#1372 Wildcard symbol ('any') with logical operators at custom query…

… for bond is missing at SMARTS (#1386)

api/tests/integration/ref/formats/smarts.py.out

@@ -96,3 +96,7 @@ Smarts [C]!-[C] loaded as smarts - OK.
 Smarts [C]-,=[C] loaded as smarts - OK.
 Smarts [C]-;=[C] loaded as smarts - OK.
 Smarts [C]-&=[C] loaded as smarts - OK.
+*******  Any wildcard '~' in bond custom query *******
+[#7]~,-[#6] is ok. smarts_in==smarts_out
+[#7]~,-[#6] is ok. json_in==json_out
+[#7]~,-[#6] is ok. expected string found in json

api/tests/integration/tests/formats/smarts.py

@@ -244,3 +244,7 @@ def test_smarts_load_save_through_ket(
         print("Smarts %s loaded as smarts - OK." % smarts)
     else:
         print("Smarts %s loaded as %s - FAILED" % (smarts, format))
+print("*******  Any wildcard '~' in bond custom query *******")
+smarts = "[#7]~,-[#6]"
+expected = '"bonds":[{"customQuery":"~,-","atoms":[0,1]}]}}'
+test_smarts_load_save_through_ket(smarts, expected)

core/indigo-core/molecule/query_molecule.h

@@ -102,6 +102,7 @@ namespace indigo
 
             BOND_ORDER,
             BOND_TOPOLOGY,
+            BOND_ANY,
 
             HIGHLIGHTING
         };
@@ -147,6 +148,7 @@ namespace indigo
             // Check if there is no other constraint, except specified ones
             bool hasNoConstraintExcept(int what_type);
             bool hasNoConstraintExcept(int what_type1, int what_type2);
+            bool hasNoConstraintExcept(std::vector<int> what_types);
 
             // Remove all constraints of the given type
             void removeConstraints(int what_type);
@@ -248,6 +250,7 @@ namespace indigo
         {
         public:
             Bond();
+            Bond(int type_);
             Bond(int type_, int value_);
             Bond(int type_, int value_, int direction_);
             ~Bond() override;

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

@@ -297,7 +297,7 @@ bool AromaticityMatcher::match(int* core_sub, int* core_super)
             return false;
         }
 
-        bool has_other = !qbond.hasNoConstraintExcept(QueryMolecule::BOND_ORDER, QueryMolecule::BOND_TOPOLOGY);
+        bool has_other = !qbond.hasNoConstraintExcept({QueryMolecule::BOND_ORDER, QueryMolecule::BOND_TOPOLOGY, QueryMolecule::BOND_ANY});
         if (has_other)
             throw Error("Only bond with order and topology constraints are supported");
 

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

@@ -541,6 +541,8 @@ bool MoleculeSubstructureMatcher::matchQueryBond(QueryMolecule::Bond* query, Bas
     case QueryMolecule::OP_NOT:
         return !matchQueryBond(query->child(0), target, sub_idx, super_idx, am, flags ^ MATCH_DISABLED_AS_TRUE);
 
+    case QueryMolecule::BOND_ANY:
+        return true;
     case QueryMolecule::BOND_ORDER: {
         if (flags & MATCH_BOND_TYPE)
         {

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

@@ -399,6 +399,10 @@ void QueryMolecule::writeSmartsBond(Output& output, Bond* bond, bool has_or_pare
             output.writeString("!@");
         break;
     }
+    case BOND_ANY: {
+        output.writeChar('~');
+        break;
+    }
     default:
         throw Error("Unexpected bond type: %d", bond->type);
     }
@@ -743,6 +747,9 @@ void QueryMolecule::_getBondDescription(Bond* bond, Output& out)
     case BOND_TOPOLOGY:
         out.printf("%s", bond->value == TOPOLOGY_RING ? "ring" : "chain");
         return;
+    case BOND_ANY:
+        out.writeChar('~');
+        return;
     default:
         out.printf("<constraint of type %d>", bond->type);
     }
@@ -931,6 +938,10 @@ QueryMolecule::Bond::Bond() : Node(OP_NONE), value(0), direction(0)
 {
 }
 
+QueryMolecule::Bond::Bond(int type_) : Node(type_), value(0), direction(0)
+{
+}
+
 QueryMolecule::Bond::Bond(int type_, int value_) : Node(type_), value(value_), direction(0)
 {
 }
@@ -1768,6 +1779,8 @@ bool QueryMolecule::Bond::_possibleValuePair(int what_type1, int what_value1, in
         return what_value1 == value;
     if (type == what_type2)
         return what_value2 == value;
+    if (type == BOND_ANY)
+        return true;
     return false;
 }
 
@@ -1947,6 +1960,25 @@ bool QueryMolecule::Node::hasNoConstraintExcept(int what_type1, int what_type2)
     return type == what_type1 || type == what_type2;
 }
 
+bool QueryMolecule::Node::hasNoConstraintExcept(std::vector<int> what_types)
+{
+    if (type == OP_NONE)
+        return true;
+
+    if (type == OP_AND || type == OP_OR || type == OP_NOT)
+    {
+        int i;
+
+        for (i = 0; i < children.size(); i++)
+            if (!children[i]->hasNoConstraintExcept(what_types))
+                return false;
+
+        return true;
+    }
+
+    return std::any_of(what_types.cbegin(), what_types.cend(), [this](int i) { return type == i; });
+}
+
 void QueryMolecule::Node::removeConstraints(int what_type)
 {
     if (type == what_type)

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

@@ -2636,6 +2636,13 @@ void SmilesLoader::_readBondSub(Array<char>& bond_str, _BondDesc& bond, std::uni
         else if (order == _ANY_BOND)
         {
             bond.type = order;
+            if (qbond.get() != 0)
+            {
+                if (subqbond.get() == 0)
+                    subqbond = std::make_unique<QueryMolecule::Bond>(QueryMolecule::BOND_ANY);
+                else
+                    subqbond.reset(QueryMolecule::Bond::und(subqbond.release(), new QueryMolecule::Bond(QueryMolecule::BOND_ANY)));
+            }
         }
 
         if (topology > 0)