api: added atom hybridization calculation (#751)

epam · Jun 1, 2022 · 2abfb8a · 2abfb8a
1 parent 7788786
commit 2abfb8a
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Showing 40 changed files with 1,152 additions and 365 deletions.
diff --git a/api/c/indigo/indigo.h b/api/c/indigo/indigo.h
@@ -404,6 +404,17 @@ CEXPORT int indigoAtomicNumber(int atom);
 CEXPORT int indigoIsotope(int atom);
 // Not applicable to query molecules.
 CEXPORT int indigoValence(int atom);
+// Return atom hybridization
+// S = 1,
+// SP = 2,
+// SP2 = 3,
+// SP3 = 4,
+// SP3D = 5,
+// SP3D2 = 6,
+// SP3D3 = 7,
+// SP3D4 = 8,
+// SP2D = 9
+CEXPORT int indigoGetHybridization(int atom);
 // Returns zero if valence of the atom is wrong
 CEXPORT int indigoCheckValence(int atom);
 

diff --git a/api/c/indigo/src/indigo_molecule.cpp b/api/c/indigo/src/indigo_molecule.cpp
@@ -25,6 +25,7 @@
 #include "indigo_mapping.h"
 #include "molecule/canonical_smiles_saver.h"
 #include "molecule/elements.h"
+#include "molecule/hybridization.h"
 #include "molecule/molecule_auto_loader.h"
 #include "molecule/molecule_automorphism_search.h"
 #include "molecule/molecule_fingerprint.h"
@@ -1271,6 +1272,17 @@ CEXPORT int indigoValence(int atom)
     INDIGO_END(-1);
 }
 
+CEXPORT int indigoGetHybridization(int atom)
+{
+    INDIGO_BEGIN
+    {
+        IndigoAtom& ia = IndigoAtom::cast(self.getObject(atom));
+        auto& molecule = ia.mol.asMolecule();
+        return static_cast<int>(HybridizationCalculator::calculate(molecule, ia.idx));
+    }
+    INDIGO_END(-1);
+}
+
 CEXPORT int indigoCheckValence(int atom)
 {
     INDIGO_BEGIN

diff --git a/api/cpp/src/BingoNoSQL.cpp b/api/cpp/src/BingoNoSQL.cpp
@@ -1,3 +1,21 @@
+/****************************************************************************
+ * 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 "BingoNoSQL.h"
 
 #include <bingo-nosql.h>

diff --git a/api/cpp/src/BingoNoSQL.h b/api/cpp/src/BingoNoSQL.h
@@ -1,3 +1,21 @@
+/****************************************************************************
+ * 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 "BingoResultIterator.h"

diff --git a/api/cpp/src/BingoResult.cpp b/api/cpp/src/BingoResult.cpp
@@ -1,3 +1,21 @@
+/****************************************************************************
+ * 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 <bingo-nosql.h>
 
 #include "BingoResult.h"

diff --git a/api/cpp/src/BingoResult.h b/api/cpp/src/BingoResult.h
@@ -1,3 +1,21 @@
+/****************************************************************************
+ * 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 "IndigoSession.h"

diff --git a/api/cpp/src/BingoResultIterator.cpp b/api/cpp/src/BingoResultIterator.cpp
@@ -1,3 +1,21 @@
+/****************************************************************************
+ * 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 "BingoResultIterator.h"
 
 #include <bingo-nosql.h>

diff --git a/api/cpp/src/BingoResultIterator.h b/api/cpp/src/BingoResultIterator.h
@@ -1,3 +1,21 @@
+/****************************************************************************
+ * 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 "IndigoSession.h"

diff --git a/api/cpp/src/IndigoAtom.cpp b/api/cpp/src/IndigoAtom.cpp
@@ -0,0 +1,34 @@
+/****************************************************************************
+ * 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 "IndigoAtom.h"
+
+#include <indigo.h>
+
+namespace indigo_cpp
+{
+    IndigoAtom::IndigoAtom(int id, IndigoSessionPtr session) : IndigoObject(id, std::move(session))
+    {
+    }
+
+    Hybridization IndigoAtom::getHybridization() const
+    {
+        session()->setSessionId();
+        return Hybridization(session()->_checkResult(indigoGetHybridization(id())));
+    }
+}
diff --git a/api/cpp/src/IndigoAtom.h b/api/cpp/src/IndigoAtom.h
@@ -0,0 +1,45 @@
+/****************************************************************************
+ * 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 "IndigoObject.h"
+
+namespace indigo_cpp
+{
+    enum class Hybridization
+    {
+        S = 1,
+        SP = 2,
+        SP2 = 3,
+        SP3 = 4,
+        SP3D = 5,
+        SP3D2 = 6,
+        SP3D3 = 7,
+        SP3D4 = 8,
+        SP2D = 9
+    };
+
+    class IndigoAtom : public IndigoObject
+    {
+    public:
+        explicit IndigoAtom(int id, IndigoSessionPtr session);
+
+        Hybridization getHybridization() const;
+    };
+}
diff --git a/api/cpp/src/IndigoBaseMolecule.cpp b/api/cpp/src/IndigoBaseMolecule.cpp
@@ -41,3 +41,9 @@ std::string IndigoBaseMolecule::ctfile() const
 {
     return molfile();
 }
+
+IndigoAtom IndigoBaseMolecule::getAtom(int atomIndex) const
+{
+    session()->setSessionId();
+    return IndigoAtom(session()->_checkResult(indigoGetAtom(id(), atomIndex)), session());
+}
diff --git a/api/cpp/src/IndigoBaseMolecule.h b/api/cpp/src/IndigoBaseMolecule.h
@@ -18,6 +18,7 @@
 
 #pragma once
 
+#include "IndigoAtom.h"
 #include "IndigoChemicalStructure.h"
 
 namespace indigo_cpp
@@ -35,5 +36,7 @@ namespace indigo_cpp
     public:
         std::string molfile() const;
         std::string ctfile() const override;
+
+        IndigoAtom getAtom(int atomIndex) const;
     };
 }
diff --git a/api/cpp/src/IndigoCopyableObject.cpp b/api/cpp/src/IndigoCopyableObject.cpp
@@ -1,3 +1,21 @@
+/****************************************************************************
+ * 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 "IndigoCopyableObject.h"
 
 #include <indigo.h>

diff --git a/api/cpp/src/IndigoCopyableObject.h b/api/cpp/src/IndigoCopyableObject.h
@@ -1,3 +1,21 @@
+/****************************************************************************
+ * 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 "IndigoObject.h"

diff --git a/api/cpp/src/IndigoMolecule.cpp b/api/cpp/src/IndigoMolecule.cpp
@@ -34,35 +34,42 @@ IndigoMolecule::IndigoMolecule(const IndigoMolecule& other) : IndigoBaseMolecule
 
 double IndigoMolecule::molecularWeight() const
 {
+    session()->setSessionId();
     return session()->_checkResultFloat(indigoMolecularWeight(id()));
 }
 
 double IndigoMolecule::tpsa(const bool includeSP) const
 {
+    session()->setSessionId();
     return session()->_checkResultFloat(indigoTPSA(id(), static_cast<int>(includeSP)));
 }
 
 int IndigoMolecule::numRotatableBonds() const
 {
+    session()->setSessionId();
     return session()->_checkResult(indigoNumRotatableBonds(id()));
 }
 
 int IndigoMolecule::numHydrogenBondAcceptors() const
 {
+    session()->setSessionId();
     return session()->_checkResult(indigoNumHydrogenBondAcceptors(id()));
 }
 
 int IndigoMolecule::numHydrogenBondDonors() const
 {
+    session()->setSessionId();
     return session()->_checkResult(indigoNumHydrogenBondDonors(id()));
 }
 
 double IndigoMolecule::cLogP() const
 {
+    session()->setSessionId();
     return session()->_checkResultFloat(indigoCLogP(id()));
 }
 
 double IndigoMolecule::cMolarRefractivity() const
 {
+    session()->setSessionId();
     return session()->_checkResultFloat(indigoCMolarRefractivity(id()));
 }
diff --git a/api/cpp/src/IndigoRDFileIterator.cpp b/api/cpp/src/IndigoRDFileIterator.cpp
@@ -1,3 +1,21 @@
+/****************************************************************************
+ * 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 "IndigoRDFileIterator.h"
 
 #include <indigo.h>