Fixes #1943 (#1954)

Code/GraphMol/AdjustQuery.cpp

@@ -23,7 +23,7 @@ namespace {
 bool isMapped(const Atom *atom) {
   return atom->hasProp(common_properties::molAtomMapNumber);
 }
-}
+}  // namespace
 
 namespace MolOps {
 ROMol *adjustQueryProperties(const ROMol &mol,
@@ -166,15 +166,39 @@ void adjustQueryProperties(RWMol &mol, const AdjustQueryParameters *inParams) {
       }
       qa->expandQuery(makeAtomInNRingsQuery(nRings));
     }  // end of adjust ring count
+    if (params.adjustRingChain &&
+        !((params.adjustRingChainFlags & ADJUST_IGNORECHAINS) && !nRings) &&
+        !((params.adjustRingChainFlags & ADJUST_IGNORERINGS) && nRings) &&
+        !((params.adjustRingChainFlags & ADJUST_IGNOREDUMMIES) && !atomicNum) &&
+        !((params.adjustRingChainFlags & ADJUST_IGNORENONDUMMIES) &&
+          atomicNum) &&
+        !((params.adjustRingChainFlags & ADJUST_IGNOREMAPPED) &&
+          isMapped(at))) {
+      QueryAtom *qa;
+      if (!at->hasQuery()) {
+        qa = new QueryAtom(*at);
+        const bool updateLabel = false;
+        const bool preserveProps = true;
+        mol.replaceAtom(i, qa, updateLabel, preserveProps);
+        delete qa;
+        qa = static_cast<QueryAtom *>(mol.getAtomWithIdx(i));
+        at = static_cast<Atom *>(qa);
+      } else {
+        qa = static_cast<QueryAtom *>(at);
+      }
+      ATOM_EQUALS_QUERY *nq = makeAtomInRingQuery();
+      if (!nRings) nq->setNegation(true);
+      qa->expandQuery(nq);
+    }  // end of adjust ring chain
   }    // end of loop over atoms
   if (params.makeBondsGeneric) {
     ROMol::EDGE_ITER firstB, lastB;
     boost::tie(firstB, lastB) = mol.getEdges();
     while (firstB != lastB) {
-      //Bond *bond = mol[*firstB];
+      // Bond *bond = mol[*firstB];
       ++firstB;
     }
   }
 }
-}  // end of MolOps namespace
-}  // end of RDKit namespace
+}  // namespace MolOps
+}  // namespace RDKit

Code/GraphMol/MolOps.h

@@ -286,6 +286,8 @@ struct RDKIT_GRAPHMOL_EXPORT AdjustQueryParameters {
   bool adjustHeavyDegree; /**< adjust the heavy-atom degree instead of overall
                              degree */
   boost::uint32_t adjustHeavyDegreeFlags;
+  bool adjustRingChain; /**< add ring-chain queries */
+  boost::uint32_t adjustRingChainFlags;
 
   AdjustQueryParameters()
       : adjustDegree(true),
@@ -299,7 +301,9 @@ struct RDKIT_GRAPHMOL_EXPORT AdjustQueryParameters {
         makeAtomsGeneric(false),
         makeAtomsGenericFlags(ADJUST_IGNORENONE),
         adjustHeavyDegree(false),
-        adjustHeavyDegreeFlags(ADJUST_IGNOREDUMMIES | ADJUST_IGNORECHAINS) {}
+        adjustHeavyDegreeFlags(ADJUST_IGNOREDUMMIES | ADJUST_IGNORECHAINS),
+        adjustRingChain(false),
+        adjustRingChainFlags(ADJUST_IGNORENONE) {}
 };
 //! returns a copy of a molecule with query properties adjusted
 /*!

Code/GraphMol/Wrap/MolOps.cpp

@@ -2160,7 +2160,7 @@ Attributes:\n\
   - adjustRingCount: \n\
       modified atoms have a ring-count query added based on their ring count in the query \n\
   - adjustRingCountFlags: \n\
-      controls which atoms have a ring-cout query added \n\
+      controls which atoms have a ring-count query added \n\
   - makeDummiesQueries: \n\
       dummy atoms that do not have a specified isotope are converted to any-atom queries \n\
   - aromatizeIfPossible: \n\
@@ -2173,6 +2173,10 @@ Attributes:\n\
       convert atoms to generic (any) atoms \n\
   - makeAtomsGenericFlags: \n\
       controls which atoms are made generic \n\
+  - adjustRingChain: \n\
+      modified atoms have a ring-chain query added based on whether or not they are in a ring \n\
+  - adjustRingChainFlags: \n\
+      controls which atoms have a ring-chain query added \n\
 \n\
 A note on the flags controlling which atoms/bonds are modified: \n\
    These generally limit the set of atoms/bonds to be modified.\n\
@@ -2206,7 +2210,11 @@ A note on the flags controlling which atoms/bonds are modified: \n\
         .def_readwrite("makeAtomsGeneric",
                        &MolOps::AdjustQueryParameters::makeAtomsGeneric)
         .def_readwrite("makeAtomsGenericFlags",
-                       &MolOps::AdjustQueryParameters::makeAtomsGenericFlags);
+                       &MolOps::AdjustQueryParameters::makeAtomsGenericFlags)
+        .def_readwrite("adjustRingChain",
+                       &MolOps::AdjustQueryParameters::adjustRingChain)
+        .def_readwrite("adjustRingChainFlags",
+                       &MolOps::AdjustQueryParameters::adjustRingChainFlags);
 
     docString =
         "Returns a new molecule where the query properties of atoms have been "

Code/GraphMol/molopstest.cpp

@@ -5839,6 +5839,40 @@ void testAdjustQueryProperties() {
     delete qm;
     delete aqm;
   }
+
+  {  // ring-chain membership
+    std::string smiles = "CC1CCC1";
+    ROMol *qm = SmartsToMol(smiles);
+    TEST_ASSERT(qm);
+    TEST_ASSERT(qm->getNumAtoms() == 5);
+    MolOps::AdjustQueryParameters params;
+    params.adjustRingChain = true;
+    params.adjustDegree = false;
+    ROMol *aqm = MolOps::adjustQueryProperties(*qm, &params);
+    TEST_ASSERT(aqm);
+    TEST_ASSERT(aqm->getNumAtoms() == 5);
+    {
+      smiles = "C1CCC12CCC2";
+      ROMol *m = SmilesToMol(smiles);
+      TEST_ASSERT(m);
+      MatchVectType match;
+      TEST_ASSERT(SubstructMatch(*m, *qm, match));
+      TEST_ASSERT(!SubstructMatch(*m, *aqm, match));
+      delete m;
+    }
+    {
+      smiles = "C1CCC1CCC";
+      ROMol *m = SmilesToMol(smiles);
+      TEST_ASSERT(m);
+      MatchVectType match;
+      TEST_ASSERT(SubstructMatch(*m, *qm, match));
+      TEST_ASSERT(SubstructMatch(*m, *aqm, match));
+      delete m;
+    }
+    delete qm;
+    delete aqm;
+  }
+
   BOOST_LOG(rdInfoLog) << "Finished" << std::endl;
 }