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Backmerge: #2339 - Unable to load HELM inline SMILES sugar #2345

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merged 2 commits into from
Sep 10, 2024
Merged

Backmerge: #2339 - Unable to load HELM inline SMILES sugar #2345

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df25f17
Fix bug. Update UTs
AliaksandrDziarkach Sep 10, 2024
3dceb54
Fix UT
AliaksandrDziarkach Sep 10, 2024
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1 change: 1 addition & 0 deletions api/tests/integration/ref/formats/helm_to_ket.py.out
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Original file line number Diff line number Diff line change
Expand Up @@ -10,6 +10,7 @@ helm_peptide.ket:SUCCEED
helm_rna_without_base.ket:SUCCEED
helm_simple_rna.ket:SUCCEED
helm_smiles.ket:SUCCEED
helm_smiles_sugar.ket:SUCCEED
Test 'CHEM1{[A6OH]}|PEPTIDE1{A}$CHEM1,PEPTIDE1,1:R2-3:R1$$$V2.0': got expected error 'Polymer 'PEPTIDE1' does not contains monomer with number 3.'
Test 'CHEM1{[A6OH]}|PEPTIDE1{A}$CHEM1,PEPTIDE1,1:R4-1:R1$$$V2.0': got expected error 'Unknown attachment point 'R4' in monomer A6OH'
Test 'CHEM1{[A6OH]}|PEPTIDE1{A}$CHEM10,PEPTIDE1,1:R2-1:R1$$$V2.0': got expected error 'Polymer 'CHEM10' not found.'
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1 change: 1 addition & 0 deletions api/tests/integration/tests/formats/helm_to_ket.py
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Expand Up @@ -40,6 +40,7 @@ def find_diff(a, b):
"helm_mixed_custom": "RNA1{[dR](A:10+C:20+G:30+T:50)P.[dR](A:10+C:20+G:30+T:50)P.[dR](A+C+G+T)}$$$$V2.0",
"aminoacids_variants": "PEPTIDE1{(D+N).(L+I).(E+Q).(A+C+D+E+F+G+H+I+K+L+M+N+O+P+Q+R+S+T+U+V+W+Y)}$$$$V2.0",
"helm_smiles": "PEPTIDE1{G.[[*]N[C@@H](C=O)C([*])=O |$_R1;;;;;;_R2;$|].C}|PEPTIDE2{G.[[*:1]N[C@@H](C=O)C([*:2])=O].C}$$$$",
"helm_smiles_sugar": "RNA1{[C([*:3])[C@@H](O[*:2])CO[*:1]](A)P}$$$$V2.0",
}

lib = indigo.loadMonomerLibraryFromFile(
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