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fix: Binding Affinity Analyzer - add support for special keys in processed data document (#1087)
1 parent b1e8573 commit 1619638

3 files changed

Lines changed: 42 additions & 36 deletions

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‎src/allotropy/allotrope/converter.py‎

Lines changed: 11 additions & 5 deletions
Original file line numberDiff line numberDiff line change
@@ -82,6 +82,10 @@
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"o2_saturation": "O2 saturation",
8383
"pco2": "pCO2",
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"po2": "pO2",
85+
"binding_on_rate_measurement_datum__kon_": "binding on rate measurement datum (kon)",
86+
"binding_off_rate_measurement_datum__koff_": "binding off rate measurement datum (koff)",
87+
"equilibrium_dissociation_constant__KD_": "equilibrium dissociation constant (KD)",
88+
"maximum_binding_capacity__Rmax_": "maximum binding capacity (Rmax)",
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}
8690
SPECIAL_KEYS_INVERSE: dict[str, str] = dict(
8791
cast(tuple[str, str], reversed(item)) for item in SPECIAL_KEYS.items()
@@ -337,11 +341,13 @@ def structure_custom_information_document(val: dict[str, Any], name: str) -> Any
337341
structured_value = value
338342
if isinstance(value, list):
339343
structured_value = [
340-
structure_custom_information_document(v, key)
341-
if isinstance(v, dict)
342-
else value
343-
if isinstance(v, list)
344-
else v
344+
(
345+
structure_custom_information_document(v, key)
346+
if isinstance(v, dict)
347+
else value
348+
if isinstance(v, list)
349+
else v
350+
)
345351
for v in value
346352
]
347353
elif isinstance(value, dict):

‎src/allotropy/allotrope/schemas/adm/binding-affinity-analyzer/WD/2024/12/binding-affinity-analyzer.schema.json‎

Lines changed: 3 additions & 3 deletions
Original file line numberDiff line numberDiff line change
@@ -180,7 +180,7 @@
180180
"$ref": "http://purl.allotrope.org/json-schemas/adm/core/REC/2024/09/core.schema#/$defs/tQuantityValue"
181181
},
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{
183-
"$ref": "http://purl.allotrope.org/json-schemas/qudt/REC/2024/09/units.schema#/$defs/PerMolarPerSecond"
183+
"$ref": "http://purl.allotrope.org/json-schemas/qudt/REC/2024/09/units.schema#/$defs/M-1s-1"
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}
185185
]
186186
},
@@ -192,7 +192,7 @@
192192
"$ref": "http://purl.allotrope.org/json-schemas/adm/core/REC/2024/09/core.schema#/$defs/tQuantityValue"
193193
},
194194
{
195-
"$ref": "http://purl.allotrope.org/json-schemas/qudt/REC/2024/09/units.schema#/$defs/PerSecond"
195+
"$ref": "http://purl.allotrope.org/json-schemas/qudt/REC/2024/09/units.schema#/$defs/s^-1"
196196
}
197197
]
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},
@@ -216,7 +216,7 @@
216216
"$ref": "http://purl.allotrope.org/json-schemas/adm/core/REC/2024/09/core.schema#/$defs/tQuantityValue"
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},
218218
{
219-
"$ref": "http://purl.allotrope.org/json-schemas/qudt/REC/2024/09/units.schema#/$defs/ResponseUnit"
219+
"$ref": "http://purl.allotrope.org/json-schemas/qudt/REC/2024/09/units.schema#/$defs/RU"
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}
221221
]
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}

‎tests/parsers/cytiva_biacore_insight/testdata/Cytiva_Biacore_Insight_Example01.json‎

Lines changed: 28 additions & 28 deletions
Original file line numberDiff line numberDiff line change
@@ -7491,19 +7491,19 @@
74917491
"Curve analysis": "No",
74927492
"Kinetics Model": "1:1 binding"
74937493
},
7494-
"binding on rate measurement datum kon ": {
7494+
"binding on rate measurement datum (kon)": {
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"value": 700000.0,
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"unit": "M-1s-1"
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},
7498-
"binding off rate measurement datum koff ": {
7498+
"binding off rate measurement datum (koff)": {
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"value": 0.7,
75007500
"unit": "s^-1"
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},
7502-
"equilibrium dissociation constant KD ": {
7502+
"equilibrium dissociation constant (KD)": {
75037503
"value": 5e-07,
75047504
"unit": "M"
75057505
},
7506-
"maximum binding capacity Rmax ": {
7506+
"maximum binding capacity (Rmax)": {
75077507
"value": 100.0,
75087508
"unit": "RU"
75097509
},
@@ -8440,19 +8440,19 @@
84408440
"Curve analysis": "No",
84418441
"Kinetics Model": "1:1 binding"
84428442
},
8443-
"binding on rate measurement datum kon ": {
8443+
"binding on rate measurement datum (kon)": {
84448444
"value": 800000.0,
84458445
"unit": "M-1s-1"
84468446
},
8447-
"binding off rate measurement datum koff ": {
8447+
"binding off rate measurement datum (koff)": {
84488448
"value": 0.8,
84498449
"unit": "s^-1"
84508450
},
8451-
"equilibrium dissociation constant KD ": {
8451+
"equilibrium dissociation constant (KD)": {
84528452
"value": 5e-07,
84538453
"unit": "M"
84548454
},
8455-
"maximum binding capacity Rmax ": {
8455+
"maximum binding capacity (Rmax)": {
84568456
"value": 100.0,
84578457
"unit": "RU"
84588458
},
@@ -9389,19 +9389,19 @@
93899389
"Curve analysis": "No",
93909390
"Kinetics Model": "1:1 binding"
93919391
},
9392-
"binding on rate measurement datum kon ": {
9392+
"binding on rate measurement datum (kon)": {
93939393
"value": 900000.0,
93949394
"unit": "M-1s-1"
93959395
},
9396-
"binding off rate measurement datum koff ": {
9396+
"binding off rate measurement datum (koff)": {
93979397
"value": 0.9,
93989398
"unit": "s^-1"
93999399
},
9400-
"equilibrium dissociation constant KD ": {
9400+
"equilibrium dissociation constant (KD)": {
94019401
"value": 5e-07,
94029402
"unit": "M"
94039403
},
9404-
"maximum binding capacity Rmax ": {
9404+
"maximum binding capacity (Rmax)": {
94059405
"value": 100.0,
94069406
"unit": "RU"
94079407
},
@@ -10338,19 +10338,19 @@
1033810338
"Curve analysis": "No",
1033910339
"Kinetics Model": "1:1 binding"
1034010340
},
10341-
"binding on rate measurement datum kon ": {
10341+
"binding on rate measurement datum (kon)": {
1034210342
"value": 1000000.0,
1034310343
"unit": "M-1s-1"
1034410344
},
10345-
"binding off rate measurement datum koff ": {
10345+
"binding off rate measurement datum (koff)": {
1034610346
"value": 1.0,
1034710347
"unit": "s^-1"
1034810348
},
10349-
"equilibrium dissociation constant KD ": {
10349+
"equilibrium dissociation constant (KD)": {
1035010350
"value": 5e-07,
1035110351
"unit": "M"
1035210352
},
10353-
"maximum binding capacity Rmax ": {
10353+
"maximum binding capacity (Rmax)": {
1035410354
"value": 100.0,
1035510355
"unit": "RU"
1035610356
},
@@ -11287,19 +11287,19 @@
1128711287
"Curve analysis": "No",
1128811288
"Kinetics Model": "1:1 binding"
1128911289
},
11290-
"binding on rate measurement datum kon ": {
11290+
"binding on rate measurement datum (kon)": {
1129111291
"value": 1100000.0,
1129211292
"unit": "M-1s-1"
1129311293
},
11294-
"binding off rate measurement datum koff ": {
11294+
"binding off rate measurement datum (koff)": {
1129511295
"value": 1.1,
1129611296
"unit": "s^-1"
1129711297
},
11298-
"equilibrium dissociation constant KD ": {
11298+
"equilibrium dissociation constant (KD)": {
1129911299
"value": 5e-07,
1130011300
"unit": "M"
1130111301
},
11302-
"maximum binding capacity Rmax ": {
11302+
"maximum binding capacity (Rmax)": {
1130311303
"value": 100.0,
1130411304
"unit": "RU"
1130511305
},
@@ -13159,19 +13159,19 @@
1315913159
"Curve analysis": "No",
1316013160
"Kinetics Model": "1:1 binding"
1316113161
},
13162-
"binding on rate measurement datum kon ": {
13162+
"binding on rate measurement datum (kon)": {
1316313163
"value": 1200000.0,
1316413164
"unit": "M-1s-1"
1316513165
},
13166-
"binding off rate measurement datum koff ": {
13166+
"binding off rate measurement datum (koff)": {
1316713167
"value": 1.2,
1316813168
"unit": "s^-1"
1316913169
},
13170-
"equilibrium dissociation constant KD ": {
13170+
"equilibrium dissociation constant (KD)": {
1317113171
"value": 5e-07,
1317213172
"unit": "M"
1317313173
},
13174-
"maximum binding capacity Rmax ": {
13174+
"maximum binding capacity (Rmax)": {
1317513175
"value": 100.0,
1317613176
"unit": "RU"
1317713177
},
@@ -14108,19 +14108,19 @@
1410814108
"Curve analysis": "No",
1410914109
"Kinetics Model": "1:1 binding"
1411014110
},
14111-
"binding on rate measurement datum kon ": {
14111+
"binding on rate measurement datum (kon)": {
1411214112
"value": 1300000.0,
1411314113
"unit": "M-1s-1"
1411414114
},
14115-
"binding off rate measurement datum koff ": {
14115+
"binding off rate measurement datum (koff)": {
1411614116
"value": 1.3,
1411714117
"unit": "s^-1"
1411814118
},
14119-
"equilibrium dissociation constant KD ": {
14119+
"equilibrium dissociation constant (KD)": {
1412014120
"value": 5e-07,
1412114121
"unit": "M"
1412214122
},
14123-
"maximum binding capacity Rmax ": {
14123+
"maximum binding capacity (Rmax)": {
1412414124
"value": 100.0,
1412514125
"unit": "RU"
1412614126
},

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