#1319 Directional bonds not work with SMART

Use constatnts for Biovia values
epam · Oct 13, 2023 · f6ee266 · f6ee266
1 parent 787ca28
commit f6ee266
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Showing 4 changed files with 27 additions and 18 deletions.
diff --git a/core/indigo-core/molecule/base_molecule.h b/core/indigo-core/molecule/base_molecule.h
@@ -82,6 +82,15 @@ namespace indigo
         BOND_EITHER = 3
     };
 
+    enum
+    {
+        BIOVIA_STEREO_NO = 0,
+        BIOVIA_STEREO_UP = 1,
+        BIOVIA_STEREO_DOUBLE_CISTRANS = 3,
+        BIOVIA_STEREO_ETHER = 4,
+        BIOVIA_STEREO_DOWN = 6,
+    }
+
     enum layout_orientation_value
     {
         UNCPECIFIED,

diff --git a/core/indigo-core/molecule/src/inchi_wrapper.cpp b/core/indigo-core/molecule/src/inchi_wrapper.cpp
@@ -261,15 +261,15 @@ void InchiWrapper::parseInchiOutput(const InchiOutput& inchi_output, Molecule& m
                 throw Molecule::Error("Indigo-InChI: ALTERN-typed bonds are not supported");
             int bond_idx = mol.addBond(atom_indices[i], atom_indices[nei], bond_order);
 
-            if (bond_stereo == 1)
+            if (bond_stereo == BIOVIA_STEREO_UP)
                 mol.setBondDirection(bond_idx, BOND_UP);
-            else if (bond_stereo == 6)
+            else if (bond_stereo == BIOVIA_STEREO_DOWN)
                 mol.setBondDirection(bond_idx, BOND_DOWN);
-            else if (bond_stereo == 4)
+            else if (bond_stereo == BIOVIA_STEREO_ETHER)
                 mol.setBondDirection(bond_idx, BOND_EITHER);
-            else if (bond_stereo == 3)
+            else if (bond_stereo == BIOVIA_STEREO_DOUBLE_CISTRANS)
                 mol.cis_trans.ignore(bond_idx);
-            else if (bond_stereo != 0)
+            else if (bond_stereo != BIOVIA_STEREO_NO)
                 throw Error("unknown number for bond stereo: %d", bond_stereo);
         }
     }

diff --git a/core/indigo-core/molecule/src/molecule_json_loader.cpp b/core/indigo-core/molecule/src/molecule_json_loader.cpp
@@ -633,26 +633,26 @@ void MoleculeJsonLoader::parseBonds(const rapidjson::Value& bonds, BaseMolecule&
             int direction = 0;
             if (_pqmol && stereo && order == BOND_SINGLE)
             {
-                if (stereo == 1)
+                if (stereo == BIOVIA_STEREO_UP)
                     direction = BOND_UP;
-                else if (stereo == 6)
+                else if (stereo == BIOVIA_STEREO_DOWN)
                     direction = BOND_DOWN;
             }
             bond_idx = _pmol ? _pmol->addBond_Silent(a1, a2, order) : addBondToMoleculeQuery(a1, a2, order, topology, direction);
             if (stereo)
             {
                 switch (stereo)
                 {
-                case 1:
+                case BIOVIA_STEREO_UP:
                     mol.setBondDirection(bond_idx, BOND_UP);
                     break;
-                case 3:
+                case BIOVIA_STEREO_DOUBLE_CISTRANS:
                     mol.cis_trans.ignore(bond_idx);
                     break;
-                case 4:
+                case BIOVIA_STEREO_ETHER:
                     mol.setBondDirection(bond_idx, BOND_EITHER);
                     break;
-                case 6:
+                case BIOVIA_STEREO_DOWN:
                     mol.setBondDirection(bond_idx, BOND_DOWN);
                     break;
                 default:

diff --git a/core/indigo-core/molecule/src/molfile_loader.cpp b/core/indigo-core/molecule/src/molfile_loader.cpp
@@ -587,22 +587,22 @@ void MolfileLoader::_readCtab2000()
         else
         {
             int direction = 0;
-            if (stereo == 1)
+            if (stereo == BIOVIA_STEREO_UP)
                 direction = BOND_UP;
-            else if (stereo == 6)
+            else if (stereo == BIOVIA_STEREO_DOWN)
                 direction = BOND_DOWN;
             _qmol->addBond(beg - 1, end - 1, QueryMolecule::createQueryMoleculeBond(order, topology, direction));
         }
 
-        if (stereo == 1)
+        if (stereo == BIOVIA_STEREO_UP)
             _bmol->setBondDirection(bond_idx, BOND_UP);
-        else if (stereo == 6)
+        else if (stereo == BIOVIA_STEREO_DOWN)
             _bmol->setBondDirection(bond_idx, BOND_DOWN);
-        else if (stereo == 4)
+        else if (stereo == BIOVIA_STEREO_ETHER)
             _bmol->setBondDirection(bond_idx, BOND_EITHER);
-        else if (stereo == 3)
+        else if (stereo == BIOVIA_STEREO_DOUBLE_CISTRANS)
             _ignore_cistrans[bond_idx] = 1;
-        else if (stereo != 0)
+        else if (stereo != BIOVIA_STEREO_NO)
             throw Error("unknown number for bond stereo: %d", stereo);
 
         _bmol->reaction_bond_reacting_center[bond_idx] = rcenter;