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fix: Binding Affinity Analyzer - add support for special keys in processed data document #1087

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Merged
slopez-b merged 3 commits into from
Sep 29, 2025
+42 −36
Merged

fix: Binding Affinity Analyzer - add support for special keys in processed data document #1087

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7a64d44
support special keys from binding affinity analyzer processed data do…
slopez-b Sep 25, 2025
d7da824
Merge branch 'main' into slopez/fix-binding-affinity-schema-special-keys
slopez-b Sep 26, 2025
34dd930
Merge branch 'main' into slopez/fix-binding-affinity-schema-special-keys
slopez-b Sep 29, 2025
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16 changes: 11 additions & 5 deletions src/allotropy/allotrope/converter.py
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Original file line number Diff line number Diff line change
Expand Up @@ -82,6 +82,10 @@
"o2_saturation": "O2 saturation",
"pco2": "pCO2",
"po2": "pO2",
"binding_on_rate_measurement_datum__kon_": "binding on rate measurement datum (kon)",
"binding_off_rate_measurement_datum__koff_": "binding off rate measurement datum (koff)",
"equilibrium_dissociation_constant__KD_": "equilibrium dissociation constant (KD)",
"maximum_binding_capacity__Rmax_": "maximum binding capacity (Rmax)",
}
SPECIAL_KEYS_INVERSE: dict[str, str] = dict(
cast(tuple[str, str], reversed(item)) for item in SPECIAL_KEYS.items()
Expand Down Expand Up @@ -337,11 +341,13 @@ def structure_custom_information_document(val: dict[str, Any], name: str) -> Any
structured_value = value
if isinstance(value, list):
structured_value = [
structure_custom_information_document(v, key)
if isinstance(v, dict)
else value
if isinstance(v, list)
else v
(
structure_custom_information_document(v, key)
if isinstance(v, dict)
else value
if isinstance(v, list)
else v
)
for v in value
]
elif isinstance(value, dict):
Expand Down
6 changes: 3 additions & 3 deletions ...pe/schemas/adm/binding-affinity-analyzer/WD/2024/12/binding-affinity-analyzer.schema.json
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Original file line number Diff line number Diff line change
Expand Up @@ -180,7 +180,7 @@
"$ref": "http://purl.allotrope.org/json-schemas/adm/core/REC/2024/09/core.schema#/$defs/tQuantityValue"
},
{
"$ref": "http://purl.allotrope.org/json-schemas/qudt/REC/2024/09/units.schema#/$defs/PerMolarPerSecond"
"$ref": "http://purl.allotrope.org/json-schemas/qudt/REC/2024/09/units.schema#/$defs/M-1s-1"
}
]
},
Expand All @@ -192,7 +192,7 @@
"$ref": "http://purl.allotrope.org/json-schemas/adm/core/REC/2024/09/core.schema#/$defs/tQuantityValue"
},
{
"$ref": "http://purl.allotrope.org/json-schemas/qudt/REC/2024/09/units.schema#/$defs/PerSecond"
"$ref": "http://purl.allotrope.org/json-schemas/qudt/REC/2024/09/units.schema#/$defs/s^-1"
}
]
},
Expand All @@ -216,7 +216,7 @@
"$ref": "http://purl.allotrope.org/json-schemas/adm/core/REC/2024/09/core.schema#/$defs/tQuantityValue"
},
{
"$ref": "http://purl.allotrope.org/json-schemas/qudt/REC/2024/09/units.schema#/$defs/ResponseUnit"
"$ref": "http://purl.allotrope.org/json-schemas/qudt/REC/2024/09/units.schema#/$defs/RU"
}
]
}
Expand Down
56 changes: 28 additions & 28 deletions tests/parsers/cytiva_biacore_insight/testdata/Cytiva_Biacore_Insight_Example01.json
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Original file line number Diff line number Diff line change
Expand Up @@ -7491,19 +7491,19 @@
"Curve analysis": "No",
"Kinetics Model": "1:1 binding"
},
"binding on rate measurement datum kon ": {
"binding on rate measurement datum (kon)": {
"value": 700000.0,
"unit": "M-1s-1"
},
"binding off rate measurement datum koff ": {
"binding off rate measurement datum (koff)": {
"value": 0.7,
"unit": "s^-1"
},
"equilibrium dissociation constant KD ": {
"equilibrium dissociation constant (KD)": {
"value": 5e-07,
"unit": "M"
},
"maximum binding capacity Rmax ": {
"maximum binding capacity (Rmax)": {
"value": 100.0,
"unit": "RU"
},
Expand Down Expand Up @@ -8440,19 +8440,19 @@
"Curve analysis": "No",
"Kinetics Model": "1:1 binding"
},
"binding on rate measurement datum kon ": {
"binding on rate measurement datum (kon)": {
"value": 800000.0,
"unit": "M-1s-1"
},
"binding off rate measurement datum koff ": {
"binding off rate measurement datum (koff)": {
"value": 0.8,
"unit": "s^-1"
},
"equilibrium dissociation constant KD ": {
"equilibrium dissociation constant (KD)": {
"value": 5e-07,
"unit": "M"
},
"maximum binding capacity Rmax ": {
"maximum binding capacity (Rmax)": {
"value": 100.0,
"unit": "RU"
},
Expand Down Expand Up @@ -9389,19 +9389,19 @@
"Curve analysis": "No",
"Kinetics Model": "1:1 binding"
},
"binding on rate measurement datum kon ": {
"binding on rate measurement datum (kon)": {
"value": 900000.0,
"unit": "M-1s-1"
},
"binding off rate measurement datum koff ": {
"binding off rate measurement datum (koff)": {
"value": 0.9,
"unit": "s^-1"
},
"equilibrium dissociation constant KD ": {
"equilibrium dissociation constant (KD)": {
"value": 5e-07,
"unit": "M"
},
"maximum binding capacity Rmax ": {
"maximum binding capacity (Rmax)": {
"value": 100.0,
"unit": "RU"
},
Expand Down Expand Up @@ -10338,19 +10338,19 @@
"Curve analysis": "No",
"Kinetics Model": "1:1 binding"
},
"binding on rate measurement datum kon ": {
"binding on rate measurement datum (kon)": {
"value": 1000000.0,
"unit": "M-1s-1"
},
"binding off rate measurement datum koff ": {
"binding off rate measurement datum (koff)": {
"value": 1.0,
"unit": "s^-1"
},
"equilibrium dissociation constant KD ": {
"equilibrium dissociation constant (KD)": {
"value": 5e-07,
"unit": "M"
},
"maximum binding capacity Rmax ": {
"maximum binding capacity (Rmax)": {
"value": 100.0,
"unit": "RU"
},
Expand Down Expand Up @@ -11287,19 +11287,19 @@
"Curve analysis": "No",
"Kinetics Model": "1:1 binding"
},
"binding on rate measurement datum kon ": {
"binding on rate measurement datum (kon)": {
"value": 1100000.0,
"unit": "M-1s-1"
},
"binding off rate measurement datum koff ": {
"binding off rate measurement datum (koff)": {
"value": 1.1,
"unit": "s^-1"
},
"equilibrium dissociation constant KD ": {
"equilibrium dissociation constant (KD)": {
"value": 5e-07,
"unit": "M"
},
"maximum binding capacity Rmax ": {
"maximum binding capacity (Rmax)": {
"value": 100.0,
"unit": "RU"
},
Expand Down Expand Up @@ -13159,19 +13159,19 @@
"Curve analysis": "No",
"Kinetics Model": "1:1 binding"
},
"binding on rate measurement datum kon ": {
"binding on rate measurement datum (kon)": {
"value": 1200000.0,
"unit": "M-1s-1"
},
"binding off rate measurement datum koff ": {
"binding off rate measurement datum (koff)": {
"value": 1.2,
"unit": "s^-1"
},
"equilibrium dissociation constant KD ": {
"equilibrium dissociation constant (KD)": {
"value": 5e-07,
"unit": "M"
},
"maximum binding capacity Rmax ": {
"maximum binding capacity (Rmax)": {
"value": 100.0,
"unit": "RU"
},
Expand Down Expand Up @@ -14108,19 +14108,19 @@
"Curve analysis": "No",
"Kinetics Model": "1:1 binding"
},
"binding on rate measurement datum kon ": {
"binding on rate measurement datum (kon)": {
"value": 1300000.0,
"unit": "M-1s-1"
},
"binding off rate measurement datum koff ": {
"binding off rate measurement datum (koff)": {
"value": 1.3,
"unit": "s^-1"
},
"equilibrium dissociation constant KD ": {
"equilibrium dissociation constant (KD)": {
"value": 5e-07,
"unit": "M"
},
"maximum binding capacity Rmax ": {
"maximum binding capacity (Rmax)": {
"value": 100.0,
"unit": "RU"
},
Expand Down
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