Backmerge: #2357 - Export to HELM doesn't work if we connect peptide …

…TO molecule (#2370)
epam · Sep 16, 2024 · 04356f1 · 04356f1
1 parent 163acd3
commit 04356f1
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Showing 3 changed files with 14 additions and 3 deletions.
diff --git a/api/tests/integration/tests/formats/ket_to_helm.py b/api/tests/integration/tests/formats/ket_to_helm.py
@@ -47,7 +47,7 @@ def find_diff(a, b):
     "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)}$$$$V2.0",
     "dna_variants": "RNA1{[dR](C,G,T)P.[dR](A,C,G,T)}$$$$V2.0",
     "rna_variants": "RNA1{R(G,T)P.R(A,C,G,T)}$$$$V2.0",
-    "helm_monomer_molecule": "PEPTIDE1{A}|PEPTIDE2{G}|CHEM1{[C(N[*:2])=C[*:1] |$;;_R2;;_R1$|]}$CHEM1,PEPTIDE1,1:R2-1:R1$$$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/ref/helm_monomer_molecule.ket b/api/tests/integration/tests/formats/ref/helm_monomer_molecule.ket
@@ -22,6 +22,17 @@
                     "monomerId": "monomer98",
                     "attachmentPointId": "R1"
                 }
+            },
+            {
+                "connectionType": "single",
+                "endpoint1": {
+                    "monomerId": "monomer102",
+                    "attachmentPointId": "R2"
+                },
+                "endpoint2": {
+                    "moleculeId": "mol0",
+                    "atomId": "1"
+                }
             }
         ],
         "templates": [

diff --git a/core/indigo-core/molecule/src/ket_document.cpp b/core/indigo-core/molecule/src/ket_document.cpp
@@ -410,7 +410,7 @@ void KetDocument::parseSimplePolymers(std::vector<std::deque<std::string>>& sequ
         bool has_ap_1 = ep1.hasStringProp("attachmentPointId");
         bool has_atom_1 = ep1.hasStringProp("atomId");
         bool has_ap_2 = ep2.hasStringProp("attachmentPointId");
-        bool has_atom_2 = ep1.hasStringProp("atomId");
+        bool has_atom_2 = ep2.hasStringProp("atomId");
         if ((has_ap_1 || has_atom_1) != (has_ap_2 || has_atom_2))
             throw Error("Connection with only one attachment point id.");
         if (!(has_ap_1 || has_atom_1))
@@ -433,7 +433,7 @@ void KetDocument::parseSimplePolymers(std::vector<std::deque<std::string>>& sequ
         auto& mon2_class = id_to_class.at(mon_id_2);
 
         auto& ap_id_1 = has_mon_1 ? ep1.getStringProp("attachmentPointId") : ep1.getStringProp("atomId");
-        auto& ap_id_2 = has_mon_1 ? ep2.getStringProp("attachmentPointId") : ep1.getStringProp("atomId");
+        auto& ap_id_2 = has_mon_2 ? ep2.getStringProp("attachmentPointId") : ep2.getStringProp("atomId");
 
         ap_to_connection.emplace(std::make_pair(mon_id_1, ap_id_1), connection);
         ap_to_connection.emplace(std::make_pair(mon_id_2, ap_id_2), connection);