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nickccollinsnickccollins
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Look for Absolute SMILES instead of Canonical (#29)
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‎examples/chem-sync-local-flask/local_app/lib/pub_chem.py‎

Lines changed: 1 addition & 1 deletion
Original file line numberDiff line numberDiff line change
@@ -45,7 +45,7 @@ def get_by_cid(cid: str) -> dict[str, Any]:
4545
synonyms_json = _pubchem_get(f"cid/{cid}/synonyms/JSON")
4646
compound_json = result_json["PC_Compounds"][0]
4747
name = synonyms_json["InformationList"]["Information"][0]["Synonym"][0]
48-
smiles = _get_compound_string_prop(compound_json, label="SMILES", name="Canonical")
48+
smiles = _get_compound_string_prop(compound_json, label="SMILES", name="Absolute")
4949
mono_isotopic_weight = _get_compound_string_prop(compound_json, label="Weight", name="MonoIsotopic")
5050
molecular_weight = _get_compound_string_prop(compound_json, label="Molecular Weight")
5151
return {

‎examples/chem-sync-local-flask/tests/files/pubchem/compound.json‎

Lines changed: 27 additions & 27 deletions
Original file line numberDiff line numberDiff line change
@@ -158,7 +158,7 @@
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"conformers": [
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{
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"x": [
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3.732,
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3.7321,
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6.3301,
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4.5981,
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2.866,
@@ -240,7 +240,7 @@
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"label": "Compound",
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"name": "Canonicalized",
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"datatype": 5,
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"release": "2021.10.14"
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"release": "2025.04.14"
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},
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"value": {
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"ival": 1
@@ -254,7 +254,7 @@
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"version": "3.4.8.18",
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"software": "Cactvs",
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"source": "Xemistry GmbH",
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"release": "2021.10.14"
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"release": "2025.04.14"
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},
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"value": {
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"fval": 212
@@ -269,7 +269,7 @@
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"version": "3.4.8.18",
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"software": "Cactvs",
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"source": "Xemistry GmbH",
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"release": "2021.10.14"
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"release": "2025.04.14"
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},
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"value": {
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"ival": 4
@@ -284,7 +284,7 @@
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"version": "3.4.8.18",
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"software": "Cactvs",
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"source": "Xemistry GmbH",
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"release": "2021.10.14"
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"release": "2025.04.14"
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},
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"value": {
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"ival": 1
@@ -299,7 +299,7 @@
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"version": "3.4.8.18",
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"software": "Cactvs",
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"source": "Xemistry GmbH",
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"release": "2021.10.14"
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"release": "2025.04.14"
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},
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"value": {
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"ival": 3
@@ -315,7 +315,7 @@
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"version": "3.4.8.18",
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"software": "Cactvs",
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"source": "Xemistry GmbH",
318-
"release": "2021.10.14"
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"release": "2025.04.14"
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},
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"value": {
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"binary": "00000371C0703800000000000000000000000000000000000000300000000000000000010000001A00000800000C04809800320E80000600880220D208000208002420000888010608C80C273684351A827B60A5E01108B98788C8208E00000000000800000000000000100000000000000000"
@@ -329,7 +329,7 @@
329329
"version": "2.7.0",
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"software": "Lexichem TK",
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"source": "OpenEye Scientific Software",
332-
"release": "2021.10.14"
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"release": "2025.04.14"
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},
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"value": {
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"sval": "2-acetoxybenzoic acid"
@@ -343,7 +343,7 @@
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"version": "2.7.0",
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"software": "Lexichem TK",
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"source": "OpenEye Scientific Software",
346-
"release": "2021.10.14"
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"release": "2025.04.14"
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},
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"value": {
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"sval": "2-acetyloxybenzoic acid"
@@ -357,7 +357,7 @@
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"version": "2.7.0",
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"software": "Lexichem TK",
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"source": "OpenEye Scientific Software",
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"release": "2021.10.14"
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"release": "2025.04.14"
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},
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"value": {
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"sval": "2-acetyloxybenzoic acid"
@@ -371,7 +371,7 @@
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"version": "2.7.0",
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"software": "Lexichem TK",
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"source": "OpenEye Scientific Software",
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"release": "2021.10.14"
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"release": "2025.04.14"
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},
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"value": {
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"sval": "2-acetyloxybenzoic acid"
@@ -385,7 +385,7 @@
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"version": "2.7.0",
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"software": "Lexichem TK",
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"source": "OpenEye Scientific Software",
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"release": "2021.10.14"
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"release": "2025.04.14"
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},
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"value": {
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"sval": "2-acetyloxybenzoic acid"
@@ -399,7 +399,7 @@
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"version": "2.7.0",
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"software": "Lexichem TK",
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"source": "OpenEye Scientific Software",
402-
"release": "2021.10.14"
402+
"release": "2025.04.14"
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},
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"value": {
405405
"sval": "2-acetoxybenzoic acid"
@@ -410,10 +410,10 @@
410410
"label": "InChI",
411411
"name": "Standard",
412412
"datatype": 1,
413-
"version": "1.0.6",
413+
"version": "1.07.2",
414414
"software": "InChI",
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"source": "iupac.org",
416-
"release": "2021.10.14"
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"release": "2025.04.14"
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},
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"value": {
419419
"sval": "InChI=1S/C9H8O4/c1-6(10)13-8-5-3-2-4-7(8)9(11)12/h2-5H,1H3,(H,11,12)"
@@ -424,10 +424,10 @@
424424
"label": "InChIKey",
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"name": "Standard",
426426
"datatype": 1,
427-
"version": "1.0.6",
427+
"version": "1.07.2",
428428
"software": "InChI",
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"source": "iupac.org",
430-
"release": "2021.10.14"
430+
"release": "2025.04.14"
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},
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"value": {
433433
"sval": "BSYNRYMUTXBXSQ-UHFFFAOYSA-N"
@@ -440,7 +440,7 @@
440440
"datatype": 7,
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"version": "3.0",
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"source": "sioc-ccbg.ac.cn",
443-
"release": "2021.10.14"
443+
"release": "2025.04.14"
444444
},
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"value": {
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"fval": 1.2
@@ -454,7 +454,7 @@
454454
"version": "2.2",
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"software": "PubChem",
456456
"source": "ncbi.nlm.nih.gov",
457-
"release": "2021.10.14"
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"release": "2025.04.14"
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},
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"value": {
460460
"sval": "180.04225873"
@@ -467,7 +467,7 @@
467467
"version": "2.2",
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"software": "PubChem",
469469
"source": "ncbi.nlm.nih.gov",
470-
"release": "2021.10.14"
470+
"release": "2025.04.14"
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},
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"value": {
473473
"sval": "C9H8O4"
@@ -480,7 +480,7 @@
480480
"version": "2.2",
481481
"software": "PubChem",
482482
"source": "ncbi.nlm.nih.gov",
483-
"release": "2021.10.14"
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"release": "2025.04.14"
484484
},
485485
"value": {
486486
"sval": "180.16"
@@ -489,12 +489,12 @@
489489
{
490490
"urn": {
491491
"label": "SMILES",
492-
"name": "Canonical",
492+
"name": "Absolute",
493493
"datatype": 1,
494494
"version": "2.3.0",
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"software": "OEChem",
496496
"source": "OpenEye Scientific Software",
497-
"release": "2021.10.14"
497+
"release": "2025.04.14"
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},
499499
"value": {
500500
"sval": "CC(=O)OC1=CC=CC=C1C(=O)O"
@@ -503,12 +503,12 @@
503503
{
504504
"urn": {
505505
"label": "SMILES",
506-
"name": "Isomeric",
506+
"name": "Connectivity",
507507
"datatype": 1,
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"version": "2.3.0",
509509
"software": "OEChem",
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"source": "OpenEye Scientific Software",
511-
"release": "2021.10.14"
511+
"release": "2025.06.30"
512512
},
513513
"value": {
514514
"sval": "CC(=O)OC1=CC=CC=C1C(=O)O"
@@ -523,7 +523,7 @@
523523
"version": "3.4.8.18",
524524
"software": "Cactvs",
525525
"source": "Xemistry GmbH",
526-
"release": "2021.10.14"
526+
"release": "2025.04.14"
527527
},
528528
"value": {
529529
"fval": 63.6
@@ -537,7 +537,7 @@
537537
"version": "2.2",
538538
"software": "PubChem",
539539
"source": "ncbi.nlm.nih.gov",
540-
"release": "2021.10.14"
540+
"release": "2025.04.14"
541541
},
542542
"value": {
543543
"sval": "180.04225873"

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