#1272 After opening a saved Extended SMILES file Single Up Bond is changed to Single Down Bond (#1273)

Author: even1024

api/c/indigo/src/indigo_layout.cpp

@@ -58,6 +58,9 @@ CEXPORT int indigoLayout(int object)
             ml.max_iterations = self.layout_max_iterations;
             ml.bond_length = MoleculeLayout::DEFAULT_BOND_LENGTH;
             ml.layout_orientation = (layout_orientation_value)self.layout_orientation;
+            bool has_atropisomery = mol->hasAtropisomericCenter();
+            if (has_atropisomery)
+                ml.respect_existing_layout = true;
 
             TimeoutCancellationHandler cancellation(self.cancellation_timeout);
             ml.setCancellationHandler(&cancellation);
@@ -66,8 +69,8 @@ CEXPORT int indigoLayout(int object)
 
             if (obj.type != IndigoObject::SUBMOLECULE)
             {
-                // Not for submolecule yet
-                mol->clearBondDirections();
+                if (!has_atropisomery)
+                    mol->clearBondDirections();
                 try
                 {
                     mol->markBondsStereocenters();

api/tests/integration/ref/formats/smiles.py.out

@@ -74,3 +74,4 @@ CCCCC |Sg:n:1,2,3::hh|
 *** Atropisomers ***
 atropisomer:
 C1=CC=C(C)C(C2=C(N)C=C(C)C=C2)=C1O |o1:5,r,wU:5.4|
+C1=CC=C(C)C(C2=C(N)C=C(C)C=C2)=C1O |o1:5,r,wU:5.4|

api/tests/integration/tests/formats/smiles.py

@@ -120,4 +120,7 @@
 mols_smiles = ["C1C(O)=C(C2C=CC(C)=CC=2N)C(C)=CC=1 |o1:3,r,wU:3.12|"]
 for sm in mols_smiles:
     print("atropisomer:")
-    print(indigo.loadMolecule(sm).smiles())
+    mol = indigo.loadMolecule(sm)
+    print(mol.smiles())
+    mol.layout()
+    print(mol.smiles())

core/indigo-core/layout/src/molecule_layout.cpp

@@ -26,7 +26,7 @@ using namespace indigo;
 
 IMPL_ERROR(MoleculeLayout, "molecule_layout");
 
-MoleculeLayout::MoleculeLayout(BaseMolecule& molecule, bool smart_layout) : _molecule(molecule), _smart_layout(smart_layout)
+MoleculeLayout::MoleculeLayout(BaseMolecule& molecule, bool smart_layout) : _molecule(molecule), _smart_layout(smart_layout), respect_existing_layout(false)
 {
     _hasMulGroups = _molecule.sgroups.getSGroupCount(SGroup::SG_TYPE_MUL) > 0;
     _init(smart_layout);
@@ -36,7 +36,6 @@ MoleculeLayout::MoleculeLayout(BaseMolecule& molecule, bool smart_layout) : _mol
 void MoleculeLayout::_init(bool smart_layout)
 {
     bond_length = 1.f;
-    respect_existing_layout = false;
     filter = 0;
     _smart_layout = smart_layout;
     if (_smart_layout)

core/indigo-core/molecule/base_molecule.h

@@ -426,6 +426,7 @@ namespace indigo
         const int* getPyramidStereocenters(int idx) const;
         void markBondsStereocenters();
         void markBondStereocenters(int atom_idx);
+        bool hasAtropisomericCenter();
 
         void addStereocenters(int atom_idx, int type, int group, const int pyramid[4]);
         void addStereocenters(int atom_idx, int type, int group, bool inverse_pyramid);

core/indigo-core/molecule/src/base_molecule.cpp

@@ -4196,6 +4196,17 @@ void BaseMolecule::markBondsStereocenters()
     stereocenters.markBonds(*this);
 }
 
+bool BaseMolecule::hasAtropisomericCenter()
+{
+    for (int i = stereocenters.begin(); i != stereocenters.end(); i = stereocenters.next(i))
+    {
+        auto atom_idx = stereocenters.getAtomIndex(i);
+        if (stereocenters.isAtropisomeric(atom_idx))
+            return true;
+    }
+    return false;
+}
+
 void BaseMolecule::markBondStereocenters(int atom_idx)
 {
     stereocenters.markBond(*this, atom_idx);

core/indigo-core/molecule/src/molecule_stereocenters.cpp

@@ -1676,10 +1676,11 @@ void MoleculeStereocenters::markBond(BaseMolecule& baseMolecule, int atom_idx)
 
 void MoleculeStereocenters::markBonds(BaseMolecule& baseMolecule)
 {
-    int i;
-
-    for (i = _stereocenters.begin(); i != _stereocenters.end(); i = _stereocenters.next(i))
-        markBond(baseMolecule, _stereocenters.key(i));
+    for (int i = _stereocenters.begin(); i != _stereocenters.end(); i = _stereocenters.next(i))
+    {
+        if (!_stereocenters.value(i).is_atropisomeric)
+            markBond(baseMolecule, _stereocenters.key(i));
+    }
 }
 
 bool MoleculeStereocenters::isAutomorphism(BaseMolecule& mol, const Array<int>& mapping, const Filter* filter)