#2460 - Load/save hydrogen bonds from/to HELM, KET and MOL (#2571)

epam · Oct 23, 2024 · d807ea1 · d807ea1
1 parent 83a67a4
commit d807ea1
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Showing 24 changed files with 3,113 additions and 18 deletions.
diff --git a/.github/workflows/indigo-ci.yaml b/.github/workflows/indigo-ci.yaml
@@ -314,7 +314,7 @@ jobs:
           path: dist/
       - name: Test Linux
         if: ${{ startsWith(matrix.os, 'ubuntu') }}
-        uses: uraimo/run-on-arch-action@v2.0.5
+        uses: uraimo/run-on-arch-action@v2.8.1
         with:
           arch: aarch64
           distro: ubuntu20.04
@@ -446,7 +446,7 @@ jobs:
           path: dist/
       - name: Test Linux
         if: ${{ startsWith(matrix.os, 'ubuntu') }}
-        uses: uraimo/run-on-arch-action@v2.0.5
+        uses: uraimo/run-on-arch-action@v2.8.1
         with:
           arch: aarch64
           distro: ubuntu20.04

diff --git a/api/tests/integration/ref/formats/helm_to_ket.py.out b/api/tests/integration/ref/formats/helm_to_ket.py.out
@@ -3,6 +3,7 @@ helm_aminoacids_variants.ket:SUCCEED
 helm_annotations.ket:SUCCEED
 helm_chem_peptide.ket:SUCCEED
 helm_chem_rna.ket:SUCCEED
+helm_chem_rna_hydro.ket:SUCCEED
 helm_fractional_ratio.ket:SUCCEED
 helm_mixed_base.ket:SUCCEED
 helm_mixed_custom.ket:SUCCEED

diff --git a/api/tests/integration/ref/formats/ket_to_helm.py.out b/api/tests/integration/ref/formats/ket_to_helm.py.out
@@ -4,6 +4,7 @@ helm_aminoacids_variants.ket:SUCCEED
 helm_annotations.ket:SUCCEED
 helm_chem_peptide.ket:SUCCEED
 helm_chem_rna.ket:SUCCEED
+helm_chem_rna_hydro.ket:SUCCEED
 helm_connetion_separator.ket:SUCCEED
 helm_cycled_polymer.ket:SUCCEED
 helm_fractional_ratio.ket FAILED : expected 'PEPTIDE1{(A:1.5+C:.1+G:3.)}$$$$V2.0', got 'PEPTIDE1{(A:1.5+C:0.1+G:3)}$$$$V2.0'

diff --git a/api/tests/integration/ref/formats/ket_to_mol.py.out b/api/tests/integration/ref/formats/ket_to_mol.py.out
@@ -4,6 +4,7 @@ accl_no_class.ket:SUCCEED
 acgt_1412.ket:SUCCEED
 anacyclamide.ket:SUCCEED
 chem.ket:SUCCEED
+chem_rna_hydro.ket:SUCCEED
 conj_no_class.ket:SUCCEED
 conjugate.ket:SUCCEED
 cysteine.ket:SUCCEED

diff --git a/api/tests/integration/ref/formats/mol_to_ket.py.out b/api/tests/integration/ref/formats/mol_to_ket.py.out
@@ -10,6 +10,7 @@ anacyclamide.ket:SUCCEED
 apamine.ket:SUCCEED
 atropisomer.ket:SUCCEED
 chem.ket:SUCCEED
+chem_rna_hydro.ket:SUCCEED
 conjugate.ket:SUCCEED
 cysteine.ket:SUCCEED
 dcysteine.ket:SUCCEED

diff --git a/api/tests/integration/tests/formats/helm_to_ket.py b/api/tests/integration/tests/formats/helm_to_ket.py
@@ -43,6 +43,7 @@ def find_diff(a, b):
     "helm_smiles_sugar": "RNA1{[C([*:3])[C@@H](O[*:2])CO[*:1]](A)P}$$$$V2.0",
     "helm_no_left_ap": "PEPTIDE1{[DACys].C}$$$$V2.0",
     "helm_fractional_ratio": "PEPTIDE1{(A:1.5+C:0.1+G:3)}$$$$V2.0",
+    "helm_chem_rna_hydro": "CHEM1{[MCC]}|RNA1{R(U)P}$CHEM1,RNA1,1:pair-3:pair$$$V2.0",
 }
 
 lib = indigo.loadMonomerLibraryFromFile(

diff --git a/api/tests/integration/tests/formats/ket_to_helm.py b/api/tests/integration/tests/formats/ket_to_helm.py
@@ -52,6 +52,7 @@ def find_diff(a, b):
     "helm_smiles": "PEPTIDE1{G.[[*:1]NC(C(=O)[*:2])C=O |$_R1;;;;;_R2;;$|].C}|PEPTIDE2{G.[[*:1]NC(C(=O)[*:2])C=O |$_R1;;;;;_R2;;$|].C}$$$$V2.0",
     "helm_smiles_sugar": "RNA1{[C(C(CO[*:1])O[*:2])[*:3] |$;;;;_R1;;_R2;_R3$|](A)P}$$$$V2.0",
     "helm_molecule_2418": "PEPTIDE1{A}|CHEM1{[C1C=CC=CC=1[*:1] |$;;;;;;_R1$|]}$PEPTIDE1,CHEM1,1:R1-1:R1$$$V2.0",
+    "helm_chem_rna_hydro": "CHEM1{[MCC]}|RNA1{R(U)P}$CHEM1,RNA1,1:pair-3:pair$$$V2.0",
 }
 
 for filename in sorted(helm_data.keys()):

diff --git a/api/tests/integration/tests/formats/ket_to_mol.py b/api/tests/integration/tests/formats/ket_to_mol.py
@@ -68,6 +68,7 @@ def find_diff(a, b):
     ("macro/sa-mono", "auto"),
     ("macro/R2R3R4", "auto"),
     ("5amd", "2000"),
+    ("chem_rna_hydro", "3000"),
 ]
 
 files.sort(key=lambda x: x[0])

diff --git a/api/tests/integration/tests/formats/mol_to_ket.py b/api/tests/integration/tests/formats/mol_to_ket.py
@@ -49,6 +49,7 @@ def find_diff(a, b):
     "taspoglutide",
     "1972-case1",
     "1972-case2",
+    "chem_rna_hydro",
 ]
 
 files.sort()