Any]) –
- class sbmlutils.factory.UncertParameter(type, value=None, var=None, unit=None)[source]¶
UncertParameter.
FIXME: This is an SBase!
- Parameters
type (str) –
value (Optional[float]) –
var (Optional[str]) –
unit (UnitType) –
- class sbmlutils.factory.UncertSpan(type, valueLower=None, varLower=None, valueUpper=None, varUpper=None, unit=None)[source]¶
UncertSpan.
FIXME: This is an SBase!
- Parameters
type (str) –
valueLower (Optional[float]) –
varLower (Optional[str]) –
valueUpper (Optional[float]) –
varUpper (Optional[str]) –
unit (UnitType) –
- class sbmlutils.factory.Uncertainty(sid=None, formula=None, uncertParameters=None, uncertSpans=None, name=None, sboTerm=None, metaId=None, annotations=None, notes=None, keyValuePairs=None, port=None, replacedBy=None)[source]¶
Bases:
Sbase
Uncertainty.
Uncertainty information for Sbase.
- Parameters
sid (Optional[str]) –
formula (Optional[str]) –
uncertParameters (Optional[List[UncertParameter]]) –
uncertSpans (Optional[List[UncertSpan]]) –
name (Optional[str]) –
sboTerm (Optional[str]) –
metaId (Optional[str]) –
annotations (OptionalAnnotationsType) –
notes (Optional[str]) –
keyValuePairs (Optional[List[KeyValuePair]]) –
port (Any) –
replacedBy (Optional[Any]) –
- class sbmlutils.factory.ExchangeReaction(species_id, compartment=None, fast=False, reversible=True, lowerFluxBound=None, upperFluxBound=None, geneProductAssociation=None, name=None, metaId=None, annotations=None, notes=None, keyValuePairs=None, port=None, uncertainties=None, replacedBy=None)[source]¶
Bases:
Reaction
Exchange reactions define substances which can be exchanged.
This is important for FBC models.
EXCHANGE_IMPORT (-INF, 0): is defined as negative flux through the exchange reaction, i.e. the upper bound must be 0, the lower bound some negative value,
e.g. -INF
- EXCHANGE_EXPORT (0, INF): is defined as positive flux through the exchange reaction,
i.e. the lower bound must be 0, the upper bound some positive value, e.g. INF
- Parameters
species_id (str) –
compartment (Optional[str]) –
fast (bool) –
reversible (bool) –
lowerFluxBound (Optional[str]) –
upperFluxBound (Optional[str]) –
geneProductAssociation (Optional[str]) –
name (Optional[str]) –
metaId (Optional[str]) –
annotations (OptionalAnnotationsType) –
notes (Optional[str]) –
keyValuePairs (Optional[List[KeyValuePair]]) –
port (Any) –
uncertainties (Optional[List[Uncertainty]]) –
replacedBy (Optional[Any]) –
- class sbmlutils.factory.GeneProduct(sid, label, associatedSpecies=None, name=None, sboTerm=None, metaId=None, annotations=None, notes=None, keyValuePairs=None, port=None, uncertainties=None, replacedBy=None)[source]¶
Bases:
Sbase
GeneProduct.
GeneProduct is a new FBC class derived from SBML SBase that inherits metaid and sboTerm, as well as the subcomponents for Annotation and Notes. The purpose of this class is to define a single gene product. It implements two required attributes id and label as well as two optional attributes name and associatedSpecies.
- Parameters
sid (str) –
label (str) –
associatedSpecies (Optional[str]) –
name (Optional[str]) –
sboTerm (Optional[str]) –
metaId (Optional[str]) –
annotations (OptionalAnnotationsType) –
notes (Optional[str]) –
keyValuePairs (Optional[List[KeyValuePair]]) –
port (Any) –
uncertainties (Optional[List[Uncertainty]]) –
replacedBy (Optional[Any]) –
- class sbmlutils.factory.UserDefinedConstraintComponent(coefficient, variable, variableType=None, sid=None, name=None, sboTerm=None, metaId=None, annotations=None, notes=None, keyValuePairs=None, port=None, uncertainties=None, replacedBy=None)[source]¶
Bases:
Sbase
UserDefinedConstraintComponent.
- Parameters
coefficient (float) –
variable (str) –
variableType (Optional[str]) –
sid (Optional[str]) –
name (Optional[str]) –
sboTerm (Optional[str]) –
metaId (Optional[str]) –
annotations (OptionalAnnotationsType) –
notes (Optional[str]) –
keyValuePairs (Optional[List[KeyValuePair]]) –
port (Any) –
uncertainties (Optional[List[Uncertainty]]) –
replacedBy (Optional[Any]) –
- class sbmlutils.factory.UserDefinedConstraint(lowerBound, upperBound, components=None, variableType=libsbml.FBC_VARIABLE_TYPE_LINEAR, sid=None, name=None, sboTerm=None, metaId=None, annotations=None, notes=None, keyValuePairs=None, port=None, uncertainties=None, replacedBy=None)[source]¶
Bases:
Sbase
UserDefinedConstraint.
The FBC UserDefinedConstraint class is derived from SBML SBase and inherits metaid and sboTerm, as well as the subcomponents for Annotation and Notes. It’s purpose is to define non-stoichiometric constraints, that is constraints that are not necessarily defined by the stoichiometrically coupled reaction network. In order to achieve, we defined a new type of linear constraint, the UserDefinedConstraint
- Parameters
lowerBound (str) –
upperBound (str) –
components (Optional[Union[List[UserDefinedConstraintComponent], Dict[str, float]]]) –
variableType (str) –
sid (Optional[str]) –
name (Optional[str]) –
sboTerm (Optional[str]) –
metaId (Optional[str]) –
annotations (OptionalAnnotationsType) –
notes (Optional[str]) –
keyValuePairs (Optional[List[KeyValuePair]]) –
port (Any) –
uncertainties (Optional[List[Uncertainty]]) –
replacedBy (Optional[Any]) –
- class sbmlutils.factory.FluxObjective(reaction, coefficient, variableType, sid=None, name=None, sboTerm=None, metaId=None, annotations=None, notes=None, keyValuePairs=None, port=None, uncertainties=None, replacedBy=None)[source]¶
Bases:
Sbase
FluxObjective.
- Parameters
reaction (str) –
coefficient (float) –
variableType (str) –
sid (Optional[str]) –
name (Optional[str]) –
sboTerm (Optional[str]) –
metaId (Optional[str]) –
annotations (OptionalAnnotationsType) –
notes (Optional[str]) –
keyValuePairs (Optional[List[KeyValuePair]]) –
port (Any) –
uncertainties (Optional[List[Uncertainty]]) –
replacedBy (Optional[Any]) –
- class sbmlutils.factory.Objective(sid, objectiveType=libsbml.OBJECTIVE_TYPE_MAXIMIZE, active=True, fluxObjectives=None, variableType=libsbml.FBC_VARIABLE_TYPE_LINEAR, name=None, sboTerm=None, metaId=None, annotations=None, notes=None, keyValuePairs=None, port=None, uncertainties=None, replacedBy=None)[source]¶
Bases:
Sbase
Objective.
- Parameters
sid (str) –
objectiveType (str) –
active (bool) –
fluxObjectives (Optional[Union[List[FluxObjective], Dict[str, float]]]) –
variableType (str) –
name (Optional[str]) –
sboTerm (Optional[str]) –
metaId (Optional[str]) –
annotations (OptionalAnnotationsType) –
notes (Optional[str]) –
keyValuePairs (Optional[List[KeyValuePair]]) –
port (Any) –
uncertainties (Optional[List[Uncertainty]]) –
replacedBy (Optional[Any]) –
- class sbmlutils.factory.ModelDefinition(sid, name=None, sboTerm=None, metaId=None, annotations=None, notes=None, keyValuePairs=None, units=None, compartments=None, species=None)[source]¶
Bases:
Sbase
ModelDefinition.
- Parameters
sid (str) –
name (Optional[str]) –
sboTerm (Optional[str]) –
metaId (Optional[str]) –
annotations (OptionalAnnotationsType) –
notes (Optional[str]) –
keyValuePairs (Optional[List[KeyValuePair]]) –
units (Optional[Type[Units]]) –
compartments (Optional[List[Compartment]]) –
species (Optional[List[Species]]) –
- class sbmlutils.factory.ExternalModelDefinition(sid, source, modelRef, md5=None, name=None, sboTerm=None, metaId=None, annotations=None, notes=None, keyValuePairs=None)[source]¶
Bases:
Sbase
ExternalModelDefinition.
- Parameters
sid (str) –
source (str) –
modelRef (str) –
md5 (Optional[str]) –
name (Optional[str]) –
sboTerm (Optional[str]) –
metaId (Optional[str]) –
annotations (OptionalAnnotationsType) –
notes (Optional[str]) –
keyValuePairs (Optional[List[KeyValuePair]]) –
- class sbmlutils.factory.Submodel(sid, modelRef=None, timeConversionFactor=None, extentConversionFactor=None, name=None, sboTerm=None, metaId=None, annotations=None, notes=None, keyValuePairs=None)[source]¶
Bases:
Sbase
Submodel.
- Parameters
sid (str) –
modelRef (Optional[str]) –
timeConversionFactor (Optional[str]) –
extentConversionFactor (Optional[str]) –
name (Optional[str]) –
sboTerm (Optional[str]) –
metaId (Optional[str]) –
annotations (OptionalAnnotationsType) –
notes (Optional[str]) –
keyValuePairs (Optional[List[KeyValuePair]]) –
- class sbmlutils.factory.ReplacedElement(sid, elementRef, submodelRef, deletion=None, conversionFactor=None, portRef=None, idRef=None, unitRef=None, metaIdRef=None, name=None, sboTerm=None, metaId=None, annotations=None, notes=None, keyValuePairs=None)[source]¶
Bases:
SbaseRef
ReplacedElement.
- Parameters
sid (str) –
elementRef (str) –
submodelRef (str) –
deletion (Optional[str]) –
conversionFactor (Optional[str]) –
portRef (Optional[str]) –
idRef (Optional[str]) –
unitRef (Optional[str]) –
metaIdRef (Optional[str]) –
name (Optional[str]) –
sboTerm (Optional[str]) –
metaId (Optional[str]) –
annotations (OptionalAnnotationsType) –
notes (Optional[str]) –
keyValuePairs (Optional[List[KeyValuePair]]) –
- class sbmlutils.factory.ReplacedBy(sid, elementRef, submodelRef, portRef=None, idRef=None, unitRef=None, metaIdRef=None, name=None, sboTerm=None, metaId=None, annotations=None, notes=None, keyValuePairs=None)[source]¶
Bases:
SbaseRef
ReplacedBy.
- Parameters
sid (str) –
elementRef (str) –
submodelRef (str) –
portRef (Optional[str]) –
idRef (Optional[str]) –
unitRef (Optional[str]) –
metaIdRef (Optional[str]) –
name (Optional[str]) –
sboTerm (Optional[str]) –
metaId (Optional[str]) –
annotations (OptionalAnnotationsType) –
notes (Optional[str]) –
keyValuePairs (Optional[List[KeyValuePair]]) –
- class sbmlutils.factory.Deletion(sid, submodelRef, portRef=None, idRef=None, unitRef=None, metaIdRef=None, name=None, sboTerm=None, metaId=None, annotations=None, notes=None, keyValuePairs=None)[source]¶
Bases:
SbaseRef
Deletion.
- Parameters
sid (str) –
submodelRef (str) –
portRef (Optional[str]) –
idRef (Optional[str]) –
unitRef (Optional[str]) –
metaIdRef (Optional[str]) –
name (Optional[str]) –
sboTerm (Optional[str]) –
metaId (Optional[str]) –
annotations (OptionalAnnotationsType) –
notes (Optional[str]) –
keyValuePairs (Optional[List[KeyValuePair]]) –
- class sbmlutils.factory.Port(sid, portRef=None, idRef=None, unitRef=None, metaIdRef=None, portType=PortType.PORT, name=None, sboTerm=None, metaId=None, annotations=None, notes=None, keyValuePairs=None)[source]¶
Bases:
SbaseRef
Port.
Ports are stored in an optional child ListOfPorts object, which, if present, must contain one or more Port objects. All of the Ports present in the ListOfPorts collectively define the ‘port interface’ of the Model.
- Parameters
sid (str) –
portRef (Optional[str]) –
idRef (Optional[str]) –
unitRef (Optional[str]) –
metaIdRef (Optional[str]) –
portType (Optional[PortType]) –
name (Optional[str]) –
sboTerm (Optional[str]) –
metaId (Optional[str]) –
annotations (OptionalAnnotationsType) –
notes (Optional[str]) –
keyValuePairs (Optional[List[KeyValuePair]]) –
- class sbmlutils.factory.ModelDict[source]¶
Bases:
TypedDict
ModelDict.
The ModelDict allows to define the Model as dictionary and then use:
md: ModelDict Model(**md)
For model construction. If possible use the Model object directly.
- class sbmlutils.factory.Model(sid, name=None, sboTerm=None, metaId=None, annotations=None, notes=None, keyValuePairs=None, packages=None, creators=None, model_units=None, units=None, objects=None, external_model_definitions=None, model_definitions=None, submodels=None, functions=None, compartments=None, species=None, parameters=None, assignments=None, rules=None, rate_rules=None, algebraic_rules=None, reactions=None, events=None, constraints=None, ports=None, replaced_elements=None, deletions=None, user_defined_constraints=None, objectives=None, gene_products=None, layouts=None)[source]¶
Bases:
Sbase
,sbmlutils.utils.FrozenClass
,pydantic.BaseModel
Model.
- Parameters
sid (str) –
name (Optional[str]) –
sboTerm (Optional[str]) –
metaId (Optional[str]) –
annotations (OptionalAnnotationsType) –
notes (Optional[str]) –
keyValuePairs (Optional[List[KeyValuePair]]) –
packages (Optional[List[Package]]) –
creators (Optional[List[pymetadata.core.creator.Creator]]) –
model_units (Optional[ModelUnits]) –
units (Optional[Type[Units]]) –
objects (Optional[List[Sbase]]) –
external_model_definitions (Optional[List[ExternalModelDefinition]]) –
model_definitions (Optional[List[ModelDefinition]]) –
submodels (Optional[List[Submodel]]) –
functions (Optional[List[Function]]) –
compartments (Optional[List[Compartment]]) –
species (Optional[List[Species]]) –
parameters (Optional[List[Parameter]]) –
assignments (Optional[List[InitialAssignment]]) –
rules (Optional[List[AssignmentRule]]) –
rate_rules (Optional[List[RateRule]]) –
algebraic_rules (Optional[List[AlgebraicRule]]) –
reactions (Optional[List[Reaction]]) –
events (Optional[List[Event]]) –
constraints (Optional[List[Constraint]]) –
ports (Optional[List[Port]]) –
replaced_elements (Optional[List[ReplacedElement]]) –
deletions (Optional[List[Deletion]]) –
user_defined_constraints (Optional[List[UserDefinedConstraint]]) –
objectives (Optional[List[Objective]]) –
gene_products (Optional[List[GeneProduct]]) –
layouts (Optional[List]) –
- create_sbml(doc)[source]¶
Create Model.
To create the complete SBMLDocument with the model use:
doc = Document(model=model).create_sbml()
- Parameters
doc (libsbml.SBMLDocument) –
- Return type
libsbml.Model
- class sbmlutils.factory.Document(model, sid=None, name=None, sboTerm=None, metaId=None, annotations=None, notes=None, keyValuePairs=None, sbml_level=SBML_LEVEL, sbml_version=SBML_VERSION)[source]¶
Bases:
Sbase
Document.
- Parameters
model (Model) –
sid (Optional[str]) –
name (Optional[str]) –
sboTerm (Optional[str]) –
metaId (Optional[str]) –
annotations (OptionalAnnotationsType) –
notes (Optional[str]) –
keyValuePairs (Optional[List[KeyValuePair]]) –
sbml_level (int) –
sbml_version (int) –
- sbmlutils.factory.create_model(model, filepath, sbml_level=SBML_LEVEL, sbml_version=SBML_VERSION, validate=True, validation_options=None, show_sbml=False, annotations=None)[source]¶
Create SBML model from models.
This is the entry point for creating models. If multiple models are provided these are merged in the process of model creation. See merge_models for more details.
Additional model annotations can be provided via a file.
- Parameters
model (Union[Model, Iterable[Model]]) – Model or iterable of Model instances which are merged in single model
filepath (pathlib.Path) – Path to write the SBML model to
sbml_level (int) – set SBML level for model generation
sbml_version (int) – set SBML version for model generation
validate (bool) – boolean flag to validate the SBML file
validation_options (Optional[sbmlutils.validation.ValidationOptions]) – options for model validation
show_sbml (bool) – boolean flag to show SBML
annotations (Optional[pathlib.Path]) – Path to annotations file
- Returns
FactoryResult
- Return type