Added fingerprints to GeneralizedSubstruct search and extended SWIG wrappers (#6991)

* Added fingerprints to GeneralizedSubstruct search

* Small change to fire tests

* Edits from code review

* Updated swig - newobject not required for GeneralizedSubstruct fingerprint methods

* GeneralizedSubstruct only supports unique_ptr in SWIG4.1

Code/JavaWrappers/GeneralizedSubstruct.i

@@ -1,10 +1,21 @@
 
+
+#if SWIG_VERSION >= 0x040101                 
+%include <std_unique_ptr.i>
+%unique_ptr(ExplicitBitVect)
+#endif
+
 %{
 #include <GraphMol/GeneralizedSubstruct/XQMol.h>
 %}
 // %include "std_unique_ptr.i"
 // %unique_ptr(ExtendedQueryMol)
 
+#if SWIG_VERSION < 0x040101                 
+%ignore patternFingerprintTargetMol(const ROMol &mol, unsigned int fpSize = 2048U);
+%ignore patternFingerprintQuery(unsigned int fpSize = 2048U) const;
+#endif
+
 %ignore ExtendedQueryMol(std::unique_ptr<RWMol> mol);
 %ignore ExtendedQueryMol(std::unique_ptr<MolBundle> mol);
 %ignore ExtendedQueryMol(std::unique_ptr<TautomerQuery> mol);
@@ -14,3 +25,9 @@
 
 %include "GraphMol/GeneralizedSubstruct/XQMol.h";
 
+%extend RDKit::GeneralizedSubstruct::ExtendedQueryMol  {
+  std::vector< std::vector<std::pair<int, int> > > getSubstructMatches(RDKit::ROMol &target,RDKit::SubstructMatchParameters ps = RDKit::SubstructMatchParameters()){
+    std::vector<RDKit::MatchVectType> mvs = SubstructMatch(target, *($self),ps);
+    return mvs;
+  };
+}

Code/JavaWrappers/csharp_wrapper/GraphMolCSharp.i

@@ -245,6 +245,7 @@ typedef unsigned long long int	uintmax_t;
 %include "../MolHash.i"
 %include "../Abbreviations.i"
 %include "../Streams.i"
+%include "../GeneralizedSubstruct.i"
 
 
 // Create a class to throw various sorts of errors for testing.  Required for unit tests in ErrorHandlingTests.java

Code/JavaWrappers/csharp_wrapper/RDKitCSharpTest/GeneralizedSubstructTest.cs

@@ -0,0 +1,56 @@
+using GraphMolWrap;
+using Xunit;
+
+namespace RdkitTests
+{
+    public class GeneralizedSubstructTest
+    {
+        private bool FingerprintsMatch(ExtendedQueryMol queryMol, RWMol target)
+        {
+            var queryFingerprint = queryMol.patternFingerprintQuery();
+            var targetFingerprint = RDKFuncs.patternFingerprintTargetMol(target);
+            Assert.True(queryFingerprint.getNumOnBits() > 0);
+            Assert.True(targetFingerprint.getNumOnBits() > 0);
+            var match = RDKFuncs.AllProbeBitsMatch(queryFingerprint, targetFingerprint);
+            return match;
+        }
+
+        [Fact]
+        public void TestControlSteps()
+        {
+            var queryMol = RWMol.MolFromSmiles("COCC1OC(N)=N1 |LN:1:1.3|");
+            var xqm1 = RDKFuncs.createExtendedQueryMol(queryMol);
+            var xqm2 = RDKFuncs.createExtendedQueryMol(queryMol, false);
+            var xqm3 = RDKFuncs.createExtendedQueryMol(queryMol, true, false);
+            var xqm4 = RDKFuncs.createExtendedQueryMol(queryMol, false, false);
+
+            var mol1 = RWMol.MolFromSmiles("COCC1OC(N)=N1");
+            Assert.Equal(1, xqm1.getSubstructMatches(mol1).Count);
+            Assert.Equal(1, xqm2.getSubstructMatches(mol1).Count);
+            Assert.Equal(1, xqm3.getSubstructMatches(mol1).Count);
+            Assert.Equal(1, xqm4.getSubstructMatches(mol1).Count);
+            Assert.True(FingerprintsMatch(xqm1, mol1));
+            Assert.True(FingerprintsMatch(xqm2, mol1));
+            Assert.True(FingerprintsMatch(xqm3, mol1));
+            Assert.True(FingerprintsMatch(xqm4, mol1));
+
+            var mol2 = RWMol.MolFromSmiles("COCC1OC(=N)N1");
+            Assert.Equal(1, xqm1.getSubstructMatches(mol2).Count);
+            Assert.Equal(1, xqm2.getSubstructMatches(mol2).Count);
+            Assert.Equal(0, xqm3.getSubstructMatches(mol2).Count);
+            Assert.Equal(0, xqm4.getSubstructMatches(mol2).Count);
+            Assert.True(FingerprintsMatch(xqm1, mol2));
+            Assert.True(FingerprintsMatch(xqm2, mol2));
+            Assert.False(FingerprintsMatch(xqm3, mol2));
+            Assert.False(FingerprintsMatch(xqm4, mol2));
+
+            var mol3 = RWMol.MolFromSmiles("COOCC1OC(N)=N1");
+            Assert.Equal(1, xqm1.getSubstructMatches(mol3).Count);
+            Assert.Equal(0, xqm2.getSubstructMatches(mol3).Count);
+            Assert.Equal(1, xqm3.getSubstructMatches(mol3).Count);
+            Assert.Equal(0, xqm4.getSubstructMatches(mol3).Count);
+            Assert.True(FingerprintsMatch(xqm1, mol3));
+            Assert.True(FingerprintsMatch(xqm3, mol3));
+        }
+    }
+}