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Merged
JR-1991 merged 4 commits into from
Sep 22, 2025
Merged

Add fit flag for Parameter #85

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0bfa14d
Update specs submodule to latest commit
JR-1991 Sep 22, 2025
85c29e4
Add 'fit' parameter to Parameter model and context
JR-1991 Sep 22, 2025
71a7a86
Handle non-fitted parameters, including pre-defined standard errors
jmrohwer Sep 22, 2025
d64745d
Write standard error back to enzymeml doc after fitting
jmrohwer Sep 22, 2025
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24 changes: 18 additions & 6 deletions pyenzyme/thinlayers/psyces.py
View file
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Original file line number Diff line number Diff line change
Expand Up @@ -232,7 +232,16 @@ def optimize(self, method="leastsq"):

self.parameters = parameters

return self.minimizer.minimize(method=method)
result = self.minimizer.minimize(method=method)
# add standard error if available in enzmldoc and if param.fit=False
# (e.g. if parameter was fitted before)
for param in self.enzmldoc.parameters:
if not param.fit and param.stderr is not None:
if param.symbol in result.params:
result.params[param.symbol].stderr = param.stderr

return result


def write(self) -> v2.EnzymeMLDocument:
"""
Expand All @@ -255,16 +264,18 @@ def write(self) -> v2.EnzymeMLDocument:
>>> pe.write_enzymeml(optimized_doc, "optimized_model.json")
"""
nu_enzmldoc = self.enzmldoc.model_copy(deep=True)
results = self.minimizer.result.params.valuesdict() # type: ignore
results = self.minimizer.result.params # type: ignore

for name, value in results.items():
for name in results:
query = nu_enzmldoc.filter_parameters(symbol=name)

if len(query) == 0:
raise ValueError(f"Parameter {name} not found")

parameter = query[0]
parameter.value = value
parameter.value = results[name].value
if results[name].stderr is not None:
parameter.stderr = results[name].stderr

return nu_enzmldoc

Expand All @@ -286,8 +297,9 @@ def _initialize_parameters(self):
for param in self.enzmldoc.parameters:
# Build kwargs dictionary with conditional assignments
kwargs = {
**({"min": param.lower_bound} if param.lower_bound is not None else {}),
**({"max": param.upper_bound} if param.upper_bound is not None else {}),
**({'min': param.lower_bound} if param.lower_bound is not None else {}),
**({'max': param.upper_bound} if param.upper_bound is not None else {}),
**({'vary': param.fit}),
}

# Determine parameter value
Expand Down
35 changes: 21 additions & 14 deletions pyenzyme/versions/v2.py
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Original file line number Diff line number Diff line change
Expand Up @@ -201,8 +201,8 @@ class EnzymeMLDocument(BaseModel):
serialization_alias="@context",
default_factory=lambda: {
"enzml": "http://www.enzymeml.org/v2/",
"schema": "https://schema.org/",
"OBO": "http://purl.obolibrary.org/obo/",
"schema": "https://schema.org/",
"name": "schema:title",
"created": "schema:dateCreated",
"modified": "schema:dateModified",
Expand Down Expand Up @@ -603,6 +603,7 @@ def add_to_parameters(
initial_value: Optional[float] = None,
upper_bound: Optional[float] = None,
lower_bound: Optional[float] = None,
fit: Optional[bool] = True,
stderr: Optional[float] = None,
constant: Optional[bool] = True,
**kwargs,
Expand All @@ -616,6 +617,7 @@ def add_to_parameters(
"initial_value": initial_value,
"upper_bound": upper_bound,
"lower_bound": lower_bound,
"fit": fit,
"stderr": stderr,
"constant": constant,
}
Expand Down Expand Up @@ -659,8 +661,8 @@ class Creator(BaseModel):
serialization_alias="@context",
default_factory=lambda: {
"enzml": "http://www.enzymeml.org/v2/",
"schema": "https://schema.org/",
"OBO": "http://purl.obolibrary.org/obo/",
"schema": "https://schema.org/",
"given_name": "schema:givenName",
"family_name": "schema:familyName",
"mail": "schema:email",
Expand Down Expand Up @@ -773,8 +775,8 @@ class Vessel(BaseModel):
serialization_alias="@context",
default_factory=lambda: {
"enzml": "http://www.enzymeml.org/v2/",
"schema": "https://schema.org/",
"OBO": "http://purl.obolibrary.org/obo/",
"schema": "https://schema.org/",
"id": {
"@id": "schema:identifier",
"@type": "@id",
Expand Down Expand Up @@ -911,8 +913,8 @@ class Protein(BaseModel):
serialization_alias="@context",
default_factory=lambda: {
"enzml": "http://www.enzymeml.org/v2/",
"schema": "https://schema.org/",
"OBO": "http://purl.obolibrary.org/obo/",
"schema": "https://schema.org/",
"id": {
"@id": "schema:identifier",
"@type": "@id",
Expand Down Expand Up @@ -1044,8 +1046,8 @@ class Complex(BaseModel):
serialization_alias="@context",
default_factory=lambda: {
"enzml": "http://www.enzymeml.org/v2/",
"schema": "https://schema.org/",
"OBO": "http://purl.obolibrary.org/obo/",
"schema": "https://schema.org/",
"id": {
"@id": "schema:identifier",
"@type": "@id",
Expand Down Expand Up @@ -1195,8 +1197,8 @@ class SmallMolecule(BaseModel):
serialization_alias="@context",
default_factory=lambda: {
"enzml": "http://www.enzymeml.org/v2/",
"schema": "https://schema.org/",
"OBO": "http://purl.obolibrary.org/obo/",
"schema": "https://schema.org/",
"id": {
"@id": "schema:identifier",
"@type": "@id",
Expand Down Expand Up @@ -1330,8 +1332,8 @@ class Reaction(BaseModel):
serialization_alias="@context",
default_factory=lambda: {
"enzml": "http://www.enzymeml.org/v2/",
"schema": "https://schema.org/",
"OBO": "http://purl.obolibrary.org/obo/",
"schema": "https://schema.org/",
"id": {
"@id": "schema:identifier",
"@type": "@id",
Expand Down Expand Up @@ -1517,8 +1519,8 @@ class ReactionElement(BaseModel):
serialization_alias="@context",
default_factory=lambda: {
"enzml": "http://www.enzymeml.org/v2/",
"schema": "https://schema.org/",
"OBO": "http://purl.obolibrary.org/obo/",
"schema": "https://schema.org/",
"species_id": {
"@id": "schema:identifier",
"@type": "@id",
Expand Down Expand Up @@ -1622,8 +1624,8 @@ class ModifierElement(BaseModel):
serialization_alias="@context",
default_factory=lambda: {
"enzml": "http://www.enzymeml.org/v2/",
"schema": "https://schema.org/",
"OBO": "http://purl.obolibrary.org/obo/",
"schema": "https://schema.org/",
"species_id": {
"@id": "schema:identifier",
"@type": "@id",
Expand Down Expand Up @@ -1738,8 +1740,8 @@ class Equation(BaseModel):
serialization_alias="@context",
default_factory=lambda: {
"enzml": "http://www.enzymeml.org/v2/",
"schema": "https://schema.org/",
"OBO": "http://purl.obolibrary.org/obo/",
"schema": "https://schema.org/",
"species_id": {
"@id": "schema:identifier",
"@type": "@id",
Expand Down Expand Up @@ -1874,8 +1876,8 @@ class Variable(BaseModel):
serialization_alias="@context",
default_factory=lambda: {
"enzml": "http://www.enzymeml.org/v2/",
"schema": "https://schema.org/",
"OBO": "http://purl.obolibrary.org/obo/",
"schema": "https://schema.org/",
"id": {
"@id": "schema:identifier",
"@type": "@id",
Expand Down Expand Up @@ -1989,6 +1991,11 @@ class Parameter(BaseModel):
description="""Lower bound for the parameter value that was used
for the parameter estimation""",
)
fit: Optional[bool] = Field(
default=True,
description="""Whether this parameter should be varied or not in
the context of an optimization.""",
)
stderr: Optional[float] = Field(
default=None,
description="""Standard error of the estimated parameter.""",
Expand All @@ -2014,8 +2021,8 @@ class Parameter(BaseModel):
serialization_alias="@context",
default_factory=lambda: {
"enzml": "http://www.enzymeml.org/v2/",
"schema": "https://schema.org/",
"OBO": "http://purl.obolibrary.org/obo/",
"schema": "https://schema.org/",
"id": {
"@id": "schema:identifier",
"@type": "@id",
Expand Down Expand Up @@ -2141,8 +2148,8 @@ class Measurement(BaseModel):
serialization_alias="@context",
default_factory=lambda: {
"enzml": "http://www.enzymeml.org/v2/",
"schema": "https://schema.org/",
"OBO": "http://purl.obolibrary.org/obo/",
"schema": "https://schema.org/",
"id": {
"@id": "schema:identifier",
"@type": "@id",
Expand Down Expand Up @@ -2330,8 +2337,8 @@ class MeasurementData(BaseModel):
serialization_alias="@context",
default_factory=lambda: {
"enzml": "http://www.enzymeml.org/v2/",
"schema": "https://schema.org/",
"OBO": "http://purl.obolibrary.org/obo/",
"schema": "https://schema.org/",
"species_id": {
"@type": "@id",
},
Expand Down
2 changes: 1 addition & 1 deletion specs
Open in desktop
Submodule specs updated 35 files
+25 −0 .github/workflows/docs.yml
+0 −63 .github/workflows/gen.yml
+0 −31 .github/workflows/generate-docs.yml
+13 −5 README.md
+1 −0 docs/CNAME
+1 −1 docs/js/validation.js
+9 −4 docs/usage.md
+0 −27 enzymeml-go/.gitignore
+0 −61 enzymeml-go/README.md
+0 −24 enzymeml-go/examples/database_example/Readme.md
+0 −93 enzymeml-go/examples/database_example/enzymeml_doc_1.json
+0 −192 enzymeml-go/examples/database_example/main.go
+0 −15 enzymeml-go/go.mod
+0 −16 enzymeml-go/go.sum
+0 −482 enzymeml-go/src/database/database.go
+0 −330 enzymeml-go/src/v2.go
+0 −2,895 enzymeml-jl/Manifest.toml
+0 −12 enzymeml-jl/Project.toml
+0 −51 enzymeml-jl/README.md
+0 −2,901 enzymeml-jl/examples/Manifest.toml
+0 −2 enzymeml-jl/examples/Project.toml
+0 −44 enzymeml-jl/examples/basic.jl
+ − enzymeml-jl/examples/basic.png
+0 −107 enzymeml-jl/examples/test.json
+0 −30 enzymeml-jl/src/EnzymeML.jl
+0 −123 enzymeml-jl/src/System.jl
+0 −725 enzymeml-jl/src/V2.jl
+0 −88 enzymeml-jl/src/V2Utils.jl
+0 −66 enzymeml-ts/.gitignore
+0 −20 enzymeml-ts/package.json
+0 −482 enzymeml-ts/src/index.ts
+0 −584 enzymeml-ts/src/v2.ts
+0 −11 enzymeml-ts/tsconfig.json
+0 −7 gen.toml
+4 −0 specifications/v2.md