diff --git a/src/allotropy/allotrope/schema_mappers/adm/binding_affinity_analyzer/benchling/_2024/_12/binding_affinity_analyzer.py b/src/allotropy/allotrope/schema_mappers/adm/binding_affinity_analyzer/benchling/_2024/_12/binding_affinity_analyzer.py index a7bd2206f..4941b5b81 100644 --- a/src/allotropy/allotrope/schema_mappers/adm/binding_affinity_analyzer/benchling/_2024/_12/binding_affinity_analyzer.py +++ b/src/allotropy/allotrope/schema_mappers/adm/binding_affinity_analyzer/benchling/_2024/_12/binding_affinity_analyzer.py @@ -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 @@ -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 @@ -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: @@ -249,60 +255,76 @@ 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 - ), + # Create report point aggregate document (only for the first processed data document) + 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 ) + # Create processed data documents - one for each analysis model + 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_, + ), + # Only include report points in the first processed data document + 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( @@ -361,14 +383,9 @@ 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 ), ) diff --git a/src/allotropy/allotrope/schemas.py b/src/allotropy/allotrope/schemas.py index e7f81fd6d..06e2b5e39 100644 --- a/src/allotropy/allotrope/schemas.py +++ b/src/allotropy/allotrope/schemas.py @@ -85,7 +85,7 @@ def validate_asm_schema(asm_dict: dict[str, Any]) -> None: resolver = jsonschema.RefResolver( base_uri=schema.get("$id", ""), referrer=schema, - store=store, + store=store, # type: ignore[arg-type] ) validator = jsonschema.validators.Draft202012Validator( schema, resolver=resolver, format_checker=FORMAT_CHECKER diff --git a/src/allotropy/parsers/cytiva_biacore_insight/cytiva_biacore_insight_data_creator.py b/src/allotropy/parsers/cytiva_biacore_insight/cytiva_biacore_insight_data_creator.py index f94bc5e5c..6a5be08ae 100644 --- a/src/allotropy/parsers/cytiva_biacore_insight/cytiva_biacore_insight_data_creator.py +++ b/src/allotropy/parsers/cytiva_biacore_insight/cytiva_biacore_insight_data_creator.py @@ -20,6 +20,7 @@ MeasurementGroup, MeasurementType, Metadata, + ProcessedData, ReportPoint, ) from allotropy.parsers.constants import NOT_APPLICABLE @@ -113,77 +114,106 @@ 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: + # Create ProcessedData for each kinetics model + processed_data_list = [] + + if measurement.kinetics: + # If we have kinetics data, create one ProcessedData per model + for kinetics in measurement.kinetics: + # Determine chi-squared label based on model type + 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]: diff --git a/src/allotropy/parsers/cytiva_biacore_insight/cytiva_biacore_insight_structure.py b/src/allotropy/parsers/cytiva_biacore_insight/cytiva_biacore_insight_structure.py index 2d6f9ecbf..60c6c3e4f 100644 --- a/src/allotropy/parsers/cytiva_biacore_insight/cytiva_biacore_insight_structure.py +++ b/src/allotropy/parsers/cytiva_biacore_insight/cytiva_biacore_insight_structure.py @@ -381,47 +381,71 @@ def get_data_processing_doc(reader: CytivaBiacoreInsightReader) -> DictType | No @dataclass(frozen=True) class KineticsData: + model_name: str # "1:1 binding", "Steady state affinity", etc. acceptance_state: str | None = None curve_markers: str | None = None - kinetics_model: str | None = None binding_on_rate_measurement_datum: float | None = None binding_off_rate_measurement_datum: float | None = None equilibrium_dissociation_constant: float | None = None maximum_binding_capacity: float | None = None kinetics_chi_squared: float | None = None tc: float | None = None + u_value: float | None = None # U-value for kinetics analysis offset: float | None = None # Affinity-specific field - is_affinity_measurement: bool = False # Track if this is from Affinity analysis @staticmethod - def create(kinetics_data: SeriesData) -> KineticsData: - # Detect if this is affinity data by checking which chi-squared column is present - kinetics_chi = kinetics_data.get(float, "Kinetics Chi² (RU²)") - affinity_chi = kinetics_data.get(float, "Affinity Chi² (RU²)") - is_affinity = kinetics_chi is None and affinity_chi is not None + def create_from_kinetics_model(kinetics_data: SeriesData) -> KineticsData | None: + """Create KineticsData from 1:1 binding model columns.""" + model = kinetics_data.get(str, "Kinetics model") + if model is None: + return None + # For kinetics model, use the first set of columns (ka, kd, Rmax, KD, U-value) + # When duplicate columns exist, SeriesData.get with duplicate_strategy="first" returns first value return KineticsData( + model_name=model, acceptance_state=kinetics_data.get(str, "Acceptance state"), curve_markers=kinetics_data.get(str, "Curve markers"), - # Try "Kinetics model" first, fall back to "Affinity model" - kinetics_model=( - kinetics_data.get(str, "Kinetics model") - or kinetics_data.get(str, "Affinity model") - ), binding_on_rate_measurement_datum=kinetics_data.get(float, "ka (1/Ms)"), binding_off_rate_measurement_datum=kinetics_data.get(float, "kd (1/s)"), - equilibrium_dissociation_constant=kinetics_data.get(float, "KD (M)"), - maximum_binding_capacity=kinetics_data.get(float, "Rmax (RU)"), - # Try "Kinetics Chi²" first, fall back to "Affinity Chi²" - kinetics_chi_squared=kinetics_chi or affinity_chi, + equilibrium_dissociation_constant=kinetics_data.get( + float, "KD (M)", duplicate_strategy="first" + ), + maximum_binding_capacity=kinetics_data.get( + float, "Rmax (RU)", duplicate_strategy="first" + ), + kinetics_chi_squared=kinetics_data.get(float, "Kinetics Chi² (RU²)"), + u_value=kinetics_data.get(float, "U-value"), + tc=kinetics_data.get(float, "tc"), + ) + + @staticmethod + def create_from_affinity_model(kinetics_data: SeriesData) -> KineticsData | None: + """Create KineticsData from Steady state affinity model columns.""" + model = kinetics_data.get(str, "Affinity model") + if model is None: + return None + + # For affinity model, use the second set of columns (KD, Rmax, offset) + # When duplicate columns exist, SeriesData.get with duplicate_strategy="last" returns last value + return KineticsData( + model_name=model, + acceptance_state=kinetics_data.get(str, "Acceptance state"), + curve_markers=kinetics_data.get(str, "Curve markers"), + equilibrium_dissociation_constant=kinetics_data.get( + float, "KD (M)", duplicate_strategy="last" + ), + maximum_binding_capacity=kinetics_data.get( + float, "Rmax (RU)", duplicate_strategy="last" + ), + kinetics_chi_squared=kinetics_data.get(float, "Affinity Chi² (RU²)"), + offset=kinetics_data.get(float, "offset (RU)"), tc=kinetics_data.get(float, "tc"), - offset=kinetics_data.get(float, "offset (RU)"), # Affinity-specific - is_affinity_measurement=is_affinity, ) class EvaluationKinetics: - _data: dict[str, KineticsData] + _data: dict[str, list[KineticsData]] def __init__(self, kinetics_table: pd.DataFrame) -> None: def _get_key(row: pd.Series[Any]) -> str: @@ -430,28 +454,45 @@ def _get_key(row: pd.Series[Any]) -> str: # For affinity data, we might have multiple capture solutions # Build key with all available capture solutions capture_solution = row.get("Capture 1 Solution", "") + # Handle None, NaN, or pd.NA values for capture_solution + if capture_solution is None or ( + isinstance(capture_solution, float) and np.isnan(capture_solution) + ): + capture_solution = "" analyte_solution = row.get("Analyte 1 Solution", "") return f"{channel_or_flowcell} {capture_solution} {analyte_solution}" self._data = {} if not kinetics_table.empty and len(kinetics_table.columns) > 0: - self._data = { - _get_key(row): KineticsData.create(SeriesData(row)) - for _, row in kinetics_table.iterrows() - } + for _, row in kinetics_table.iterrows(): + series_data = SeriesData(row) + key = _get_key(row) + + # Try to create both kinetics and affinity models + models = [] + if kinetics_model := KineticsData.create_from_kinetics_model( + series_data + ): + models.append(kinetics_model) + if affinity_model := KineticsData.create_from_affinity_model( + series_data + ): + models.append(affinity_model) + + if models: + self._data[key] = models def get_data( self, channel: int | str, capture_solution: str | None, analyte_solution: str | None, - ) -> KineticsData: - empty = KineticsData() + ) -> list[KineticsData]: if analyte_solution is None: - return empty + return [] # Handle cases where capture_solution might be None (treat as empty string) capture_key = capture_solution if capture_solution is not None else "" - return self._data.get(f"{channel} {capture_key} {analyte_solution}", empty) + return self._data.get(f"{channel} {capture_key} {analyte_solution}", []) class EvaluationConcentration: @@ -567,7 +608,7 @@ class MeasurementData: ligand_identifier: str | None device_control_document: list[DeviceControlDocument] sample_custom_info: dict[str, Any | None] - kinetics: KineticsData + kinetics: list[KineticsData] report_point_data: list[ReportPointData] @staticmethod diff --git a/src/allotropy/parsers/cytiva_biacore_t200_control/cytiva_biacore_t200_control_data_creator.py b/src/allotropy/parsers/cytiva_biacore_t200_control/cytiva_biacore_t200_control_data_creator.py index 9043ef959..9932c9713 100644 --- a/src/allotropy/parsers/cytiva_biacore_t200_control/cytiva_biacore_t200_control_data_creator.py +++ b/src/allotropy/parsers/cytiva_biacore_t200_control/cytiva_biacore_t200_control_data_creator.py @@ -25,6 +25,7 @@ Measurement, MeasurementGroup, Metadata, + ProcessedData, ReportPoint, ) from allotropy.allotrope.schema_mappers.data_cube import DataCube, DataCubeComponent @@ -148,64 +149,78 @@ def create_measurements( device_control_custom_info: DictType, data: Data, ) -> list[Measurement]: - return [ - Measurement( - identifier=measurement.identifier, - type_=measurement.type_, - sample_identifier=measurement.sample_identifier, - location_identifier=measurement.location_identifier, - sample_role_type=measurement.sample_role_type, - concentration=measurement.concentration, - device_control_document=[ - DeviceControlDocument( - device_type=measurement.device_type, - flow_cell_identifier=measurement.flow_cell_identifier, - flow_path=measurement.flow_path, - flow_rate=measurement.flow_rate, - contact_time=measurement.contact_time, - dilution=measurement.dilution, - device_control_custom_info=dict( - device_control_custom_info - ), # copy to avoid modifying the original + measurements = [] + for measurement in measurements_data: + # Create report points + report_points = ( + [ + ReportPoint( + identifier=rp_data.identifier, + identifier_role=rp_data.identifier_role, + absolute_resonance=rp_data.absolute_resonance, + relative_resonance=rp_data.relative_resonance, + time_setting=rp_data.time_setting, + custom_info=rp_data.custom_info, ) - ], - sample_custom_info={ - **data.application_template_details.get_nested( - "racks" - ).get_keys_as_dict( - { - "Rack1": (str, "_Rack1", None), - "Rack2": (str, "_Rack2", None), - "Lock Positions": (bool, "_LockPositions", None), - } - ), - "molecular weight": quantity_or_none( - TQuantityValueDalton, measurement.molecular_weight - ), - **measurement.sample_custom_info, - }, - sensorgram_data_cube=_get_sensorgram_datacube(measurement.sensorgram_data), - report_point_data=( - [ - ReportPoint( - identifier=rp_data.identifier, - identifier_role=rp_data.identifier_role, - absolute_resonance=rp_data.absolute_resonance, - relative_resonance=rp_data.relative_resonance, - time_setting=rp_data.time_setting, - custom_info=rp_data.custom_info, + for rp_data in measurement.report_point_data + ] + if measurement.report_point_data is not None + else None + ) + + # Wrap report points in a ProcessedData object (required by new schema) + processed_data = ( + [ProcessedData(model_name="N/A")] if report_points is not None else None + ) + + measurements.append( + Measurement( + identifier=measurement.identifier, + type_=measurement.type_, + sample_identifier=measurement.sample_identifier, + location_identifier=measurement.location_identifier, + sample_role_type=measurement.sample_role_type, + concentration=measurement.concentration, + device_control_document=[ + DeviceControlDocument( + device_type=measurement.device_type, + flow_cell_identifier=measurement.flow_cell_identifier, + flow_path=measurement.flow_path, + flow_rate=measurement.flow_rate, + contact_time=measurement.contact_time, + dilution=measurement.dilution, + device_control_custom_info=dict( + device_control_custom_info + ), # copy to avoid modifying the original ) - for rp_data in measurement.report_point_data - ] - if measurement.report_point_data is not None - else None - ), - # for Mobilization experiments - method_name=measurement.method_name, - ligand_identifier=measurement.ligand_identifier, + ], + sample_custom_info={ + **data.application_template_details.get_nested( + "racks" + ).get_keys_as_dict( + { + "Rack1": (str, "_Rack1", None), + "Rack2": (str, "_Rack2", None), + "Lock Positions": (bool, "_LockPositions", None), + } + ), + "molecular weight": quantity_or_none( + TQuantityValueDalton, measurement.molecular_weight + ), + **measurement.sample_custom_info, + }, + sensorgram_data_cube=_get_sensorgram_datacube( + measurement.sensorgram_data + ), + report_point_data=report_points, + processed_data=processed_data, + # for Mobilization experiments + method_name=measurement.method_name, + ligand_identifier=measurement.ligand_identifier, + ) ) - for measurement in measurements_data - ] + + return measurements def create_measurement_groups(data: Data) -> list[MeasurementGroup]: diff --git a/src/allotropy/parsers/cytiva_biacore_t200_evaluation/cytiva_biacore_t200_evaluation_data_creator.py b/src/allotropy/parsers/cytiva_biacore_t200_evaluation/cytiva_biacore_t200_evaluation_data_creator.py index 17487ebb1..269c81a3a 100644 --- a/src/allotropy/parsers/cytiva_biacore_t200_evaluation/cytiva_biacore_t200_evaluation_data_creator.py +++ b/src/allotropy/parsers/cytiva_biacore_t200_evaluation/cytiva_biacore_t200_evaluation_data_creator.py @@ -22,6 +22,7 @@ MeasurementGroup, MeasurementType, Metadata, + ProcessedData, ReportPoint, ) from allotropy.allotrope.schema_mappers.data_cube import DataCube, DataCubeComponent @@ -381,6 +382,53 @@ def _normalize_flow_cell_id(value: Any) -> str: # Extract kinetic analysis data using precomputed mapping (if present) kinetic_data = kinetic_map.get(fc_id) if kinetic_map is not None else None + # Extract kinetic parameters + kon = _extract_kinetic_parameter(kinetic_data, "parameters", ["ka", "kon"]) + koff = _extract_kinetic_parameter(kinetic_data, "parameters", ["kd", "koff"]) + kd = _extract_kinetic_parameter( + kinetic_data, "calculated", ["Kd_M", "KD", "kd"] + ) + rmax = _extract_kinetic_parameter(kinetic_data, "parameters", ["Rmax", "rmax"]) + + # Create processed data object if we have kinetic data + processed_data_list = None + if kinetic_data is not None: + processed_data_list = [ + ProcessedData( + model_name=kinetic_data.get("model", "N/A") + if isinstance(kinetic_data, dict) + else "N/A", + binding_on_rate_measurement_datum__kon_=kon, + binding_off_rate_measurement_datum__koff_=koff, + equilibrium_dissociation_constant__kd_=kd, + maximum_binding_capacity__rmax_=rmax, + processed_data_custom_info={ + "kinetics chi squared": { + "value": _extract_chi2_value(kinetic_data), + "unit": "(unitless)", + }, + "ka error": { + "value": _extract_kinetic_parameter_error( + kinetic_data, ["ka", "kon"] + ), + "unit": "M-1s-1", + }, + "kd error": { + "value": _extract_kinetic_parameter_error( + kinetic_data, ["kd", "koff"] + ), + "unit": "s^-1", + }, + "Rmax error": { + "value": _extract_kinetic_parameter_error( + kinetic_data, ["Rmax", "rmax"] + ), + "unit": "RU", + }, + }, + ) + ] + measurements.append( Measurement( identifier=random_uuid_str(), @@ -409,44 +457,7 @@ def _normalize_flow_cell_id(value: Any) -> str: df_fc, cycle=cycle_num, flow_cell=fc_id ), report_point_data=report_points, - # Kinetic analysis fields - binding_on_rate_measurement_datum__kon_=_extract_kinetic_parameter( - kinetic_data, "parameters", ["ka", "kon"] - ), - binding_off_rate_measurement_datum__koff_=_extract_kinetic_parameter( - kinetic_data, "parameters", ["kd", "koff"] - ), - equilibrium_dissociation_constant__kd_=_extract_kinetic_parameter( - kinetic_data, "calculated", ["Kd_M", "KD", "kd"] - ), - maximum_binding_capacity__rmax_=_extract_kinetic_parameter( - kinetic_data, "parameters", ["Rmax", "rmax"] - ), - # Attach custom kinetic analysis values for processed data custom info - processed_data_custom_info={ - "kinetics chi squared": { - "value": _extract_chi2_value(kinetic_data), - "unit": "(unitless)", - }, - "ka error": { - "value": _extract_kinetic_parameter_error( - kinetic_data, ["ka", "kon"] - ), - "unit": "M-1s-1", - }, - "kd error": { - "value": _extract_kinetic_parameter_error( - kinetic_data, ["kd", "koff"] - ), - "unit": "s^-1", - }, - "Rmax error": { - "value": _extract_kinetic_parameter_error( - kinetic_data, ["Rmax", "rmax"] - ), - "unit": "RU", - }, - }, + processed_data=processed_data_list, ) ) diff --git a/tests/parsers/cytiva_biacore_insight/testdata/Affinity.json b/tests/parsers/cytiva_biacore_insight/testdata/Affinity.json index 70b0d5f16..d9e0cb3df 100644 --- a/tests/parsers/cytiva_biacore_insight/testdata/Affinity.json +++ b/tests/parsers/cytiva_biacore_insight/testdata/Affinity.json @@ -5226,6 +5226,17 @@ "processed data aggregate document": { "processed data document": [ { + "data processing document": { + "Kinetics Model": "Steady state affinity" + }, + "equilibrium dissociation constant (KD)": { + "value": 1.0056400658698e-05, + "unit": "M" + }, + "maximum binding capacity (Rmax)": { + "value": 3.06774374813797, + "unit": "RU" + }, "report point aggregate document": { "report point document": [ { @@ -5489,6 +5500,16 @@ } } ] + }, + "custom information document": { + "Affinity Chi squared": { + "value": 0.168765684434212, + "unit": "RU^2" + }, + "offset": { + "value": 0.0, + "unit": "RU" + } } } ] @@ -5928,6 +5949,17 @@ "processed data aggregate document": { "processed data document": [ { + "data processing document": { + "Kinetics Model": "Steady state affinity" + }, + "equilibrium dissociation constant (KD)": { + "value": 1.93376304172776e-05, + "unit": "M" + }, + "maximum binding capacity (Rmax)": { + "value": 5.27162963964191, + "unit": "RU" + }, "report point aggregate document": { "report point document": [ { @@ -6191,6 +6223,16 @@ } } ] + }, + "custom information document": { + "Affinity Chi squared": { + "value": 0.104646601669138, + "unit": "RU^2" + }, + "offset": { + "value": 0.0, + "unit": "RU" + } } } ] @@ -6630,6 +6672,17 @@ "processed data aggregate document": { "processed data document": [ { + "data processing document": { + "Kinetics Model": "Steady state affinity" + }, + "equilibrium dissociation constant (KD)": { + "value": 1.04545738849952e-06, + "unit": "M" + }, + "maximum binding capacity (Rmax)": { + "value": 76.7842829472756, + "unit": "RU" + }, "report point aggregate document": { "report point document": [ { @@ -6893,6 +6946,16 @@ } } ] + }, + "custom information document": { + "Affinity Chi squared": { + "value": 1.21767585431671, + "unit": "RU^2" + }, + "offset": { + "value": 0.0, + "unit": "RU" + } } } ] @@ -7332,6 +7395,17 @@ "processed data aggregate document": { "processed data document": [ { + "data processing document": { + "Kinetics Model": "Steady state affinity" + }, + "equilibrium dissociation constant (KD)": { + "value": 4.53519326648544e-05, + "unit": "M" + }, + "maximum binding capacity (Rmax)": { + "value": 0.00135862070067624, + "unit": "RU" + }, "report point aggregate document": { "report point document": [ { @@ -7595,6 +7669,16 @@ } } ] + }, + "custom information document": { + "Affinity Chi squared": { + "value": 0.123572911524383, + "unit": "RU^2" + }, + "offset": { + "value": 0.0, + "unit": "RU" + } } } ] @@ -9072,6 +9156,17 @@ "processed data aggregate document": { "processed data document": [ { + "data processing document": { + "Kinetics Model": "Steady state affinity" + }, + "equilibrium dissociation constant (KD)": { + "value": 1.0056400658698e-05, + "unit": "M" + }, + "maximum binding capacity (Rmax)": { + "value": 3.06774374813797, + "unit": "RU" + }, "report point aggregate document": { "report point document": [ { @@ -9335,6 +9430,16 @@ } } ] + }, + "custom information document": { + "Affinity Chi squared": { + "value": 0.168765684434212, + "unit": "RU^2" + }, + "offset": { + "value": 0.0, + "unit": "RU" + } } } ] @@ -9774,6 +9879,17 @@ "processed data aggregate document": { "processed data document": [ { + "data processing document": { + "Kinetics Model": "Steady state affinity" + }, + "equilibrium dissociation constant (KD)": { + "value": 1.93376304172776e-05, + "unit": "M" + }, + "maximum binding capacity (Rmax)": { + "value": 5.27162963964191, + "unit": "RU" + }, "report point aggregate document": { "report point document": [ { @@ -10037,6 +10153,16 @@ } } ] + }, + "custom information document": { + "Affinity Chi squared": { + "value": 0.104646601669138, + "unit": "RU^2" + }, + "offset": { + "value": 0.0, + "unit": "RU" + } } } ] @@ -10476,6 +10602,17 @@ "processed data aggregate document": { "processed data document": [ { + "data processing document": { + "Kinetics Model": "Steady state affinity" + }, + "equilibrium dissociation constant (KD)": { + "value": 1.04545738849952e-06, + "unit": "M" + }, + "maximum binding capacity (Rmax)": { + "value": 76.7842829472756, + "unit": "RU" + }, "report point aggregate document": { "report point document": [ { @@ -10739,6 +10876,16 @@ } } ] + }, + "custom information document": { + "Affinity Chi squared": { + "value": 1.21767585431671, + "unit": "RU^2" + }, + "offset": { + "value": 0.0, + "unit": "RU" + } } } ] @@ -11178,6 +11325,17 @@ "processed data aggregate document": { "processed data document": [ { + "data processing document": { + "Kinetics Model": "Steady state affinity" + }, + "equilibrium dissociation constant (KD)": { + "value": 4.53519326648544e-05, + "unit": "M" + }, + "maximum binding capacity (Rmax)": { + "value": 0.00135862070067624, + "unit": "RU" + }, "report point aggregate document": { "report point document": [ { @@ -11441,6 +11599,16 @@ } } ] + }, + "custom information document": { + "Affinity Chi squared": { + "value": 0.123572911524383, + "unit": "RU^2" + }, + "offset": { + "value": 0.0, + "unit": "RU" + } } } ] @@ -12918,6 +13086,17 @@ "processed data aggregate document": { "processed data document": [ { + "data processing document": { + "Kinetics Model": "Steady state affinity" + }, + "equilibrium dissociation constant (KD)": { + "value": 1.0056400658698e-05, + "unit": "M" + }, + "maximum binding capacity (Rmax)": { + "value": 3.06774374813797, + "unit": "RU" + }, "report point aggregate document": { "report point document": [ { @@ -13181,6 +13360,16 @@ } } ] + }, + "custom information document": { + "Affinity Chi squared": { + "value": 0.168765684434212, + "unit": "RU^2" + }, + "offset": { + "value": 0.0, + "unit": "RU" + } } } ] @@ -13620,6 +13809,17 @@ "processed data aggregate document": { "processed data document": [ { + "data processing document": { + "Kinetics Model": "Steady state affinity" + }, + "equilibrium dissociation constant (KD)": { + "value": 1.93376304172776e-05, + "unit": "M" + }, + "maximum binding capacity (Rmax)": { + "value": 5.27162963964191, + "unit": "RU" + }, "report point aggregate document": { "report point document": [ { @@ -13883,6 +14083,16 @@ } } ] + }, + "custom information document": { + "Affinity Chi squared": { + "value": 0.104646601669138, + "unit": "RU^2" + }, + "offset": { + "value": 0.0, + "unit": "RU" + } } } ] @@ -14322,6 +14532,17 @@ "processed data aggregate document": { "processed data document": [ { + "data processing document": { + "Kinetics Model": "Steady state affinity" + }, + "equilibrium dissociation constant (KD)": { + "value": 1.04545738849952e-06, + "unit": "M" + }, + "maximum binding capacity (Rmax)": { + "value": 76.7842829472756, + "unit": "RU" + }, "report point aggregate document": { "report point document": [ { @@ -14585,6 +14806,16 @@ } } ] + }, + "custom information document": { + "Affinity Chi squared": { + "value": 1.21767585431671, + "unit": "RU^2" + }, + "offset": { + "value": 0.0, + "unit": "RU" + } } } ] @@ -15024,6 +15255,17 @@ "processed data aggregate document": { "processed data document": [ { + "data processing document": { + "Kinetics Model": "Steady state affinity" + }, + "equilibrium dissociation constant (KD)": { + "value": 4.53519326648544e-05, + "unit": "M" + }, + "maximum binding capacity (Rmax)": { + "value": 0.00135862070067624, + "unit": "RU" + }, "report point aggregate document": { "report point document": [ { @@ -15287,6 +15529,16 @@ } } ] + }, + "custom information document": { + "Affinity Chi squared": { + "value": 0.123572911524383, + "unit": "RU^2" + }, + "offset": { + "value": 0.0, + "unit": "RU" + } } } ] @@ -16764,6 +17016,17 @@ "processed data aggregate document": { "processed data document": [ { + "data processing document": { + "Kinetics Model": "Steady state affinity" + }, + "equilibrium dissociation constant (KD)": { + "value": 1.0056400658698e-05, + "unit": "M" + }, + "maximum binding capacity (Rmax)": { + "value": 3.06774374813797, + "unit": "RU" + }, "report point aggregate document": { "report point document": [ { @@ -17027,6 +17290,16 @@ } } ] + }, + "custom information document": { + "Affinity Chi squared": { + "value": 0.168765684434212, + "unit": "RU^2" + }, + "offset": { + "value": 0.0, + "unit": "RU" + } } } ] @@ -17466,6 +17739,17 @@ "processed data aggregate document": { "processed data document": [ { + "data processing document": { + "Kinetics Model": "Steady state affinity" + }, + "equilibrium dissociation constant (KD)": { + "value": 1.93376304172776e-05, + "unit": "M" + }, + "maximum binding capacity (Rmax)": { + "value": 5.27162963964191, + "unit": "RU" + }, "report point aggregate document": { "report point document": [ { @@ -17729,6 +18013,16 @@ } } ] + }, + "custom information document": { + "Affinity Chi squared": { + "value": 0.104646601669138, + "unit": "RU^2" + }, + "offset": { + "value": 0.0, + "unit": "RU" + } } } ] @@ -18168,6 +18462,17 @@ "processed data aggregate document": { "processed data document": [ { + "data processing document": { + "Kinetics Model": "Steady state affinity" + }, + "equilibrium dissociation constant (KD)": { + "value": 1.04545738849952e-06, + "unit": "M" + }, + "maximum binding capacity (Rmax)": { + "value": 76.7842829472756, + "unit": "RU" + }, "report point aggregate document": { "report point document": [ { @@ -18431,6 +18736,16 @@ } } ] + }, + "custom information document": { + "Affinity Chi squared": { + "value": 1.21767585431671, + "unit": "RU^2" + }, + "offset": { + "value": 0.0, + "unit": "RU" + } } } ] @@ -18870,6 +19185,17 @@ "processed data aggregate document": { "processed data document": [ { + "data processing document": { + "Kinetics Model": "Steady state affinity" + }, + "equilibrium dissociation constant (KD)": { + "value": 4.53519326648544e-05, + "unit": "M" + }, + "maximum binding capacity (Rmax)": { + "value": 0.00135862070067624, + "unit": "RU" + }, "report point aggregate document": { "report point document": [ { @@ -19133,6 +19459,16 @@ } } ] + }, + "custom information document": { + "Affinity Chi squared": { + "value": 0.123572911524383, + "unit": "RU^2" + }, + "offset": { + "value": 0.0, + "unit": "RU" + } } } ] @@ -20610,6 +20946,17 @@ "processed data aggregate document": { "processed data document": [ { + "data processing document": { + "Kinetics Model": "Steady state affinity" + }, + "equilibrium dissociation constant (KD)": { + "value": 1.0056400658698e-05, + "unit": "M" + }, + "maximum binding capacity (Rmax)": { + "value": 3.06774374813797, + "unit": "RU" + }, "report point aggregate document": { "report point document": [ { @@ -20873,6 +21220,16 @@ } } ] + }, + "custom information document": { + "Affinity Chi squared": { + "value": 0.168765684434212, + "unit": "RU^2" + }, + "offset": { + "value": 0.0, + "unit": "RU" + } } } ] @@ -21312,6 +21669,17 @@ "processed data aggregate document": { "processed data document": [ { + "data processing document": { + "Kinetics Model": "Steady state affinity" + }, + "equilibrium dissociation constant (KD)": { + "value": 1.93376304172776e-05, + "unit": "M" + }, + "maximum binding capacity (Rmax)": { + "value": 5.27162963964191, + "unit": "RU" + }, "report point aggregate document": { "report point document": [ { @@ -21575,6 +21943,16 @@ } } ] + }, + "custom information document": { + "Affinity Chi squared": { + "value": 0.104646601669138, + "unit": "RU^2" + }, + "offset": { + "value": 0.0, + "unit": "RU" + } } } ] @@ -22014,6 +22392,17 @@ "processed data aggregate document": { "processed data document": [ { + "data processing document": { + "Kinetics Model": "Steady state affinity" + }, + "equilibrium dissociation constant (KD)": { + "value": 1.04545738849952e-06, + "unit": "M" + }, + "maximum binding capacity (Rmax)": { + "value": 76.7842829472756, + "unit": "RU" + }, "report point aggregate document": { "report point document": [ { @@ -22277,6 +22666,16 @@ } } ] + }, + "custom information document": { + "Affinity Chi squared": { + "value": 1.21767585431671, + "unit": "RU^2" + }, + "offset": { + "value": 0.0, + "unit": "RU" + } } } ] @@ -22716,6 +23115,17 @@ "processed data aggregate document": { "processed data document": [ { + "data processing document": { + "Kinetics Model": "Steady state affinity" + }, + "equilibrium dissociation constant (KD)": { + "value": 4.53519326648544e-05, + "unit": "M" + }, + "maximum binding capacity (Rmax)": { + "value": 0.00135862070067624, + "unit": "RU" + }, "report point aggregate document": { "report point document": [ { @@ -22979,6 +23389,16 @@ } } ] + }, + "custom information document": { + "Affinity Chi squared": { + "value": 0.123572911524383, + "unit": "RU^2" + }, + "offset": { + "value": 0.0, + "unit": "RU" + } } } ] @@ -24456,6 +24876,17 @@ "processed data aggregate document": { "processed data document": [ { + "data processing document": { + "Kinetics Model": "Steady state affinity" + }, + "equilibrium dissociation constant (KD)": { + "value": 1.0056400658698e-05, + "unit": "M" + }, + "maximum binding capacity (Rmax)": { + "value": 3.06774374813797, + "unit": "RU" + }, "report point aggregate document": { "report point document": [ { @@ -24719,6 +25150,16 @@ } } ] + }, + "custom information document": { + "Affinity Chi squared": { + "value": 0.168765684434212, + "unit": "RU^2" + }, + "offset": { + "value": 0.0, + "unit": "RU" + } } } ] @@ -25158,6 +25599,17 @@ "processed data aggregate document": { "processed data document": [ { + "data processing document": { + "Kinetics Model": "Steady state affinity" + }, + "equilibrium dissociation constant (KD)": { + "value": 1.93376304172776e-05, + "unit": "M" + }, + "maximum binding capacity (Rmax)": { + "value": 5.27162963964191, + "unit": "RU" + }, "report point aggregate document": { "report point document": [ { @@ -25421,6 +25873,16 @@ } } ] + }, + "custom information document": { + "Affinity Chi squared": { + "value": 0.104646601669138, + "unit": "RU^2" + }, + "offset": { + "value": 0.0, + "unit": "RU" + } } } ] @@ -25860,6 +26322,17 @@ "processed data aggregate document": { "processed data document": [ { + "data processing document": { + "Kinetics Model": "Steady state affinity" + }, + "equilibrium dissociation constant (KD)": { + "value": 1.04545738849952e-06, + "unit": "M" + }, + "maximum binding capacity (Rmax)": { + "value": 76.7842829472756, + "unit": "RU" + }, "report point aggregate document": { "report point document": [ { @@ -26123,6 +26596,16 @@ } } ] + }, + "custom information document": { + "Affinity Chi squared": { + "value": 1.21767585431671, + "unit": "RU^2" + }, + "offset": { + "value": 0.0, + "unit": "RU" + } } } ] @@ -26562,6 +27045,17 @@ "processed data aggregate document": { "processed data document": [ { + "data processing document": { + "Kinetics Model": "Steady state affinity" + }, + "equilibrium dissociation constant (KD)": { + "value": 4.53519326648544e-05, + "unit": "M" + }, + "maximum binding capacity (Rmax)": { + "value": 0.00135862070067624, + "unit": "RU" + }, "report point aggregate document": { "report point document": [ { @@ -26825,6 +27319,16 @@ } } ] + }, + "custom information document": { + "Affinity Chi squared": { + "value": 0.123572911524383, + "unit": "RU^2" + }, + "offset": { + "value": 0.0, + "unit": "RU" + } } } ] @@ -28302,6 +28806,17 @@ "processed data aggregate document": { "processed data document": [ { + "data processing document": { + "Kinetics Model": "Steady state affinity" + }, + "equilibrium dissociation constant (KD)": { + "value": 1.0056400658698e-05, + "unit": "M" + }, + "maximum binding capacity (Rmax)": { + "value": 3.06774374813797, + "unit": "RU" + }, "report point aggregate document": { "report point document": [ { @@ -28565,6 +29080,16 @@ } } ] + }, + "custom information document": { + "Affinity Chi squared": { + "value": 0.168765684434212, + "unit": "RU^2" + }, + "offset": { + "value": 0.0, + "unit": "RU" + } } } ] @@ -29004,6 +29529,17 @@ "processed data aggregate document": { "processed data document": [ { + "data processing document": { + "Kinetics Model": "Steady state affinity" + }, + "equilibrium dissociation constant (KD)": { + "value": 1.93376304172776e-05, + "unit": "M" + }, + "maximum binding capacity (Rmax)": { + "value": 5.27162963964191, + "unit": "RU" + }, "report point aggregate document": { "report point document": [ { @@ -29267,6 +29803,16 @@ } } ] + }, + "custom information document": { + "Affinity Chi squared": { + "value": 0.104646601669138, + "unit": "RU^2" + }, + "offset": { + "value": 0.0, + "unit": "RU" + } } } ] @@ -29706,6 +30252,17 @@ "processed data aggregate document": { "processed data document": [ { + "data processing document": { + "Kinetics Model": "Steady state affinity" + }, + "equilibrium dissociation constant (KD)": { + "value": 1.04545738849952e-06, + "unit": "M" + }, + "maximum binding capacity (Rmax)": { + "value": 76.7842829472756, + "unit": "RU" + }, "report point aggregate document": { "report point document": [ { @@ -29969,6 +30526,16 @@ } } ] + }, + "custom information document": { + "Affinity Chi squared": { + "value": 1.21767585431671, + "unit": "RU^2" + }, + "offset": { + "value": 0.0, + "unit": "RU" + } } } ] @@ -30408,6 +30975,17 @@ "processed data aggregate document": { "processed data document": [ { + "data processing document": { + "Kinetics Model": "Steady state affinity" + }, + "equilibrium dissociation constant (KD)": { + "value": 4.53519326648544e-05, + "unit": "M" + }, + "maximum binding capacity (Rmax)": { + "value": 0.00135862070067624, + "unit": "RU" + }, "report point aggregate document": { "report point document": [ { @@ -30671,6 +31249,16 @@ } } ] + }, + "custom information document": { + "Affinity Chi squared": { + "value": 0.123572911524383, + "unit": "RU^2" + }, + "offset": { + "value": 0.0, + "unit": "RU" + } } } ] @@ -32148,6 +32736,17 @@ "processed data aggregate document": { "processed data document": [ { + "data processing document": { + "Kinetics Model": "Steady state affinity" + }, + "equilibrium dissociation constant (KD)": { + "value": 1.0056400658698e-05, + "unit": "M" + }, + "maximum binding capacity (Rmax)": { + "value": 3.06774374813797, + "unit": "RU" + }, "report point aggregate document": { "report point document": [ { @@ -32411,6 +33010,16 @@ } } ] + }, + "custom information document": { + "Affinity Chi squared": { + "value": 0.168765684434212, + "unit": "RU^2" + }, + "offset": { + "value": 0.0, + "unit": "RU" + } } } ] @@ -32850,6 +33459,17 @@ "processed data aggregate document": { "processed data document": [ { + "data processing document": { + "Kinetics Model": "Steady state affinity" + }, + "equilibrium dissociation constant (KD)": { + "value": 1.93376304172776e-05, + "unit": "M" + }, + "maximum binding capacity (Rmax)": { + "value": 5.27162963964191, + "unit": "RU" + }, "report point aggregate document": { "report point document": [ { @@ -33113,6 +33733,16 @@ } } ] + }, + "custom information document": { + "Affinity Chi squared": { + "value": 0.104646601669138, + "unit": "RU^2" + }, + "offset": { + "value": 0.0, + "unit": "RU" + } } } ] @@ -33552,6 +34182,17 @@ "processed data aggregate document": { "processed data document": [ { + "data processing document": { + "Kinetics Model": "Steady state affinity" + }, + "equilibrium dissociation constant (KD)": { + "value": 1.04545738849952e-06, + "unit": "M" + }, + "maximum binding capacity (Rmax)": { + "value": 76.7842829472756, + "unit": "RU" + }, "report point aggregate document": { "report point document": [ { @@ -33815,6 +34456,16 @@ } } ] + }, + "custom information document": { + "Affinity Chi squared": { + "value": 1.21767585431671, + "unit": "RU^2" + }, + "offset": { + "value": 0.0, + "unit": "RU" + } } } ] @@ -34254,6 +34905,17 @@ "processed data aggregate document": { "processed data document": [ { + "data processing document": { + "Kinetics Model": "Steady state affinity" + }, + "equilibrium dissociation constant (KD)": { + "value": 4.53519326648544e-05, + "unit": "M" + }, + "maximum binding capacity (Rmax)": { + "value": 0.00135862070067624, + "unit": "RU" + }, "report point aggregate document": { "report point document": [ { @@ -34517,6 +35179,16 @@ } } ] + }, + "custom information document": { + "Affinity Chi squared": { + "value": 0.123572911524383, + "unit": "RU^2" + }, + "offset": { + "value": 0.0, + "unit": "RU" + } } } ] @@ -35994,6 +36666,17 @@ "processed data aggregate document": { "processed data document": [ { + "data processing document": { + "Kinetics Model": "Steady state affinity" + }, + "equilibrium dissociation constant (KD)": { + "value": 1.0056400658698e-05, + "unit": "M" + }, + "maximum binding capacity (Rmax)": { + "value": 3.06774374813797, + "unit": "RU" + }, "report point aggregate document": { "report point document": [ { @@ -36257,6 +36940,16 @@ } } ] + }, + "custom information document": { + "Affinity Chi squared": { + "value": 0.168765684434212, + "unit": "RU^2" + }, + "offset": { + "value": 0.0, + "unit": "RU" + } } } ] @@ -36696,6 +37389,17 @@ "processed data aggregate document": { "processed data document": [ { + "data processing document": { + "Kinetics Model": "Steady state affinity" + }, + "equilibrium dissociation constant (KD)": { + "value": 1.93376304172776e-05, + "unit": "M" + }, + "maximum binding capacity (Rmax)": { + "value": 5.27162963964191, + "unit": "RU" + }, "report point aggregate document": { "report point document": [ { @@ -36959,6 +37663,16 @@ } } ] + }, + "custom information document": { + "Affinity Chi squared": { + "value": 0.104646601669138, + "unit": "RU^2" + }, + "offset": { + "value": 0.0, + "unit": "RU" + } } } ] @@ -37398,6 +38112,17 @@ "processed data aggregate document": { "processed data document": [ { + "data processing document": { + "Kinetics Model": "Steady state affinity" + }, + "equilibrium dissociation constant (KD)": { + "value": 1.04545738849952e-06, + "unit": "M" + }, + "maximum binding capacity (Rmax)": { + "value": 76.7842829472756, + "unit": "RU" + }, "report point aggregate document": { "report point document": [ { @@ -37661,6 +38386,16 @@ } } ] + }, + "custom information document": { + "Affinity Chi squared": { + "value": 1.21767585431671, + "unit": "RU^2" + }, + "offset": { + "value": 0.0, + "unit": "RU" + } } } ] @@ -38100,6 +38835,17 @@ "processed data aggregate document": { "processed data document": [ { + "data processing document": { + "Kinetics Model": "Steady state affinity" + }, + "equilibrium dissociation constant (KD)": { + "value": 4.53519326648544e-05, + "unit": "M" + }, + "maximum binding capacity (Rmax)": { + "value": 0.00135862070067624, + "unit": "RU" + }, "report point aggregate document": { "report point document": [ { @@ -38363,6 +39109,16 @@ } } ] + }, + "custom information document": { + "Affinity Chi squared": { + "value": 0.123572911524383, + "unit": "RU^2" + }, + "offset": { + "value": 0.0, + "unit": "RU" + } } } ] @@ -95528,7 +96284,7 @@ "file name": "Experiment_Name", "UNC path": "Root\\", "ASM converter name": "allotropy_cytiva_biacore_insight", - "ASM converter version": "0.1.116", + "ASM converter version": "0.1.117", "software name": "Biacore Insight Evaluation", "software version": "6.0.7.1750" }, diff --git a/tests/parsers/cytiva_biacore_insight/testdata/Cytiva_Biacore_Insight_Example01.json b/tests/parsers/cytiva_biacore_insight/testdata/Cytiva_Biacore_Insight_Example01.json index 556c440b9..7c9922c90 100644 --- a/tests/parsers/cytiva_biacore_insight/testdata/Cytiva_Biacore_Insight_Example01.json +++ b/tests/parsers/cytiva_biacore_insight/testdata/Cytiva_Biacore_Insight_Example01.json @@ -38509,7 +38509,7 @@ "file name": "evaluation_name", "UNC path": "my_evaluation_path", "ASM converter name": "allotropy_cytiva_biacore_insight", - "ASM converter version": "0.1.116", + "ASM converter version": "0.1.117", "software name": "Biacore Insight Evaluation", "software version": "6.0.0.0000" }, diff --git a/tests/parsers/cytiva_biacore_insight/testdata/Insight evaluaiton software kinetics and affinity.json b/tests/parsers/cytiva_biacore_insight/testdata/Insight evaluaiton software kinetics and affinity.json new file mode 100644 index 000000000..629e64528 --- /dev/null +++ b/tests/parsers/cytiva_biacore_insight/testdata/Insight evaluaiton software kinetics and affinity.json @@ -0,0 +1,224712 @@ +{ + "$asm.manifest": "http://purl.allotrope.org/manifests/binding-affinity-analyzer/WD/2024/12/binding-affinity-analyzer.manifest", + "binding affinity analyzer aggregate document": { + "binding affinity analyzer document": [ + { + "measurement aggregate document": { + "measurement document": [ + { + "device control aggregate document": { + "device control document": [ + { + "device type": "Binding Affinity Analyzer", + "sample temperature setting": { + "value": 25.0, + "unit": "degC" + }, + "flow cell identifier": "1", + "custom information document": { + "Analyte 1 Contact time": { + "value": 60.0, + "unit": "s" + }, + "Analyte 1 Dissociation time": { + "value": 60.0, + "unit": "s" + }, + "Analyte 1 Flow rate": { + "value": 30.0, + "unit": "µL/min" + }, + "Analyte 2 Contact time": { + "value": 60.0, + "unit": "s" + }, + "Analyte 2 Dissociation time": { + "value": 60.0, + "unit": "s" + }, + "Analyte 2 Flow rate": { + "value": 30.0, + "unit": "µL/min" + }, + "Analyte 3 Contact time": { + "value": 60.0, + "unit": "s" + }, + "Analyte 3 Dissociation time": { + "value": 60.0, + "unit": "s" + }, + "Analyte 3 Flow rate": { + "value": 30.0, + "unit": "µL/min" + }, + "Regeneration 1 Contact time": { + "value": 30.0, + "unit": "s" + }, + "Regeneration 1 Flow rate": { + "value": 30.0, + "unit": "µL/min" + }, + "Regeneration 2 Contact time": { + "value": 30.0, + "unit": "s" + }, + "Regeneration 2 Flow rate": { + "value": 30.0, + "unit": "µL/min" + }, + "Regeneration 3 Contact time": { + "value": 30.0, + "unit": "s" + }, + "Regeneration 3 Flow rate": { + "value": 30.0, + "unit": "µL/min" + }, + "Included": "Yes", + "Sensorgram type": "Reference", + "Level": { + "value": 118.123435000001, + "unit": "RU" + } + } + } + ] + }, + "measurement identifier": "CYTIVA_BIACORE_INSIGHT_TEST_ID_0", + "sample document": { + "sample identifier": "Run1_Cycle1", + "custom information document": { + "Run": 1, + "Cycle": 1, + "Channel": "1", + "Analyte 1 Solution": "Sample_1", + "Analyte 1 Plate id": "Rack 1", + "Analyte 1 Position": "A1", + "Analyte 1 Control type": "Not a control", + "Analyte 2 Solution": "Sample_1", + "Analyte 2 Plate id": "Rack 1", + "Analyte 2 Position": "A1", + "Analyte 2 Control type": "Not a control", + "Analyte 3 Solution": "Sample_1", + "Analyte 3 Plate id": "Rack 1", + "Analyte 3 Position": "A1", + "Analyte 3 Control type": "Not a control", + "Regeneration 1 Solution": "Regeneration_Solution", + "Regeneration 1 Plate id": "Rack 1", + "Regeneration 1 Position": "D1", + "Regeneration 1 Control type": "Not a control", + "Regeneration 2 Solution": "Regeneration_Solution", + "Regeneration 2 Plate id": "Rack 1", + "Regeneration 2 Position": "D1", + "Regeneration 2 Control type": "Not a control", + "Regeneration 3 Solution": "Regeneration_Solution", + "Regeneration 3 Plate id": "Rack 1", + "Regeneration 3 Position": "D1", + "Regeneration 3 Control type": "Not a control" + } + }, + "detection type": "Surface Plasmon Resonance", + "processed data aggregate document": { + "processed data document": [ + { + "data processing document": { + "Blank subtraction": "No", + "Molecular weight adjustment": "No", + "Capture/ligand adjustment": "No", + "Adjustment for controls": "No", + "Curve analysis": "No" + }, + "report point aggregate document": { + "report point document": [ + { + "absolute resonance": { + "value": 25058.6283, + "unit": "RU" + }, + "report point identifier": "CYTIVA_BIACORE_INSIGHT_TEST_ID_1", + "identifier role": "Analyte baseline_1", + "relative resonance": { + "value": 0.0, + "unit": "RU" + }, + "time setting": { + "value": 24.7000007629395, + "unit": "s" + }, + "custom information document": { + "Step purpose": "Conditioning", + "Window": { + "value": 5.0, + "unit": "s" + }, + "Baseline": "Yes" + } + }, + { + "absolute resonance": { + "value": 25262.1509, + "unit": "RU" + }, + "report point identifier": "CYTIVA_BIACORE_INSIGHT_TEST_ID_2", + "identifier role": "Analyte binding early_1", + "relative resonance": { + "value": 203.5226, + 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"CYTIVA_BIACORE_INSIGHT_TEST_ID_2988", + "data source feature": "Absolute Response" + } + ] + } + }, + { + "calculated data name": "Standard deviation", + "calculated result": { + "value": 0.358681775788143, + "unit": "(unitless)" + }, + "calculated data identifier": "CYTIVA_BIACORE_INSIGHT_TEST_ID_10861", + "data source aggregate document": { + "data source document": [ + { + "data source identifier": "CYTIVA_BIACORE_INSIGHT_TEST_ID_2988", + "data source feature": "Absolute Response" + } + ] + } + }, + { + "calculated data name": "LRSD", + "calculated result": { + "value": 0.480206578969955, + "unit": "(unitless)" + }, + "calculated data identifier": "CYTIVA_BIACORE_INSIGHT_TEST_ID_10862", + "data source aggregate document": { + "data source document": [ + { + "data source identifier": "CYTIVA_BIACORE_INSIGHT_TEST_ID_2989", + "data source feature": "Absolute Response" + } + ] + } + }, + { + "calculated data name": "Slope", + "calculated result": { + "value": -0.497888147830963, + "unit": "RU/s" + }, + "calculated data identifier": "CYTIVA_BIACORE_INSIGHT_TEST_ID_10863", + "data source aggregate document": { + "data source document": [ + { + "data source identifier": "CYTIVA_BIACORE_INSIGHT_TEST_ID_2989", + "data source feature": "Absolute Response" + } + ] + } + }, + { + "calculated data name": "Standard deviation", + "calculated result": { + "value": 0.8796755020476, + "unit": "(unitless)" + }, + "calculated data identifier": "CYTIVA_BIACORE_INSIGHT_TEST_ID_10864", + "data source aggregate document": { + "data source document": [ + { + "data source identifier": "CYTIVA_BIACORE_INSIGHT_TEST_ID_2989", + "data source feature": "Absolute Response" + } + ] + } + } + ] + }, + "data system document": { + "ASM file identifier": "Insight evaluaiton software kinetics and affinity.json", + "data system instance identifier": "N/A", + "file name": "Experiment_Name (unsaved changes)", + "UNC path": "Root\\Runs\\Experiment_Name", + "ASM converter name": "allotropy_cytiva_biacore_insight", + "ASM converter version": "0.1.117", + "software name": "Biacore Insight Evaluation", + "software version": "6.0.7.1750" + }, + "device system document": { + "device identifier": "Biacore", + "model number": "Biacore 1K+", + "equipment serial number": "1234", + "product manufacturer": "Cytiva" + } + } +} diff --git a/tests/parsers/cytiva_biacore_insight/testdata/Insight evaluaiton software kinetics and affinity.xlsx b/tests/parsers/cytiva_biacore_insight/testdata/Insight evaluaiton software kinetics and affinity.xlsx new file mode 100644 index 000000000..36d72c6bf Binary files /dev/null and b/tests/parsers/cytiva_biacore_insight/testdata/Insight evaluaiton software kinetics and affinity.xlsx differ diff --git a/tests/parsers/cytiva_biacore_t200_evaluation/testdata/biacore_evaluation_module_example.json b/tests/parsers/cytiva_biacore_t200_evaluation/testdata/biacore_evaluation_module_example.json index 9082df6bd..18629e4d9 100644 --- a/tests/parsers/cytiva_biacore_t200_evaluation/testdata/biacore_evaluation_module_example.json +++ b/tests/parsers/cytiva_biacore_t200_evaluation/testdata/biacore_evaluation_module_example.json @@ -391,6 +391,18 @@ } }, "detection type": "surface plasmon resonance", + "processed data aggregate document": { + "processed data document": [ + { + "custom information document": { + "kinetics chi squared": { + "value": 11.90239373089, + "unit": "(unitless)" + } + } + } + ] + }, "sensorgram data cube": { "label": "Cycle1_FlowCell3", "cube-structure": { @@ -1139,6 +1151,18 @@ } }, "detection type": "surface plasmon resonance", + "processed data aggregate document": { + "processed data document": [ + { + "custom information document": { + "kinetics chi squared": { + "value": 11.90239373089, + "unit": "(unitless)" + } + } + } + ] + }, "sensorgram data cube": { "label": "Cycle2_FlowCell3", "cube-structure": { @@ -1887,6 +1911,18 @@ } }, "detection type": "surface plasmon resonance", + "processed data aggregate document": { + "processed data document": [ + { + "custom information document": { + "kinetics chi squared": { + "value": 11.90239373089, + "unit": "(unitless)" + } + } + } + ] + }, "sensorgram data cube": { "label": "Cycle3_FlowCell3", "cube-structure": { @@ -2635,6 +2671,18 @@ } }, "detection type": "surface plasmon resonance", + "processed data aggregate document": { + "processed data document": [ + { + "custom information document": { + "kinetics chi squared": { + "value": 11.90239373089, + "unit": "(unitless)" + } + } + } + ] + }, "sensorgram data cube": { "label": "Cycle4_FlowCell3", "cube-structure": { @@ -3001,7 +3049,7 @@ "file name": "biacore_evaluation_module_example.bme", "UNC path": "tests/parsers/cytiva_biacore_t200_evaluation/testdata/biacore_evaluation_module_example.bme", "ASM converter name": "allotropy_cytiva_biacore_t200_evaluation", - "ASM converter version": "0.1.106", + "ASM converter version": "0.1.117", "software name": "Biacore T200 Evaluation Software", "software version": "3.2.1", "custom information document": {