#3604 Add api methods to interact with atoms and bonds in s-groups (#3625)

Author: even1024

api/c/indigo/indigo.h

@@ -614,6 +614,12 @@ CEXPORT int indigoGetSGroupNumCrossBonds(int sgroup);
 CEXPORT int indigoCreateCrossBonds(int sgroup);
 CEXPORT int indigoClearSGroupCrossBonds(int sgroup);
 
+// Issue #3604: New SGroup API methods
+CEXPORT int indigoAddSGroup(int molecule, const char* type, int extindex);
+CEXPORT int indigoSetSGroupAtoms(int sgroup, int natoms, int* atoms);
+CEXPORT int indigoSetSGroupBonds(int sgroup, int nbonds, int* bonds);
+CEXPORT int indigoIterateSGroupCrossBonds(int sgroup);
+
 CEXPORT int indigoAddSGroupAttachmentPoint(int sgroup, int aidx, int lvidx, const char* apid);
 CEXPORT int indigoDeleteSGroupAttachmentPoint(int sgroup, int index);
 // Returns iterator of superatom attachment points (SAP entries) for a superatom S-group.

api/c/indigo/src/indigo_abbreviations_expand.cpp

@@ -762,7 +762,7 @@ namespace indigo
 
             int sid = mol.sgroups.addSGroup(SGroup::SG_TYPE_SUP);
             Superatom& super = (Superatom&)mol.sgroups.getSGroup(sid);
-            super.subscript.readString(mol.getPseudoAtom(v), true);
+            super.label.readString(mol.getPseudoAtom(v), true);
             for (int ve = expanded.vertexBegin(); ve != expanded.vertexEnd(); ve = expanded.vertexNext(ve))
                 super.atoms.push(mapping[ve]);
 

api/c/indigo/src/indigo_molecule.cpp

@@ -1188,7 +1188,7 @@ IndigoObject* IndigoSGroupAtomsIter::next()
     return new IndigoAtom(_mol, _sgroup.atoms[_idx]);
 }
 
-IndigoSGroupBondsIter::IndigoSGroupBondsIter(BaseMolecule& mol, SGroup& sgroup) : IndigoObject(SGROUP_ATOMS_ITER), _mol(mol), _sgroup(sgroup)
+IndigoSGroupBondsIter::IndigoSGroupBondsIter(BaseMolecule& mol, SGroup& sgroup) : IndigoObject(SGROUP_BONDS_ITER), _mol(mol), _sgroup(sgroup)
 {
     _idx = -1;
 }
@@ -1199,7 +1199,7 @@ IndigoSGroupBondsIter::~IndigoSGroupBondsIter()
 
 bool IndigoSGroupBondsIter::hasNext()
 {
-    return _idx + 1 < _sgroup.bonds.size();
+    return _idx + 1 < _sgroup.getBonds().size();
 }
 
 IndigoObject* IndigoSGroupBondsIter::next()
@@ -1208,7 +1208,30 @@ IndigoObject* IndigoSGroupBondsIter::next()
         return 0;
 
     _idx++;
-    return new IndigoBond(_mol, _sgroup.bonds[_idx]);
+    return new IndigoBond(_mol, _sgroup.getBonds()[_idx]);
+}
+
+IndigoSGroupXBondsIter::IndigoSGroupXBondsIter(BaseMolecule& mol, SGroup& sgroup) : IndigoObject(SGROUP_BONDS_ITER), _mol(mol), _sgroup(sgroup)
+{
+    _idx = -1;
+}
+
+IndigoSGroupXBondsIter::~IndigoSGroupXBondsIter()
+{
+}
+
+bool IndigoSGroupXBondsIter::hasNext()
+{
+    return _idx + 1 < _sgroup.xbonds.size();
+}
+
+IndigoObject* IndigoSGroupXBondsIter::next()
+{
+    if (!hasNext())
+        return 0;
+
+    _idx++;
+    return new IndigoBond(_mol, _sgroup.xbonds[_idx]);
 }
 
 int _indigoIterateAtoms(Indigo& self, int molecule, int type)
@@ -1352,7 +1375,7 @@ CEXPORT int indigoCountBonds(int molecule)
 
         auto sg = _getSGroupFromObject(obj);
         if (sg)
-            return sg.get().bonds.size();
+            return sg.get().getBonds().size();
 
         BaseMolecule& mol = obj.getBaseMolecule();
 

api/c/indigo/src/indigo_molecule.h

@@ -559,6 +559,22 @@ class IndigoSGroupBondsIter : public IndigoObject
     int _idx;
 };
 
+// Iterates xbonds (crossing bonds) directly, not polymorphic getBonds()
+class IndigoSGroupXBondsIter : public IndigoObject
+{
+public:
+    IndigoSGroupXBondsIter(BaseMolecule& mol, SGroup& sgroup);
+    ~IndigoSGroupXBondsIter() override;
+
+    IndigoObject* next() override;
+    bool hasNext() override;
+
+protected:
+    BaseMolecule& _mol;
+    SGroup& _sgroup;
+    int _idx;
+};
+
 class IndigoMoleculeComponent : public IndigoObject
 {
 public: