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feat: Cytiva Biacore T200 Evaluation -- Update parser to extract kinetics data (kd, ka, RMax, chi-squared, errors) #1183

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Merged
nathan-stender merged 13 commits into from
Apr 22, 2026
Merged

feat: Cytiva Biacore T200 Evaluation -- Update parser to extract kinetics data (kd, ka, RMax, chi-squared, errors) #1183

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2d08d4e
feat: Support multiple analysis models in Cytiva Biacore Insight parser
james-leinas Apr 10, 2026
1b8288c
feat: Update T200 parsers to support ProcessedData list structure
james-leinas Apr 10, 2026
cde3f97
fix: Return list of KineticsData from EvaluationKinetics.get_data
james-leinas Apr 10, 2026
13c6b9b
test: Update T200 Evaluation expected outputs for ProcessedData struc…
james-leinas Apr 10, 2026
d3bfeaf
test: Update Insight expected outputs - merge dynamic extraction and …
james-leinas Apr 10, 2026
68f50c2
lint
james-leinas Apr 10, 2026
bbb9f7e
Merge remote-tracking branch 'origin/main' into jleinas-biacore-insig…
james-leinas Apr 10, 2026
17d7520
feat: Add support for newer Fits structure in Biacore T200 Evaluation…
james-leinas Apr 16, 2026
952a5e6
chore: Apply linting and update test data file identifiers
james-leinas Apr 16, 2026
9dde330
feat: Extract affinity analysis data (KD, Rmax) from Biacore T200 Eva…
james-leinas Apr 17, 2026
a51554b
Merge main into jleinas-biacore-evaluation-kinetics
nathan-stender Apr 21, 2026
5a0d01e
fix: Remove dead isinstance(dict) check in T200 Evaluation model_name
nathan-stender Apr 21, 2026
f3da5b1
style: Fix black formatting
nathan-stender Apr 21, 2026
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152 changes: 84 additions & 68 deletions ...ma_mappers/adm/binding_affinity_analyzer/benchling/_2024/_12/binding_affinity_analyzer.py
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Original file line number Diff line number Diff line change
Expand Up @@ -46,7 +46,7 @@
from allotropy.parsers.utils.calculated_data_documents.definition import (
CalculatedDocument,
)
from allotropy.parsers.utils.values import assert_not_none, has_value, quantity_or_none
from allotropy.parsers.utils.values import assert_not_none, quantity_or_none
from allotropy.types import DictType


Expand Down Expand Up @@ -108,6 +108,19 @@ class DeviceControlDocument:
device_control_custom_info: DictType | None = None


@dataclass(frozen=True)
class ProcessedData:
"""Represents a single processed data document (one analysis model)."""

model_name: str
binding_on_rate_measurement_datum__kon_: float | None = None
binding_off_rate_measurement_datum__koff_: float | None = None
equilibrium_dissociation_constant__kd_: float | None = None
maximum_binding_capacity__rmax_: float | None = None
processed_data_custom_info: DictType | None = None
data_processing_document: DictType | None = None


@dataclass(frozen=True)
class Measurement:
identifier: str
Expand All @@ -126,19 +139,12 @@ class Measurement:
# Sensorgram
sensorgram_data_cube: DataCube | None = None

# Processed Data
binding_on_rate_measurement_datum__kon_: float | None = None
binding_off_rate_measurement_datum__koff_: float | None = None
equilibrium_dissociation_constant__kd_: float | None = None
maximum_binding_capacity__rmax_: float | None = None
processed_data_custom_info: DictType | None = None
# Processed Data - supports multiple analysis models
processed_data: list[ProcessedData] | None = None

# Report point
report_point_data: list[ReportPoint] | None = None

# Data processing
data_processing_document: DictType | None = None


@dataclass(frozen=True)
class MeasurementGroup:
Expand Down Expand Up @@ -249,60 +255,75 @@ def _get_measurement_document_item(
def _get_surface_plasmon_resonance_measurement_document(
self, measurement: Measurement, metadata: Metadata
) -> MeasurementDocumentItem:
processed_data_document = ProcessedDataDocumentItem(
data_processing_document=(
{
key: value
for key, value in measurement.data_processing_document.items()
if value is not None
}
if measurement.data_processing_document
else None
),
binding_on_rate_measurement_datum__kon_=quantity_or_none(
TQuantityValuePerMolarPerSecond,
measurement.binding_on_rate_measurement_datum__kon_,
),
binding_off_rate_measurement_datum__koff_=quantity_or_none(
TQuantityValuePerSecond,
measurement.binding_off_rate_measurement_datum__koff_,
),
equilibrium_dissociation_constant__kd_=quantity_or_none(
TQuantityValueMolar,
measurement.equilibrium_dissociation_constant__kd_,
),
maximum_binding_capacity__rmax_=quantity_or_none(
TQuantityValueResponseUnit,
measurement.maximum_binding_capacity__rmax_,
),
report_point_aggregate_document=(
ReportPointAggregateDocument(
report_point_document=[
add_custom_information_document(
ReportPointDocumentItem(
report_point_identifier=report_point.identifier,
identifier_role=report_point.identifier_role,
absolute_resonance=TQuantityValueResponseUnit(
value=report_point.absolute_resonance
),
relative_resonance=quantity_or_none(
TQuantityValueResponseUnit,
report_point.relative_resonance,
),
time_setting=TQuantityValueSecondTime(
value=report_point.time_setting
),
# Report points are measurement-level data but the schema nests them
# inside ProcessedDataDocumentItem, so we attach them to the first entry.
report_point_aggregate = (
ReportPointAggregateDocument(
report_point_document=[
add_custom_information_document(
ReportPointDocumentItem(
report_point_identifier=report_point.identifier,
identifier_role=report_point.identifier_role,
absolute_resonance=TQuantityValueResponseUnit(
value=report_point.absolute_resonance
),
custom_info_doc=report_point.custom_info,
)
for report_point in measurement.report_point_data
]
)
if measurement.report_point_data
else None
),
relative_resonance=quantity_or_none(
TQuantityValueResponseUnit,
report_point.relative_resonance,
),
time_setting=TQuantityValueSecondTime(
value=report_point.time_setting
),
),
custom_info_doc=report_point.custom_info,
)
for report_point in measurement.report_point_data
]
)
if measurement.report_point_data
else None
)

processed_data_documents = []
if measurement.processed_data:
for idx, proc_data in enumerate(measurement.processed_data):
doc = ProcessedDataDocumentItem(
data_processing_document=(
{
key: value
for key, value in proc_data.data_processing_document.items()
if value is not None
}
if proc_data.data_processing_document
else None
),
binding_on_rate_measurement_datum__kon_=quantity_or_none(
TQuantityValuePerMolarPerSecond,
proc_data.binding_on_rate_measurement_datum__kon_,
),
binding_off_rate_measurement_datum__koff_=quantity_or_none(
TQuantityValuePerSecond,
proc_data.binding_off_rate_measurement_datum__koff_,
),
equilibrium_dissociation_constant__kd_=quantity_or_none(
TQuantityValueMolar,
proc_data.equilibrium_dissociation_constant__kd_,
),
maximum_binding_capacity__rmax_=quantity_or_none(
TQuantityValueResponseUnit,
proc_data.maximum_binding_capacity__rmax_,
),
report_point_aggregate_document=report_point_aggregate
if idx == 0
else None,
)
processed_data_documents.append(
add_custom_information_document(
doc,
custom_info_doc=proc_data.processed_data_custom_info,
)
)

return MeasurementDocumentItem(
measurement_identifier=measurement.identifier,
sample_document=add_custom_information_document(
Expand Down Expand Up @@ -361,14 +382,9 @@ def _get_surface_plasmon_resonance_measurement_document(
),
processed_data_aggregate_document=(
ProcessedDataAggregateDocument(
processed_data_document=[
add_custom_information_document(
processed_data_document,
custom_info_doc=measurement.processed_data_custom_info,
)
]
processed_data_document=processed_data_documents
)
if has_value(processed_data_document)
if processed_data_documents
else None
),
)
Expand Down
151 changes: 89 additions & 62 deletions src/allotropy/parsers/cytiva_biacore_insight/cytiva_biacore_insight_data_creator.py
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Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -20,6 +20,7 @@
MeasurementGroup,
MeasurementType,
Metadata,
ProcessedData,
ReportPoint,
)
from allotropy.parsers.constants import NOT_APPLICABLE
Expand Down Expand Up @@ -113,77 +114,103 @@ def _get_measurements(
) -> list[Measurement]:
data_processing_document = dict(metadata.data_processing_document or {})

return [
Measurement(
identifier=measurement.identifier,
sample_identifier=measurement.sample_identifier,
type_=MeasurementType.SURFACE_PLASMON_RESONANCE,
method_name=measurement.method_name,
ligand_identifier=measurement.ligand_identifier,
device_control_document=measurement.device_control_document,
sample_custom_info=measurement.sample_custom_info,
binding_on_rate_measurement_datum__kon_=(
measurement.kinetics.binding_on_rate_measurement_datum
),
binding_off_rate_measurement_datum__koff_=(
measurement.kinetics.binding_off_rate_measurement_datum
),
equilibrium_dissociation_constant__kd_=(
measurement.kinetics.equilibrium_dissociation_constant
),
maximum_binding_capacity__rmax_=(
measurement.kinetics.maximum_binding_capacity
),
processed_data_custom_info=_clean_custom_info(
{
(
"Affinity Chi squared"
if measurement.kinetics.is_affinity_measurement
else "Kinetics Chi squared"
): (
TQuantityValue(value=v, unit="RU^2")
if (v := measurement.kinetics.kinetics_chi_squared) is not None
else None
measurements = []
for measurement in measurement_data:
processed_data_list = []

if measurement.kinetics:
for kinetics in measurement.kinetics:
chi_squared_label = (
"Affinity Chi squared"
if "affinity" in kinetics.model_name.lower()
else "Kinetics Chi squared"
)

processed_data = ProcessedData(
model_name=kinetics.model_name,
binding_on_rate_measurement_datum__kon_=(
kinetics.binding_on_rate_measurement_datum
),
"tc": quantity_or_none(
TQuantityValueUnitless, measurement.kinetics.tc
binding_off_rate_measurement_datum__koff_=(
kinetics.binding_off_rate_measurement_datum
),
"offset": quantity_or_none(
TQuantityValueResponseUnit,
measurement.kinetics.offset,
equilibrium_dissociation_constant__kd_=(
kinetics.equilibrium_dissociation_constant
),
}
),
report_point_data=[
ReportPoint(
identifier=rp.identifier,
identifier_role=rp.identifier_role,
absolute_resonance=rp.absolute_resonance,
time_setting=rp.time_setting,
relative_resonance=rp.relative_resonance,
custom_info=_clean_custom_info(
maximum_binding_capacity__rmax_=(kinetics.maximum_binding_capacity),
processed_data_custom_info=_clean_custom_info(
{
"Step purpose": rp.step_purpose,
"Window": quantity_or_none(
TQuantityValueSecondTime, rp.window
chi_squared_label: (
TQuantityValue(value=v, unit="RU^2")
if (v := kinetics.kinetics_chi_squared) is not None
else None
),
"tc": quantity_or_none(TQuantityValueUnitless, kinetics.tc),
"U-value": quantity_or_none(
TQuantityValueUnitless, kinetics.u_value
),
"offset": quantity_or_none(
TQuantityValueResponseUnit,
kinetics.offset,
),
"Baseline": rp.baseline,
}
),
data_processing_document=_clean_custom_info(
{
**data_processing_document,
"Acceptance State": kinetics.acceptance_state,
"Curve Markers": kinetics.curve_markers,
"Kinetics Model": kinetics.model_name,
}
),
)
processed_data_list.append(processed_data)
else:
# If no kinetics data, create a single ProcessedData with just data processing info
processed_data_list.append(
ProcessedData(
model_name="N/A", # No model when there's no kinetics data
data_processing_document=_clean_custom_info(
data_processing_document
)
if data_processing_document
else None,
)
for rp in measurement.report_point_data
],
data_processing_document=_clean_custom_info(
{
**data_processing_document,
"Acceptance State": measurement.kinetics.acceptance_state,
"Curve Markers": measurement.kinetics.curve_markers,
"Kinetics Model": measurement.kinetics.kinetics_model,
}
),
)

measurements.append(
Measurement(
identifier=measurement.identifier,
sample_identifier=measurement.sample_identifier,
type_=MeasurementType.SURFACE_PLASMON_RESONANCE,
method_name=measurement.method_name,
ligand_identifier=measurement.ligand_identifier,
device_control_document=measurement.device_control_document,
sample_custom_info=measurement.sample_custom_info,
processed_data=processed_data_list,
report_point_data=[
ReportPoint(
identifier=rp.identifier,
identifier_role=rp.identifier_role,
absolute_resonance=rp.absolute_resonance,
time_setting=rp.time_setting,
relative_resonance=rp.relative_resonance,
custom_info=_clean_custom_info(
{
"Step purpose": rp.step_purpose,
"Window": quantity_or_none(
TQuantityValueSecondTime, rp.window
),
"Baseline": rp.baseline,
}
),
)
for rp in measurement.report_point_data
],
)
)
for measurement in measurement_data
]

return measurements


def create_calculated_data(data: Data) -> list[CalculatedDocument]:
Expand Down
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