atrop layout

epam · Sep 14, 2023 · e97f85e · e97f85e
1 parent 0bb224e
commit e97f85e
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Showing 5 changed files with 23 additions and 8 deletions.
diff --git a/api/c/indigo/src/indigo_layout.cpp b/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 = 1.6f;
             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();

diff --git a/core/indigo-core/layout/src/molecule_layout.cpp b/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)

diff --git a/core/indigo-core/molecule/base_molecule.h b/core/indigo-core/molecule/base_molecule.h
@@ -421,6 +421,7 @@ 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);

diff --git a/core/indigo-core/molecule/src/base_molecule.cpp b/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);

diff --git a/core/indigo-core/molecule/src/molecule_stereocenters.cpp b/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)