diff --git a/Code/GraphMol/MolDraw2D/MolDraw2DSVG.h b/Code/GraphMol/MolDraw2D/MolDraw2DSVG.h
index ab05286ba..8736ac1d9 100644
--- a/Code/GraphMol/MolDraw2D/MolDraw2DSVG.h
+++ b/Code/GraphMol/MolDraw2D/MolDraw2DSVG.h
@@ -69,8 +69,8 @@ class RDKIT_MOLDRAW2D_EXPORT MolDraw2DSVG : public MolDraw2D {
   std::string getDrawingText() const { return d_ss.str(); };
 
   using MolDraw2D::tagAtoms;  // Avoid overload warning.
-
-  void tagAtoms(const ROMol &mol, double radius = 0.2,
+  void tagAtoms(const ROMol &mol) { tagAtoms(mol, 0.2); }
+  void tagAtoms(const ROMol &mol, double radius,
                 const std::map<std::string, std::string> &events = {});
 
   void addMoleculeMetadata(const ROMol &mol, int confId = -1) const;
diff --git a/Code/JavaWrappers/CMakeLists.txt b/Code/JavaWrappers/CMakeLists.txt
index 96533b567..9ea971048 100644
--- a/Code/JavaWrappers/CMakeLists.txt
+++ b/Code/JavaWrappers/CMakeLists.txt
@@ -20,6 +20,7 @@ if(RDK_BUILD_INCHI_SUPPORT)
   set(swigRDKitLibList "${swigRDKitLibList}RDInchiLib;${INCHI_LIBRARIES};")
 endif(RDK_BUILD_INCHI_SUPPORT)
 set(swigRDKitLibList "${swigRDKitLibList}"
+  "SubstructLibrary;"
   "MolStandardize;FilterCatalog;Catalogs;FMCS;MolDraw2D;FileParsers;SmilesParse;"
   "Depictor;SubstructMatch;ChemReactions;Fingerprints;ChemTransforms;"
   "Subgraphs;GraphMol;DataStructs;Trajectory;Descriptors;"
diff --git a/Code/JavaWrappers/SubstructLibrary.i b/Code/JavaWrappers/SubstructLibrary.i
new file mode 100644
index 000000000..ef25ceedd
--- /dev/null
+++ b/Code/JavaWrappers/SubstructLibrary.i
@@ -0,0 +1,96 @@
+/*
+ *  Copyright (c) 2015, Novartis Institutes for BioMedical Research Inc.
+ *  All rights reserved.
+ *
+ * Redistribution and use in source and binary forms, with or without
+ * modification, are permitted provided that the following conditions are
+ * met:
+ *
+ *     * Redistributions of source code must retain the above copyright
+ *       notice, this list of conditions and the following disclaimer.
+ *     * Redistributions in binary form must reproduce the above
+ *       copyright notice, this list of conditions and the following
+ *       disclaimer in the documentation and/or other materials provided
+ *       with the distribution.
+ *     * Neither the name of Novartis Institutes for BioMedical Research Inc.
+ *       nor the names of its contributors may be used to endorse or promote
+ *       products derived from this software without specific prior written permission.
+ *
+ * THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS
+ * "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT
+ * LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR
+ * A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT
+ * OWNER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL,
+ * SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT
+ * LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE,
+ * DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY
+ * THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT
+ * (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE
+ * OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
+ */
+
+//%import "ROMol.i"
+%include "std_vector.i"
+
+
+%{
+#include <GraphMol/SubstructLibrary/SubstructLibrary.h>
+%}
+%shared_ptr(RDKit::MolHolderBase)
+%shared_ptr(RDKit::MolHolder)
+%shared_ptr(RDKit::CachedMolHolder)
+%shared_ptr(RDKit::CachedSmilesMolHolder)
+%shared_ptr(RDKit::CachedTrustedSmilesMolHolder)
+%shared_ptr(RDKit::FPHolderBase)
+%shared_ptr(RDKit::PatternHolder)
+
+%template(UChar_Vect) std::vector<unsigned char>;
+
+%typemap(javacode) RDKit::SubstructLibrary %{
+     public static SubstructLibrary Deserialize(byte[] b) {
+     UChar_Vect vec = new UChar_Vect();
+     vec.reserve(b.length);
+     for (int size=0;size<b.length;++size) {
+       vec.add(b[size]);
+     }
+     return new SubstructLibrary(vec);
+   }
+%}
+
+%extend RDKit::SubstructLibrary {
+  SubstructLibrary(const std::vector<unsigned char> & data ) {
+    std::string str(data.begin(), data.end());
+    return new RDKit::SubstructLibrary(str);
+  }
+
+  bool canSerialize() const {
+    return RDKit::SubstructLibraryCanSerialize();
+  }
+}
+
+
+#ifdef SWIGJAVA
+%typemap(jni) std::string RDKit::SubstructLibrary::Serialize "jbyteArray"
+%typemap(jtype) std::string RDKit::SubstructLibrary::Serialize "byte[]"
+%typemap(jstype) std::string RDKit::SubstructLibrary::Serialize "byte[]"
+%typemap(javaout) std::string RDKit::SubstructLibrary::Serialize {
+  return $jnicall;
+}
+%typemap(out) std::string RDKit::SubstructLibrary::Serialize {
+  $result = JCALL1(NewByteArray, jenv, $1.size());
+  JCALL4(SetByteArrayRegion, jenv, $result, 0, $1.size(), (const jbyte*)$1.c_str());
+}
+#endif
+
+%include <GraphMol/SubstructLibrary/SubstructLibrary.h>
+
+%pragma(java) modulecode=%{
+   public static SubstructLibrary SubstructLibraryDeserialize(byte[] b) {
+     UChar_Vect vec = new UChar_Vect();
+     vec.reserve(b.length);
+     for (int size=0;size<b.length;++size) {
+       vec.add(b[size]);
+     }
+     return new SubstructLibrary(vec);
+   }
+%}
diff --git a/Code/JavaWrappers/csharp_wrapper/GraphMolCSharp.i b/Code/JavaWrappers/csharp_wrapper/GraphMolCSharp.i
index 364854d29..68601828f 100644
--- a/Code/JavaWrappers/csharp_wrapper/GraphMolCSharp.i
+++ b/Code/JavaWrappers/csharp_wrapper/GraphMolCSharp.i
@@ -246,6 +246,7 @@ typedef unsigned long long int	uintmax_t;
 %include "../MolDraw2D.i"
 %include "../FilterCatalog.i"
 %include "../Trajectory.i"
+%include "../SubstructLibrary.i"
 
 // Create a class to throw various sorts of errors for testing.  Required for unit tests in ErrorHandlingTests.java
 #ifdef INCLUDE_ERROR_GENERATOR
diff --git a/Code/JavaWrappers/gmwrapper/CMakeLists.txt b/Code/JavaWrappers/gmwrapper/CMakeLists.txt
index 48f5c9f2a..216012f8e 100644
--- a/Code/JavaWrappers/gmwrapper/CMakeLists.txt
+++ b/Code/JavaWrappers/gmwrapper/CMakeLists.txt
@@ -340,6 +340,11 @@ ADD_TEST(JavaFilterCatalogTests
 	-cp "${JUNIT_JAR}${PATH_SEP}${CMAKE_JAVA_TEST_OUTDIR}${PATH_SEP}${CMAKE_CURRENT_SOURCE_DIR}/org.RDKit.jar"
 	org.RDKit.FilterCatalogTests)
 
+ADD_TEST(JavaSubstructLibraryTests
+    java -Djava.library.path=${CMAKE_CURRENT_SOURCE_DIR}
+	-cp "${JUNIT_JAR}${PATH_SEP}${CMAKE_JAVA_TEST_OUTDIR}${PATH_SEP}${CMAKE_CURRENT_SOURCE_DIR}/org.RDKit.jar"
+	org.RDKit.SubstructLibraryTests)
+
 ADD_TEST(JavaDiversityPickerTests
 	    java -Djava.library.path=${CMAKE_CURRENT_SOURCE_DIR}
 		-cp "${JUNIT_JAR}${PATH_SEP}${CMAKE_JAVA_TEST_OUTDIR}${PATH_SEP}${CMAKE_CURRENT_SOURCE_DIR}/org.RDKit.jar"
diff --git a/Code/JavaWrappers/gmwrapper/GraphMolJava.i b/Code/JavaWrappers/gmwrapper/GraphMolJava.i
index b21ad452f..2a20d1024 100644
--- a/Code/JavaWrappers/gmwrapper/GraphMolJava.i
+++ b/Code/JavaWrappers/gmwrapper/GraphMolJava.i
@@ -224,6 +224,7 @@ typedef unsigned long long int	uintmax_t;
 %include "../FilterCatalog.i"
 %include "../Trajectory.i"
 %include "../MolStandardize.i"
+%include "../SubstructLibrary.i"
 
 // Create a class to throw various sorts of errors for testing.  Required for unit tests in ErrorHandlingTests.java
 #ifdef INCLUDE_ERROR_GENERATOR
diff --git a/Code/JavaWrappers/gmwrapper/src-test/org/RDKit/SubstructLibraryTests.java b/Code/JavaWrappers/gmwrapper/src-test/org/RDKit/SubstructLibraryTests.java
new file mode 100644
index 000000000..b1ff0c0f6
--- /dev/null
+++ b/Code/JavaWrappers/gmwrapper/src-test/org/RDKit/SubstructLibraryTests.java
@@ -0,0 +1,246 @@
+/* 
+ *
+ *  Copyright (c) 2018, Novartis Institutes for BioMedical Research Inc.
+ *  All rights reserved.
+ * 
+ * Redistribution and use in source and binary forms, with or without
+ * modification, are permitted provided that the following conditions are
+ * met: 
+ *
+ *     * Redistributions of source code must retain the above copyright 
+ *       notice, this list of conditions and the following disclaimer.
+ *     * Redistributions in binary form must reproduce the above
+ *       copyright notice, this list of conditions and the following 
+ *       disclaimer in the documentation and/or other materials provided 
+ *       with the distribution.
+ *     * Neither the name of Novartis Institutes for BioMedical Research Inc. 
+ *       nor the names of its contributors may be used to endorse or promote 
+ *       products derived from this software without specific prior written permission.
+ *
+ * THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS
+ * "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT
+ * LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR
+ * A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT
+ * OWNER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL,
+ * SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT
+ * LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE,
+ * DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY
+ * THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT
+ * (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE
+ * OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
+ */
+package org.RDKit;
+
+import static org.junit.Assert.*;
+import org.junit.*;
+    
+public class SubstructLibraryTests extends GraphMolTest {
+	private ROMol mol;
+        private ROMol m;
+
+	@Before public void setUp() {
+	}
+
+	@Test 
+	public void test1Basics() {
+            SubstructLibrary lib = new SubstructLibrary();
+            assertEquals(0, lib.size());
+            // mol holders
+            MolHolder mh = new MolHolder();
+            assertEquals(0, mh.size());
+            CachedMolHolder cmh = new CachedMolHolder();
+            assertEquals(0, cmh.size());
+            CachedSmilesMolHolder csmh = new CachedSmilesMolHolder();
+            assertEquals(0, csmh.size());
+            CachedTrustedSmilesMolHolder ctsmh = new CachedTrustedSmilesMolHolder();
+            assertEquals(0, ctsmh.size());
+
+            // fpholder - can we create it...
+            PatternHolder ph = new PatternHolder();
+
+            // Now lets make some molecules
+            mol = RWMol.MolFromSmiles("c1ccccc1");
+            String smiles = mol.MolToSmiles();
+            
+            mh.addMol(mol);
+            assertEquals(1, mh.size());
+            cmh.addMol(mol);
+            assertEquals(1, cmh.size());
+            csmh.addMol(mol);
+            assertEquals(1, csmh.size());
+            ctsmh.addMol(mol);
+            assertEquals(1, ctsmh.size());
+            
+            m = mh.getMol(0);
+            assertEquals(smiles, m.MolToSmiles());
+            m = cmh.getMol(0);
+            assertEquals(smiles, m.MolToSmiles());
+            m = csmh.getMol(0);
+            assertEquals(smiles, m.MolToSmiles());
+            m = ctsmh.getMol(0);
+            assertEquals(smiles, m.MolToSmiles());
+
+            mol = RWMol.MolFromSmiles("CCN");
+            smiles = mol.MolToSmiles();
+
+            mh.addMol(mol);
+            assertEquals(2, mh.size());
+            cmh.addMol(mol);
+            assertEquals(2, mh.size());
+            
+            csmh.addSmiles("CCN");
+            assertEquals(2, csmh.size());
+            ctsmh.addSmiles("CCN");
+            assertEquals(2, ctsmh.size());
+
+            m = mh.getMol(1);
+            assertEquals(smiles, m.MolToSmiles());
+            m = cmh.getMol(1);
+            assertEquals(smiles, m.MolToSmiles());
+            m = csmh.getMol(1);
+            assertEquals(smiles, m.MolToSmiles());
+            m = ctsmh.getMol(1);
+            assertEquals(smiles, m.MolToSmiles());
+	}
+
+
+  	@Test 
+	public void test2Basics() {
+            MolHolder mh = new MolHolder();
+            assertEquals(0, mh.size());
+            CachedMolHolder cmh = new CachedMolHolder();
+            assertEquals(0, cmh.size());
+            CachedSmilesMolHolder csmh = new CachedSmilesMolHolder();
+            assertEquals(0, csmh.size());
+            CachedTrustedSmilesMolHolder ctsmh = new CachedTrustedSmilesMolHolder();
+            assertEquals(0, ctsmh.size());
+            mol = RWMol.MolFromSmiles("c1ccccc1");
+            // mol holder
+            SubstructLibrary lib = new SubstructLibrary(mh);
+            SubstructLibrary lib2;
+            lib.addMol(mol);
+            
+            UInt_Vect matches = lib.getMatches(mol);
+            assertEquals(1, matches.size());
+
+            if(lib.canSerialize()) {
+                byte pickle[] = lib.Serialize();
+                assertTrue(pickle != null);
+                lib2 = SubstructLibrary.Deserialize(pickle);
+                assertFalse(lib2 == null);
+                assertEquals(lib.size(), 1);
+                matches = lib.getMatches(mol);
+                assertEquals(1, matches.size());
+            }
+            
+            // cached mol holder
+            lib = new SubstructLibrary(cmh);
+            lib.addMol(mol);
+
+            matches = lib.getMatches(mol);
+            assertEquals(1, matches.size());
+
+            if(lib.canSerialize()) {
+                byte pickle[] = lib.Serialize();
+                assertTrue(pickle != null);
+                lib2 = SubstructLibrary.Deserialize(pickle);
+                assertFalse(lib2 == null);
+                assertEquals(lib.size(), 1);
+                matches = lib.getMatches(mol);
+                assertEquals(1, matches.size());
+            }
+
+            // cached smiles mol holder
+            lib = new SubstructLibrary(csmh);
+            lib.addMol(mol);
+
+            matches = lib.getMatches(mol);
+            assertEquals(1, matches.size());
+
+            if(lib.canSerialize()) {
+                byte pickle[] = lib.Serialize();
+                assertTrue(pickle != null);
+                lib2 = SubstructLibrary.Deserialize(pickle);
+                assertFalse(lib2 == null);
+                assertEquals(lib.size(), 1);
+                matches = lib.getMatches(mol);
+                assertEquals(1, matches.size());
+            }
+            
+            // cached trusted smiles mol holder
+            lib = new SubstructLibrary(ctsmh);
+            lib.addMol(mol);
+
+            matches = lib.getMatches(mol);
+            assertEquals(1, matches.size());
+
+            if(lib.canSerialize()) {
+                byte pickle[] = lib.Serialize();
+                assertTrue(pickle != null);
+                lib2 = SubstructLibrary.Deserialize(pickle);
+                assertFalse(lib2 == null);
+                assertEquals(lib.size(), 1);
+                matches = lib.getMatches(mol);
+                assertEquals(1, matches.size());
+            }
+            
+        }
+
+  	@Test 
+	public void test3Basics() {
+            MolHolder mh = new MolHolder();
+            PatternHolder pat = new PatternHolder();
+            assertEquals(0, mh.size());
+            CachedMolHolder cmh = new CachedMolHolder();
+            assertEquals(0, cmh.size());
+            CachedSmilesMolHolder csmh = new CachedSmilesMolHolder();
+            assertEquals(0, csmh.size());
+            CachedTrustedSmilesMolHolder ctsmh = new CachedTrustedSmilesMolHolder();
+            assertEquals(0, ctsmh.size());
+            mol = RWMol.MolFromSmiles("c1ccccc1");
+            // mol holder
+            SubstructLibrary lib = new SubstructLibrary(mh, pat);
+            lib.addMol(mol);
+            
+            UInt_Vect matches = lib.getMatches(mol);
+            assertEquals(1, matches.size());
+
+            // cached mol holder
+            try {
+              lib = new SubstructLibrary(cmh, pat);
+              lib.addMol(mol);
+              assertTrue(false); // shouldn't get here can't share patternholder and addmol
+            } catch(Exception e) {
+              // ok to get here
+            }
+            cmh = new CachedMolHolder();
+            pat = new PatternHolder();
+            lib = new SubstructLibrary(cmh, pat);
+            lib.addMol(mol);
+            matches = lib.getMatches(mol);
+            assertEquals(1, matches.size());
+
+            // cached smiles mol holder
+            pat = new PatternHolder();
+            lib = new SubstructLibrary(csmh, pat);
+            lib.addMol(mol);
+
+            matches = lib.getMatches(mol);
+            assertEquals(1, matches.size());
+            
+            // cached trusted smiles mol holder
+            pat = new PatternHolder();
+            lib = new SubstructLibrary(ctsmh, pat);
+            lib.addMol(mol);
+
+            matches = lib.getMatches(mol);
+            assertEquals(1, matches.size());
+        }
+
+    
+  
+	public static void main(String args[]) {
+		org.junit.runner.JUnitCore.main("org.RDKit.SubstructLibraryTests");
+	}
+
+}