Backmerge #1362 Valence is not added to the SMARTS file (#1379)

epam · Oct 26, 2023 · ced8aeb · ced8aeb
1 parent af912fb
commit ced8aeb
Show file tree

Hide file tree

Showing 4 changed files with 20 additions and 5 deletions.
diff --git a/api/tests/integration/ref/formats/smarts.py.out b/api/tests/integration/ref/formats/smarts.py.out
@@ -74,12 +74,18 @@ Ok expected smarts generated
 [#6,#7;a]:[o] is ok. expected string found in json
 [c,n,o]:[o] is ok. json_in==json_out
 [c,n,o]:[o] is ok. expected string found in json
+[c,C,c] is ok. smarts_in==smarts_out
 [c,C,c] is ok. json_in==json_out
 [c,C,c] is ok. expected string found in json
+[C,c] is ok. smarts_in==smarts_out
 [C,c] is ok. json_in==json_out
 [C,c] is ok. expected string found in json
+[C,c,n,o] is ok. smarts_in==smarts_out
 [C,c,n,o] is ok. json_in==json_out
 [C,c,n,o] is ok. expected string found in json
+[#7;v4]-[#6] is ok. smarts_in==smarts_out
+[#7;v4]-[#6] is ok. json_in==json_out
+[#7;v4]-[#6] is ok. expected string found in json
  *** SMARTS specific ***
 Smarts [C,N] loaded as smarts - OK.
 Smarts [C;N] loaded as smarts - OK.

diff --git a/api/tests/integration/tests/formats/smarts.py b/api/tests/integration/tests/formats/smarts.py
@@ -215,13 +215,16 @@ def test_smarts_load_save_through_ket(
 test_smarts_load_save_through_ket(smarts, expected, False)
 smarts = "[c,C,c]"
 expected = '"atoms":[{"label":"C","location":[0.0,0.0,0.0],"queryProperties":{"customQuery":"c,C,c"}}]'
-test_smarts_load_save_through_ket(smarts, expected, False)
+test_smarts_load_save_through_ket(smarts, expected)
 smarts = "[C,c]"
 expected = '"atoms":[{"label":"C","location":[0.0,0.0,0.0],"queryProperties":{"customQuery":"C,c"}}]'
-test_smarts_load_save_through_ket(smarts, expected, False)
+test_smarts_load_save_through_ket(smarts, expected)
 smarts = "[C,c,n,o]"
 expected = '"atoms":[{"label":"","location":[0.0,0.0,0.0],"queryProperties":{"customQuery":"C,c,n,o"}}]'
-test_smarts_load_save_through_ket(smarts, expected, False)
+test_smarts_load_save_through_ket(smarts, expected)
+smarts = "[#7;v4]-[#6]"
+expected = '"atoms":[{"label":"N","location":[0.0,0.0,0.0],"explicitValence":4},{"label":"C","location":[1.0,0.0,0.0]}]'
+test_smarts_load_save_through_ket(smarts, expected)
 print(" *** SMARTS specific ***")
 smarts_list = [
     "[C,N]",

diff --git a/core/indigo-core/molecule/src/molecule_json_loader.cpp b/core/indigo-core/molecule/src/molecule_json_loader.cpp
@@ -178,7 +178,7 @@ int MoleculeJsonLoader::addAtomToMoleculeQuery(const char* label, int element, i
     {
         if (valence == 15)
             valence = 0;
-        atom.reset(QueryMolecule::Atom::und(atom.release(), new QueryMolecule::Atom(QueryMolecule::ATOM_VALENCE, valence)));
+        atom.reset(QueryMolecule::Atom::und(atom.release(), new QueryMolecule::Atom(QueryMolecule::ATOM_TOTAL_BOND_ORDER, valence)));
     }
 
     if (isotope != 0)

diff --git a/core/indigo-core/molecule/src/molecule_json_saver.cpp b/core/indigo-core/molecule/src/molecule_json_saver.cpp
@@ -930,7 +930,13 @@ void MoleculeJsonSaver::saveAtoms(BaseMolecule& mol, JsonWriter& writer)
             writer.Int(charge);
         }
 
-        if (evalence > 0)
+        int total_bond_count = 0;
+        if (_pqmol && _pqmol->getAtom(i).sureValue(QueryMolecule::ATOM_TOTAL_BOND_ORDER, total_bond_count))
+        {
+            writer.Key("explicitValence");
+            writer.Int(total_bond_count);
+        }
+        else if (evalence > 0)
         {
             writer.Key("explicitValence");
             writer.Int(evalence);