#1355 Error appears when pressing 'Layout" (#1364)

epam · Oct 23, 2023 · 73a99f4 · 73a99f4
1 parent e6374ee
commit 73a99f4
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Showing 4 changed files with 21 additions and 3 deletions.
diff --git a/api/tests/integration/ref/formats/smarts.py.out b/api/tests/integration/ref/formats/smarts.py.out
@@ -61,3 +61,5 @@ smarts loaded OK
 [!#6!#7!#8] is ok. smarts_in==smarts_out
 [!#6!#7!#8] is ok. json_in==json_out
 [!#6!#7!#8] is ok. expected string found in json
+#1355 Error appeared at save query molecule with RSite as smarts
+Ok expected smarts generated
diff --git a/api/tests/integration/tests/formats/smarts.py b/api/tests/integration/tests/formats/smarts.py
@@ -184,3 +184,15 @@ def test_smarts_load_save_through_ket(smarts_in, expected_str):
     "[!#6!#7!#8]",
     '"atoms":[{"type":"atom-list","notList":true,"elements":["C","N","O"],"location":[0.0,0.0,0.0]}]',
 )
+print("#1355 Error appeared at save query molecule with RSite as smarts")
+m = indigo.loadQueryMolecule(
+    "S=CC(F)CCCCC[C@@](CCO)/C=C/[C@@](N)CCC[C]C([13C]CC([C+2]CC(CC%91)CC(C)CCC)CCC)CC%92.[*:2]%92.[*:1]%91 |$;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;_R2;_R1$,rb:32:*,u:3|"
+)
+smarts = m.smarts()
+expected = "[#16]=[#6]-[#6](-[#6]-[#6]-[#6]-[#6]-[#6]-[#6@](-[#6]=[#6]-[#6@](-[#6]-[#6]-[#6]-[#6]-[#6](-[#6]-[#6]%91)-[13;#6]-[#6]-[#6](-[#6]-[#6]-[#6])-[#6;+2]-[#6]-[#6](-[#6]-[#6](-[#6]-[#6]-[#6])-[#6;x0])-[#6]-[#6]%92)-[#7])-[#6]-[#6]-[#8])-[#9;$([*,#1]=,#,:[*,#1])].[*:2]-%91.[*:1]-%92"
+if smarts == expected:
+    print("Ok expected smarts generated")
+else:
+    print(
+        "Fail. Expected smarts is\n%s\nbut generated\n%s" % (expected, smarts)
+    )
diff --git a/core/indigo-core/molecule/src/molecule_json_saver.cpp b/core/indigo-core/molecule/src/molecule_json_saver.cpp
@@ -686,7 +686,8 @@ void MoleculeJsonSaver::saveAtoms(BaseMolecule& mol, JsonWriter& writer)
         int radical = 0;
         int query_atom_type = QueryMolecule::QUERY_ATOM_UNKNOWN;
         std::map<int, const QueryMolecule::Atom*> query_atom_properties;
-        if (mol.isRSite(i))
+        bool is_rSite = mol.isRSite(i);
+        if (is_rSite)
         {
             mol.getAllowedRGroups(i, rg_list);
             writer.Key("type");
@@ -810,7 +811,7 @@ void MoleculeJsonSaver::saveAtoms(BaseMolecule& mol, JsonWriter& writer)
         bool ecflag = mol.reaction_atom_exact_change[i];
         int hcount = MoleculeSavers::getHCount(mol, i, anum, charge);
 
-        if (_pqmol)
+        if (_pqmol && !is_rSite) // No custom query for RSite
         {
             bool needCustomQuery = query_atom_type == QueryMolecule::QUERY_ATOM_UNKNOWN;
             std::map<int, const char*> qprops{{QueryMolecule::ATOM_SSSR_RINGS, "ringMembership"},
@@ -908,7 +909,7 @@ void MoleculeJsonSaver::saveAtoms(BaseMolecule& mol, JsonWriter& writer)
                 writer.Int(query_atom_properties[QueryMolecule::ATOM_IMPLICIT_H]->value_min);
             }
         }
-        else
+        else if (_pmol)
         {
             if (Molecule::shouldWriteHCount(mol.asMolecule(), i) && hcount > 0)
             {

diff --git a/core/indigo-core/molecule/src/query_molecule.cpp b/core/indigo-core/molecule/src/query_molecule.cpp
@@ -678,6 +678,9 @@ void QueryMolecule::writeSmartsAtom(Output& output, Atom* atom, int aam, int chi
         }
         break;
     }
+    case ATOM_RSITE:
+        output.printf("*:%d", atom->value_min);
+        break;
 
     default: {
         throw Error("Unknown atom attribute %d", atom->type);