Merge branch 'release/1.24' into bugfix/2303-broken-import-seq-rna-r

epam · Sep 16, 2024 · d778650 · d778650
2 parents 60af756 + ea5daf0
commit d778650
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Showing 18 changed files with 2,403 additions and 92 deletions.
diff --git a/api/tests/integration/ref/formats/ket_to_fasta.py.out b/api/tests/integration/ref/formats/ket_to_fasta.py.out
@@ -2,4 +2,5 @@
 1822-peptide.fasta:SUCCEED
 1843-rna.fasta:SUCCEED
 1950-mixed-seq.fasta:SUCCEED
+2341-no-analog.fasta:SUCCEED
 nucleotides.fasta:SUCCEED
diff --git a/api/tests/integration/ref/formats/ket_to_idt.py.out b/api/tests/integration/ref/formats/ket_to_idt.py.out
@@ -18,6 +18,7 @@ idt_i2moera_t.ket:SUCCEED
 idt_many_molecules.ket:SUCCEED
 idt_mixed.ket:SUCCEED
 idt_mixed_custom.ket:SUCCEED
+idt_mixed_ketcher.ket:SUCCEED
 idt_mixed_std.ket:SUCCEED
 idt_mod_phosphates.ket:SUCCEED
 idt_modifications.ket:SUCCEED

diff --git a/api/tests/integration/tests/formats/ket_to_fasta.py b/api/tests/integration/tests/formats/ket_to_fasta.py
@@ -27,6 +27,7 @@ def find_diff(a, b):
     "1843-rna",
     "1950-mixed-seq",
     "nucleotides",
+    "2341-no-analog",
 ]
 
 lib = indigo.loadMonomerLibraryFromFile(
@@ -35,9 +36,9 @@ def find_diff(a, b):
 
 files.sort()
 for filename in files:
-    mol = indigo.loadMoleculeFromFile(os.path.join(root, filename + ".ket"))
+    mol = indigo.loadKetDocumentFromFile(os.path.join(root, filename + ".ket"))
     # with open(os.path.join(ref_path, filename) + ".fasta", "w") as file:
-    #     file.write(mol.fasta())
+    #     file.write(mol.fasta(lib))
     with open(os.path.join(ref_path, filename) + ".fasta", "r") as file:
         seq_ref = file.read()
     seq = mol.fasta(lib)

diff --git a/api/tests/integration/tests/formats/ket_to_helm.py b/api/tests/integration/tests/formats/ket_to_helm.py
@@ -45,9 +45,9 @@ def find_diff(a, b):
     "helm_mixed_base": "RNA1{[dR](A)P.[dR](A+G)P.[dR](A)P.[dR](G+C)}$$$$V2.0",
     "helm_mixed_custom": "RNA1{[dR](A:10+[Xan]:20+G:30+T:50)P.[dR](A:10+C:20+G:30+T:50)P.[dR](A+C+G+T)}$$$$V2.0",
     "helm_aminoacids_variants": "PEPTIDE1{([Dha]+N).(L+I).(E+Q).(A+C+D+E+F+G+H+I+K+L+M+N+O+P+Q+R+S+T+U+V+W+Y)}$$$$V2.0",
-    "dna_variants": "RNA1{[dR](C+G+T)P.[dR](A+C+G+T)}$$$$V2.0",
+    "dna_variants": "RNA1{[dR](C,G,T)P.[dR](A,C,G,T)}$$$$V2.0",
     "rna_variants": "RNA1{R(A+G)P.R(G+T)P.R(A+C+G+T)}$$$$V2.0",
-    "helm_monomer_molecule": "PEPTIDE1{A}|PEPTIDE2{G}|CHEM1{[C(N[*:2])=C[*:1] |$;;_R2;;_R1$|]}$CHEM1,PEPTIDE1,1:R2-1:R1$$$V2.0",
+    "helm_monomer_molecule": "PEPTIDE1{A}|PEPTIDE2{G}|CHEM1{[C(N[*:2])=C[*:1] |$;;_R2;;_R1$|]}$CHEM1,PEPTIDE1,1:R2-1:R1|PEPTIDE2,CHEM1,1:R2-1:R1$$$V2.0",
 }
 
 for filename in sorted(helm_data.keys()):

diff --git a/api/tests/integration/tests/formats/ket_to_idt.py b/api/tests/integration/tests/formats/ket_to_idt.py
@@ -64,6 +64,7 @@ def find_diff(a, b):
     "idt_mixed_std": "ARAS",
     "idt_mixed_custom": "(N1:10203050)(N1)N",
     "idt_rna_dna_mixed_custom": "r(R1:50003000)(R1)",
+    "idt_mixed_ketcher": "KrK(K1:00003070)r(K2:00003070)",
 }
 
 for filename in sorted(idt_data.keys()):