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Merged
AliaksandrDziarkach merged 6 commits into from
Nov 11, 2026
Merged

Update seqid generation #4052

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475453b
Update seqid generation
AliaksandrDziarkach Nov 9, 2026
bd2a53f
Fix UTs
AliaksandrDziarkach Nov 10, 2026
f35a6aa
Fix UT
AliaksandrDziarkach Nov 10, 2026
37220b4
Fix UT
AliaksandrDziarkach Nov 10, 2026
be668f4
Fix UT
AliaksandrDziarkach Nov 11, 2026
9a46b40
Fix UT
AliaksandrDziarkach Nov 11, 2026
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2 changes: 1 addition & 1 deletion api/tests/integration/ref/formats/idt_unresolved.py.out
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Original file line number Diff line number Diff line change
Expand Up @@ -3,4 +3,4 @@ Sequence saver: Can't save chem 'i3AmPr' to sequence format
molecule CDXML saver: i3AmPr cannot be written in CDXML/CDX format.
molfile saver: i3AmPr cannot be written in MDL Molfile format.
SMILES saver: i3AmPr cannot be written in SMILES/SMARTS format.
CML saver: i3AmPr cannot be written in CML format.
CML saver: i3AmPr cannot be written in CML format.
1 change: 1 addition & 0 deletions api/tests/integration/ref/formats/ket_errors.py.out
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Original file line number Diff line number Diff line change
@@ -1,3 +1,4 @@
*** KET errors ***
Test 'ket_invalid_seqid_0': got expected error 'Invalid "seqid" value'
Test 'ket_invalid_seqid_1': got expected error 'Invalid "seqid" value'
Test 'ket_invalid_seqid_not_int': got expected error 'Invalid "seqid" value'
1 change: 1 addition & 0 deletions api/tests/integration/tests/formats/ket_errors.py
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Original file line number Diff line number Diff line change
Expand Up @@ -24,6 +24,7 @@
ket_errors = {
"ket_invalid_seqid_0": 'Invalid "seqid" value',
"ket_invalid_seqid_1": 'Invalid "seqid" value',
"ket_invalid_seqid_not_int": 'Invalid "seqid" value',
}
for filename in sorted(ket_errors.keys()):
error = ket_errors[filename]
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4 changes: 2 additions & 2 deletions api/tests/integration/tests/formats/molecules/4004-no-seqid-base.ket
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Original file line number Diff line number Diff line change
Expand Up @@ -61,7 +61,7 @@
"monomer1": {
"type": "monomer",
"id": "1",
"seqid": "5",
"seqid": 5,
"position": {
"x": 1.25,
"y": -1.25
Expand All @@ -72,7 +72,7 @@
"monomer2": {
"type": "monomer",
"id": "2",
"seqid": "5",
"seqid": 5,
"position": {
"x": 2.75,
"y": -1.25
Expand Down
166 changes: 166 additions & 0 deletions api/tests/integration/tests/formats/molecules/ket_invalid_seqid_not_int.ket
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@@ -0,0 +1,166 @@
{
"ket_version": "2.0.0",
"root": {
"nodes": [
{
"$ref": "monomer0"
}
],
"connections": [],
"templates": [
{
"$ref": "monomerTemplate-A___Alanine"
}
]
},
"monomer0": {
"type": "monomer",
"id": "0",
"seqid": "0",
"position": {
"x": 1.25,
"y": -1.25
},
"alias": "A",
"templateId": "A___Alanine"
},
"monomerTemplate-A___Alanine": {
"type": "monomerTemplate",
"atoms": [
{
"label": "N",
"location": [
-0.866,
-0.25,
0
]
},
{
"label": "C",
"location": [
0,
0.25,
0
],
"stereoLabel": "abs",
"stereoParity": 1
},
{
"label": "H",
"location": [
-1.732,
0.25,
0
]
},
{
"label": "C",
"location": [
0.866,
-0.25,
0
]
},
{
"label": "O",
"location": [
1.732,
0.25,
0
]
},
{
"label": "O",
"location": [
0.866,
-1.25,
0
]
},
{
"label": "C",
"location": [
0,
1.25,
0
]
}
],
"bonds": [
{
"type": 1,
"atoms": [
0,
1
]
},
{
"type": 1,
"atoms": [
0,
2
]
},
{
"type": 1,
"atoms": [
1,
3
]
},
{
"type": 1,
"atoms": [
3,
4
]
},
{
"type": 2,
"atoms": [
3,
5
]
},
{
"type": 1,
"atoms": [
1,
6
],
"stereo": 1
}
],
"class": "AminoAcid",
"classHELM": "PEPTIDE",
"id": "A___Alanine",
"fullName": "Alanine",
"alias": "A",
"aliasHELM": "A",
"aliasBILN": "A",
"attachmentPoints": [
{
"attachmentAtom": 0,
"leavingGroup": {
"atoms": [
2
]
},
"type": "left"
},
{
"attachmentAtom": 3,
"leavingGroup": {
"atoms": [
4
]
},
"type": "right"
}
],
"modificationTypes": [
"Natural amino acid"
],
"naturalAnalogShort": "A"
}
}
11 changes: 0 additions & 11 deletions api/tests/integration/tests/formats/ref/AxoLabs_ACsGsU.ket
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Expand Up @@ -174,7 +174,6 @@
"monomer0": {
"type": "monomer",
"id": "0",
"seqid": 1,
"position": {
"x": 0.000000,
"y": -0.000000
Expand All @@ -185,7 +184,6 @@
"monomer1": {
"type": "monomer",
"id": "1",
"seqid": 1,
"position": {
"x": 0.000000,
"y": -1.500000
Expand All @@ -196,7 +194,6 @@
"monomer2": {
"type": "monomer",
"id": "2",
"seqid": 1,
"position": {
"x": 1.500000,
"y": -0.000000
Expand All @@ -207,7 +204,6 @@
"monomer3": {
"type": "monomer",
"id": "3",
"seqid": 2,
"position": {
"x": 3.000000,
"y": -0.000000
Expand All @@ -218,7 +214,6 @@
"monomer4": {
"type": "monomer",
"id": "4",
"seqid": 2,
"position": {
"x": 3.000000,
"y": -1.500000
Expand All @@ -229,7 +224,6 @@
"monomer5": {
"type": "monomer",
"id": "5",
"seqid": 2,
"position": {
"x": 4.500000,
"y": -0.000000
Expand All @@ -240,7 +234,6 @@
"monomer6": {
"type": "monomer",
"id": "6",
"seqid": 3,
"position": {
"x": 6.000000,
"y": -0.000000
Expand All @@ -251,7 +244,6 @@
"monomer7": {
"type": "monomer",
"id": "7",
"seqid": 3,
"position": {
"x": 6.000000,
"y": -1.500000
Expand All @@ -262,7 +254,6 @@
"monomer8": {
"type": "monomer",
"id": "8",
"seqid": 3,
"position": {
"x": 7.500000,
"y": -0.000000
Expand All @@ -273,7 +264,6 @@
"monomer9": {
"type": "monomer",
"id": "9",
"seqid": 4,
"position": {
"x": 9.000000,
"y": -0.000000
Expand All @@ -284,7 +274,6 @@
"monomer10": {
"type": "monomer",
"id": "10",
"seqid": 4,
"position": {
"x": 9.000000,
"y": -1.500000
Expand Down
8 changes: 0 additions & 8 deletions api/tests/integration/tests/formats/ref/AxoLabs_brackets.ket
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Original file line number Diff line number Diff line change
Expand Up @@ -120,7 +120,6 @@
"monomer0": {
"type": "monomer",
"id": "0",
"seqid": 1,
"position": {
"x": 0.000000,
"y": -0.000000
Expand All @@ -131,7 +130,6 @@
"monomer1": {
"type": "monomer",
"id": "1",
"seqid": 1,
"position": {
"x": 0.000000,
"y": -1.500000
Expand All @@ -142,7 +140,6 @@
"monomer2": {
"type": "monomer",
"id": "2",
"seqid": 1,
"position": {
"x": 1.500000,
"y": -0.000000
Expand All @@ -153,7 +150,6 @@
"monomer3": {
"type": "monomer",
"id": "3",
"seqid": 2,
"position": {
"x": 3.000000,
"y": -0.000000
Expand All @@ -164,7 +160,6 @@
"monomer4": {
"type": "monomer",
"id": "4",
"seqid": 2,
"position": {
"x": 3.000000,
"y": -1.500000
Expand All @@ -175,7 +170,6 @@
"monomer5": {
"type": "monomer",
"id": "5",
"seqid": 2,
"position": {
"x": 4.500000,
"y": -0.000000
Expand All @@ -186,7 +180,6 @@
"monomer6": {
"type": "monomer",
"id": "6",
"seqid": 3,
"position": {
"x": 6.000000,
"y": -0.000000
Expand All @@ -197,7 +190,6 @@
"monomer7": {
"type": "monomer",
"id": "7",
"seqid": 3,
"position": {
"x": 6.000000,
"y": -1.500000
Expand Down
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