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JR-1991JR-1991
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Add 'fit' parameter to Parameter model and context
Introduces an optional 'fit' boolean to the Parameter model and related method, indicating if a parameter should be varied during optimization. Also reorders the '@context' dictionary entries for consistency across multiple classes.
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Lines changed: 21 additions & 14 deletions

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‎pyenzyme/versions/v2.py‎

Lines changed: 21 additions & 14 deletions
Original file line numberDiff line numberDiff line change
@@ -201,8 +201,8 @@ class EnzymeMLDocument(BaseModel):
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serialization_alias="@context",
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default_factory=lambda: {
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"enzml": "http://www.enzymeml.org/v2/",
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"schema": "https://schema.org/",
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"OBO": "http://purl.obolibrary.org/obo/",
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"schema": "https://schema.org/",
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"name": "schema:title",
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"created": "schema:dateCreated",
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"modified": "schema:dateModified",
@@ -603,6 +603,7 @@ def add_to_parameters(
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initial_value: Optional[float] = None,
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upper_bound: Optional[float] = None,
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lower_bound: Optional[float] = None,
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fit: Optional[bool] = True,
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stderr: Optional[float] = None,
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constant: Optional[bool] = True,
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**kwargs,
@@ -616,6 +617,7 @@ def add_to_parameters(
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"initial_value": initial_value,
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"upper_bound": upper_bound,
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"lower_bound": lower_bound,
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"fit": fit,
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"stderr": stderr,
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"constant": constant,
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}
@@ -659,8 +661,8 @@ class Creator(BaseModel):
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serialization_alias="@context",
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default_factory=lambda: {
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"enzml": "http://www.enzymeml.org/v2/",
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"schema": "https://schema.org/",
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"OBO": "http://purl.obolibrary.org/obo/",
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"schema": "https://schema.org/",
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"given_name": "schema:givenName",
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"family_name": "schema:familyName",
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"mail": "schema:email",
@@ -773,8 +775,8 @@ class Vessel(BaseModel):
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serialization_alias="@context",
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default_factory=lambda: {
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"enzml": "http://www.enzymeml.org/v2/",
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"schema": "https://schema.org/",
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"OBO": "http://purl.obolibrary.org/obo/",
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"schema": "https://schema.org/",
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"id": {
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"@id": "schema:identifier",
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"@type": "@id",
@@ -911,8 +913,8 @@ class Protein(BaseModel):
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serialization_alias="@context",
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default_factory=lambda: {
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"enzml": "http://www.enzymeml.org/v2/",
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"schema": "https://schema.org/",
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"OBO": "http://purl.obolibrary.org/obo/",
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"schema": "https://schema.org/",
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"id": {
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"@id": "schema:identifier",
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"@type": "@id",
@@ -1044,8 +1046,8 @@ class Complex(BaseModel):
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serialization_alias="@context",
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default_factory=lambda: {
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"enzml": "http://www.enzymeml.org/v2/",
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"schema": "https://schema.org/",
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"OBO": "http://purl.obolibrary.org/obo/",
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"schema": "https://schema.org/",
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"id": {
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"@id": "schema:identifier",
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"@type": "@id",
@@ -1195,8 +1197,8 @@ class SmallMolecule(BaseModel):
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serialization_alias="@context",
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default_factory=lambda: {
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"enzml": "http://www.enzymeml.org/v2/",
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"schema": "https://schema.org/",
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"OBO": "http://purl.obolibrary.org/obo/",
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"schema": "https://schema.org/",
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"id": {
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"@id": "schema:identifier",
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"@type": "@id",
@@ -1330,8 +1332,8 @@ class Reaction(BaseModel):
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serialization_alias="@context",
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default_factory=lambda: {
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"enzml": "http://www.enzymeml.org/v2/",
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"schema": "https://schema.org/",
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"OBO": "http://purl.obolibrary.org/obo/",
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"schema": "https://schema.org/",
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"id": {
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"@id": "schema:identifier",
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"@type": "@id",
@@ -1517,8 +1519,8 @@ class ReactionElement(BaseModel):
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serialization_alias="@context",
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default_factory=lambda: {
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"enzml": "http://www.enzymeml.org/v2/",
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"schema": "https://schema.org/",
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"OBO": "http://purl.obolibrary.org/obo/",
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"schema": "https://schema.org/",
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"species_id": {
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"@id": "schema:identifier",
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"@type": "@id",
@@ -1622,8 +1624,8 @@ class ModifierElement(BaseModel):
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serialization_alias="@context",
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default_factory=lambda: {
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"enzml": "http://www.enzymeml.org/v2/",
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"schema": "https://schema.org/",
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"OBO": "http://purl.obolibrary.org/obo/",
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"schema": "https://schema.org/",
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"species_id": {
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"@id": "schema:identifier",
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"@type": "@id",
@@ -1738,8 +1740,8 @@ class Equation(BaseModel):
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serialization_alias="@context",
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default_factory=lambda: {
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"enzml": "http://www.enzymeml.org/v2/",
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"schema": "https://schema.org/",
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"OBO": "http://purl.obolibrary.org/obo/",
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"schema": "https://schema.org/",
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"species_id": {
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"@id": "schema:identifier",
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"@type": "@id",
@@ -1874,8 +1876,8 @@ class Variable(BaseModel):
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serialization_alias="@context",
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default_factory=lambda: {
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"enzml": "http://www.enzymeml.org/v2/",
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"schema": "https://schema.org/",
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"OBO": "http://purl.obolibrary.org/obo/",
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"schema": "https://schema.org/",
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"id": {
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"@id": "schema:identifier",
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"@type": "@id",
@@ -1989,6 +1991,11 @@ class Parameter(BaseModel):
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description="""Lower bound for the parameter value that was used
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for the parameter estimation""",
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)
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fit: Optional[bool] = Field(
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default=True,
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description="""Whether this parameter should be varied or not in
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the context of an optimization.""",
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)
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stderr: Optional[float] = Field(
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default=None,
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description="""Standard error of the estimated parameter.""",
@@ -2014,8 +2021,8 @@ class Parameter(BaseModel):
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serialization_alias="@context",
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default_factory=lambda: {
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"enzml": "http://www.enzymeml.org/v2/",
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"schema": "https://schema.org/",
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"OBO": "http://purl.obolibrary.org/obo/",
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"schema": "https://schema.org/",
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"id": {
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"@id": "schema:identifier",
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"@type": "@id",
@@ -2141,8 +2148,8 @@ class Measurement(BaseModel):
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serialization_alias="@context",
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default_factory=lambda: {
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"enzml": "http://www.enzymeml.org/v2/",
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"schema": "https://schema.org/",
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"OBO": "http://purl.obolibrary.org/obo/",
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"schema": "https://schema.org/",
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"id": {
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"@id": "schema:identifier",
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"@type": "@id",
@@ -2330,8 +2337,8 @@ class MeasurementData(BaseModel):
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serialization_alias="@context",
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default_factory=lambda: {
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"enzml": "http://www.enzymeml.org/v2/",
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"schema": "https://schema.org/",
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"OBO": "http://purl.obolibrary.org/obo/",
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"schema": "https://schema.org/",
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"species_id": {
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"@type": "@id",
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},

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