core: molecule: fix saving aliases order in SMILES saver

epam · Aug 26, 2023 · 03717cc · 03717cc
1 parent 964da3f
commit 03717cc
Show file tree

Hide file tree

Showing 5 changed files with 50 additions and 3 deletions.
diff --git a/api/wasm/indigo-ketcher/test/test.js b/api/wasm/indigo-ketcher/test/test.js
@@ -689,6 +689,20 @@ M  END
             });
             options.delete();
         });
+        test("reactionComponents", "complex_1", () => {
+            let options = new indigo.MapStringString();
+            assert.deepStrictEqual(JSON.parse(indigo.reactionComponents("[#6:1][C:2](=[O:3])[OH1:4].[C:5][N:6]>>[#6:1][C:2](=[O:3])[N:6][C:5] |$R1;;;OH;R2;NHR3;R1;;;NR3;R2$|", options)), {
+                "reactants": ["CC([OH])=O |$R1;;OH;$|", "CN |$R2;NHR3$|"],
+                "catalysts": [],
+                "products": ["CC(NC)=O |$R1;;NR3;R2;$|"]
+            });
+            assert.deepStrictEqual(JSON.parse(indigo.reactionComponents("[#6:1][C:2](=[O:3])[OH1:4].[C:5][N:6]>>[#6:1][C:2](=[O:3])[N:6][C:5] |$R1;;;OH;R2;NHR3;R1;;;NR3;R2$|", options)), {
+                "reactants": ["CC([OH])=O |$R1;;OH;$|", "CN |$R2;NHR3$|"],
+                "catalysts": [],
+                "products": ["CC(NC)=O |$R1;;NR3;R2;$|"]
+            });
+            options.delete();
+        });
     }
 
     // Run tests

diff --git a/core/indigo-core/molecule/src/smiles_saver.cpp b/core/indigo-core/molecule/src/smiles_saver.cpp
@@ -1669,9 +1669,9 @@ void SmilesSaver::_writePseudoAtoms()
         {
             writeSpecialAtom(_written_atoms[i], _output);
         }
-        else if (mol.isAlias(i))
+        else if (mol.isAlias(_written_atoms[i]))
         {
-            writePseudoAtom(mol.getAlias(i), _output);
+            writePseudoAtom(mol.getAlias(_written_atoms[i]), _output);
         }
     }
 

diff --git a/core/indigo-core/tests/common.cpp b/core/indigo-core/tests/common.cpp
@@ -163,3 +163,21 @@ std::string IndigoCoreTest::saverReactionJson(BaseReaction& reaction)
     std::string result(buffer.ptr());
     return result;
 }
+
+std::string IndigoCoreTest::smiles(Molecule& m)
+{
+    Array<char> smiles;
+    ArrayOutput output(smiles);
+    SmilesSaver saver(output);
+    saver.saveMolecule(m);
+    return {smiles.ptr(), static_cast<std::size_t>(smiles.size())};
+}
+
+std::string IndigoCoreTest::smiles(QueryMolecule& m)
+{
+    Array<char> smiles;
+    ArrayOutput output(smiles);
+    SmilesSaver saver(output);
+    saver.saveQueryMolecule(m);
+    return {smiles.ptr(), static_cast<std::size_t>(smiles.size())};
+}
diff --git a/core/indigo-core/tests/common.h.in b/core/indigo-core/tests/common.h.in
@@ -32,5 +32,7 @@ namespace indigo
         std::string saveReactionCML(Reaction& reaction);
         std::string saverReactionJson(BaseReaction& reaction);
         static std::string dataPath(const char* dataPathSuffix);
+        static std::string smiles(Molecule& m);
+        static std::string smiles(QueryMolecule& m);
     };
 }
diff --git a/core/indigo-core/tests/tests/molecule.cpp b/core/indigo-core/tests/tests/molecule.cpp
@@ -27,7 +27,6 @@
 #include <molecule/tpsa.h>
 
 #include "common.h"
-#include "molecule/elements.h"
 
 using namespace std;
 using namespace indigo;
@@ -306,3 +305,17 @@ TEST_F(IndigoCoreMoleculeTest, pKa)
         EXPECT_NEAR(6.5, Crippen::pKa(molecule), 0.01);
     }
 }
+
+TEST_F(IndigoCoreMoleculeTest, atom_reorder_query)
+{
+    QueryMolecule molecule;
+    loadQueryMolecule("[A:1][C:2](=[O:3])[OH1:4] |$R1;;;OH$|", molecule);
+    EXPECT_STREQ("*C([OH])=O |$R1;;OH;$|", smiles(molecule).c_str());
+}
+
+TEST_F(IndigoCoreMoleculeTest, atom_reorder_nonquery)
+{
+    Molecule molecule;
+    loadMolecule("SC(=N)O |$R1;;;OH$|", molecule);
+    EXPECT_STREQ("SC(O)=N |$R1;;OH;$|", smiles(molecule).c_str());
+}