Issue #521: core: replace MultiMap with standard library container

Partial implementation: replace MultiMap in MoleculeRGroupsComposition class - Part 2
epam · Dec 6, 2022 · d119d96 · d119d96
1 parent 1d1e43c
commit d119d96
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Showing 3 changed files with 19 additions and 18 deletions.
diff --git a/api/tests/integration/ref/composition/basic.py.out b/api/tests/integration/ref/composition/basic.py.out
@@ -367,15 +367,15 @@ molecule 01: C1(C2CCCC2)=C(C2CCCC2)C=CC=C1 |RG:_R1={C1CCCC1},{C1CCCC1}|
 		fragment 1: C1CCCC1
 		fragment 2: C1CCCC1
 ===================================================
-molecule 02: C1(C2CCCCC2)=C(C2CCCC2)C=CC=C1 |RG:_R1={C1CCCCC1},{C1CCCC1}|
+molecule 02: C1(C2CCCCC2)=C(C2CCCC2)C=CC=C1 |RG:_R1={C1CCCC1},{C1CCCCC1}|
 	rgroup 1
-		fragment 1: C1CCCCC1
-		fragment 2: C1CCCC1
+		fragment 1: C1CCCC1
+		fragment 2: C1CCCCC1
 ===================================================
-molecule 03: C1(C2=CC=CC=C2)=C(C2CCCC2)C=CC=C1 |RG:_R1={C1=CC=CC=C1},{C1CCCC1}|
+molecule 03: C1(C2=CC=CC=C2)=C(C2CCCC2)C=CC=C1 |RG:_R1={C1CCCC1},{C1=CC=CC=C1}|
 	rgroup 1
-		fragment 1: C1=CC=CC=C1
-		fragment 2: C1CCCC1
+		fragment 1: C1CCCC1
+		fragment 2: C1=CC=CC=C1
 ===================================================
 molecule 04: C1(C2CCCC2)=C(C2CCCCC2)C=CC=C1 |RG:_R1={C1CCCC1},{C1CCCCC1}|
 	rgroup 1
@@ -387,10 +387,10 @@ molecule 05: C1(C2CCCCC2)=C(C2CCCCC2)C=CC=C1 |RG:_R1={C1CCCCC1},{C1CCCCC1}|
 		fragment 1: C1CCCCC1
 		fragment 2: C1CCCCC1
 ===================================================
-molecule 06: C1(C2=CC=CC=C2)=C(C2CCCCC2)C=CC=C1 |RG:_R1={C1=CC=CC=C1},{C1CCCCC1}|
+molecule 06: C1(C2=CC=CC=C2)=C(C2CCCCC2)C=CC=C1 |RG:_R1={C1CCCCC1},{C1=CC=CC=C1}|
 	rgroup 1
-		fragment 1: C1=CC=CC=C1
-		fragment 2: C1CCCCC1
+		fragment 1: C1CCCCC1
+		fragment 2: C1=CC=CC=C1
 ===================================================
 molecule 07: C1(C2CCCC2)=C(C2=CC=CC=C2)C=CC=C1 |RG:_R1={C1CCCC1},{C1=CC=CC=C1}|
 	rgroup 1

diff --git a/core/indigo-core/molecule/molecule_rgroups_composition.h b/core/indigo-core/molecule/molecule_rgroups_composition.h
@@ -19,10 +19,10 @@
 #ifndef __molecule_rgroups_composition__
 #define __molecule_rgroups_composition__
 
+#include <map>
 #include <memory>
 
 #include "base_cpp/array.h"
-#include "base_cpp/multimap.h"
 #include "molecule/molecule.h"
 
 namespace indigo
@@ -240,13 +240,13 @@ namespace indigo
 
         inline Fragment _fragment_coordinates(int rsite, int fragment) const
         {
-            const RedBlackSet<int>& rs = _rsite2rgroup[_rsite2vertex.at(rsite)];
-
             int r = -1;
             int f = fragment;
-            for (int i = rs.begin(); i != rs.end(); i = rs.next(i))
+            const auto it_end = _rsite2rgroup.upper_bound(_rsite2vertex.at(rsite));
+
+            for (auto it = _rsite2rgroup.lower_bound(_rsite2vertex.at(rsite)); it != it_end; it++)
             {
-                r = rs.key(i);
+                r = it->second;
                 int size = _rgroup2size[r];
                 if (f >= size)
                 {
@@ -281,7 +281,7 @@ namespace indigo
 
         Array<int> _limits;
         Array<int> _rgroup2size;
-        MultiMap<int, int> _rsite2rgroup;
+        std::multimap<int, int> _rsite2rgroup;
         RedBlackMap<int, int> _rsite2vertex;
 
         mutable std::unique_ptr<Attachments> _ats;

diff --git a/core/indigo-core/molecule/src/molecule_rgroups_composition.cpp b/core/indigo-core/molecule/src/molecule_rgroups_composition.cpp
@@ -16,8 +16,6 @@
  * limitations under the License.
  ***************************************************************************/
 
-#include <map>
-
 #include "base_cpp/array.h"
 #include "molecule/base_molecule.h"
 
@@ -44,7 +42,10 @@ MoleculeRGroupsComposition::MoleculeRGroupsComposition(BaseMolecule& mol)
 
         Array<int> rgroups;
         _mol.getAllowedRGroups(vertex, rgroups);
-        _rsite2rgroup.insert(vertex, rgroups);
+        for (const auto& rgroup : rgroups)
+        {
+            _rsite2rgroup.emplace(vertex, rgroup);
+        }
 
         int total = 0;
         for (int i = 0; i < rgroups.size(); i++)