#1349 Symbol for topology chain is missing in SMARTS file (#1354)

epam · Oct 19, 2023 · 2e0b7ae · 2e0b7ae
1 parent 4369a05
commit 2e0b7ae
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Showing 5 changed files with 25 additions and 3 deletions.
diff --git a/api/tests/integration/ref/deco/deco_recursive_smarts.py.out b/api/tests/integration/ref/deco/deco_recursive_smarts.py.out
@@ -8,8 +8,8 @@ full scaffold:
     0.0000    0.0000    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
     0.0000    0.0000    0.0000 R#  0  0  0  0  0  0  0  0  0  0  0  0
     0.0000    0.0000    0.0000 R#  0  0  0  0  0  0  0  0  0  0  0  0
-  1  2  1  0  0  0  0
-  2  3  1  0  0  0  0
+  1  2  1  0  0  2  0
+  2  3  1  0  0  2  0
   3  4  2  0  0  0  0
   5  2  1  0  0  0  0
   6  4  1  0  0  0  0

diff --git a/api/tests/integration/ref/formats/smarts.py.out b/api/tests/integration/ref/formats/smarts.py.out
@@ -47,3 +47,9 @@ CC[C+5]CCCCC
 [C;@@] is ok. smarts_in==smarts_out
 [C;@@] is ok. json_in==json_out
 [C;@@] is ok. expected string found in json
+[#6]-;@[#6] is ok. smarts_in==smarts_out
+[#6]-;@[#6] is ok. json_in==json_out
+[#6]-;@[#6] is ok. expected string found in json
+[#6]-;!@[#6] is ok. smarts_in==smarts_out
+[#6]-;!@[#6] is ok. json_in==json_out
+[#6]-;!@[#6] is ok. expected string found in json
diff --git a/api/tests/integration/tests/formats/smarts.py b/api/tests/integration/tests/formats/smarts.py
@@ -168,3 +168,9 @@ def test_smarts_load_save_through_ket(smarts_in, expected_str):
     "[C;@@]",
     '"atoms":[{"label":"C","location":[0.0,0.0,0.0],"queryProperties":{"aromaticity":"aliphatic","chirality":"clockwise"}}]',
 )
+test_smarts_load_save_through_ket(
+    "[#6]-;@[#6]", '"bonds":[{"type":1,"topology":1,"atoms":[0,1]}]'
+)
+test_smarts_load_save_through_ket(
+    "[#6]-;!@[#6]", '"bonds":[{"type":1,"topology":2,"atoms":[0,1]}]'
+)
diff --git a/core/indigo-core/molecule/src/query_molecule.cpp b/core/indigo-core/molecule/src/query_molecule.cpp
@@ -395,6 +395,8 @@ void QueryMolecule::writeSmartsBond(Output& output, Bond* bond, bool has_or_pare
     case BOND_TOPOLOGY: {
         if (bond->value == TOPOLOGY_RING)
             output.writeChar('@');
+        else
+            output.writeString("!@");
         break;
     }
     default:

diff --git a/core/indigo-core/molecule/src/smiles_loader.cpp b/core/indigo-core/molecule/src/smiles_loader.cpp
@@ -2631,7 +2631,15 @@ void SmilesLoader::_readBondSub(Array<char>& bond_str, _BondDesc& bond, std::uni
             scanner.skip(1);
             if (qbond.get() == 0)
                 throw Error("'@' ring bond is allowed only for queries");
-            topology = TOPOLOGY_RING;
+            if (neg)
+            {
+                topology = TOPOLOGY_CHAIN;
+                neg = false;
+            }
+            else
+            {
+                topology = TOPOLOGY_RING;
+            }
         }
         else
             throw Error("Character #%d is unexpected during bond parsing", next);