api: added numRotatableBonds, numHydrogenBondAcceptors, numHydrogenBo…

…ndDonors (#748)
epam · May 30, 2022 · 234d55e · 234d55e
1 parent 5f933b7
commit 234d55e
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Showing 18 changed files with 494 additions and 1 deletion.
diff --git a/api/c/indigo/indigo.h b/api/c/indigo/indigo.h
@@ -669,6 +669,9 @@ CEXPORT double indigoMostAbundantMass(int molecule);
 CEXPORT double indigoMonoisotopicMass(int molecule);
 CEXPORT const char* indigoMassComposition(int molecule);
 CEXPORT double indigoTPSA(int molecule, int includeSP);
+CEXPORT int indigoNumRotatableBonds(int molecule);
+CEXPORT int indigoNumHydrogenBondAcceptors(int molecule);
+CEXPORT int indigoNumHydrogenBondDonors(int molecule);
 
 CEXPORT const char* indigoCanonicalSmiles(int molecule);
 CEXPORT const char* indigoLayeredCode(int molecule);

diff --git a/api/c/indigo/src/indigo_calc.cpp b/api/c/indigo/src/indigo_calc.cpp
@@ -1,4 +1,5 @@
 #include <base_cpp/output.h>
+#include <molecule/lipinski.h>
 #include <molecule/molecule_gross_formula.h>
 #include <molecule/molecule_mass.h>
 #include <molecule/tpsa.h>
@@ -141,7 +142,52 @@ CEXPORT double indigoTPSA(const int molecule, const int includeSP)
             auto& mol = obj.getMolecule();
             return TPSA::calculate(mol, static_cast<bool>(includeSP));
         }
-        throw IndigoError("incorrect object type for TPSA calculation: %s", obj.debugInfo());
+        throw IndigoError("incorrect object type for TPSA calculation: %s, should be molecule", obj.debugInfo());
+    }
+    INDIGO_END(-1);
+}
+
+CEXPORT int indigoNumRotatableBonds(const int molecule)
+{
+    INDIGO_BEGIN
+    {
+        auto& obj = self.getObject(molecule);
+        if (IndigoMolecule::is(obj))
+        {
+            auto& mol = obj.getMolecule();
+            return Lipinski::getNumRotatableBonds(mol);
+        }
+        throw IndigoError("incorrect object type for calculation number of rotatable bonds: %s, should be molecule", obj.debugInfo());
+    }
+    INDIGO_END(-1);
+}
+
+CEXPORT int indigoNumHydrogenBondAcceptors(const int molecule)
+{
+    INDIGO_BEGIN
+    {
+        auto& obj = self.getObject(molecule);
+        if (IndigoMolecule::is(obj))
+        {
+            auto& mol = obj.getMolecule();
+            return Lipinski::getNumHydrogenBondAcceptors(mol);
+        }
+        throw IndigoError("incorrect object type for calculation number of hydrogen bond acceptors: %s, should be molecule", obj.debugInfo());
+    }
+    INDIGO_END(-1);
+}
+
+CEXPORT int indigoNumHydrogenBondDonors(const int molecule)
+{
+    INDIGO_BEGIN
+    {
+        auto& obj = self.getObject(molecule);
+        if (IndigoMolecule::is(obj))
+        {
+            auto& mol = obj.getMolecule();
+            return Lipinski::getNumHydrogenBondDonors(mol);
+        }
+        throw IndigoError("incorrect object type for calculation number of hydrogen bond donors: %s, should be molecule", obj.debugInfo());
     }
     INDIGO_END(-1);
 }
diff --git a/api/cpp/src/IndigoMolecule.cpp b/api/cpp/src/IndigoMolecule.cpp
@@ -36,3 +36,23 @@ double IndigoMolecule::molecularWeight() const
 {
     return session()->_checkResultFloat(indigoMolecularWeight(id()));
 }
+
+double IndigoMolecule::tpsa(const bool includeSP) const
+{
+    return session()->_checkResultFloat(indigoTPSA(id(), static_cast<int>(includeSP)));
+}
+
+int IndigoMolecule::numRotatableBonds() const
+{
+    return session()->_checkResult(indigoNumRotatableBonds(id()));
+}
+
+int IndigoMolecule::numHydrogenBondAcceptors() const
+{
+    return session()->_checkResult(indigoNumHydrogenBondAcceptors(id()));
+}
+
+int IndigoMolecule::numHydrogenBondDonors() const
+{
+    return session()->_checkResult(indigoNumHydrogenBondDonors(id()));
+}
diff --git a/api/cpp/src/IndigoMolecule.h b/api/cpp/src/IndigoMolecule.h
@@ -35,6 +35,10 @@ namespace indigo_cpp
         ~IndigoMolecule() final = default;
 
         double molecularWeight() const;
+        double tpsa(bool includeSP = false) const;
+        int numRotatableBonds() const;
+        int numHydrogenBondAcceptors() const;
+        int numHydrogenBondDonors() const;
     };
 
     using IndigoMoleculeSPtr = std::shared_ptr<IndigoMolecule>;

diff --git a/api/cpp/tests/basic/molecule.cpp b/api/cpp/tests/basic/molecule.cpp
@@ -0,0 +1,109 @@
+/****************************************************************************
+ * 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 <IndigoMolecule.h>
+
+#include "common.h"
+
+using namespace indigo_cpp;
+
+TEST(Molecule, molecularWeight)
+{
+    const auto& session = IndigoSession::create();
+    {
+        const auto& molecule = session->loadMolecule(METHANE);
+        EXPECT_NEAR(16.042, molecule.molecularWeight(), 0.01);
+    }
+    {
+        const auto& molecule = session->loadMolecule(CAFFEINE);
+        EXPECT_NEAR(194.191, molecule.molecularWeight(), 0.01);
+    }
+    {
+        const auto& molecule = session->loadMolecule(SULFASALAZINE);
+        EXPECT_NEAR(398.393, molecule.molecularWeight(), 0.01);
+    }
+}
+
+TEST(Molecule, tpsa)
+{
+    const auto& session = IndigoSession::create();
+    {
+        const auto& molecule = session->loadMolecule(METHANE);
+        EXPECT_NEAR(0.0, molecule.tpsa(), 0.01);
+        EXPECT_NEAR(0.0, molecule.tpsa(true), 0.01);
+    }
+    {
+        const auto& molecule = session->loadMolecule(CAFFEINE);
+        EXPECT_NEAR(58.44, molecule.tpsa(), 0.01);
+        EXPECT_NEAR(58.44, molecule.tpsa(true), 0.01);
+    }
+    {
+        const auto& molecule = session->loadMolecule(SULFASALAZINE);
+        EXPECT_NEAR(141.31, molecule.tpsa(), 0.01);
+        EXPECT_NEAR(149.69, molecule.tpsa(true), 0.01);
+    }
+}
+
+TEST(Molecule, numRotatableBonds)
+{
+    const auto& session = IndigoSession::create();
+    {
+        const auto& molecule = session->loadMolecule(METHANE);
+        EXPECT_EQ(0, molecule.numRotatableBonds());
+    }
+    {
+        const auto& molecule = session->loadMolecule(CAFFEINE);
+        EXPECT_EQ(0, molecule.numRotatableBonds());
+    }
+    {
+        const auto& molecule = session->loadMolecule(SULFASALAZINE);
+        EXPECT_EQ(6, molecule.numRotatableBonds());
+    }
+}
+
+TEST(Molecule, numHydrogenBondAcceptors)
+{
+    const auto& session = IndigoSession::create();
+    {
+        const auto& molecule = session->loadMolecule(METHANE);
+        EXPECT_EQ(0, molecule.numHydrogenBondAcceptors());
+    }
+    {
+        const auto& molecule = session->loadMolecule(CAFFEINE);
+        EXPECT_EQ(6, molecule.numHydrogenBondAcceptors());
+    }
+    {
+        const auto& molecule = session->loadMolecule(SULFASALAZINE);
+        EXPECT_EQ(9, molecule.numHydrogenBondAcceptors());
+    }
+}
+
+TEST(Molecule, numHydrogenBondDonors)
+{
+    const auto& session = IndigoSession::create();
+    {
+        const auto& molecule = session->loadMolecule(CAFFEINE);
+        EXPECT_EQ(0, molecule.numHydrogenBondDonors());
+    }
+    {
+        const auto& molecule = session->loadMolecule(SULFASALAZINE);
+        EXPECT_EQ(3, molecule.numHydrogenBondDonors());
+    }
+}
diff --git a/api/cpp/tests/common.h.in b/api/cpp/tests/common.h.in
@@ -2,6 +2,10 @@
 
 #include <string>
 
+#define METHANE "C"
+#define CAFFEINE "CN1C=NC2=C1C(=O)N(C(=O)N2C)C"
+#define SULFASALAZINE "C1=CC=NC(=C1)NS(=O)(=O)C2=CC=C(C=C2)N=NC3=CC(=C(C=C3)O)C(=O)O"
+
 namespace indigo_cpp
 {
     std::string dataPath(const char* dataPathSuffix);

diff --git a/api/dotnet/src/IndigoLib.cs b/api/dotnet/src/IndigoLib.cs
@@ -813,6 +813,15 @@ public static extern int indigoSetSGroupBrackets(int sgroup, int brk_style, floa
         [DllImport("indigo"), SuppressUnmanagedCodeSecurity]
         public static extern double indigoTPSA(int molecule, bool includeSP);
 
+        [DllImport("indigo"), SuppressUnmanagedCodeSecurity]
+        public static extern int indigoNumRotatableBonds(int molecule);
+
+        [DllImport("indigo"), SuppressUnmanagedCodeSecurity]
+        public static extern int indigoNumHydrogenBondAcceptors(int molecule);
+
+        [DllImport("indigo"), SuppressUnmanagedCodeSecurity]
+        public static extern int indigoNumHydrogenBondDonors(int molecule);
+
         [DllImport("indigo"), SuppressUnmanagedCodeSecurity]
         public static extern byte* indigoCanonicalSmiles(int molecule);
 

diff --git a/api/dotnet/src/IndigoObject.cs b/api/dotnet/src/IndigoObject.cs
@@ -1397,6 +1397,24 @@ public double tpsa(bool includeSP = false)
             return dispatcher.checkResult(IndigoLib.indigoTPSA(self, includeSP));
         }
 
+        public int numRotatableBonds()
+        {
+            dispatcher.setSessionID();
+            return dispatcher.checkResult(IndigoLib.indigoNumRotatableBonds(self));
+        }
+
+        public int numHydrogenBondAcceptors()
+        {
+            dispatcher.setSessionID();
+            return dispatcher.checkResult(IndigoLib.indigoNumHydrogenBondAcceptors(self));
+        }
+
+        public int numHydrogenBondDonors()
+        {
+            dispatcher.setSessionID();
+            return dispatcher.checkResult(IndigoLib.indigoNumHydrogenBondDonors(self));
+        }
+
         public string canonicalSmiles()
         {
             dispatcher.setSessionID();

diff --git a/api/java/indigo/src/main/java/com/epam/indigo/IndigoLib.java b/api/java/indigo/src/main/java/com/epam/indigo/IndigoLib.java
@@ -599,6 +599,12 @@ int indigoSetSGroupBrackets(
 
     double indigoTPSA(int molecule, boolean includeSP);
 
+    int indigoNumRotatableBonds(int molecule);
+
+    int indigoNumHydrogenBondAcceptors(int molecule);
+
+    int indigoNumHydrogenBondDonors(int molecule);
+
     Pointer indigoCanonicalSmiles(int molecule);
 
     Pointer indigoLayeredCode(int molecule);

diff --git a/api/java/indigo/src/main/java/com/epam/indigo/IndigoObject.java b/api/java/indigo/src/main/java/com/epam/indigo/IndigoObject.java
@@ -825,6 +825,21 @@ public double tpsa(boolean includeSP) {
         return Indigo.checkResultDouble(this, lib.indigoTPSA(self, includeSP));
     }
 
+    public int numRotatableBonds() {
+        dispatcher.setSessionID();
+        return Indigo.checkResult(this, lib.indigoNumRotatableBonds(self));
+    }
+
+    public int numHydrogenBondAcceptors() {
+        dispatcher.setSessionID();
+        return Indigo.checkResult(this, lib.indigoNumHydrogenBondAcceptors(self));
+    }
+
+    public int numHydrogenBondDonors() {
+        dispatcher.setSessionID();
+        return Indigo.checkResult(this, lib.indigoNumHydrogenBondDonors(self));
+    }
+
     public String canonicalSmiles() {
         dispatcher.setSessionID();
         return Indigo.checkResultString(this, lib.indigoCanonicalSmiles(self));

diff --git a/api/python/indigo/__init__.py b/api/python/indigo/__init__.py
@@ -3230,6 +3230,39 @@ def tpsa(self, includeSP=False):
             Indigo._lib.indigoTPSA(self.id, includeSP)
         )
 
+    def numRotatableBonds(self):
+        """Molecule method returns the number of rotatable bonds
+
+        Returns:
+            int: number of rotatable bonds
+        """
+        self.dispatcher._setSessionId()
+        return self.dispatcher._checkResult(
+            Indigo._lib.indigoNumRotatableBonds(self.id)
+        )
+
+    def numHydrogenBondAcceptors(self):
+        """Molecule method returns the number of hydrogen bond acceptors
+
+        Returns:
+            float: number of hydrogen bond acceptors
+        """
+        self.dispatcher._setSessionId()
+        return self.dispatcher._checkResult(
+            Indigo._lib.indigoNumHydrogenBondAcceptors(self.id)
+        )
+
+    def numHydrogenBondDonors(self):
+        """Molecule method returns the number of hydrogen bond donors
+
+        Returns:
+            float: number of hydrogen bond donors
+        """
+        self.dispatcher._setSessionId()
+        return self.dispatcher._checkResult(
+            Indigo._lib.indigoNumHydrogenBondDonors(self.id)
+        )
+
     def canonicalSmiles(self):
         """Molecule or reaction method returns canonical smiles
 
@@ -5029,6 +5062,12 @@ def __init__(self, path=None):
         Indigo._lib.indigoMassComposition.argtypes = [c_int]
         Indigo._lib.indigoTPSA.restype = c_double
         Indigo._lib.indigoTPSA.argtypes = [c_int, c_int]
+        Indigo._lib.indigoNumRotatableBonds.restype = c_int
+        Indigo._lib.indigoNumRotatableBonds.argtypes = [c_int]
+        Indigo._lib.indigoNumHydrogenBondAcceptors.restype = c_int
+        Indigo._lib.indigoNumHydrogenBondAcceptors.argtypes = [c_int]
+        Indigo._lib.indigoNumHydrogenBondDonors.restype = c_int
+        Indigo._lib.indigoNumHydrogenBondDonors.argtypes = [c_int]
         Indigo._lib.indigoCanonicalSmiles.restype = c_char_p
         Indigo._lib.indigoCanonicalSmiles.argtypes = [c_int]
         Indigo._lib.indigoCanonicalSmarts.restype = c_char_p

diff --git a/api/tests/integration/ref/calc/lipinski.py.out b/api/tests/integration/ref/calc/lipinski.py.out