#1260: fix SMARTS saver for non-query entities with atom mappings (#1261

)

api/cpp/src/IndigoBaseReaction.cpp

@@ -17,12 +17,18 @@
  ***************************************************************************/
 
 #include "IndigoBaseReaction.h"
-#include "IndigoSession.h"
+
+#include <array>
 
 #include <indigo.h>
 
 using namespace indigo_cpp;
 
+namespace
+{
+    const std::array<const char*, 4> AUTOMAP_MODES{"discard", "keep", "alter", "clear"};
+}
+
 IndigoBaseReaction::IndigoBaseReaction(const int id, IndigoSessionPtr session) : IndigoChemicalStructure(id, std::move(session))
 {
 }
@@ -41,3 +47,9 @@ std::string IndigoBaseReaction::ctfile() const
 {
     return rxnfile();
 }
+
+void IndigoBaseReaction::automap(const IndigoAutomapMode& mode)
+{
+    session()->setSessionId();
+    session()->_checkResult(indigoAutomap(id(), AUTOMAP_MODES.at(static_cast<size_t>(mode))));
+}

api/cpp/src/IndigoBaseReaction.h

@@ -22,6 +22,14 @@
 
 namespace indigo_cpp
 {
+    enum class IndigoAutomapMode
+    {
+        DISCARD = 0,
+        KEEP,
+        ALTER,
+        CLEAR
+    };
+
     class IndigoBaseReaction : public IndigoChemicalStructure
     {
     protected:
@@ -35,5 +43,7 @@ namespace indigo_cpp
     public:
         std::string rxnfile() const;
         std::string ctfile() const override;
+
+        void automap(const IndigoAutomapMode& mode);
     };
 }

api/cpp/src/IndigoChemicalStructure.cpp

@@ -61,6 +61,12 @@ std::string IndigoChemicalStructure::smiles() const
     return session()->_checkResultString(indigoSmiles(id()));
 }
 
+std::string IndigoChemicalStructure::smarts() const
+{
+    session()->setSessionId();
+    return session()->_checkResultString(indigoSmarts(id()));
+}
+
 std::string IndigoChemicalStructure::canonicalSmiles() const
 {
     session()->setSessionId();

api/cpp/src/IndigoChemicalStructure.h

@@ -40,6 +40,8 @@ namespace indigo_cpp
 
         std::string smiles() const;
 
+        std::string smarts() const;
+
         std::string cml() const;
 
         std::string inchi() const;

api/cpp/src/IndigoQueryReaction.cpp

@@ -0,0 +1,29 @@
+/****************************************************************************
+ * 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.
+ ***************************************************************************/
+
+#include "IndigoQueryReaction.h"
+
+using namespace indigo_cpp;
+
+IndigoQueryReaction::IndigoQueryReaction(const int id, IndigoSessionPtr session) : IndigoBaseReaction(id, std::move(session))
+{
+}
+
+IndigoQueryReaction::IndigoQueryReaction(const IndigoQueryReaction& other) : IndigoBaseReaction(other)
+{
+}

api/cpp/src/IndigoQueryReaction.h

@@ -0,0 +1,35 @@
+/****************************************************************************
+ * 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.
+ ***************************************************************************/
+
+#pragma once
+
+#include "IndigoBaseReaction.h"
+
+namespace indigo_cpp
+{
+    class IndigoQueryReaction final : public IndigoBaseReaction
+    {
+    public:
+        IndigoQueryReaction(int id, IndigoSessionPtr session);
+        IndigoQueryReaction(IndigoQueryReaction&&) = default;
+        IndigoQueryReaction& operator=(IndigoQueryReaction&&) = default;
+        IndigoQueryReaction(const IndigoQueryReaction&);
+        IndigoQueryReaction& operator=(const IndigoQueryReaction&) = default;
+        ~IndigoQueryReaction() final = default;
+    };
+}

api/cpp/src/IndigoSession.cpp

@@ -206,3 +206,9 @@ IndigoReaction IndigoSession::loadReaction(const std::string& data)
     setSessionId();
     return {_checkResult(indigoLoadReactionFromString(data.c_str())), shared_from_this()};
 }
+
+IndigoReaction IndigoSession::loadQueryReaction(const std::string& data)
+{
+    setSessionId();
+    return {_checkResult(indigoLoadQueryReactionFromString(data.c_str())), shared_from_this()};
+}

api/cpp/src/IndigoSession.h

@@ -64,9 +64,12 @@ namespace indigo_cpp
         IndigoMolecule loadMolecule(const std::string& data);
         IndigoMolecule loadMoleculeFromFile(const std::string& path);
 
+        IndigoQueryMolecule loadQueryMolecule(const std::string& data);
+
         IndigoReaction loadReaction(const std::string& data);
 
-        IndigoQueryMolecule loadQueryMolecule(const std::string& data);
+        IndigoReaction loadQueryReaction(const std::string& data);
+
         IndigoWriteBuffer writeBuffer();
         IndigoIterator<IndigoReaction> iterateRDFile(const std::string& path);
         IndigoIterator<IndigoMolecule> iterateSDFile(const std::string& path);

api/cpp/tests/basic/reaction.cpp

@@ -0,0 +1,41 @@
+/****************************************************************************
+ * 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.
+ ***************************************************************************/
+
+#include <gtest/gtest.h>
+
+#include <IndigoReaction.h>
+
+#include "common.h"
+
+using namespace indigo_cpp;
+
+TEST(Reaction, automapReactionSmarts)
+{
+    const auto& session = IndigoSession::create();
+    auto reaction = session->loadReaction("[C:1]=[C:2][C:3].[C:4]=[C:5][C:6]>>[C:3][C:2]=[C:5][C:6]");
+    reaction.automap(IndigoAutomapMode::CLEAR);
+    ASSERT_STREQ("[#6]=[#6]-[#6].[#6]=[#6]-[#6]>>[#6]-[#6]=[#6]-[#6] |^3:0,3,^1:1,4,7,8|", reaction.smarts().c_str());
+}
+
+TEST(Reaction, automapQueryReactionSmarts)
+{
+    const auto& session = IndigoSession::create();
+    auto reaction = session->loadQueryReaction("[C:1]=[C:2][C:3].[C:4]=[C:5][C:6]>>[C:3][C:2]=[C:5][C:6] |$;;R1;;;R2;R1;;;R2$|");
+    reaction.automap(IndigoAutomapMode::CLEAR);
+    ASSERT_STREQ("[#6]=[#6]-[#6].[#6]=[#6]-[#6]>>[#6]-[#6]=[#6]-[#6] |$;;R1;;;R2;R1;;;R2$|", reaction.smarts().c_str());
+}

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

@@ -878,6 +878,11 @@ void SmilesSaver::_writeSmartsAtom(int idx, QueryMolecule::Atom* atom, int chira
     case QueryMolecule::OP_AND: {
         for (i = 0; i < atom->children.size(); i++)
         {
+            if (atom->children[i]->type == QueryMolecule::ATOM_RADICAL || atom->children[i]->type == QueryMolecule::ATOM_VALENCE)
+            {
+                continue;
+            }
+
             if (i > 0)
                 _output.writeChar(has_or_parent ? '&' : ';');
             _writeSmartsAtom(idx, (QueryMolecule::Atom*)atom->children[i], chirality, depth + 1, has_or_parent, has_not_parent);
@@ -887,6 +892,11 @@ void SmilesSaver::_writeSmartsAtom(int idx, QueryMolecule::Atom* atom, int chira
     case QueryMolecule::OP_OR: {
         for (i = 0; i < atom->children.size(); i++)
         {
+            if (atom->children[i]->type == QueryMolecule::ATOM_RADICAL || atom->children[i]->type == QueryMolecule::ATOM_VALENCE)
+            {
+                continue;
+            }
+
             if (i > 0)
                 _output.printf(has_not_parent ? "!" : ",");
             _writeSmartsAtom(idx, (QueryMolecule::Atom*)atom->children[i], chirality, depth + 1, true, has_not_parent);