diff --git a/create_database/tuple_reader/RecoIndexer.cc b/create_database/tuple_reader/GraphDef.cc
similarity index 86%
rename from create_database/tuple_reader/RecoIndexer.cc
rename to create_database/tuple_reader/GraphDef.cc
index 8e807b2..3bfaff9 100644
--- a/create_database/tuple_reader/RecoIndexer.cc
+++ b/create_database/tuple_reader/GraphDef.cc
@@ -1,16 +1,16 @@
-#include "RecoIndexer.h"
 #include "BDtaunuDef.h"
+#include "GraphDef.h"
 
 #include <cmath>
 #include <cstdlib>
 #include <cassert>
 #include <initializer_list>
 
-RecoIndexer::RecoIndexer() : 
+RecoGraph::RecoIndexer::RecoIndexer() : 
   nY(0), nB(0), nD(0), nC(0), 
   nh(0), nl(0), ngamma(0) {};
 
-RecoIndexer::RecoIndexer(
+RecoGraph::RecoIndexer::RecoIndexer(
     int _nY, int _nB, int _nD, 
     int _nC, int _nh, int _nl, int _ngamma) : 
     nY(_nY), nB(_nB), nD(_nD), nC(_nC), 
@@ -23,7 +23,7 @@ RecoIndexer::RecoIndexer(
 // C candidates: ... continue pattern.
 // h candidates: ... continue pattern.
 // gamma candidates: ... continue pattern.
-int RecoIndexer::operator()(int lund, int idx) const {
+int RecoGraph::RecoIndexer::operator()(int lund, int idx) const {
 
   int abslund = std::abs(lund);
   switch (abslund) {
@@ -54,7 +54,7 @@ int RecoIndexer::operator()(int lund, int idx) const {
   return -1;
 }
 
-void RecoIndexer::clear() {
+void RecoGraph::RecoIndexer::clear() {
   nY = 0;
   nB = 0;
   nD = 0;
@@ -64,7 +64,7 @@ void RecoIndexer::clear() {
   ngamma = 0;
 }
 
-void RecoIndexer::set(std::initializer_list<int> l) {
+void RecoGraph::RecoIndexer::set(std::initializer_list<int> l) {
 
   assert(l.size() == 7);
 
diff --git a/create_database/tuple_reader/GraphDef.h b/create_database/tuple_reader/GraphDef.h
index e38c9c7..36625b3 100644
--- a/create_database/tuple_reader/GraphDef.h
+++ b/create_database/tuple_reader/GraphDef.h
@@ -1,8 +1,11 @@
 #ifndef __GRAPHDEF_H_
 #define __GRAPHDEF_H_
 
+#include <initializer_list>
 #include <boost/graph/adjacency_list.hpp>
 
+#include "BDtaunuDef.h"
+
 namespace boost {
   enum vertex_lund_id_t { vertex_lund_id };
   BOOST_INSTALL_PROPERTY(vertex, lund_id);
@@ -33,8 +36,85 @@ typedef typename boost::property_map<Graph, boost::vertex_lund_id_t>::type LundI
 typedef typename boost::property_map<Graph, boost::vertex_reco_index_t>::type RecoIndexPropertyMap;
 typedef typename boost::property_map<Graph, boost::vertex_block_index_t>::type BlockIndexPropertyMap;
 
+struct RecoLepton {
+  int l_block_idx = -1;
+  int pi_block_idx = -1;
+  int tau_mode = static_cast<int>(bdtaunu::TauType::null);
+};
+
+struct RecoD {
+  RecoD() = default;
+  int D_mode = static_cast<int>(bdtaunu::RecoDTypeCatalogue::DType::null);
+  int Dstar_mode = static_cast<int>(bdtaunu::RecoDTypeCatalogue::DstarType::NoDstar);
+};
+
+struct RecoB {
+  RecoB() = default;
+  int flavor = static_cast<int>(bdtaunu::BFlavor::null);
+  RecoD *D = nullptr;
+  RecoLepton *Lepton = nullptr;
+};
+
+struct RecoY {
+  RecoY() = default;
+  RecoB *tagB = nullptr;
+  RecoB *sigB = nullptr;
+};
+
+/** @brief This class assigns a unique index to each reconstructed particle.
+ *
+ * @detail 
+ * # Motivation
+ * The need for every reconstructed particle of the event to have a unique
+ * index arises primarily in accessessing vertex information in the BGL graph. 
+ * However, such an indexing is more convenient to use than the existing 
+ * BtaTupleMaker indexing. 
+ *
+ * # Implementation
+ * This class builds a hash function from the reco particle's index in the 
+ * BtaTupleMaker block to a unique index. 
+ *
+ * See RecoIndexer.cc for details.
+ */
+class RecoIndexer {
+
+  private:
+    int nY, nB, nD, nC, nh, nl, ngamma;
+
+  public:
+    RecoIndexer();
+    RecoIndexer(int _nY, int _nB, int _nD, 
+                int _nC, int _nh, int _nl, int _ngamma);
+    RecoIndexer(const RecoIndexer &r) = default;
+    RecoIndexer &operator=(const RecoIndexer &r) = default;
+    ~RecoIndexer() {};
+
+    //! Given the lundId and block index, return the unique reco index.
+    int operator()(int lund, int idx) const;
+
+    //! Return total number of reco particles in this event. 
+    int total() const { return nY + nB + nD + nC + nh + nl + ngamma; }
+
+    //! Set the total number of each type of reco particle.
+    /*! The list order is { nY, nB, nD, nC, nh, nl, ngamma } */
+    void set(std::initializer_list<int> l);
+
+    //! Clear cache.
+    void clear();
+};
+
 }
 
+
+
+
+
+
+
+
+
+
+
 namespace boost {
   enum vertex_mc_index_t { vertex_mc_index };
   BOOST_INSTALL_PROPERTY(vertex, mc_index);
@@ -56,6 +136,25 @@ typedef typename boost::graph_traits<Graph>::adjacency_iterator AdjacencyIterato
 typedef typename boost::property_map<Graph, boost::vertex_lund_id_t>::type LundIdPropertyMap;
 typedef typename boost::property_map<Graph, boost::vertex_mc_index_t>::type McIndexPropertyMap;
 
+struct McTau {
+  McTau() = default;
+  int mc_type = static_cast<int>(bdtaunu::TauMcType::null);
+};
+
+struct McB {
+  McB() = default;
+  int flavor = static_cast<int>(bdtaunu::BFlavor::null);
+  int mc_type = static_cast<int>(bdtaunu::McBTypeCatalogue::BMcType::null);
+  McTau *tau = nullptr;
+};
+
+struct McY {
+  McY() = default;
+  bool isBBbar = true;
+  McB *B1 = nullptr;
+  McB *B2 = nullptr;
+};
+
 }
 
 #endif
diff --git a/create_database/tuple_reader/Makefile b/create_database/tuple_reader/Makefile
index 5e328d1..56a05fd 100644
--- a/create_database/tuple_reader/Makefile
+++ b/create_database/tuple_reader/Makefile
@@ -13,10 +13,10 @@ LIBNAME = libTupleReader.so
 PKG_LIBPATH = lib
 
 # package Contents
-SOURCES = BDtaunuDef.cc \
+SOURCES = BDtaunuDef.cc GraphDef.cc \
           BDtaunuHelpers.cc UpsilonCandidate.cc \
 					RootReader.cc BDtaunuReader.cc BDtaunuMcReader.cc \
-					RecoIndexer.cc RecoGraphVisitors.cc RecoGraphManager.cc \
+					RecoGraphVisitors.cc RecoGraphManager.cc \
 					McGraphManager.cc McGraphVisitors.cc
 
 # Dependencies
diff --git a/create_database/tuple_reader/McGraphManager.cc b/create_database/tuple_reader/McGraphManager.cc
index 9c55fdf..0b2a6f1 100644
--- a/create_database/tuple_reader/McGraphManager.cc
+++ b/create_database/tuple_reader/McGraphManager.cc
@@ -8,7 +8,6 @@
 
 #include "BDtaunuDef.h"
 #include "GraphDef.h"
-#include "Particles.h"
 #include "BDtaunuMcReader.h"
 #include "McGraphManager.h"
 #include "BDtaunuGraphWriter.h"
diff --git a/create_database/tuple_reader/McGraphManager.h b/create_database/tuple_reader/McGraphManager.h
index d4e04e4..ef5e745 100644
--- a/create_database/tuple_reader/McGraphManager.h
+++ b/create_database/tuple_reader/McGraphManager.h
@@ -7,7 +7,6 @@
 
 #include "GraphManager.h"
 #include "GraphDef.h"
-#include "Particles.h"
 #include "McGraphVisitors.h"
 
 class BDtaunuMcReader;
@@ -112,13 +111,13 @@ class McGraphManager : public GraphManager {
     void clear();
 
     //! Returns pointer to the MC truth \f$\Upsilon(4S)\f$ if it exists, nullptr otherwise.
-    const McY* get_mcY() const;
+    const McGraph::McY* get_mcY() const;
 
     //! Returns pointer to one of the MC truth \f$B\f$ if it exists, nullptr otherwise.
-    const McB* get_mcB1() const;
+    const McGraph::McB* get_mcB1() const;
 
     //! Returns pointer to the other MC truth \f$B\f$ if it exists, nullptr otherwise.
-    const McB* get_mcB2() const;
+    const McGraph::McB* get_mcB2() const;
 
   private:
 
@@ -138,9 +137,9 @@ class McGraphManager : public GraphManager {
     void ClearGraph();
 
     // Graph analysis
-    std::map<McGraph::Vertex, McY> Y_map;
-    std::map<McGraph::Vertex, McB> B_map;
-    std::map<McGraph::Vertex, McTau> Tau_map;
+    std::map<McGraph::Vertex, McGraph::McY> Y_map;
+    std::map<McGraph::Vertex, McGraph::McB> B_map;
+    std::map<McGraph::Vertex, McGraph::McTau> Tau_map;
     void ClearAnalysis();
 
 };
diff --git a/create_database/tuple_reader/McGraphVisitors.cc b/create_database/tuple_reader/McGraphVisitors.cc
index 77eba01..60ca695 100644
--- a/create_database/tuple_reader/McGraphVisitors.cc
+++ b/create_database/tuple_reader/McGraphVisitors.cc
@@ -4,7 +4,6 @@
 
 #include "BDtaunuDef.h"
 #include "GraphDef.h"
-#include "Particles.h"
 #include "McGraphVisitors.h"
 #include "McGraphManager.h"
 
@@ -70,7 +69,7 @@ void McGraphDfsVisitor::AnalyzeY(const Vertex &u, const Graph &g) {
 // Analyze B meson. The quantities computed are:
 // 1. B flavor. 
 // 2. Pointer to daughter tau. 
-// 3. MC type. See Particles.h.
+// 3. MC type. See GraphDef.h.
 void McGraphDfsVisitor::AnalyzeB(const Vertex &u, const Graph &g) {
 
   McB mcB;
@@ -98,7 +97,7 @@ void McGraphDfsVisitor::AnalyzeB(const Vertex &u, const Graph &g) {
 }
 
 // Analyze tau. The quantities computed are:
-// 1. MC type. See Particles.h.
+// 1. MC type. See GraphDef.h.
 void McGraphDfsVisitor::AnalyzeTau(const Vertex &u, const Graph &g) {
 
   McTau mcTau;
diff --git a/create_database/tuple_reader/Particles.h b/create_database/tuple_reader/Particles.h
deleted file mode 100644
index d16e5fd..0000000
--- a/create_database/tuple_reader/Particles.h
+++ /dev/null
@@ -1,63 +0,0 @@
-#ifndef _PARTICLES_H_
-#define _PARTICLES_H_
-
-#include "BDtaunuDef.h"
-#include "GraphDef.h"
-
-/** @file Particles.h 
- * Information of specific types of particles that are computed
- * during graph traversal (see RecoGraphManager.h or McGraphManager.h).
- */
-
-struct RecoB;
-struct RecoD;
-struct RecoLepton;
-
-struct RecoY {
-  RecoY() = default;
-  RecoB *tagB = nullptr;
-  RecoB *sigB = nullptr;
-};
-
-struct RecoB {
-  RecoB() = default;
-  int flavor = static_cast<int>(bdtaunu::BFlavor::null);
-  RecoD *D = nullptr;
-  RecoLepton *Lepton = nullptr;
-};
-
-struct RecoD {
-  RecoD() = default;
-  int D_mode = static_cast<int>(bdtaunu::RecoDTypeCatalogue::DType::null);
-  int Dstar_mode = static_cast<int>(bdtaunu::RecoDTypeCatalogue::DstarType::NoDstar);
-};
-
-struct RecoLepton {
-  int l_block_idx = -1;
-  int pi_block_idx = -1;
-  int tau_mode = static_cast<int>(bdtaunu::TauType::null);
-};
-
-struct McB;
-struct McTau;
-
-struct McY {
-  McY() = default;
-  bool isBBbar = true;
-  McB *B1 = nullptr;
-  McB *B2 = nullptr;
-};
-
-struct McB {
-  McB() = default;
-  int flavor = static_cast<int>(bdtaunu::BFlavor::null);
-  int mc_type = static_cast<int>(bdtaunu::McBTypeCatalogue::BMcType::null);
-  McTau *tau = nullptr;
-};
-
-struct McTau {
-  McTau() = default;
-  int mc_type = static_cast<int>(bdtaunu::TauMcType::null);
-};
-
-#endif
diff --git a/create_database/tuple_reader/RecoGraphManager.cc b/create_database/tuple_reader/RecoGraphManager.cc
index 394f519..602b241 100644
--- a/create_database/tuple_reader/RecoGraphManager.cc
+++ b/create_database/tuple_reader/RecoGraphManager.cc
@@ -7,7 +7,6 @@
 #include <boost/graph/graphviz.hpp>
 
 #include "GraphDef.h"
-#include "Particles.h"
 #include "BDtaunuReader.h"
 #include "RecoGraphManager.h"
 #include "BDtaunuGraphWriter.h"
@@ -127,7 +126,7 @@ void RecoGraphManager::AddCandidates(
   // Each vertex has the following information attached:
   // 
   // 1. vertex_reco_index: The unique reco particle index assigned by 
-  // reco_indxer (See RecoIndexer.h). This tracks which 
+  // reco_indexer (See GraphDef.h). This tracks which 
   // vertex a particlar reco particle is associated with. 
   //
   // 2. vertex_block_index: This is the index of where this reco particle 
diff --git a/create_database/tuple_reader/RecoGraphManager.h b/create_database/tuple_reader/RecoGraphManager.h
index b6deeef..6e29e30 100644
--- a/create_database/tuple_reader/RecoGraphManager.h
+++ b/create_database/tuple_reader/RecoGraphManager.h
@@ -5,10 +5,8 @@
 #include <vector>
 #include <map>
 
-#include "GraphManager.h"
 #include "GraphDef.h"
-#include "Particles.h"
-#include "RecoIndexer.h"
+#include "GraphManager.h"
 #include "RecoGraphVisitors.h"
 
 class BDtaunuReader;
@@ -101,7 +99,7 @@ class BDtaunuReader;
  * #### Graph analysis
  * We use BGL's generic algorithms and visitor classes to analyze the graph. 
  * Since we are often interested in specific reco particles, we cache `map`s
- * of specific particles and its satellite data (see Particles.h); the contents of the 
+ * of specific particles and its satellite data (see GraphDef.h); the contents of the 
  * `map`s can be reported to the supervising class for analysis. 
  *
  */
@@ -137,8 +135,8 @@ class RecoGraphManager : public GraphManager {
     //! Get the unique reco particle index. See RecoIndexer.h.
     int get_reco_index(int lund, int i) const { return reco_indexer(lund, i); }
 
-    //! Access information about the `i`th Y candidate. See Particles.h.
-    const RecoY* get_recoY(int i) const;
+    //! Access information about the `i`th Y candidate. See GraphDef.h.
+    const RecoGraph::RecoY* get_recoY(int i) const;
 
   private:
 
@@ -149,7 +147,7 @@ class RecoGraphManager : public GraphManager {
     RecoGraph::Graph g;
 
     // Graph construction
-    RecoIndexer reco_indexer;
+    RecoGraph::RecoIndexer reco_indexer;
     std::map<int, RecoGraph::Vertex> reco_vertex_map;
     void ClearGraph();
     void AddCandidates(
@@ -158,10 +156,10 @@ class RecoGraphManager : public GraphManager {
         std::vector<int*> &CandDauLund);
 
     // Graph analysis
-    std::map<RecoGraph::Vertex, RecoY> Y_map;
-    std::map<RecoGraph::Vertex, RecoB> B_map;
-    std::map<RecoGraph::Vertex, RecoD> D_map;
-    std::map<RecoGraph::Vertex, RecoLepton> Lepton_map;
+    std::map<RecoGraph::Vertex, RecoGraph::RecoY> Y_map;
+    std::map<RecoGraph::Vertex, RecoGraph::RecoB> B_map;
+    std::map<RecoGraph::Vertex, RecoGraph::RecoD> D_map;
+    std::map<RecoGraph::Vertex, RecoGraph::RecoLepton> Lepton_map;
     void ClearAnalysis();
 };
 
diff --git a/create_database/tuple_reader/RecoGraphVisitors.cc b/create_database/tuple_reader/RecoGraphVisitors.cc
index 228ace1..6377478 100644
--- a/create_database/tuple_reader/RecoGraphVisitors.cc
+++ b/create_database/tuple_reader/RecoGraphVisitors.cc
@@ -3,7 +3,6 @@
 #include <cassert>
 
 #include "GraphDef.h"
-#include "Particles.h"
 #include "RecoGraphVisitors.h"
 #include "RecoGraphManager.h"
 
@@ -113,7 +112,7 @@ void RecoGraphDfsVisitor::AnalyzeDstar(const Vertex &u, const Graph &g) {
 }
 
 // Analyze "Leptons". These are either actual leptons are placeholder 
-// hadron for the tau of the B decay. See Particles.h for more info.
+// hadron for the tau of the B decay. See GraphDef.h for more info.
 // The quantities computed are:
 // 1. The tau decay mode. For actual leptons, this is what the 
 // tau mode would have been if it were actually from a tau decay. 
diff --git a/create_database/tuple_reader/RecoGraphVisitors.h b/create_database/tuple_reader/RecoGraphVisitors.h
index 6f26fa7..49e6737 100644
--- a/create_database/tuple_reader/RecoGraphVisitors.h
+++ b/create_database/tuple_reader/RecoGraphVisitors.h
@@ -24,7 +24,7 @@ class RecoGraphManager;
  * #Purpose
  *
  * This class computes analysis information associated with particular
- * types of reconstructed particles. See Particles.h for the quantities 
+ * types of reconstructed particles. See GraphDef.h for the quantities 
  * computed. 
  *
  * Since most quantities about a reconstructed particle can only be 
diff --git a/create_database/tuple_reader/RecoIndexer.h b/create_database/tuple_reader/RecoIndexer.h
deleted file mode 100644
index ce7fa03..0000000
--- a/create_database/tuple_reader/RecoIndexer.h
+++ /dev/null
@@ -1,50 +0,0 @@
-#ifndef _RECOINDEXER_H_
-#define _RECOINDEXER_H_
-
-/** @file RecoIndexer.h */
-
-#include <initializer_list>
-
-/** @brief This class assigns a unique index to each reconstructed particle.
- *
- * @detail 
- * # Motivation
- * The need for every reconstructed particle of the event to have a unique
- * index arises primarily in accessessing vertex information in the BGL graph. 
- * However, such an indexing is more convenient to use than the existing 
- * BtaTupleMaker indexing. 
- *
- * # Implementation
- * This class builds a hash function from the reco particle's index in the 
- * BtaTupleMaker block to a unique index. 
- *
- * See RecoIndexer.cc for details.
- */
-class RecoIndexer {
-
-  private:
-    int nY, nB, nD, nC, nh, nl, ngamma;
-
-  public:
-    RecoIndexer();
-    RecoIndexer(int _nY, int _nB, int _nD, 
-                int _nC, int _nh, int _nl, int _ngamma);
-    RecoIndexer(const RecoIndexer &r) = default;
-    RecoIndexer &operator=(const RecoIndexer &r) = default;
-    ~RecoIndexer() {};
-
-    //! Given the lundId and block index, return the unique reco index.
-    int operator()(int lund, int idx) const;
-
-    //! Return total number of reco particles in this event. 
-    int total() const { return nY + nB + nD + nC + nh + nl + ngamma; }
-
-    //! Set the total number of each type of reco particle.
-    /*! The list order is { nY, nB, nD, nC, nh, nl, ngamma } */
-    void set(std::initializer_list<int> l);
-
-    //! Clear cache.
-    void clear();
-};
-
-#endif