#2472 - Support for three letter sequences #4944
GitHub Actions / windows-latest-x86_64-java_test_report
failed
Oct 30, 2024 in 0s
283 tests run, 281 passed, 0 skipped, 2 failed.
Annotations
Check failure on line 1 in api\c\tests\unit\tests\formats.cpp
github-actions / windows-latest-x86_64-java_test_report
formats.ket_to_seq3letter
[ERROR]
Raw output
Error:
Traceback (most recent call last):
File "api/tests/integration/test.py", line 368, in run_test_module
runpy.run_path(module_filename, run_name="__main__")
File "D:\a\Indigo\Indigo\jython.jar\Lib\runpy$py.class", line 240, in run_path
return _run_module_code(code, init_globals, run_name, path_name)
File "D:\a\Indigo\Indigo\jython.jar\Lib\runpy$py.class", line 81, in _run_module_code
_run_code(code, mod_globals, init_globals,
File "D:\a\Indigo\Indigo\jython.jar\Lib\runpy$py.class", line 72, in _run_code
exec code in run_globals
File "D:\a\Indigo\Indigo\api\tests\integration\tests\formats\ket_to_seq3letter.py", line 36, in <module>
file.write(doc.sequence3Letter(lib))
AttributeError: 'com.epam.indigo.IndigoObject' object has no attribute 'sequence3Letter'
Check failure on line 1 in api\c\tests\unit\tests\formats.cpp
github-actions / windows-latest-x86_64-java_test_report
formats.seq3letter_to_ket
[FAILED]
Raw output
Diff:
- peptides_3letter : SUCCEED
+ peptides_3letter : FAILED
+ ---
+ +++
+ @@ -1,5334 +1,5 @@
+ {
+ "root": {
+ - "nodes": [
+ - {
+ - "$ref": "monomer0"
+ - },
+ - {
+ - "$ref": "monomer1"
+ - },
+ - {
+ - "$ref": "monomer2"
+ - },
+ - {
+ - "$ref": "monomer3"
+ - },
+ - {
+ - "$ref": "monomer4"
+ - },
+ - {
+ - "$ref": "monomer5"
+ - },
+ - {
+ - "$ref": "monomer6"
+ - },
+ - {
+ - "$ref": "monomer7"
+ - },
+ - {
+ - "$ref": "monomer8"
+ - },
+ - {
+ - "$ref": "monomer9"
+ - },
+ - {
+ - "$ref": "monomer10"
+ - },
+ - {
+ - "$ref": "monomer11"
+ - },
+ - {
+ - "$ref": "monomer12"
+ - },
+ - {
+ - "$ref": "monomer13"
+ - },
+ - {
+ - "$ref": "monomer14"
+ - },
+ - {
+ - "$ref": "monomer15"
+ - },
+ - {
+ - "$ref": "monomer16"
+ - },
+ - {
+ - "$ref": "monomer17"
+ - },
+ - {
+ - "$ref": "monomer18"
+ - },
+ - {
+ - "$ref": "monomer19"
+ - },
+ - {
+ - "$ref": "monomer20"
+ - },
+ - {
+ - "$ref": "monomer21"
+ - },
+ - {
+ - "$ref": "ambiguousMonomer-22"
+ - },
+ - {
+ - "$ref": "ambiguousMonomer-23"
+ - },
+ - {
+ - "$ref": "ambiguousMonomer-24"
+ - },
+ - {
+ - "$ref": "ambiguousMonomer-25"
+ - }
+ - ],
+ - "connections": [
+ - {
+ - "connectionType": "single",
+ - "endpoint1": {
+ - "monomerId": "monomer0",
+ - "attachmentPointId": "R2"
+ - },
+ - "endpoint2": {
+ - "monomerId": "monomer1",
+ - "attachmentPointId": "R1"
+ - }
+ - },
+ - {
+ - "connectionType": "single",
+ - "endpoint1": {
+ - "monomerId": "monomer1",
+ - "attachmentPointId": "R2"
+ - },
+ - "endpoint2": {
+ - "monomerId": "monomer2",
+ - "attachmentPointId": "R1"
+ - }
+ - },
+ - {
+ - "connectionType": "single",
+ - "endpoint1": {
+ - "monomerId": "monomer2",
+ - "attachmentPointId": "R2"
+ - },
+ - "endpoint2": {
+ - "monomerId": "monomer3",
+ - "attachmentPointId": "R1"
+ - }
+ - },
+ - {
+ - "connectionType": "single",
+ - "endpoint1": {
+ - "monomerId": "monomer3",
+ - "attachmentPointId": "R2"
+ - },
+ - "endpoint2": {
+ - "monomerId": "monomer4",
+ - "attachmentPointId": "R1"
+ - }
+ - },
+ - {
+ - "connectionType": "single",
+ - "endpoint1": {
+ - "monomerId": "monomer4",
+ - "attachmentPointId": "R2"
+ - },
+ - "endpoint2": {
+ - "monomerId": "monomer5",
+ - "attachmentPointId": "R1"
+ - }
+ - },
+ - {
+ - "connectionType": "single",
+ - "endpoint1": {
+ - "monomerId": "monomer5",
+ - "attachmentPointId": "R2"
+ - },
+ - "endpoint2": {
+ - "monomerId": "monomer6",
+ - "attachmentPointId": "R1"
+ - }
+ - },
+ - {
+ - "connectionType": "single",
+ - "endpoint1": {
+ - "monomerId": "monomer6",
+ - "attachmentPointId": "R2"
+ - },
+ - "endpoint2": {
+ - "monomerId": "monomer7",
+ - "attachmentPointId": "R1"
+ - }
+ - },
+ - {
+ - "connectionType": "single",
+ - "endpoint1": {
+ - "monomerId": "monomer7",
+ - "attachmentPointId": "R2"
+ - },
+ - "endpoint2": {
+ - "monomerId": "monomer8",
+ - "attachmentPointId": "R1"
+ - }
+ - },
+ - {
+ - "connectionType": "single",
+ - "endpoint1": {
+ - "monomerId": "monomer8",
+ - "attachmentPointId": "R2"
+ - },
+ - "endpoint2": {
+ - "monomerId": "monomer9",
+ - "attachmentPointId": "R1"
+ - }
+ - },
+ - {
+ - "connectionType": "single",
+ - "endpoint1": {
+ - "monomerId": "monomer9",
+ - "attachmentPointId": "R2"
+ - },
+ - "endpoint2": {
+ - "monomerId": "monomer10",
+ - "attachmentPointId": "R1"
+ - }
+ - },
+ - {
+ - "connectionType": "single",
+ - "endpoint1": {
+ - "monomerId": "monomer10",
+ - "attachmentPointId": "R2"
+ - },
+ - "endpoint2": {
+ - "monomerId": "monomer11",
+ - "attachmentPointId": "R1"
+ - }
+ - },
+ - {
+ - "connectionType": "single",
+ - "endpoint1": {
+ - "monomerId": "monomer11",
+ - "attachmentPointId": "R2"
+ - },
+ - "endpoint2": {
+ - "monomerId": "monomer12",
+ - "attachmentPointId": "R1"
+ - }
+ - },
+ - {
+ - "connectionType": "single",
+ - "endpoint1": {
+ - "monomerId": "monomer12",
+ - "attachmentPointId": "R2"
+ - },
+ - "endpoint2": {
+ - "monomerId": "monomer13",
+ - "attachmentPointId": "R1"
+ - }
+ - },
+ - {
+ - "connectionType": "single",
+ - "endpoint1": {
+ - "monomerId": "monomer13",
+ - "attachmentPointId": "R2"
+ - },
+ - "endpoint2": {
+ - "monomerId": "monomer14",
+ - "attachmentPointId": "R1"
+ - }
+ - },
+ - {
+ - "connectionType": "single",
+ - "endpoint1": {
+ - "monomerId": "monomer14",
+ - "attachmentPointId": "R2"
+ - },
+ - "endpoint2": {
+ - "monomerId": "monomer15",
+ - "attachmentPointId": "R1"
+ - }
+ - },
+ - {
+ - "connectionType": "single",
+ - "endpoint1": {
+ - "monomerId": "monomer15",
+ - "attachmentPointId": "R2"
+ - },
+ - "endpoint2": {
+ - "monomerId": "monomer16",
+ - "attachmentPointId": "R1"
+ - }
+ - },
+ - {
+ - "connectionType": "single",
+ - "endpoint1": {
+ - "monomerId": "monomer16",
+ - "attachmentPointId": "R2"
+ - },
+ - "endpoint2": {
+ - "monomerId": "monomer17",
+ - "attachmentPointId": "R1"
+ - }
+ - },
+ - {
+ - "connectionType": "single",
+ - "endpoint1": {
+ - "monomerId": "monomer17",
+ - "attachmentPointId": "R2"
+ - },
+ - "endpoint2": {
+ - "monomerId": "monomer18",
+ - "attachmentPointId": "R1"
+ - }
+ - },
+ - {
+ - "connectionType": "single",
+ - "endpoint1": {
+ - "monomerId": "monomer18",
+ - "attachmentPointId": "R2"
+ - },
+ - "endpoint2": {
+ - "monomerId": "monomer19",
+ - "attachmentPointId": "R1"
+ - }
+ - },
+ - {
+ - "connectionType": "single",
+ - "endpoint1": {
+ - "monomerId": "monomer19",
+ - "attachmentPointId": "R2"
+ - },
+ - "endpoint2": {
+ - "monomerId": "monomer20",
+ - "attachmentPointId": "R1"
+ - }
+ - },
+ - {
+ - "connectionType": "single",
+ - "endpoint1": {
+ - "monomerId": "monomer20",
+ - "attachmentPointId": "R2"
+ - },
+ - "endpoint2": {
+ - "monomerId": "monomer21",
+ - "attachmentPointId": "R1"
+ - }
+ - },
+ - {
+ - "connectionType": "single",
+ - "endpoint1": {
+ - "monomerId": "monomer21",
+ - "attachmentPointId": "R2"
+ - },
+ - "endpoint2": {
+ - "monomerId": "ambiguousMonomer-22",
+ - "attachmentPointId": "R1"
+ - }
+ - },
+ - {
+ - "connectionType": "single",
+ - "endpoint1": {
+ - "monomerId": "ambiguousMonomer-22",
+ - "attachmentPointId": "R2"
+ - },
+ - "endpoint2": {
+ - "monomerId": "ambiguousMonomer-23",
+ - "attachmentPointId": "R1"
+ - }
+ - },
+ - {
+ - "connectionType": "single",
+ - "endpoint1": {
+ - "monomerId": "ambiguousMonomer-23",
+ - "attachmentPointId": "R2"
+ - },
+ - "endpoint2": {
+ - "monomerId": "ambiguousMonomer-24",
+ - "attachmentPointId": "R1"
+ - }
+ - },
+ - {
+ - "connectionType": "single",
+ - "endpoint1": {
+ - "monomerId": "ambiguousMonomer-24",
+ - "attachmentPointId": "R2"
+ - },
+ - "endpoint2": {
+ - "monomerId": "ambiguousMonomer-25",
+ - "attachmentPointId": "R1"
+ - }
+ - }
+ - ],
+ - "templates": [
+ - {
+ - "$ref": "monomerTemplate-A___Alanine"
+ - },
+ - {
+ - "$ref": "monomerTemplate-R___Arginine"
+ - },
+ - {
+ - "$ref": "monomerTemplate-N___Asparagine"
+ - },
+ - {
+ - "$ref": "monomerTemplate-D___Aspartic acid"
+ - },
+ - {
+ - "$ref": "monomerTemplate-C___Cysteine"
+ - },
+ - {
+ - "$ref": "monomerTemplate-Q___Glutamine"
+ - },
+ - {
+ - "$ref": "monomerTemplate-E___Glutamic acid"
+ - },
+ - {
+ - "$ref": "monomerTemplate-G___Glycine"
+ - },
+ - {
+ - "$ref": "monomerTemplate-H___Histidine"
+ - },
+ - {
+ - "$ref": "monomerTemplate-I___Isoleucine"
+ - },
+ - {
+ - "$ref": "monomerTemplate-L___Leucine"
+ - },
+ - {
+ - "$ref": "monomerTemplate-K___Lysine"
+ - },
+ - {
+ - "$ref": "monomerTemplate-M___Methionine"
+ - },
+ - {
+ - "$ref": "monomerTemplate-F___Phenylalanine"
+ - },
+ - {
+ - "$ref": "monomerTemplate-P___Proline"
+ - },
+ - {
+ - "$ref": "monomerTemplate-S___Serine"
+ - },
+ - {
+ - "$ref": "monomerTemplate-T___Threonine"
+ - },
+ - {
+ - "$ref": "monomerTemplate-W___Tryptophan"
+ - },
+ - {
+ - "$ref": "monomerTemplate-Y___Tyrosine"
+ - },
+ - {
+ - "$ref": "monomerTemplate-V___Valine"
+ - },
+ - {
+ - "$ref": "monomerTemplate-U___Selenocysteine"
+ - },
+ - {
+ - "$ref": "monomerTemplate-O___Pyrrolysine"
+ - },
+ - {
+ - "$ref": "ambiguousMonomerTemplate-B"
+ - },
+ - {
+ - "$ref": "ambiguousMonomerTemplate-J"
+ - },
+ - {
+ - "$ref": "ambiguousMonomerTemplate-X"
+ - },
+ - {
+ - "$ref": "ambiguousMonomerTemplate-Z"
+ - }
+ - ]
+ - },
+ - "monomer0": {
+ - "type": "monomer",
+ - "id": "0",
+ - "seqid": 1,
+ - "position": {
+ - "x": 0.000000,
+ - "y": -0.000000
+ - },
+ - "alias": "A",
+ - "templateId": "A___Alanine"
+ - },
+ - "monomer1": {
+ - "type": "monomer",
+ - "id": "1",
+ - "seqid": 2,
+ - "position": {
+ - "x": 1.600000,
+ - "y": -0.000000
+ - },
+ - "alias": "R",
+ - "templateId": "R___Arginine"
+ - },
+ - "monomer2": {
+ - "type": "monomer",
+ - "id": "2",
+ - "seqid": 3,
+ - "position": {
+ - "x": 3.200000,
+ - "y": -0.000000
+ - },
+ - "alias": "N",
+ - "templateId": "N___Asparagine"
+ - },
+ - "monomer3": {
+ - "type": "monomer",
+ - "id": "3",
+ - "seqid": 4,
+ - "position": {
+ - "x": 4.800000,
+ - "y": -0.000000
+ - },
+ - "alias": "D",
+ - "templateId": "D___Aspartic acid"
+ - },
+ - "monomer4": {
+ - "type": "monomer",
+ - "id": "4",
+ - "seqid": 5,
+ - "position": {
+ - "x": 6.400000,
+ - "y": -0.000000
+ - },
+ - "alias": "C",
+ - "templateId": "C___Cysteine"
+ - },
+ - "monomer5": {
+ - "type": "monomer",
+ - "id": "5",
+ - "seqid": 6,
+ - "position": {
+ - "x": 8.000000,
+ - "y": -0.000000
+ - },
+ - "alias": "Q",
+ - "templateId": "Q___Glutamine"
+ - },
+ - "monomer6": {
+ - "type": "monomer",
+ - "id": "6",
+ - "seqid": 7,
+ - "position": {
+ - "x": 9.600000,
+ - "y": -0.000000
+ - },
+ - "alias": "E",
+ - "templateId": "E___Glutamic acid"
+ - },
+ - "monomer7": {
+ - "type": "monomer",
+ - "id": "7",
+ - "seqid": 8,
+ - "position": {
+ - "x": 11.200000,
+ - "y": -0.000000
+ - },
+ - "alias": "G",
+ - "templateId": "G___Glycine"
+ - },
+ - "monomer8": {
+ - "type": "monomer",
+ - "id": "8",
+ - "seqid": 9,
+ - "position": {
+ - "x": 12.800000,
+ - "y": -0.000000
+ - },
+ - "alias": "H",
+ - "templateId": "H___Histidine"
+ - },
+ - "monomer9": {
+ - "type": "monomer",
+ - "id": "9",
+ - "seqid": 10,
+ - "position": {
+ - "x": 14.400001,
+ - "y": -0.000000
+ - },
+ - "alias": "I",
+ - "templateId": "I___Isoleucine"
+ - },
+ - "monomer10": {
+ - "type": "monomer",
+ - "id": "10",
+ - "seqid": 11,
+ - "position": {
+ - "x": 16.000000,
+ - "y": -0.000000
+ - },
+ - "alias": "L",
+ - "templateId": "L___Leucine"
+ - },
+ - "monomer11": {
+ - "type": "monomer",
+ - "id": "11",
+ - "seqid": 12,
+ - "position": {
+ - "x": 17.600000,
+ - "y": -0.000000
+ - },
+ - "alias": "K",
+ - "templateId": "K___Lysine"
+ - },
+ - "monomer12": {
+ - "type": "monomer",
+ - "id": "12",
+ - "seqid": 13,
+ - "position": {
+ - "x": 19.200001,
+ - "y": -0.000000
+ - },
+ - "alias": "M",
+ - "templateId": "M___Methionine"
+ - },
+ - "monomer13": {
+ - "type": "monomer",
+ - "id": "13",
+ - "seqid": 14,
+ - "position": {
+ - "x": 20.800001,
+ - "y": -0.000000
+ - },
+ - "alias": "F",
+ - "templateId": "F___Phenylalanine"
+ - },
+ - "monomer14": {
+ - "type": "monomer",
+ - "id": "14",
+ - "seqid": 15,
+ - "position": {
+ - "x": 22.400000,
+ - "y": -0.000000
+ - },
+ - "alias": "P",
+ - "templateId": "P___Proline"
+ - },
+ - "monomer15": {
+ - "type": "monomer",
+ - "id": "15",
+ - "seqid": 16,
+ - "position": {
+ - "x": 24.000000,
+ - "y": -0.000000
+ - },
+ - "alias": "S",
+ - "templateId": "S___Serine"
+ - },
+ - "monomer16": {
+ - "type": "monomer",
+ - "id": "16",
+ - "seqid": 17,
+ - "position": {
+ - "x": 25.600000,
+ - "y": -0.000000
+ - },
+ - "alias": "T",
+ - "templateId": "T___Threonine"
+ - },
+ - "monomer17": {
+ - "type": "monomer",
+ - "id": "17",
+ - "seqid": 18,
+ - "position": {
+ - "x": 27.200001,
+ - "y": -0.000000
+ - },
+ - "alias": "W",
+ - "templateId": "W___Tryptophan"
+ - },
+ - "monomer18": {
+ - "type": "monomer",
+ - "id": "18",
+ - "seqid": 19,
+ - "position": {
+ - "x": 28.800001,
+ - "y": -0.000000
+ - },
+ - "alias": "Y",
+ - "templateId": "Y___Tyrosine"
+ - },
+ - "monomer19": {
+ - "type": "monomer",
+ - "id": "19",
+ - "seqid": 20,
+ - "position": {
+ - "x": 30.400000,
+ - "y": -0.000000
+ - },
+ - "alias": "V",
+ - "templateId": "V___Valine"
+ - },
+ - "monomer20": {
+ - "type": "monomer",
+ - "id": "20",
+ - "seqid": 21,
+ - "position": {
+ - "x": 32.000000,
+ - "y": -0.000000
+ - },
+ - "alias": "U",
+ - "templateId": "U___Selenocysteine"
+ - },
+ - "monomer21": {
+ - "type": "monomer",
+ - "id": "21",
+ - "seqid": 22,
+ - "position": {
+ - "x": 33.600002,
+ - "y": -0.000000
+ - },
+ - "alias": "O",
+ - "templateId": "O___Pyrrolysine"
+ - },
+ - "ambiguousMonomer-22": {
+ - "type": "ambiguousMonomer",
+ - "id": "22",
+ - "position": {
+ - "x": 35.200001,
+ - "y": -0.000000
+ - },
+ - "seqid": 23,
+ - "alias": "B",
+ - "templateId": "B"
+ - },
+ - "ambiguousMonomer-23": {
+ - "type": "ambiguousMonomer",
+ - "id": "23",
+ - "position": {
+ - "x": 36.799999,
+ - "y": -0.000000
+ - },
+ - "seqid": 24,
+ - "alias": "J",
+ - "templateId": "J"
+ - },
+ - "ambiguousMonomer-24": {
+ - "type": "ambiguousMonomer",
+ - "id": "24",
+ - "position": {
+ - "x": 38.400002,
+ - "y": -0.000000
+ - },
+ - "seqid": 25,
+ - "alias": "X",
+ - "templateId": "X"
+ - },
+ - "ambiguousMonomer-25": {
+ - "type": "ambiguousMonomer",
+ - "id": "25",
+ - "position": {
+ - "x": 40.000000,
+ - "y": -0.000000
+ - },
+ - "seqid": 26,
+ - "alias": "Z",
+ - "templateId": "Z"
+ - },
+ - "monomerTemplate-A___Alanine": {
+ - "type": "monomerTemplate",
+ - "id": "A___Alanine",
+ - "class": "AminoAcid",
+ - "classHELM": "PEPTIDE",
+ - "fullName": "Alanine",
+ - "alias": "A",
+ - "naturalAnalogShort": "A",
+ - "attachmentPoints": [
+ - {
+ - "attachmentAtom": 0,
+ - "type": "left",
+ - "leavingGroup": {
+ - "atoms": [
+ - 6
+ - ]
+ - }
+ - },
+ - {
+ - "attachmentAtom": 3,
+ - "type": "right",
+ - "leavingGroup": {
+ - "atoms": [
+ - 5
+ - ]
+ - }
+ - }
+ - ],
+ - "atoms": [
+ - {
+ - "label": "N",
+ - "location": [
+ - -1.254900,
+ - -0.392000,
+ - 0.000000
+ - ]
+ - },
+ - {
+ - "label": "C",
+ - "location": [
+ - -0.272000,
+ - 0.263300,
+ - 0.000000
+ - ],
+ - "stereoLabel": "abs"
+ - },
+ - {
+ - "label": "C",
+ - "location": [
+ - -0.310300,
+ - 1.739300,
+ - 0.000000
+ - ]
+ - },
+ - {
+ - "label": "C",
+ - "location": [
+ - 1.052300,
+ - -0.392000,
+ - 0.000000
+ - ]
+ - },
+ - {
+ - "label": "O",
+ - "location": [
+ - 1.082900,
+ - -1.572200,
+ - 0.000000
+ - ]
+ - },
+ - {
+ - "label": "O",
+ - "location": [
+ - 2.035300,
+ - 0.263300,
+ - 0.000000
+ - ]
+ - },
+ - {
+ - "label": "H",
+ - "location": [
+ - -2.333400,
+ - 0.090500,
+ - 0.000000
+ - ]
+ - }
+ - ],
+ - "bonds": [
+ - {
+ - "type": 1,
+ - "atoms": [
+ - 1,
+ - 0
+ - ]
+ - },
+ - {
+ - "type": 1,
+ - "atoms": [
+ - 1,
+ - 2
+ - ],
+ - "stereo": 1
+ - },
+ - {
+ - "type": 1,
+ - "atoms": [
+ - 1,
+ - 3
+ - ]
+ - },
+ - {
+ - "type": 2,
+ - "atoms": [
+ - 3,
+ - 4
+ - ]
+ - },
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