#1322 Reaction cannon be saved

Add 'original_format' support to reactions Add UTs
epam · Oct 12, 2023 · ef6afe7 · ef6afe7
1 parent 5ee0dbc
commit ef6afe7
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Showing 10 changed files with 98 additions and 33 deletions.
diff --git a/api/c/indigo/src/indigo_misc.cpp b/api/c/indigo/src/indigo_misc.cpp
@@ -1484,3 +1484,51 @@ CEXPORT const char* indigoJson(int item)
     }
     INDIGO_END(0);
 }
+
+CEXPORT const char* indigoGetOriginalFormat(int item)
+{
+    INDIGO_BEGIN
+    {
+        IndigoObject& obj = self.getObject(item);
+        int original_format = BaseMolecule::UNKNOWN;
+        if (IndigoBaseMolecule::is(obj))
+        {
+            BaseMolecule& mol = obj.getBaseMolecule();
+            original_format = mol.original_format;
+        }
+        else if (IndigoBaseReaction::is(obj))
+        {
+            BaseReaction& rxn = obj.getBaseReaction();
+            original_format = rxn.original_format;
+        }
+        else
+            throw IndigoError("indigoSaveJson(): expected molecule, got %s", obj.debugInfo());
+
+        switch (original_format)
+        {
+        case BaseMolecule::CML:
+            return "chemical/x-cml";
+        case BaseMolecule::CDXML:
+            return "chemical/x-cdxml";
+        case BaseMolecule::CDX:
+            return "chemical/x-cdx";
+        case BaseMolecule::RDF:
+            return "chemical/x-mdl-rdfile";
+        case BaseMolecule::SMILES:
+            return "chemical/x-daylight-smiles";
+        case BaseMolecule::CXSMILES:
+            return "chemical/x-chemaxon-cxsmiles";
+        case BaseMolecule::SMARTS:
+            return "chemical/x-daylight-smarts";
+        case BaseMolecule::MOL:
+            return "chemical/x-mdl-molfile";
+        case BaseMolecule::RXN:
+            return "chemical/x-mdl-rxnfile";
+        case BaseMolecule::KET:
+            return "chemical/x-indigo-ket";
+        default:
+            return "unknown";
+        }
+    }
+    INDIGO_END(0);
+}
diff --git a/api/c/indigo/src/indigo_molecule.cpp b/api/c/indigo/src/indigo_molecule.cpp
@@ -3784,34 +3784,6 @@ CEXPORT int indigoCountComponentBonds(int molecule, int index)
     INDIGO_END(-1);
 }
 
-CEXPORT const char* indigoGetOriginalFormat(int item)
-{
-    INDIGO_BEGIN
-    {
-        IndigoObject& obj = self.getObject(item);
-        if (IndigoBaseMolecule::is(obj))
-        {
-            BaseMolecule& mol = obj.getBaseMolecule();
-            switch (mol.original_format)
-            {
-            case BaseMolecule::SMARTS:
-                return "chemical/x-daylight-smarts";
-            case BaseMolecule::SMILES:
-                return "chemical/x-daylight-smiles";
-            case BaseMolecule::MOL:
-                return "chemical/x-mdl-molfile";
-            case BaseMolecule::RXN:
-                return "chemical/x-mdl-rxnfile";
-            default:
-                return "unknown";
-            }
-        }
-        else
-            throw IndigoError("indigoSaveJson(): expected molecule, got %s", obj.debugInfo());
-    }
-    INDIGO_END(0);
-}
-
 CEXPORT int indigoCreateMolecule()
 {
     INDIGO_BEGIN

diff --git a/api/tests/integration/ref/basic/get_original_format.py.out b/api/tests/integration/ref/basic/get_original_format.py.out
@@ -2,3 +2,7 @@
 Molecule "N[CH](C)C(=O)O" : got "chemical/x-daylight-smiles" - OK
 ******  Test get original format: smarts  ***
 Molecule "([#6]1-[#6]-[#6]-1.[#6])" : got "chemical/x-daylight-smarts" - OK
+******  Test get original format: reaction  ***
+Molecule "N[CH](C)C(=O)O>>N[CH](C)C" : got "chemical/x-daylight-smiles" - OK
+******  Test get original format: reaction smarts  ***
+Molecule "([#6]1-[#6]-[#6]-1.[#6])>>([#6]1-[#6]-[#6]-1.[#6]=O)" : got "chemical/x-daylight-smarts" - OK
diff --git a/api/tests/integration/tests/basic/get_original_format.py b/api/tests/integration/tests/basic/get_original_format.py
@@ -11,14 +11,14 @@
 indigo = Indigo()
 
 
-def test_mol(molecule, mol, expected):
-    original_format = mol.getOriginalFormat()
+def test_mol(smarts, obj, expected):
+    original_format = obj.getOriginalFormat()
     if original_format == expected:
-        print('Molecule "%s" : got "%s" - OK' % (molecule, expected))
+        print('Molecule "%s" : got "%s" - OK' % (smarts, expected))
     else:
         print(
             'Molecule "%s" failed: expected original format "%s", got "%s"'
-            % (molecule, expected, original_format)
+            % (smarts, expected, original_format)
         )
 
 
@@ -31,3 +31,13 @@ def test_mol(molecule, mol, expected):
 molecule = "([#6]1-[#6]-[#6]-1.[#6])"
 mol = indigo.loadSmarts(molecule)
 test_mol(molecule, mol, "chemical/x-daylight-smarts")
+
+print("******  Test get original format: reaction  ***")
+molecule = "N[CH](C)C(=O)O>>N[CH](C)C"
+mol = indigo.loadReaction(molecule)
+test_mol(molecule, mol, "chemical/x-daylight-smiles")
+
+print("******  Test get original format: reaction smarts  ***")
+molecule = "([#6]1-[#6]-[#6]-1.[#6])>>([#6]1-[#6]-[#6]-1.[#6]=O)"
+mol = indigo.loadReactionSmarts(molecule)
+test_mol(molecule, mol, "chemical/x-daylight-smarts")
diff --git a/api/wasm/indigo-ketcher/test/test.js b/api/wasm/indigo-ketcher/test/test.js
@@ -512,6 +512,23 @@ M  END
             options.delete();
         });
 
+        test("convert", "rsmiles-app-json", () => {
+            let options = new indigo.MapStringString();
+            options.set("output-content-type", "application/json");
+            const rsmiles = indigo.convert(rxn_smiles, "smiles", options);
+            assert.equal(rsmiles, '{"struct":"C1C=CC=CC=1.N>>C1N=CC=CC=1.[CH3-]","format":"smiles","original_format":"chemical/x-daylight-smiles"}');
+            options.delete();
+        });
+
+        test("convert", "rsmiles-input-format-smarts", () => {
+            let options = new indigo.MapStringString();
+            options.set("output-content-type", "application/json");
+            options.set("input-format", "chemical/x-daylight-smarts");
+            const rsmiles = indigo.convert(rxn_smiles, "smiles", options);
+            assert.equal(rsmiles, '{"struct":"C1C=CC=CC=1.N>>C1N=CC=CC=1.[CH3-]","format":"smiles","original_format":"chemical/x-daylight-smarts"}');
+            options.delete();
+        });
+
     }
 
 

diff --git a/core/indigo-core/molecule/src/molecule_json_loader.cpp b/core/indigo-core/molecule/src/molecule_json_loader.cpp
@@ -1061,6 +1061,7 @@ void MoleculeJsonLoader::loadMolecule(BaseMolecule& mol, bool load_arrows)
         {
             _pmol = &pmol->asMolecule();
         }
+        mol.original_format = BaseMolecule::KET;
 
         auto& mol_node = _mol_nodes[node_idx];
         if (mol_node.HasMember("atoms"))

diff --git a/core/indigo-core/reaction/base_reaction.h b/core/indigo-core/reaction/base_reaction.h
@@ -321,6 +321,8 @@ namespace indigo
 
         Array<char> name;
 
+        int original_format;
+
         DECL_ERROR;
 
     protected:

diff --git a/core/indigo-core/reaction/src/base_reaction.cpp b/core/indigo-core/reaction/src/base_reaction.cpp
@@ -91,7 +91,8 @@ SideIter SideAuto::end()
 }
 
 BaseReaction::BaseReaction()
-    : reactants(*this, REACTANT), catalysts(*this, CATALYST), products(*this, PRODUCT), intermediates(*this, INTERMEDIATE), undefined(*this, UNDEFINED)
+    : reactants(*this, REACTANT), catalysts(*this, CATALYST), products(*this, PRODUCT), intermediates(*this, INTERMEDIATE), undefined(*this, UNDEFINED),
+      original_format(BaseMolecule::UNKNOWN)
 {
     clear();
 }

diff --git a/core/indigo-core/reaction/src/reaction_json_loader.cpp b/core/indigo-core/reaction/src/reaction_json_loader.cpp
@@ -68,6 +68,8 @@ void ReactionJsonLoader::loadReaction(BaseReaction& rxn)
     else
         throw Error("unknown reaction type: %s", typeid(rxn).name());
 
+    rxn.original_format = BaseMolecule::KET;
+
     rxn.meta().clone(_pmol->meta());
     _pmol->meta().resetMetaData();
 

diff --git a/core/indigo-core/reaction/src/rsmiles_loader.cpp b/core/indigo-core/reaction/src/rsmiles_loader.cpp
@@ -64,6 +64,10 @@ void RSmilesLoader::loadReaction(Reaction& reaction)
     _rxn = &reaction;
     _brxn = &reaction;
     _qrxn = 0;
+    if (smarts_mode)
+        reaction.original_format = BaseMolecule::SMARTS;
+    else
+        reaction.original_format = BaseMolecule::SMILES;
     _loadReaction();
 }
 
@@ -72,6 +76,10 @@ void RSmilesLoader::loadQueryReaction(QueryReaction& rxn)
     _rxn = 0;
     _brxn = &rxn;
     _qrxn = &rxn;
+    if (smarts_mode)
+        rxn.original_format = BaseMolecule::SMARTS;
+    else
+        rxn.original_format = BaseMolecule::SMILES;
     _loadReaction();
 }