Issue #520: core: replace RedBlackMap and RedBlackSet implementation

Partial implementation: replace RedBlackMap in BaseMolecule class
epam · Aug 4, 2022 · 2e952b6 · 2e952b6
1 parent 774ebd6
commit 2e952b6
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Showing 4 changed files with 20 additions and 19 deletions.
diff --git a/core/indigo-core/layout/src/molecule_layout.cpp b/core/indigo-core/layout/src/molecule_layout.cpp
@@ -71,7 +71,7 @@ void MoleculeLayout::_init(bool smart_layout)
 
                 // modify the atom mapping
                 for (int j = 0; j < _atomMapping.size(); ++j)
-                    if (atomMapCollapse.find(_atomMapping[j]))
+                    if (atomMapCollapse.find(_atomMapping[j]) != atomMapCollapse.end())
                         _atomMapping[j] = atomMapCollapse.at(_atomMapping[j]);
             }
         }

diff --git a/core/indigo-core/molecule/base_molecule.h b/core/indigo-core/molecule/base_molecule.h
@@ -33,6 +33,7 @@
 #include "molecule/molecule_standardize.h"
 #include "molecule/molecule_stereocenters.h"
 #include "molecule/molecule_tgroups.h"
+#include <map>
 #include <set>
 
 #ifdef _WIN32
@@ -104,7 +105,7 @@ namespace indigo
     class DLLEXPORT BaseMolecule : public Graph
     {
     public:
-        typedef RedBlackMap<int, int> Mapping;
+        typedef std::map<int, int> Mapping;
 
         BaseMolecule();
         ~BaseMolecule() override;
@@ -462,7 +463,7 @@ namespace indigo
         Array<int> _bond_directions;
 
         Array<Vec3f> _xyz;
-        RedBlackMap<int, Vec3f> _stereo_flag_positions;
+        std::map<int, Vec3f> _stereo_flag_positions;
 
         ObjArray<Array<int>> _rsite_attachment_points;
         bool _rGroupFragment;

diff --git a/core/indigo-core/molecule/src/base_molecule.cpp b/core/indigo-core/molecule/src/base_molecule.cpp
@@ -1231,10 +1231,10 @@ void BaseMolecule::collapse(BaseMolecule& bm, int id, Mapping& mapAtom, Mapping&
         int from = group.atoms[j];
         int to = group.atoms[k];
 
-        int* to_ = mapAtom.at2(from);
-        if (to_ == 0)
-            mapAtom.insert(from, to);
-        else if (*to_ != to)
+        auto it = mapAtom.find(from);
+        if (it == mapAtom.end())
+            mapAtom.emplace(from, to);
+        else if (it->second != to)
             throw Error("Invalid mapping in MultipleGroup::collapse");
 
         if (k != j)
@@ -1244,15 +1244,15 @@ void BaseMolecule::collapse(BaseMolecule& bm, int id, Mapping& mapAtom, Mapping&
     for (int j = bm.edgeBegin(); j < bm.edgeEnd(); j = bm.edgeNext(j))
     {
         const Edge& edge = bm.getEdge(j);
-        bool in1 = mapAtom.find(edge.beg), in2 = mapAtom.find(edge.end), p1 = in1 && mapAtom.at(edge.beg) == edge.beg,
-             p2 = in2 && mapAtom.at(edge.end) == edge.end;
+        bool in1 = mapAtom.find(edge.beg) != mapAtom.end(), in2 = mapAtom.find(edge.end) != mapAtom.end();
+        bool p1 = in1 && mapAtom.at(edge.beg) == edge.beg, p2 = in2 && mapAtom.at(edge.end) == edge.end;
         if ((in1 && !p1 && !in2) || (!in1 && !p2 && in2))
         {
             int beg = in1 ? mapAtom.at(edge.beg) : edge.beg;
             int end = in2 ? mapAtom.at(edge.end) : edge.end;
             int bid = copyBaseBond(bm, beg, end, j);
-            if (!mapBondInv.find(bid))
-                mapBondInv.insert(bid, j);
+            if (mapBondInv.find(bid) == mapBondInv.end())
+                mapBondInv.emplace(bid, j);
         }
     }
 
@@ -4137,7 +4137,7 @@ void BaseMolecule::setStereoFlagPosition(int frag_index, const Vec3f& pos)
 {
     try
     {
-        _stereo_flag_positions.insert(frag_index, pos);
+        _stereo_flag_positions.emplace(frag_index, pos);
     }
     catch (Exception& ex)
     {
@@ -4146,10 +4146,10 @@ void BaseMolecule::setStereoFlagPosition(int frag_index, const Vec3f& pos)
 
 bool BaseMolecule::getStereoFlagPosition(int frag_index, Vec3f& pos)
 {
-    auto pval = _stereo_flag_positions.at2(frag_index);
-    if (pval)
+    auto it = _stereo_flag_positions.find(frag_index);
+    if (it != _stereo_flag_positions.end())
     {
-        pos = *pval;
+        pos = it->second;
         return true;
     }
     return false;

diff --git a/core/render2d/src/render_internal.cpp b/core/render2d/src/render_internal.cpp
@@ -855,7 +855,7 @@ void MoleculeRenderInternal::_cloneAndFillMappings()
     _bondMappingInv.clear();
     for (int i = clone->edgeBegin(); i < clone->edgeEnd(); i = clone->edgeNext(i))
     {
-        _bondMappingInv.insert(i, BaseMolecule::findMappedEdge(*clone, *_mol, i, _atomMappingInv.ptr()));
+        _bondMappingInv.emplace(i, BaseMolecule::findMappedEdge(*clone, *_mol, i, _atomMappingInv.ptr()));
     }
     _mol = clone;
     _own_mol = true;
@@ -928,9 +928,9 @@ void MoleculeRenderInternal::_prepareSGroups()
                                     bid = amol.addBond(said, naid, amol.getBondOrder(nbid));
                                     amol.setEdgeTopology(bid, amol.getBondTopology(nbid));
                                 }
-                                if (_bondMappingInv.find(bid))
-                                    _bondMappingInv.remove(bid);
-                                _bondMappingInv.insert(bid, _bondMappingInv.at(nbid));
+                                if (_bondMappingInv.find(bid) != _bondMappingInv.end())
+                                    _bondMappingInv.erase(bid);
+                                _bondMappingInv.emplace(bid, _bondMappingInv.at(nbid));
                             }
                         }
                     }