epam · even1024 · Aug 5, 2022 · Aug 5, 2022 · Aug 5, 2022 · Aug 5, 2022
diff --git a/api/c/bingo-nosql/src/bingo_container_set.cpp b/api/c/bingo-nosql/src/bingo_container_set.cpp
@@ -195,7 +195,7 @@ int ContainerSet::_findSimilarInc(const byte* query, SimCoef& sim_coef, double m
         if (coef < min_coef)
             continue;
 
-        sim_indices.push(SimResult(indices[i], (float)coef));
+        sim_indices.push_back(SimResult(indices[i], (float)coef));
     }
 
     return sim_indices.size();

diff --git a/api/c/bingo-nosql/src/bingo_matcher.cpp b/api/c/bingo-nosql/src/bingo_matcher.cpp
@@ -1053,9 +1053,7 @@ void TopNSimMatcher::_findTopN()
             while (BaseSimilarityMatcher::next())
             {
                 cnt++;
-                res = &_current_results.push();
-                res->id = _current_id;
-                res->sim_value = _current_sim_value;
+                res = &_current_results.emplace_back(_current_id, _current_sim_value);
                 cur_cell = currentCell();
                 if ((cnt > hits_limit * 2) && ((max_cell - cur_cell) > cells_count / 2))
                 {
@@ -1109,9 +1107,7 @@ void TopNSimMatcher::_findTopN()
             while (BaseSimilarityMatcher::next())
             {
                 cnt++;
-                res = &_current_results.push();
-                res->id = _current_id;
-                res->sim_value = _current_sim_value;
+                res = &_current_results.emplace_back(_current_id, _current_sim_value);
 
                 if (cnt > hits_limit * 2)
                 {
@@ -1186,9 +1182,7 @@ void TopNSimMatcher::_findTopN()
                 while (BaseSimilarityMatcher::next())
                 {
                     cnt++;
-                    res = &_current_results.push();
-                    res->id = _current_id;
-                    res->sim_value = _current_sim_value;
+                    res = &_current_results.emplace_back(_current_id, _current_sim_value);
                     cur_cell = currentCell();
                     if ((cnt > hits_limit * 2) && (max_cell - cur_cell) > cells_count / 2)
                     {
@@ -1246,7 +1240,7 @@ void TopNSimMatcher::_findTopN()
         for (i = 0; i < _current_results.size(); i++)
         {
             _result_ids.push(_current_results[i].id);
-            _result_sims.push(_current_results[i].sim_value);
+            _result_sims.push_back(_current_results[i].sim_value);
 
             if (i == (hits_limit - 1))
                 break;
@@ -1268,7 +1262,7 @@ void TopNSimMatcher::_initModelDistribution(Array<float>& model_thrs, Array<int>
 {
     for (int i = 0; i < 9; i++)
     {
-        model_thrs.push(_2FLOAT(1.0 - 0.1 * (i + 1)));
+        model_thrs.push_back(_2FLOAT(1.0 - 0.1 * (i + 1)));
         model_nhits_per_block.push(5 * 2 ^ (i));
     }
 }

diff --git a/api/c/bingo-nosql/src/bingo_multibit_tree.cpp b/api/c/bingo-nosql/src/bingo_multibit_tree.cpp
@@ -137,7 +137,7 @@ void MultibitTree::_build()
 
     QS_DEF(Array<bool>, is_mb);
     is_mb.clear_resize(_fp_size * 8);
-    is_mb.zerofill();
+    is_mb.fill(false);
 
     _tree_ptr = _buildNode(indices, is_mb, 0);
 }
@@ -160,7 +160,7 @@ void MultibitTree::_findLinear(_MultibitNode* node, const byte* query, int query
         if (coef < min_coef)
             continue;
 
-        sim_indices.push(SimResult(indices[fp_indices[i]], (float)coef));
+        sim_indices.push_back(SimResult(indices[fp_indices[i]], (float)coef));
     }
 }
 
@@ -207,9 +207,9 @@ void MultibitTree::_findSimilarInNode(MMFPtr<_MultibitNode> node_ptr, const byte
         _findSimilarInNode(node->right, query, query_bit_number, sim_coef, min_coef, right_indices, right_m01, right_m10);
 
     for (int i = 0; i < left_indices.size(); i++)
-        sim_indices.push(left_indices[i]);
+        sim_indices.push_back(left_indices[i]);
     for (int i = 0; i < right_indices.size(); i++)
-        sim_indices.push(right_indices[i]);
+        sim_indices.push_back(right_indices[i]);
 }
 
 MultibitTree::MultibitTree(int fp_size) : _fp_size(fp_size)

diff --git a/api/c/bingo-nosql/src/bingo_sim_coef.h b/api/c/bingo-nosql/src/bingo_sim_coef.h
@@ -10,6 +10,10 @@ namespace bingo
         int id;
         float sim_value;
 
+        SimResult() : id(0), sim_value(0)
+        {
+        }
+
         SimResult(int new_id, float new_sim_value) : id(new_id), sim_value(new_sim_value)
         {
         }

diff --git a/api/c/bingo-nosql/src/bingo_sim_storage.cpp b/api/c/bingo-nosql/src/bingo_sim_storage.cpp
@@ -118,7 +118,7 @@ int SimStorage::getIncSimilar(const byte* query, SimCoef& sim_coef, double min_c
             continue;
         size_t id = _inc_id_buffer[i];
 
-        sim_fp_indices.push(SimResult(id, _2FLOAT(coef)));
+        sim_fp_indices.push_back(SimResult(id, _2FLOAT(coef)));
     }
 
     return sim_fp_indices.size();

diff --git a/api/c/bingo-nosql/src/mmf/mmf_mapping.cpp b/api/c/bingo-nosql/src/mmf/mmf_mapping.cpp
@@ -36,7 +36,7 @@ void MMFMapping::getAll(size_t id1, Array<size_t>& id2_array)
         for (i = 0; i < it->count; i++)
         {
             if (it->buf[i].first == id1)
-                id2_array.push(it->buf[i].second);
+                id2_array.push_back(it->buf[i].second);
         }
     }
 }

diff --git a/api/c/indigo-inchi/CMakeLists.txt b/api/c/indigo-inchi/CMakeLists.txt
@@ -12,7 +12,7 @@ target_include_directories(${PROJECT_NAME}-object
 
 if (NOT EMSCRIPTEN)
     add_library(${PROJECT_NAME} SHARED $<TARGET_OBJECTS:${PROJECT_NAME}-object>)
-    target_link_libraries(${PROJECT_NAME} PRIVATE indigo indigo-core)
+    target_link_libraries(${PROJECT_NAME} PRIVATE indigo)
     target_include_directories(${PROJECT_NAME}
             PUBLIC ${CMAKE_CURRENT_SOURCE_DIR}/)
 

diff --git a/api/c/indigo/src/indigo_abbreviations_expand.cpp b/api/c/indigo/src/indigo_abbreviations_expand.cpp
@@ -687,19 +687,19 @@ namespace indigo
 
             if (on_right && !on_left)
             {
-                options.push(Options(RIGHT, RIGHT));
-                options.push(Options(LEFT, LEFT));
+                options.push_back(Options(RIGHT, RIGHT));
+                options.push_back(Options(LEFT, LEFT));
             }
             else
             {
                 if (on_right)
-                    options.push(Options(RIGHT, RIGHT));
+                    options.push_back(Options(RIGHT, RIGHT));
                 if (on_left)
                 {
-                    options.push(Options(LEFT, LEFT));
-                    options.push(Options(LEFT, RIGHT));
-                    options.push(Options(RIGHT, RIGHT));
-                    options.push(Options(LEFT, LEFT, 2));
+                    options.push_back(Options(LEFT, LEFT));
+                    options.push_back(Options(LEFT, RIGHT));
+                    options.push_back(Options(RIGHT, RIGHT));
+                    options.push_back(Options(LEFT, LEFT, 2));
                 }
             }
 
@@ -709,7 +709,7 @@ namespace indigo
             {
                 Options opt = options[i];
                 opt.ignore_case = true;
-                options.push(opt);
+                options.push_back(opt);
             }
 
             bool found = false;

diff --git a/api/c/indigo/src/indigo_deconvolution.cpp b/api/c/indigo/src/indigo_deconvolution.cpp
@@ -1035,6 +1035,11 @@ IndigoDecompositionMatch::IndigoDecompositionMatch() : IndigoObject(DECOMPOSITIO
 {
 }
 
+IndigoDecompositionMatch::IndigoDecompositionMatch(const IndigoDecompositionMatch& other) : IndigoObject(DECOMPOSITION_MATCH), deco(0), _completeScaffold(false)
+{
+    copy(const_cast<IndigoDecompositionMatch&>(other));
+}
+
 bool IndigoDeconvolution::_matchAtoms(Graph& g1, Graph& g2, const int*, int sub_idx, int super_idx, void* userdata)
 {
     if (userdata == 0)

diff --git a/api/c/indigo/src/indigo_deconvolution.h b/api/c/indigo/src/indigo_deconvolution.h
@@ -171,6 +171,8 @@ class DLLEXPORT IndigoDecompositionMatch : public IndigoObject
 {
 public:
     IndigoDecompositionMatch();
+    IndigoDecompositionMatch(const IndigoDecompositionMatch& other);
+
     Array<int> visitedAtoms;
     Array<int> scaffoldBonds;
     Array<int> scaffoldAtoms;
@@ -196,10 +198,6 @@ class DLLEXPORT IndigoDecompositionMatch : public IndigoObject
     Molecule mol_scaffold;
 
     IndigoDeconvolution* deco;
-
-private:
-    IndigoDecompositionMatch(const IndigoDecompositionMatch&); // no implicit copy
-
     bool _completeScaffold;
 };
 

diff --git a/api/c/indigo/src/indigo_molecule.cpp b/api/c/indigo/src/indigo_molecule.cpp
@@ -2051,8 +2051,8 @@ CEXPORT float indigoAlignAtoms(int molecule, int natoms, int* atom_ids, float* d
 
         for (i = 0; i < natoms; i++)
         {
-            points.push(mol.getAtomXyz(atom_ids[i]));
-            goals.push(Vec3f(desired_xyz[i * 3], desired_xyz[i * 3 + 1], desired_xyz[i * 3 + 2]));
+            points.push_back(mol.getAtomXyz(atom_ids[i]));
+            goals.push_back(Vec3f(desired_xyz[i * 3], desired_xyz[i * 3 + 1], desired_xyz[i * 3 + 2]));
         }
 
         if (points.size() < 1)
@@ -3307,13 +3307,13 @@ CEXPORT int indigoSetSGroupBrackets(int sgroup, int brk_style, float x1, float y
 
         psg->brk_style = brk_style;
         psg->brackets.clear();
-        Vec2f* brackets = psg->brackets.push();
+        std::array<Vec2f, 2> brackets;
         brackets[0].set(x1, y1);
         brackets[1].set(x2, y2);
-        brackets = psg->brackets.push();
+        psg->brackets.push_back(brackets);
         brackets[0].set(x3, y3);
         brackets[1].set(x4, y4);
-
+        psg->brackets.push_back(brackets);
         return 1;
     }
     INDIGO_END(-1);

diff --git a/api/c/indigo/src/indigo_object.cpp b/api/c/indigo/src/indigo_object.cpp
@@ -25,7 +25,7 @@
 #include "reaction/reaction.h"
 
 using IndigoObjectTypesMap = std::map<int, const char* const>;
-class IndigoObjectTypes : public IndigoObjectTypesMap, public NonCopyable
+class IndigoObjectTypes : public IndigoObjectTypesMap
 {
 public:
     IndigoObjectTypes();

diff --git a/bingo/oracle/src/oracle/bingo_fingerprints.cpp b/bingo/oracle/src/oracle/bingo_fingerprints.cpp
@@ -110,7 +110,7 @@ void BingoFingerprints::addFingerprint(OracleEnv& env, const byte* fp)
         }
         ptr += 8 * _chunk_qwords;
     }
-    _pending_block.mapping.push(_pending_block.mapping.size());
+    _pending_block.mapping.push_back(_pending_block.mapping.size());
     _pending_block.used++;
 }
 

diff --git a/bingo/oracle/src/oracle/bingo_storage.cpp b/bingo/oracle/src/oracle/bingo_storage.cpp
@@ -115,7 +115,7 @@ void BingoStorage::validateForInsert(OracleEnv& env)
             continue;
         }
 
-        _Block& block = _blocks.push();
+        _Block& block = _blocks.emplace_back();
 
         block.size = length;
     } while (statement.fetch());
@@ -244,7 +244,7 @@ void BingoStorage::validate(OracleEnv& env)
                 _index.copy((_Addr*)_shmem_array[0]->ptr(), length / sizeof(_Addr));
         }
 
-        _Block& block = _blocks.push();
+        _Block& block = _blocks.emplace_back();
 
         block.size = length;
     } while (statement.fetch());
@@ -305,7 +305,7 @@ void BingoStorage::_insertLOB(OracleEnv& env, int no)
 
     if (no > 0)
     {
-        _Block& block = _blocks.push();
+        _Block& block = _blocks.emplace_back();
 
         block.size = 0;
     }

diff --git a/bingo/oracle/src/oracle/mango_shadow_table.cpp b/bingo/oracle/src/oracle/mango_shadow_table.cpp
@@ -86,13 +86,13 @@ void MangoShadowTable::addMolecule(OracleEnv& env, const char* rowid, int blockn
         _main_table_statement->append(")");
     }
 
-    _pending_rid.push();
+    _pending_rid.emplace_back();
     strncpy(_pending_rid.top(), rowid, 19);
     _pending_blockno.push(blockno);
     _pending_offset.push(offset);
-    _pending_gross.push();
+    _pending_gross.emplace_back();
     strncpy(_pending_gross.top(), gross, 512);
-    _pending_mass.push(molecular_mass);
+    _pending_mass.push_back(molecular_mass);
 
     _pending_cmf.push(env);
     _pending_cmf.top().assignBytes(data_cmf, len_cmf);
@@ -130,9 +130,9 @@ void MangoShadowTable::addMolecule(OracleEnv& env, const char* rowid, int blockn
 
     for (int i = 0; i < hash.size(); i++)
     {
-        _pending_comp_hash.push();
+        _pending_comp_hash.emplace_back();
         snprintf(_pending_comp_hash.top(), 9, "%08X", hash[i].hash);
-        _pending_comp_rid.push();
+        _pending_comp_rid.emplace_back();
         strncpy(_pending_comp_rid.top(), rowid, 19);
         _pending_comp_count.push(hash[i].count);
         _components_table_statement_count++;
@@ -205,10 +205,10 @@ void MangoShadowTable::_flushMain(OracleEnv& env)
                 if (_pending_xyz[i].get() != 0)
                 {
                     memcpy(xyz.ptr() + i * (maxallocsize_xyz + 4), _pending_xyz[i].get(), _pending_xyz[i].getAllocSize() + 4);
-                    xyz_ind.push(0); // OCI_IND_NOTNULL
+                    xyz_ind.push_back(0); // OCI_IND_NOTNULL
                 }
                 else
-                    xyz_ind.push(-1); // OCI_IND_NULL
+                    xyz_ind.push_back(-1); // OCI_IND_NULL
             }
 
             _main_table_statement->bindRawPtrByName(":cmf", (OCIRaw*)cmf.ptr(), maxallocsize_cmf, 0);

diff --git a/bingo/postgres/src/pg_am/pg_bingo_import.cpp b/bingo/postgres/src/pg_am/pg_bingo_import.cpp
@@ -353,7 +353,7 @@ class BingoImportHandler : public BingoPgCommon::BingoSessionHandler
         for (int col_idx = 0; col_idx < _importColumns.size(); ++col_idx)
         {
             q_nulls.push(0);
-            q_oids.push(_importColumns[col_idx].type);
+            q_oids.push_back(_importColumns[col_idx].type);
 
             if (col_idx != 0)
                 query_string.printf(", ");
@@ -397,7 +397,7 @@ class BingoImportHandler : public BingoPgCommon::BingoSessionHandler
             q_values.clear();
             for (int q_idx = 0; q_idx < _importData.size(); ++q_idx)
             {
-                q_values.push(_importData[q_idx]->getDatum());
+                q_values.push_back(_importData[q_idx]->getDatum());
                 if (q_values[q_idx] == 0)
                 {
                     q_nulls[q_idx] = 'n';