Issue 6411 ROMol hasquery (rdkit#6739)

* added ROMol::hasQuery * python bindings for Mol.HasQuery * at least I checked that my Python tests were running... * hasQuery use C++11 range iterators
DavidACosgrove · Sep 25, 2023 · 4db63b8 · 4db63b8
1 parent 2761441
commit 4db63b8
Show file tree

Hide file tree

Showing 5 changed files with 50 additions and 1 deletion.
diff --git a/Code/GraphMol/ROMol.cpp b/Code/GraphMol/ROMol.cpp
@@ -543,6 +543,20 @@ ROMol::ConstHeteroatomIterator ROMol::endHeteros() const {
   return ConstHeteroatomIterator(this, getNumAtoms());
 }
 
+bool ROMol::hasQuery() const {
+  for (auto atom : atoms()) {
+    if (atom->hasQuery()) {
+      return true;
+    }
+  }
+  for (auto bond : bonds()) {
+    if (bond->hasQuery()) {
+      return true;
+    }
+  }
+  return false;
+}
+
 ROMol::QueryAtomIterator ROMol::beginQueryAtoms(QueryAtom const *what) {
   return QueryAtomIterator(this, what);
 }

diff --git a/Code/GraphMol/ROMol.h b/Code/GraphMol/ROMol.h
@@ -718,6 +718,9 @@ class RDKIT_GRAPHMOL_EXPORT ROMol : public RDProps {
   //! \overload
   ConstHeteroatomIterator endHeteros() const;
 
+  //! if the Mol has any Query atoms or bonds
+  bool hasQuery() const;
+
   //! get an AtomIterator pointing at our first Atom that matches \c query
   QueryAtomIterator beginQueryAtoms(QueryAtom const *query);
   //! \overload

diff --git a/Code/GraphMol/Wrap/Mol.cpp b/Code/GraphMol/Wrap/Mol.cpp
@@ -444,6 +444,9 @@ struct mol_wrapper {
              "instead.\n\n"
              "  NOTE: bond indices start at 0\n")
 
+        .def("HasQuery", &ROMol::hasQuery,
+             "Returns if any atom or bond in molecule has a query")
+
         // substructures
         .def("HasSubstructMatch",
              (bool (*)(const ROMol &m, const ROMol &query, bool, bool,

diff --git a/Code/GraphMol/Wrap/rough_test.py b/Code/GraphMol/Wrap/rough_test.py
@@ -7357,7 +7357,17 @@ def testHasQueryHs(self):
          (True, False))]:
       pat = Chem.MolFromSmarts(sma)
       self.assertEqual(Chem.HasQueryHs(pat), hasQHs)
-
+
+  def testMolHasQuery(self):
+    m1 = Chem.MolFromSmiles("CCO")
+    self.assertFalse(m1.HasQuery())
+
+    m2 = Chem.MolFromSmarts("[#6][#6][#8]")
+    self.assertTrue(m2.HasQuery())
+
+    m3 = Chem.MolFromSmiles("CC~O")
+    self.assertTrue(m3.HasQuery())
+
   def testMrvHandling(self):
     fn1 = os.path.join(RDConfig.RDBaseDir,'Code','GraphMol','MarvinParse','test_data','aspirin.mrv')
     mol = Chem.MolFromMrvFile(fn1)

diff --git a/Code/GraphMol/catch_graphmol.cpp b/Code/GraphMol/catch_graphmol.cpp
@@ -3418,4 +3418,23 @@ TEST_CASE(
     REQUIRE(sgs.size() == 1);
     CHECK(&sgs[0].getOwningMol() == &mol);
   }
+}
+
+TEST_CASE(
+    "ROMol hasQuery") {
+  SECTION("check false Mol.hasQuery") {
+    std::unique_ptr<ROMol> mol{SmilesToMol("CCO")};
+
+    REQUIRE(!mol->hasQuery());
+  }
+  SECTION("check true Mol.hasQuery because Atom") {
+    std::unique_ptr<ROMol> mol{SmartsToMol("[#6][#6][#8]")};
+
+    REQUIRE(mol->hasQuery());
+  }
+  SECTION("check true Mol.hashQuery because Bond") {
+    std::unique_ptr<ROMol> mol{SmilesToMol("CC~O")};
+
+    REQUIRE(mol->hasQuery());
+  }
 }