WIP: Issue #520 Replace RedBlackMap in MoleculeStereocenters

api/c/indigo/src/indigo_stereo.cpp

@@ -20,6 +20,7 @@
 #include "indigo_reaction.h"
 #include "molecule/molecule_automorphism_search.h"
 #include "molecule/molecule_exact_matcher.h"
+#include "molecule/molecule_stereocenter_iterator.h"
 #include "reaction/reaction.h"
 
 CEXPORT int indigoStereocenterType(int atom)
@@ -373,7 +374,7 @@ static int _resetSymmetric(Molecule& mol, bool cistrans, bool stereo)
     {
         QS_DEF(Array<int>, to_remove);
         to_remove.clear();
-        for (int i = mol.stereocenters.begin(); i != mol.stereocenters.end(); i = mol.stereocenters.next(i))
+        for (auto i = mol.stereocenters.begin(); i != mol.stereocenters.end(); i = mol.stereocenters.next(i))
         {
             int atom_index = mol.stereocenters.getAtomIndex(i);
             if (am.invalidStereocenter(atom_index))
@@ -530,7 +531,7 @@ static void _indigoValidateMoleculeChirality(Molecule& mol)
     QS_DEF(Molecule, mirror);
     mirror.clone(mol, 0, 0);
 
-    for (int s = mirror.stereocenters.begin(); s != mirror.stereocenters.end(); s = mirror.stereocenters.next(s))
+    for (auto s = mirror.stereocenters.begin(); s != mirror.stereocenters.end(); s = mirror.stereocenters.next(s))
     {
         int atom = mirror.stereocenters.getAtomIndex(s);
         if (mirror.stereocenters.getType(atom) == MoleculeStereocenters::ATOM_ABS)
@@ -544,7 +545,7 @@ static void _indigoValidateMoleculeChirality(Molecule& mol)
     if (!matcher.find())
         return;
 
-    for (int s = mol.stereocenters.begin(); s != mol.stereocenters.end(); s = mol.stereocenters.next(s))
+    for (auto s = mol.stereocenters.begin(); s != mol.stereocenters.end(); s = mol.stereocenters.next(s))
     {
         int atom = mol.stereocenters.getAtomIndex(s);
         if (mol.stereocenters.getType(atom) == MoleculeStereocenters::ATOM_ABS)

core/indigo-core/molecule/molecule_automorphism_search.h

@@ -19,13 +19,17 @@
 #ifndef __molecule_automorphism_search__
 #define __molecule_automorphism_search__
 
+#include <memory>
+
 #include "graph/automorphism_search.h"
+#include "molecule/molecule_stereocenter_iterator.h"
 
 namespace indigo
 {
 
     class Molecule;
     class MoleculeStereocenters;
+    class StereocenterIteratorr;
     class CancellationHandler;
 
     class MoleculeAutomorphismSearch : public AutomorphismSearch
@@ -65,7 +69,7 @@ namespace indigo
         static bool _check_automorphism(Graph& graph, const Array<int>& mapping, const void* context);
 
         static bool _isCisTransBondMappedRigid(Molecule& mol, int i, const int* mapping);
-        static bool _isStereocenterMappedRigid(Molecule& mol, int i, const int* mapping);
+        static bool _isStereocenterMappedRigid(Molecule& mol, const StereocenterIterator& it, const int* mapping);
 
         static int _compare_mapped(Graph& graph, const Array<int>& mapping1, const Array<int>& mapping2, const void* context);
 
@@ -84,7 +88,7 @@ namespace indigo
         void _getFirstApproximation(Molecule& mol);
 
         int _validCisTransBond(int idx, const Array<int>& orbits);
-        int _validStereocenter(int idx, Array<int>& orbits, int* parity = 0);
+        int _validStereocenter(const StereocenterIterator& it, Array<int>& orbits, int* parity = 0);
         int _validStereocenterByAtom(int atom_idx, Array<int>& orbits, int* parity = 0);
 
         int _treat_undef_as;
@@ -130,7 +134,8 @@ namespace indigo
         TL_CP_DECL(Array<int>, _cistrans_bond_state);
 
         // Target stereocenters and cis-trans bond for checking permutation parity
-        int _target_stereocenter, _target_bond;
+        std::unique_ptr<StereocenterIterator> _target_stereocenter; // should be replaced with std::optional after switch to C++17
+        int _target_bond;
         bool _target_stereocenter_parity_inv, _target_bond_parity_inv;
         int _fixed_atom;
 

core/indigo-core/molecule/molecule_cip_calculator.h

@@ -29,6 +29,7 @@ namespace indigo
 {
     class BaseMolecule;
     class Molecule;
+    class StereocenterIterator;
 
     enum class CIPDesc : int
     {
@@ -81,8 +82,8 @@ namespace indigo
                                                                        {"(s)", CIPDesc::s}, {"(E)", CIPDesc::E}, {"(Z)", CIPDesc::Z}};
 
     private:
-        void _calcRSStereoDescriptor(BaseMolecule& mol, BaseMolecule& unfolded_h_mol, int idx, Array<CIPDesc>& atom_cip_desc, Array<int>& stereo_passed,
-                                     bool use_stereo, Array<EquivLigand>& equiv_ligands, bool& digraph_cip_used);
+        void _calcRSStereoDescriptor(BaseMolecule& mol, BaseMolecule& unfolded_h_mol, const StereocenterIterator& id, Array<CIPDesc>& atom_cip_desc,
+                                     Array<StereocenterIterator>& stereo_passed, bool use_stereo, Array<EquivLigand>& equiv_ligands, bool& digraph_cip_used);
         void _calcEZStereoDescriptor(BaseMolecule& mol, BaseMolecule& unfolded_h_mol, int idx, Array<CIPDesc>& bond_cip_desc);
         bool _checkLigandsEquivalence(Array<int>& ligands, Array<EquivLigand>& equiv_ligands, CIPContext& context);
         static int _getNumberOfStereoDescritors(const Array<CIPDesc>& atom_cip_desc);

core/indigo-core/molecule/molecule_ionize.h

@@ -19,6 +19,11 @@
 #ifndef __molecule_ionize_h__
 #define __molecule_ionize_h__
 
+#include <map>
+#include <memory>
+#include <string>
+#include <vector>
+
 #include "base_cpp/obj_array.h"
 #include "base_cpp/red_black.h"
 #include "base_cpp/tlscont.h"
@@ -82,16 +87,16 @@ namespace indigo
         static void _checkCanonicalOrder(Molecule& mol, Molecule& can_mol, Array<int>& order);
         static void _removeExtraHydrogens(Molecule& mol);
 
-        ObjArray<QueryMolecule> acids;
-        ObjArray<QueryMolecule> basics;
-        Array<float> a_pkas;
-        Array<float> b_pkas;
+        std::vector<std::unique_ptr<QueryMolecule>> acids; // consider replacement to std::vector<QueryMolecule> after QueryMolecule will become movable
+        std::vector<std::unique_ptr<QueryMolecule>> basics;
+        std::vector<float> a_pkas;
+        std::vector<float> b_pkas;
         bool simple_model_ready = false;
 
-        RedBlackStringObjMap<Array<float>> adv_a_pkas;
-        RedBlackStringObjMap<Array<float>> adv_b_pkas;
+        std::map<std::string, std::vector<float>, std::less<>> adv_a_pkas;
+        std::map<std::string, std::vector<float>, std::less<>> adv_b_pkas;
         int level;
-        Array<float> max_deviations;
+        std::vector<float> max_deviations;
         bool advanced_model_ready = false;
     };
 

core/indigo-core/molecule/molecule_stereocenter_iterator.h

@@ -0,0 +1,53 @@
+/****************************************************************************
+ * Copyright (C) from 2009 to Present EPAM Systems.
+ *
+ * This file is part of Indigo toolkit.
+ *
+ * Licensed under the Apache License, Version 2.0 (the "License");
+ * you may not use this file except in compliance with the License.
+ * You may obtain a copy of the License at
+ *
+ * http://www.apache.org/licenses/LICENSE-2.0
+ *
+ * Unless required by applicable law or agreed to in writing, software
+ * distributed under the License is distributed on an "AS IS" BASIS,
+ * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+ * See the License for the specific language governing permissions and
+ * limitations under the License.
+ ***************************************************************************/
+
+#ifndef __molecule_stereocenter_iterator__
+#define __molecule_stereocenter_iterator__
+
+#include "base_c/defs.h"
+#include "molecule/molecule_stereocenters.h"
+
+#ifdef _WIN32
+#pragma warning(push)
+#pragma warning(disable : 4251)
+#endif
+
+namespace indigo
+{
+
+    class DLLEXPORT StereocenterIterator
+    {
+        StereocenterIterator(MoleculeStereocenters::Container::const_iterator it);
+
+        MoleculeStereocenters::Container::const_iterator _iterator;
+
+        friend class MoleculeStereocenters;
+
+    public:
+        bool operator==(const StereocenterIterator& rhs) const;
+
+        bool operator!=(const StereocenterIterator& rhs) const;
+    };
+
+} // namespace indigo
+
+#ifdef _WIN32
+#pragma warning(pop)
+#endif
+
+#endif // __molecule_stereocenter_iterator__

core/indigo-core/molecule/molecule_stereocenters.h

@@ -19,7 +19,9 @@
 #ifndef __molecule_stereocenters__
 #define __molecule_stereocenters__
 
-#include "base_cpp/red_black.h"
+#include <map>
+
+#include "base_cpp/array.h"
 #include "math/algebra.h"
 
 #ifdef _WIN32
@@ -31,10 +33,21 @@ namespace indigo
 {
     class Filter;
     class StereocentersOptions;
+    class StereocenterIterator;
     class BaseMolecule;
 
     class DLLEXPORT MoleculeStereocenters
     {
+        struct _Atom
+        {
+            int type;  // ANY, AND, OR, ABS
+            int group; // stereogroup index
+            // [X, Y, Z, W] -- atom indices or -1 for implicit hydrogen
+            // (X, Y, Z) go counterclockwise when looking from W.
+            // if there are pure (implicit) hydrogen, it is W
+            int pyramid[4];
+        };
+
     public:
         enum
         {
@@ -45,6 +58,11 @@ namespace indigo
         };
 
         explicit MoleculeStereocenters();
+        MoleculeStereocenters(const MoleculeStereocenters&) = delete; // no implicit copy
+        MoleculeStereocenters(MoleculeStereocenters&&) = default;
+
+        MoleculeStereocenters& operator=(const MoleculeStereocenters&) = delete; // no implicit copy
+        MoleculeStereocenters& operator=(MoleculeStereocenters&&) = default;
 
         void clear();
 
@@ -69,7 +87,6 @@ namespace indigo
         void add_ignore(BaseMolecule& baseMolecule, int atom_idx, int type, int group, bool inverse_pyramid);
         void add_ignore(BaseMolecule& baseMolecule, int atom_idx, int type, int group, const int pyramid[4]);
 
-        void get(int i, int& atom_idx, int& type, int& group, int* pyramid) const;
         void remove(int idx);
 
         bool exists(int atom_idx) const;
@@ -102,11 +119,12 @@ namespace indigo
 
         void flipBond(int atom_parent, int atom_from, int atom_to);
 
-        int begin() const;
-        int end() const;
-        int next(int i) const;
+        StereocenterIterator begin() const;
+        StereocenterIterator end() const;
+        StereocenterIterator next(const StereocenterIterator& it) const;
 
-        int getAtomIndex(int i) const;
+        void get(const StereocenterIterator& it, int& atom_idx, int& type, int& group, int* pyramid) const;
+        int getAtomIndex(const StereocenterIterator& it) const;
 
         bool isPossibleStereocenter(BaseMolecule& baseMolecule, int atom_idx, bool* possible_implicit_h = 0, bool* possible_lone_pair = 0);
 
@@ -121,7 +139,7 @@ namespace indigo
         static void moveMinimalToEnd(int pyramid[4]);
         static void moveElementToEnd(int pyramid[4], int element);
 
-        static bool isAutomorphism(BaseMolecule& mol, const Array<int>& mapping, const Filter* filter = NULL);
+        static bool isAutomorphism(BaseMolecule& mol, const Array<int>& mapping);
 
         DECL_ERROR;
 
@@ -130,16 +148,6 @@ namespace indigo
         static void rotatePyramid(int* pyramid);
 
     private:
-        struct _Atom
-        {
-            int type;  // ANY, AND, OR, ABS
-            int group; // stereogroup index
-            // [X, Y, Z, W] -- atom indices or -1 for implicit hydrogen
-            // (X, Y, Z) go counterclockwise when looking from W.
-            // if there are pure (implicit) hydrogen, it is W
-            int pyramid[4];
-        };
-
         struct _EdgeIndVec
         {
             int edge_idx;
@@ -157,7 +165,8 @@ namespace indigo
             int implicit_degree;
         };
 
-        RedBlackMap<int, _Atom> _stereocenters;
+        using Container = std::map<int, _Atom>;
+        Container _stereocenters;
 
         static int _sign(const Vec3f& v1, const Vec3f& v2, const Vec3f& v3);
         static int _xyzzy(const Vec3f& v1, const Vec3f& v2, const Vec3f& u);
@@ -178,7 +187,7 @@ namespace indigo
 
         int _getDirection(BaseMolecule& mol, int atom_from, int atom_to, bool bidirectional_mode);
 
-        MoleculeStereocenters(const MoleculeStereocenters&); // no implicit copy
+        friend class StereocenterIterator;
     };
 
 } // namespace indigo

core/indigo-core/molecule/src/inchi_wrapper.cpp

@@ -25,6 +25,7 @@
 #include "molecule/elements.h"
 #include "molecule/molecule.h"
 #include "molecule/molecule_dearom.h"
+#include "molecule/molecule_stereocenter_iterator.h"
 // #include "mode.h"
 
 using namespace indigo;
@@ -521,7 +522,7 @@ void InchiWrapper::generateInchiInput(Molecule& mol, inchi_Input& input, Array<i
     }
 
     // Process tetrahedral stereocenters
-    for (int i = mol.stereocenters.begin(); i != mol.stereocenters.end(); i = mol.stereocenters.next(i))
+    for (auto i = mol.stereocenters.begin(); i != mol.stereocenters.end(); i = mol.stereocenters.next(i))
     {
         int v = mol.stereocenters.getAtomIndex(i);