initial import

Code/Catalogs/Catalog.cpp

@@ -0,0 +1,15 @@
+// $Id: Catalog.cpp 4942 2006-02-17 01:19:53Z glandrum $
+//
+//  Copyright (C) 2003-2006 Rational Discovery LLC
+//
+//  @@ All Rights Reserved @@
+//
+//
+
+#include "Catalog.h"
+
+namespace RDCatalog {
+
+
+}
+    

Code/Catalogs/Catalog.h

@@ -0,0 +1,469 @@
+//
+//  Copyright (C) 2003-2006 Rational Discovery LLC
+//
+//  @@ All Rights Reserved @@
+//
+
+#ifndef __RD_CATALOG_H__
+#define __RD_CATALOG_H__
+
+// Boost graph stuff
+#include <boost/graph/graph_traits.hpp>
+#include <boost/graph/adjacency_list.hpp>
+#include <boost/property_map.hpp>
+
+// for some typedefs
+#include <RDGeneral/types.h>
+#include <RDGeneral/StreamOps.h>
+
+namespace RDCatalog {
+  const int versionMajor=1;
+  const int versionMinor=0;
+  const int versionPatch=0;
+  const int endianId=0xDEADBEEF;
+  
+  //-----------------------------------------------------------------------------
+  //! abstract base class for a catalog object
+  template <class entryType, class paramType>
+  class Catalog {
+  public:
+    //------------------------------------
+    Catalog() : d_fpLength(0), dp_cParams(0) {};
+
+    //------------------------------------
+    virtual ~Catalog(){
+      if (dp_cParams) {
+	delete dp_cParams;
+      }
+    }
+    
+    //------------------------------------
+    //! return a serialized form of the Catalog as an std::string
+    virtual std::string Serialize() const = 0;
+    
+    //------------------------------------
+    //! adds an entry to the catalog
+    /*!
+
+       \param entry          the entry to be added
+       \param updateFPLength (optional) if this is true, our internal
+          fingerprint length will also be updated.
+      
+    */
+    virtual unsigned int addEntry(entryType *entry, bool updateFPLength = true) = 0;
+    
+    //------------------------------------
+    //! returns a particular entry in the Catalog
+    virtual const entryType* getEntryWithIdx(unsigned int idx) const = 0;
+    
+    //------------------------------------
+    //! returns the number of entries
+    virtual unsigned int getNumEntries() const = 0;
+    
+    //------------------------------------
+    //! returns the length of our fingerprint
+    unsigned int getFPLength() const {return d_fpLength;}
+    
+    //------------------------------------
+    //! sets our fingerprint length
+    void setFPLength(unsigned int val) {d_fpLength = val;}
+    
+    //------------------------------------
+    //! sets our parameters by copying the \c params argument
+    void setCatalogParams(paramType *params) {
+      PRECONDITION(params,"bad parameter object");
+      //if we already have a paramter object throw an exception
+      PRECONDITION(!dp_cParams,"A parameter object already exists on the catalog" );
+      /*
+	if (dp_cParams) {
+	// we already have parameter object on the catalog
+	// can't overwrite it
+	PRECONDITION(0, "A parameter object already exist on the catalog");
+	}*/
+      dp_cParams = new paramType(*params);
+    }
+    
+    //------------------------------------
+    //! returns a pointer to our parameters
+    const paramType *getCatalogParams() const { return dp_cParams;}
+
+  protected:
+    // this is the ID that will be assigned to the next entry 
+    // added to the catalog - need not be same as the number of entries 
+    // in the catalog and does not correspond with the
+    // id of the entry in the catalog.
+    // this is more along the lines of bitId
+    unsigned int d_fpLength; //!< the length of our fingerprint
+    paramType *dp_cParams;   //!< our params object
+
+  };
+
+
+
+  //-----------------------------------------------------------------------------
+  //! A Catalog with a hierarchical structure
+  /*!
+
+    The entries of a HierarchCatalog are arranged in a directed graph
+
+    <b>The difference between <i>Indices</i> and <i>Bit Ids</i></b>
+    
+    A HierarchCatalog may contain more entries than the user is actually
+    interested in.  For example a HierarchCatalog constructed to contain
+    orders 5 through 8 may well contain information about orders 1-5,
+    in order to facilitate some search optimizations.
+
+      - <i>Bit Ids</i> refer to the "interesting" bits.  
+        So, in the above example, Bit Id \c 0 will be the first entry
+	with order 5.
+      - <i>Indices</i> refer to the underlying structure of the catalog.
+        So, in the above example, the entry with index \c 0 will be
+	the first entry	with order 1.
+
+   */
+  template <class entryType, class paramType, class orderType> 
+  class HierarchCatalog : public Catalog <entryType, paramType> {
+    // the entries in the catalog can be traversed using the edges
+    // in a desired order
+  public:
+    //! used by the BGL to set up the node properties in our graph
+    struct vertex_entry_t {
+      enum { num=1003 };
+      typedef boost::vertex_property_tag kind;
+    };
+    typedef boost::property<vertex_entry_t, entryType *> EntryProperty;
+    
+    //! the type of the graph itself:
+    typedef boost::adjacency_list<boost::vecS,
+				  boost::vecS, // FIX: should be using setS for edges so that parallel edges are never added (page 225 BGL book)
+				  // but that seems result in compile errors
+				  boost::bidirectionalS,
+				  EntryProperty> CatalogGraph;
+    
+    typedef boost::graph_traits<CatalogGraph> CAT_GRAPH_TRAITS;
+    typedef typename CAT_GRAPH_TRAITS::vertex_iterator VER_ITER;
+    typedef std::pair<VER_ITER, VER_ITER> ENT_ITER_PAIR;
+    typedef typename CAT_GRAPH_TRAITS::adjacency_iterator DOWN_ENT_ITER;
+    typedef std::pair<DOWN_ENT_ITER, DOWN_ENT_ITER> DOWN_ENT_ITER_PAIR;
+    
+    //------------------------------------
+    HierarchCatalog<entryType, paramType, orderType>() {};
+    
+    //------------------------------------
+    //! Construct by making a copy of the input \c params object
+    HierarchCatalog<entryType, paramType, orderType>(paramType *params) : Catalog<entryType,paramType>() {
+      this->setCatalogParams(params);
+    }
+
+    //------------------------------------
+    //! Construct from a \c pickle (a serialized form of the HierarchCatalog)
+    HierarchCatalog<entryType, paramType, orderType>(const std::string &pickle) {
+      this->initFromString(pickle);
+    }
+    
+    //------------------------------------
+    ~HierarchCatalog() {
+      destroy();
+    }
+
+    //------------------------------------
+    //! serializes this object to a stream
+    void toStream(std::ostream &ss) const {
+      // the i/o header:
+      RDKit::streamWrite(ss,endianId);
+      RDKit::streamWrite(ss,versionMajor);
+      RDKit::streamWrite(ss,versionMinor);
+      RDKit::streamWrite(ss,versionPatch);
+
+      // information about the catalog itself:
+      int tmpUInt;
+      tmpUInt = this->getFPLength();
+      RDKit::streamWrite(ss,tmpUInt);
+      tmpUInt = this->getNumEntries();
+      RDKit::streamWrite(ss,tmpUInt);
+
+      //std::cout << ">>>>-------------------------------" << std::endl;
+      //std::cout << "\tlength: " << getFPLength() << " " << getNumEntries() << std::endl;
+
+      // add the params object:
+      this->getCatalogParams()->toStream(ss);
+      //std::cout << "\tparams: " << getCatalogParams()->getLowerFragLength();
+      //std::cout << " " << getCatalogParams()->getUpperFragLength();
+      //std::cout << " " << getCatalogParams()->getNumFuncGroups();
+      //std::cout << std::endl;
+      
+      // write the entries in order:
+      for(unsigned int i=0;i<getNumEntries();i++){
+    	this->getEntryWithIdx(i)->toStream(ss);
+      }
+
+      // finally the adjacency list:
+      for(unsigned int i=0;i<getNumEntries();i++){
+    	RDKit::INT_VECT children=this->getDownEntryList(i);
+    	tmpUInt = children.size();
+    	RDKit::streamWrite(ss,tmpUInt);
+        for(RDKit::INT_VECT::const_iterator ivci=children.begin();
+            ivci!=children.end();
+            ivci++){
+    	   RDKit::streamWrite(ss,*ivci);
+	    }
+      }
+    }
+
+    //------------------------------------
+    //! serializes this object and returns the resulting \c pickle
+    std::string Serialize() const {
+      std::stringstream ss(std::ios_base::binary|std::ios_base::out|std::ios_base::in);
+      this->toStream(ss);
+      return ss.str();
+    }
+
+    //------------------------------------
+    //! fills the contents of this object from a stream containing a \c pickle
+    void initFromStream(std::istream &ss) {
+      int tmpInt;
+      // FIX: at the moment we ignore the header info:
+      RDKit::streamRead(ss,tmpInt);
+      RDKit::streamRead(ss,tmpInt);
+      RDKit::streamRead(ss,tmpInt);
+      RDKit::streamRead(ss,tmpInt);
+      
+      unsigned int tmpUInt;
+      RDKit::streamRead(ss,tmpUInt);// fp length
+      this->setFPLength(tmpUInt);
+      
+      unsigned int numEntries;
+      RDKit::streamRead(ss,numEntries);
+      //std::cout << "<<<-------------------------------" << std::endl;
+      //std::cout << "\tlength: " << getFPLength() << " " << numEntries << std::endl;
+
+
+      // grab the params:
+      paramType *params = new paramType();
+      params->initFromStream(ss);
+      this->setCatalogParams(params);
+
+      //std::cout << "\tparams: " << getCatalogParams()->getLowerFragLength();
+      //std::cout << " " << getCatalogParams()->getUpperFragLength();
+      //std::cout << " " << getCatalogParams()->getNumFuncGroups();
+      //std::cout << std::endl;
+
+      // now all of the entries:
+      for(unsigned int i=0;i<numEntries;i++){
+    	entryType *entry = new entryType();
+    	entry->initFromStream(ss);
+    	this->addEntry(entry,false);
+      }
+
+      // and, finally, the adjacency list:
+      for(unsigned int i=0;i<numEntries;i++){
+    	unsigned int nNeighbors;
+    	RDKit::streamRead(ss,nNeighbors);
+    	for(unsigned int j=0;j<nNeighbors;j++){
+    	  RDKit::streamRead(ss,tmpInt);
+    	  this->addEdge(i,tmpInt);
+	    }
+      }
+    }
+    
+    //------------------------------------
+    unsigned int getNumEntries() const {
+      return boost::num_vertices(d_graph);
+    }
+
+    //------------------------------------
+    //! fills the contents of this object from a string containing a \c pickle
+    void initFromString(const std::string &text){
+      std::stringstream ss(std::ios_base::binary|std::ios_base::out|std::ios_base::in);
+      // initialize the stream:
+      ss.write(text.c_str(),text.length());
+      // now start reading out values:
+      this->initFromStream(ss);
+    }
+
+    //------------------------------------
+    //! add a new entry to the catalog
+    /*!
+
+       \param entry          the entry to be added
+       \param updateFPLength (optional) if this is true, our internal
+          fingerprint length will also be updated.
+
+    */
+    unsigned int addEntry(entryType *entry, bool updateFPLength = true){ 
+      PRECONDITION(entry,"bad arguments");
+      if (updateFPLength) {
+    	unsigned int fpl = this->getFPLength();
+    	entry->setBitId(fpl);
+    	fpl++;
+    	this->setFPLength(fpl);
+      }
+      unsigned int eid = boost::add_vertex(EntryProperty(entry), d_graph);
+      orderType etype = entry->getOrder();
+      // REVIEW: this initialization is not required: the STL map, in
+      // theory, will create a new object when operator[] is called
+      // for a new item
+      if (d_orderMap.find(etype) == d_orderMap.end()) {
+    	RDKit::INT_VECT nets;
+    	d_orderMap[etype] = nets;
+      }
+      d_orderMap[etype].push_back(eid);
+      return eid;
+    }
+
+    //------------------------------------
+    //! adds an edge between two entries in the catalog
+    /*!
+      Since we are using a bidirectional graph - the order in 
+      which the ids are supplied here makes a difference
+
+      \param id1 index of the edge's beginning
+      \param id2 index of the edge's end
+
+    */
+    void addEdge(unsigned int id1, unsigned int id2) {
+      unsigned int nents = getNumEntries();
+      RANGE_CHECK(0, id1, nents-1);
+      RANGE_CHECK(0, id2, nents-1);
+      // FIX: if we boost::setS for the edgeList BGL will
+      // do the checking for duplicity (parallel edges)
+      // But for reasons unknown setS results in compile
+      // errors while using adjacent_vertices.
+      typename CAT_GRAPH_TRAITS::edge_descriptor edge;
+      bool found;
+      boost::tie(edge,found) = boost::edge(boost::vertex(id1,d_graph),
+					   boost::vertex(id2,d_graph),
+					   d_graph);
+      if (!found) {
+    	boost::add_edge(id1, id2, d_graph);
+      }
+    }
+
+    //------------------------------------
+    //! returns a pointer to our entry with a particular index 
+    const entryType *getEntryWithIdx(unsigned int idx) const {
+      RANGE_CHECK(0,idx,getNumEntries()-1);
+      int vd = boost::vertex(idx, d_graph);
+      typename boost::property_map < CatalogGraph, vertex_entry_t>::const_type 
+        pMap = boost::get(vertex_entry_t(), d_graph);
+      return pMap[vd];
+    }
+
+    //------------------------------------
+    //! returns a pointer to our entry with a particular bit ID
+    const entryType *getEntryWithBitId(unsigned int idx) const {
+      RANGE_CHECK(0,idx,this->getFPLength()-1);
+      typename boost::property_map < CatalogGraph, vertex_entry_t>::const_type 
+        pMap = boost::get(vertex_entry_t(), d_graph);
+      const entryType *res=NULL;
+      for(unsigned int i=idx;i<this->getNumEntries();i++){
+    	const entryType *e=pMap[i];
+    	if(e->getBitId()==idx){
+	     res=e;
+    	  break;
+    	}
+      }
+      return res;
+    }
+
+    //------------------------------------
+    //! returns the index of the entry with a particular bit ID
+    int getIdOfEntryWithBitId(unsigned int idx) const {
+      RANGE_CHECK(0,idx,this->getFPLength()-1);
+      typename boost::property_map < CatalogGraph, vertex_entry_t>::const_type 
+        pMap = boost::get(vertex_entry_t(), d_graph);
+      int res=-1;
+      for(unsigned int i=idx;i<this->getNumEntries();i++){
+    	const entryType *e=pMap[i];
+    	if(e->getBitId()==idx){
+    	  res=i;
+	     break;
+    	}
+      }
+      return res;
+    }
+
+    //------------------------------------
+    //! returns a list of the indices of entries below the one passed in
+    RDKit::INT_VECT getDownEntryList(unsigned int idx) const {
+      RDKit::INT_VECT res;
+      DOWN_ENT_ITER nbrIdx, endIdx;
+      boost::tie(nbrIdx, endIdx) = boost::adjacent_vertices(idx, d_graph);
+      while (nbrIdx != endIdx) {
+	res.push_back(*nbrIdx);
+	nbrIdx++;
+      }
+      //std::cout << res.size() << "\n";
+      return res;
+    }
+
+    //------------------------------------
+    //! returns a list of the indices that have a particular order 
+    const RDKit::INT_VECT &getEntriesOfOrder(orderType ord) {
+      return d_orderMap[ord];
+    }
+
+    //------------------------------------
+    //! returns a list of the indices that have a particular order
+    /*!
+      \overload
+     */
+    const RDKit::INT_VECT &getEntriesOfOrder(orderType ord) const {
+      typename std::map<orderType, RDKit::INT_VECT>::const_iterator elem;
+      elem = d_orderMap.find(ord);
+      CHECK_INVARIANT(elem!=d_orderMap.end()," catalog does not contain any entries of the order specified");
+      return elem->second;
+    }
+
+    
+  private:
+    // graphs that store the entries in the catalog in a hierachical manner
+    CatalogGraph d_graph;
+    // a  map that maps the order type of entries in the catalog to 
+    // a vector of vertex indices in the graphs above
+    // e.g.  for a catalog with molecular fragments, the order of a fragment can 
+    // simply be the number of bond in it. The list this oder maps to is all the
+    // vertex ids of these fragment in the catalog that have this many bonds in them
+    std::map<orderType, RDKit::INT_VECT> d_orderMap;
+
+    //------------------------------------
+    //! clear any memory that we've used
+    void destroy() {
+      ENT_ITER_PAIR entItP = boost::vertices(d_graph);
+      typename boost::property_map < CatalogGraph, vertex_entry_t>::type 
+        pMap = boost::get(vertex_entry_t(), d_graph);
+      while (entItP.first != entItP.second) {
+        delete pMap[*(entItP.first++)];
+      }
+    }
+
+
+    
+  };
+
+
+  //-----------------------------------------------------------------------------
+  //! a linear Catalog (analogous to an std::vector)
+  /*!
+     Here there is no particular hierarchy, simply a
+     collection of entries.
+   */
+  template <class entryType, class orderType> 
+    class LinearCatalog : public Catalog <entryType, orderType> {
+    // here there is no particular hierarchy of entries
+    // we simply model it as a vector of entries
+    // FIX: for retrieval purposes a better model map be std::map
+
+  public:
+    std::string Serialize();
+    
+    unsigned int addEntry(entryType *entry, bool updateFPLength = true);
+    
+    const entryType *getEntryWithIdx(unsigned int idx) const;
+
+  private:
+    std::vector<entryType*> d_vector;
+  };
+}
+
+#endif

Code/Catalogs/CatalogEntry.cpp

@@ -0,0 +1,13 @@
+// $Id: CatalogEntry.cpp 4942 2006-02-17 01:19:53Z glandrum $
+//
+//  Copyright (C) 2004-2006 Rational Discovery LLC
+//
+//  @@ All Rights Reserved @@
+//
+
+#include "CatalogEntry.h"
+
+namespace RDCatalog {
+  CatalogEntry::~CatalogEntry() {}
+
+}

Code/Catalogs/CatalogEntry.h

@@ -0,0 +1,45 @@
+//
+//  Copyright (C) 2003-2006 Rational Discovery LLC
+//
+//  @@ All Rights Reserved @@
+//
+#ifndef __RD_CATALOGENTRY_H__
+#define __RD_CATALOGENTRY_H__
+
+#include <iostream>
+#include <string>
+
+namespace RDCatalog {
+  
+  //! Abstract base class to be used to represent an entry in a Catalog
+  class CatalogEntry {
+  public:
+    virtual ~CatalogEntry() = 0;
+
+    //! sets our bit Id
+    void setBitId(int bid) {d_bitId = bid;}; 
+
+    //! returns our bit Id
+    int getBitId() const {return d_bitId;};
+
+    //! returns a text description of this entry
+    virtual std::string getDescription() const = 0;
+
+    //! serializes (pickles) to a stream
+    virtual void toStream(std::ostream &ss) const = 0;
+    //! returns a string with a serialized (pickled) representation
+    virtual std::string Serialize() const = 0;
+    //! initializes from a stream pickle
+    virtual void initFromStream(std::istream &ss) = 0;
+    //! initializes from a string pickle
+    virtual void initFromString(const std::string &text) = 0;
+
+
+    
+  private:
+    int d_bitId; //!< our bit Id. This needs to be signed so that we can mark uninitialized entries.
+  };
+}
+
+#endif
+    

Code/Catalogs/CatalogParams.cpp

@@ -0,0 +1,12 @@
+// $Id: CatalogParams.cpp 4942 2006-02-17 01:19:53Z glandrum $
+//
+//  Copyright (C) 2003-2006 Rational Discovery LLC
+//
+//  @@ All Rights Reserved @@
+//
+
+#include "CatalogParams.h"
+
+namespace RDCatalog {
+  CatalogParams::~CatalogParams() {};
+}

Code/Catalogs/CatalogParams.h

@@ -0,0 +1,37 @@
+//
+//  Copyright (C) 2003-2006 Rational Discovery LLC
+//
+//  @@ All Rights Reserved @@
+//
+#ifndef __RD_CATALOGPARAMS_H__
+#define __RD_CATALOGPARAMS_H__
+
+#include <string>
+
+namespace RDCatalog {
+  //! abstract base class for the container used to create a catalog
+  class CatalogParams {
+  public:
+    virtual ~CatalogParams() = 0;
+
+    //! returns our type string
+    std::string getTypeStr() const { return d_typeStr; };
+
+    //! sets our type string
+    void setTypeStr(const std::string &typeStr) { d_typeStr=typeStr; };
+
+    //! serializes (pickles) to a stream
+    virtual void toStream(std::ostream &) const = 0;
+    //! returns a string with a serialized (pickled) representation
+    virtual std::string Serialize() const = 0;
+    //! initializes from a stream pickle
+    virtual void initFromStream(std::istream &ss) = 0;
+    //! initializes from a string pickle
+    virtual void initFromString(const std::string &text) = 0;
+
+  protected:
+    std::string d_typeStr; //!< our type string
+  };
+}
+
+#endif

Code/Catalogs/Catalogs.dsp

@@ -0,0 +1,117 @@
+# Microsoft Developer Studio Project File - Name="Catalogs" - Package Owner=<4>
+# Microsoft Developer Studio Generated Build File, Format Version 6.00
+# ** DO NOT EDIT **
+
+# TARGTYPE "Win32 (x86) Static Library" 0x0104
+
+CFG=Catalogs - Win32 Debug
+!MESSAGE This is not a valid makefile. To build this project using NMAKE,
+!MESSAGE use the Export Makefile command and run
+!MESSAGE 
+!MESSAGE NMAKE /f "Catalogs.mak".
+!MESSAGE 
+!MESSAGE You can specify a configuration when running NMAKE
+!MESSAGE by defining the macro CFG on the command line. For example:
+!MESSAGE 
+!MESSAGE NMAKE /f "Catalogs.mak" CFG="Catalogs - Win32 Debug"
+!MESSAGE 
+!MESSAGE Possible choices for configuration are:
+!MESSAGE 
+!MESSAGE "Catalogs - Win32 Release" (based on "Win32 (x86) Static Library")
+!MESSAGE "Catalogs - Win32 Debug" (based on "Win32 (x86) Static Library")
+!MESSAGE 
+
+# Begin Project
+# PROP AllowPerConfigDependencies 0
+# PROP Scc_ProjName ""
+# PROP Scc_LocalPath ""
+CPP=cl.exe
+RSC=rc.exe
+
+!IF  "$(CFG)" == "Catalogs - Win32 Release"
+
+# PROP BASE Use_MFC 0
+# PROP BASE Use_Debug_Libraries 0
+# PROP BASE Output_Dir "Catalogs___Win32_Release"
+# PROP BASE Intermediate_Dir "Catalogs___Win32_Release"
+# PROP BASE Target_Dir ""
+# PROP Use_MFC 0
+# PROP Use_Debug_Libraries 0
+# PROP Output_Dir "Catalogs___Win32_Release"
+# PROP Intermediate_Dir "Catalogs___Win32_Release"
+# PROP Target_Dir ""
+# ADD BASE CPP /nologo /W3 /GX /O2 /D "WIN32" /D "NDEBUG" /D "_MBCS" /D "_LIB" /YX /FD /c
+# ADD CPP /nologo /MD /W3 /GR /GX /O2 /I "." /I "$(RDBASE)/code" /I "$(RDBASE)/code/graphmol" /I "$(RDBASE)/External/$(BOOSTBASE)" /D "WIN32" /D "NDEBUG" /D "_MBCS" /D "_LIB" /YX /FD /c
+# ADD BASE RSC /l 0x409 /d "NDEBUG"
+# ADD RSC /l 0x409 /d "NDEBUG"
+BSC32=bscmake.exe
+# ADD BASE BSC32 /nologo
+# ADD BSC32 /nologo
+LIB32=link.exe -lib
+# ADD BASE LIB32 /nologo
+# ADD LIB32 /nologo
+
+!ELSEIF  "$(CFG)" == "Catalogs - Win32 Debug"
+
+# PROP BASE Use_MFC 0
+# PROP BASE Use_Debug_Libraries 1
+# PROP BASE Output_Dir "Catalogs___Win32_Debug0"
+# PROP BASE Intermediate_Dir "Catalogs___Win32_Debug0"
+# PROP BASE Target_Dir ""
+# PROP Use_MFC 0
+# PROP Use_Debug_Libraries 1
+# PROP Output_Dir "Catalogs___Win32_Debug0"
+# PROP Intermediate_Dir "Catalogs___Win32_Debug0"
+# PROP Target_Dir ""
+# ADD BASE CPP /nologo /W3 /Gm /GX /ZI /Od /D "WIN32" /D "_DEBUG" /D "_MBCS" /D "_LIB" /YX /FD /GZ /c
+# ADD CPP /nologo /MDd /W3 /Gm /GR /GX /ZI /Od /I "." /I "$(RDBASE)/code" /I "$(RDBASE)/code/graphmol" /I "$(RDBASE)/External/$(BOOSTBASE)" /D "WIN32" /D "_DEBUG" /D "_MBCS" /D "_LIB" /FD /GZ /c
+# SUBTRACT CPP /YX
+# ADD BASE RSC /l 0x409 /d "_DEBUG"
+# ADD RSC /l 0x409 /d "_DEBUG"
+BSC32=bscmake.exe
+# ADD BASE BSC32 /nologo
+# ADD BSC32 /nologo
+LIB32=link.exe -lib
+# ADD BASE LIB32 /nologo
+# ADD LIB32 /nologo
+
+!ENDIF 
+
+# Begin Target
+
+# Name "Catalogs - Win32 Release"
+# Name "Catalogs - Win32 Debug"
+# Begin Group "Source Files"
+
+# PROP Default_Filter "cpp;c;cxx;rc;def;r;odl;idl;hpj;bat"
+# Begin Source File
+
+SOURCE=.\Catalog.cpp
+# End Source File
+# Begin Source File
+
+SOURCE=.\CatalogEntry.cpp
+# End Source File
+# Begin Source File
+
+SOURCE=.\CatalogParams.cpp
+# End Source File
+# End Group
+# Begin Group "Header Files"
+
+# PROP Default_Filter "h;hpp;hxx;hm;inl"
+# Begin Source File
+
+SOURCE=.\Catalog.h
+# End Source File
+# Begin Source File
+
+SOURCE=.\CatalogEntry.h
+# End Source File
+# Begin Source File
+
+SOURCE=.\CatalogParams.h
+# End Source File
+# End Group
+# End Target
+# End Project

Code/Catalogs/Catalogs.vcproj

@@ -0,0 +1,204 @@
+<?xml version="1.0" encoding="Windows-1252"?>
+<VisualStudioProject
+	ProjectType="Visual C++"
+	Version="7.10"
+	Name="libCatalogs"
+	SccProjectName=""
+	SccLocalPath="">
+	<Platforms>
+		<Platform
+			Name="Win32"/>
+	</Platforms>
+	<Configurations>
+		<Configuration
+			Name="Release|Win32"
+			OutputDirectory=".\Catalogs___Win32_Release"
+			IntermediateDirectory=".\Catalogs___Win32_Release"
+			ConfigurationType="4"
+			UseOfMFC="0"
+			ATLMinimizesCRunTimeLibraryUsage="FALSE"
+			CharacterSet="2">
+			<Tool
+				Name="VCCLCompilerTool"
+				Optimization="2"
+				InlineFunctionExpansion="1"
+				AdditionalIncludeDirectories=".,$(RDBASE)/code,$(RDBASE)/External/boost/include/$(BOOSTBASE)"
+				PreprocessorDefinitions="WIN32;NDEBUG;_LIB"
+				StringPooling="TRUE"
+				RuntimeLibrary="2"
+				EnableFunctionLevelLinking="TRUE"
+				RuntimeTypeInfo="TRUE"
+				UsePrecompiledHeader="2"
+				PrecompiledHeaderFile=".\Catalogs___Win32_Release/Catalogs.pch"
+				AssemblerListingLocation=".\Catalogs___Win32_Release/"
+				ObjectFile=".\Catalogs___Win32_Release/"
+				ProgramDataBaseFileName=".\Catalogs___Win32_Release/"
+				WarningLevel="3"
+				SuppressStartupBanner="TRUE"
+				CompileAs="0"/>
+			<Tool
+				Name="VCCustomBuildTool"/>
+			<Tool
+				Name="VCLibrarianTool"
+				OutputFile=".\Catalogs___Win32_Release\Catalogs.lib"
+				SuppressStartupBanner="TRUE"/>
+			<Tool
+				Name="VCMIDLTool"/>
+			<Tool
+				Name="VCPostBuildEventTool"/>
+			<Tool
+				Name="VCPreBuildEventTool"/>
+			<Tool
+				Name="VCPreLinkEventTool"/>
+			<Tool
+				Name="VCResourceCompilerTool"
+				PreprocessorDefinitions="NDEBUG"
+				Culture="1033"/>
+			<Tool
+				Name="VCWebServiceProxyGeneratorTool"/>
+			<Tool
+				Name="VCXMLDataGeneratorTool"/>
+			<Tool
+				Name="VCManagedWrapperGeneratorTool"/>
+			<Tool
+				Name="VCAuxiliaryManagedWrapperGeneratorTool"/>
+		</Configuration>
+		<Configuration
+			Name="Debug|Win32"
+			OutputDirectory=".\Catalogs___Win32_Debug0"
+			IntermediateDirectory=".\Catalogs___Win32_Debug0"
+			ConfigurationType="4"
+			UseOfMFC="0"
+			ATLMinimizesCRunTimeLibraryUsage="FALSE"
+			CharacterSet="2">
+			<Tool
+				Name="VCCLCompilerTool"
+				Optimization="0"
+				AdditionalIncludeDirectories=".,$(RDBASE)/code,$(RDBASE)/External/boost/include/$(BOOSTBASE)"
+				PreprocessorDefinitions="WIN32;_DEBUG;_LIB"
+				BasicRuntimeChecks="3"
+				RuntimeLibrary="3"
+				RuntimeTypeInfo="TRUE"
+				PrecompiledHeaderFile=".\Catalogs___Win32_Debug0/Catalogs.pch"
+				AssemblerListingLocation=".\Catalogs___Win32_Debug0/"
+				ObjectFile=".\Catalogs___Win32_Debug0/"
+				ProgramDataBaseFileName=".\Catalogs___Win32_Debug0/"
+				WarningLevel="3"
+				SuppressStartupBanner="TRUE"
+				DebugInformationFormat="4"
+				CompileAs="0"/>
+			<Tool
+				Name="VCCustomBuildTool"/>
+			<Tool
+				Name="VCLibrarianTool"
+				OutputFile=".\Catalogs___Win32_Debug0\Catalogs.lib"
+				SuppressStartupBanner="TRUE"/>
+			<Tool
+				Name="VCMIDLTool"/>
+			<Tool
+				Name="VCPostBuildEventTool"/>
+			<Tool
+				Name="VCPreBuildEventTool"/>
+			<Tool
+				Name="VCPreLinkEventTool"/>
+			<Tool
+				Name="VCResourceCompilerTool"
+				PreprocessorDefinitions="_DEBUG"
+				Culture="1033"/>
+			<Tool
+				Name="VCWebServiceProxyGeneratorTool"/>
+			<Tool
+				Name="VCXMLDataGeneratorTool"/>
+			<Tool
+				Name="VCManagedWrapperGeneratorTool"/>
+			<Tool
+				Name="VCAuxiliaryManagedWrapperGeneratorTool"/>
+		</Configuration>
+	</Configurations>
+	<References>
+	</References>
+	<Files>
+		<Filter
+			Name="Source Files"
+			Filter="cpp;c;cxx;rc;def;r;odl;idl;hpj;bat">
+			<File
+				RelativePath="Catalog.cpp">
+				<FileConfiguration
+					Name="Release|Win32">
+					<Tool
+						Name="VCCLCompilerTool"
+						Optimization="2"
+						AdditionalIncludeDirectories=""
+						PreprocessorDefinitions=""/>
+				</FileConfiguration>
+				<FileConfiguration
+					Name="Debug|Win32">
+					<Tool
+						Name="VCCLCompilerTool"
+						Optimization="0"
+						AdditionalIncludeDirectories=""
+						PreprocessorDefinitions=""
+						BasicRuntimeChecks="3"/>
+				</FileConfiguration>
+			</File>
+			<File
+				RelativePath="CatalogEntry.cpp">
+				<FileConfiguration
+					Name="Release|Win32">
+					<Tool
+						Name="VCCLCompilerTool"
+						Optimization="2"
+						AdditionalIncludeDirectories=""
+						PreprocessorDefinitions=""/>
+				</FileConfiguration>
+				<FileConfiguration
+					Name="Debug|Win32">
+					<Tool
+						Name="VCCLCompilerTool"
+						Optimization="0"
+						AdditionalIncludeDirectories=""
+						PreprocessorDefinitions=""
+						BasicRuntimeChecks="3"/>
+				</FileConfiguration>
+			</File>
+			<File
+				RelativePath="CatalogParams.cpp">
+				<FileConfiguration
+					Name="Release|Win32">
+					<Tool
+						Name="VCCLCompilerTool"
+						Optimization="2"
+						AdditionalIncludeDirectories=""
+						PreprocessorDefinitions=""/>
+				</FileConfiguration>
+				<FileConfiguration
+					Name="Debug|Win32">
+					<Tool
+						Name="VCCLCompilerTool"
+						Optimization="0"
+						AdditionalIncludeDirectories=""
+						PreprocessorDefinitions=""
+						BasicRuntimeChecks="3"/>
+				</FileConfiguration>
+			</File>
+		</Filter>
+		<Filter
+			Name="Header Files"
+			Filter="h;hpp;hxx;hm;inl">
+			<File
+				RelativePath="Catalog.h">
+			</File>
+			<File
+				RelativePath="CatalogEntry.h">
+			</File>
+			<File
+				RelativePath="CatalogParams.h">
+			</File>
+		</Filter>
+		<File
+			RelativePath=".\VTune\Catalogs.vpj">
+		</File>
+	</Files>
+	<Globals>
+	</Globals>
+</VisualStudioProject>

Code/Catalogs/Makefile

@@ -0,0 +1,14 @@
+include $(RDBASE)/Code/rdvars.make
+include $(RDBASE)/Code/rdrules.make
+CXXFLAGS=$(BASECXXFLAGS) $(VFLIBINC)
+
+SOURCES=Catalog.cpp CatalogParams.cpp CatalogEntry.cpp
+LIB=$(RDCATALOGLIB)
+
+$(LIB): $(OBJS) 
+	ar -rv $@ $?
+clean:
+	rm -f $(OBJS) $(LIB) $(DEPENDS)
+
+include $(DEPENDS)
+

Code/ChemicalFeatures/ChemicalFeature.h

@@ -0,0 +1,28 @@
+//
+//  Copyright (C) 2004-2006 Rational Discovery LLC
+//
+//  @@ All Rights Reserved @@
+//
+#ifndef __CHEMICALFEATURE_H_11012005_1310__
+#define __CHEMICALFEATURE_H_11012005_1310__
+
+#include <Geometry/point.h>
+namespace ChemicalFeatures {
+  
+  //------------------------------------------------------------------
+  //! abstract base class for chemical feature 
+  class ChemicalFeature {
+  public:
+    ChemicalFeature() {};
+    virtual ~ChemicalFeature() {};
+    
+    virtual const std::string& getType() const = 0;
+    
+    virtual const std::string& getFamily() const = 0;
+    
+    virtual RDGeom::Point3D getPos() const = 0;
+  };
+}
+
+#endif
+    

Code/ChemicalFeatures/FreeChemicalFeature.cpp

@@ -0,0 +1,63 @@
+// $Id: FreeChemicalFeature.cpp 4943 2006-02-17 01:21:27Z glandrum $
+//
+// Copyright (c) 2005-2006 greg Landrum and Rational Discovery LLC
+//
+//  @@ All Rights Reserved @@
+//
+#include "FreeChemicalFeature.h"
+#include <sstream>
+
+
+namespace ChemicalFeatures {
+  const int ci_FEAT_VERSION=0x0010; //!< version number to use in pickles
+
+  std::string FreeChemicalFeature::toString() const {
+    std::stringstream ss(std::ios_base::binary|std::ios_base::out|std::ios_base::in);
+    unsigned int tInt = ci_FEAT_VERSION;
+    ss.write((const char *)&(tInt),sizeof(tInt));
+    tInt = d_family.size()+1;
+    ss.write((const char *)&(tInt),sizeof(tInt));
+    ss.write(d_family.c_str(),tInt*sizeof(char));
+    tInt = d_type.size()+1;
+    ss.write((const char *)&(tInt),sizeof(tInt));
+    ss.write(d_type.c_str(),tInt*sizeof(char));
+    ss.write((const char *)&d_position.x,sizeof(d_position.x));
+    ss.write((const char *)&d_position.y,sizeof(d_position.y));
+    ss.write((const char *)&d_position.z,sizeof(d_position.z));
+    std::string res(ss.str());
+    return res;
+  };
+  void FreeChemicalFeature::initFromString(const std::string &pickle){
+    std::stringstream ss(pickle,
+			 std::ios_base::binary|std::ios_base::in|std::ios_base::out);
+    int version=0;
+    unsigned int tInt;
+    ss.read((char *)&tInt,sizeof(tInt));
+    switch(tInt){
+    case 0x0010:
+      version=1;
+      break;
+    default:
+      throw("Unknown version type for FreeChemicalFeature");
+    }
+
+    char *tmpChr;
+    ss.read((char *)&(tInt),sizeof(tInt));
+    tmpChr = new char[tInt];
+    ss.read(tmpChr,tInt*sizeof(char));
+    d_family = tmpChr;
+    delete [] tmpChr;
+
+    ss.read((char *)&(tInt),sizeof(tInt));
+    tmpChr = new char[tInt];
+    ss.read(tmpChr,tInt*sizeof(char));
+    d_type = tmpChr;
+    delete [] tmpChr;
+
+    ss.read((char *)&d_position.x,sizeof(d_position.x));
+    ss.read((char *)&d_position.y,sizeof(d_position.x));
+    ss.read((char *)&d_position.z,sizeof(d_position.x));
+  };
+
+  
+}

Code/ChemicalFeatures/FreeChemicalFeature.h

@@ -0,0 +1,77 @@
+//
+//  Copyright (C) 2004-2006 Rational Discovery LLC
+//
+//  @@ All Rights Reserved @@
+//
+#ifndef __FREECHEMICALFEATURE_H_13012005_1023__
+#define __FREECHEMICALFEATURE_H_13012005_1023__
+
+#include <Geometry/point.h>
+#include <ChemicalFeatures/ChemicalFeature.h>
+
+namespace ChemicalFeatures {
+
+  //------------------------------------------------------
+  //! Class for chemical features that do orignate from molecules
+  //  e.g. pharamcophores, site-maps etc.
+  class FreeChemicalFeature : public ChemicalFeature {
+    public:
+    FreeChemicalFeature(std::string family, std::string type,
+                        const RDGeom::Point3D &loc) :
+      d_family(family), d_type(type), d_position(loc) {
+    }
+
+    FreeChemicalFeature(std::string family, const RDGeom::Point3D &loc) :
+      d_family(family), d_type(""), d_position(loc) {
+    }
+
+    explicit FreeChemicalFeature(const std::string &pickle) {
+      this->initFromString(pickle);
+    }
+    FreeChemicalFeature() :
+      d_family(""), d_type(""), d_position(RDGeom::Point3D(0.0, 0.0, 0.0)) {
+    }
+
+    FreeChemicalFeature(const FreeChemicalFeature &other) : 
+      d_family(other.getFamily()), d_type(other.getType()), d_position(other.getPos())  {
+    }
+
+    ~FreeChemicalFeature() {}
+
+    const std::string& getFamily() const {
+      return d_family;
+    }
+
+    const std::string& getType() const {
+      return d_type;
+    }
+
+    RDGeom::Point3D getPos() const {
+      return d_position;
+    }
+
+    void setFamily(const std::string &family) {
+      d_family = family;
+    }
+    
+    void setType(const std::string &type) {
+      d_type = type;
+    }
+
+    void setPos(const RDGeom::Point3D &loc) {
+      d_position = loc;
+    }
+
+    std::string toString() const;
+    void initFromString(const std::string &pickle);
+    
+  private:
+    std::string d_family;
+    std::string d_type;
+    RDGeom::Point3D d_position;
+  };
+}
+  
+
+#endif
+

Code/ChemicalFeatures/Makefile

@@ -0,0 +1,18 @@
+include $(RDBASE)/Code/rdvars.make
+include $(RDBASE)/Code/rdrules.make
+CXXFLAGS=$(BASECXXFLAGS)
+
+SOURCES=FreeChemicalFeature.cpp
+LIB=libChemicalFeatures.a
+$(LIB): $(OBJS)
+	ar -rv $@ $?
+
+regrs: testExecs/main.exe
+
+testExecs/main.exe: testChemicalFeatures.o $(LIB)
+	$(CXX) $(CXXFLAGS) -o $@ testChemicalFeatures.o $(RDCHEMFEATS) $(RDGENERAL)
+
+clean:
+	rm -f $(OBJS) $(LIB) $(DEPENDS) testExecs/main.exe testChemicalFeatures.o
+
+include $(DEPENDS)

Code/ChemicalFeatures/Wrap/FreeChemicalFeature.cpp

@@ -0,0 +1,72 @@
+// $Id: FreeChemicalFeature.cpp 4944 2006-02-17 01:23:55Z glandrum $
+//
+//  Copyright (C) 2004-2006 Rational Discovery LLC
+//
+//  @@ All Rights Reserved @@
+//
+#define NO_IMPORT_ARRAY
+#include <boost/python.hpp>
+
+#include <GraphMol/RDKitBase.h>
+#include <RDGeneral/types.h>
+#include<RDGeneral/Invariant.h>
+#include <RDBoost/PySequenceHolder.h>
+#include <ChemicalFeatures/FreeChemicalFeature.h>
+
+namespace ChemicalFeatures {
+
+  // allows BitVects to be pickled
+  struct chemfeat_pickle_suite : python::pickle_suite
+  {
+    static python::tuple
+    getinitargs(const FreeChemicalFeature& self)
+    {
+      return python::make_tuple(self.toString());
+    };
+  };
+
+  
+  std::string featClassDoc="Class to represent a free chemical  feature.\n\
+    These chemical features are not derived from a molecule, though they can be matched \n\
+    to features from a molecule\n";
+  struct freefeat_wrapper {
+    static void wrap() {
+      python::class_<FreeChemicalFeature>("FreeChemicalFeature", featClassDoc.c_str(),
+					  python::init<const std::string &>()) //<>("Default Constructor"))
+        .def(python::init<>("Default Constructor"))
+        .def(python::init<std::string, std::string, const RDGeom::Point3D &>
+             (python::args("family", "type", "loc"),
+              "Constructor with family, type and location specified"))
+        .def(python::init<std::string, const RDGeom::Point3D &>
+             (python::args("family", "loc"), 
+              "constructor with family and location specified, empty type"))
+        .def("SetFamily", &FreeChemicalFeature::setFamily,
+             "Set the family of the feature")
+        .def("SetType", &FreeChemicalFeature::setType,
+             "Set the sepcific type for the feature")
+        .def("GetFamily", &FreeChemicalFeature::getFamily,
+             "Get the family of the feature",
+             python::return_value_policy<python::copy_const_reference>())
+        .def("GetType", &FreeChemicalFeature::getType,
+             "Get the sepcific type for the feature",
+             python::return_value_policy<python::copy_const_reference>())
+        .def("SetPos", &FreeChemicalFeature::setPos,
+             "Set the feature position")
+        .def("GetPos", &FreeChemicalFeature::getPos,
+             "Get the psotion for the feature")
+	.def_pickle(chemfeat_pickle_suite())
+        ;
+      //python::def("FreeChemicalFeature", ChemicalFeatures::makeFreeChemFeat,
+      //            (python::arg("family")="", python::arg("type")="",
+      //             python::arg("pos")=python::list()),
+      //            "This a kind of faking a constructor for FreeChemicalFeature");
+
+
+    };
+  }; 
+}
+
+void wrap_freefeat() {
+  ChemicalFeatures::freefeat_wrapper::wrap();
+}
+

Code/ChemicalFeatures/Wrap/rdChemicalFeatures.cpp

@@ -0,0 +1,25 @@
+// $Id: rdChemicalFeatures.cpp 4944 2006-02-17 01:23:55Z glandrum $
+//
+//  Copyright (C) 2003-2006 Rational Discovery LLC
+//     All Rights Reserved
+//
+//  @@ All Rights Reserved @@
+//
+
+#include <RDBoost/Wrap.h>
+#include <ChemicalFeatures/FreeChemicalFeature.h>
+#include <RDBoost/PySequenceHolder.h>
+
+void wrap_freefeat();
+
+
+
+BOOST_PYTHON_MODULE(rdChemicalFeatures)
+{
+  python::scope().attr("__doc__") =
+    "Module containing free chemical feature functionality\n\
+     These are feature that ar not derived from molecules. They are \n\
+     are typically derived from pharmacophores and site-map.\n";
+
+  wrap_freefeat();
+}

Code/ChemicalFeatures/Wrap/setup.py

@@ -0,0 +1,24 @@
+# Run this with:
+#  python setup.py install --install-lib=$RDBASE/Python
+from RDBuild import *
+from distutils.core import setup,Extension
+
+
+libDirs += [
+         rdLibDir,
+         os.path.join(RDConfig.RDBaseDir,'Code','Geometry'),
+         os.path.join(RDConfig.RDBaseDir,'Code','ChemicalFeatures'),
+         ]
+
+libraries += ["ChemicalFeatures","RDGeometry", "RDGeneral",] 
+
+
+setup(name="Chem.rdChemicalFeatures", version="2.0",
+      ext_modules=[Extension("Chem.rdChemicalFeatures",
+                             ["rdChemicalFeatures.cpp",
+                              "FreeChemicalFeature.cpp"],                             
+                             library_dirs=libDirs,
+                             libraries=libraries,
+                             extra_link_args=linkArgs,
+                             extra_compile_args=compileArgs)])
+

Code/ChemicalFeatures/Wrap/testFeatures.py

@@ -0,0 +1,62 @@
+import Chem
+from Chem import ChemicalFeatures
+import unittest
+import cPickle
+from Geometry import rdGeometry as geom
+
+def feq(v1,v2,tol2=1e-4):
+  return abs(v1-v2)<=tol2
+
+def lstFeq(l1, l2, tol=1.e-4):
+  if (len(l1) != len(l2)):
+    return 0
+  for i in range(len(l1)):
+    if not feq(l1[i], l2[i], tol):
+      return 0
+  return 1
+
+def ptFeq(pt1, pt2, tol=0.0001):
+  dist = pt1.Distance(pt2)
+  return feq(dist, 0.0, tol)
+
+
+class TestCase(unittest.TestCase):
+    def setUp(self):
+      pass
+
+    def testBasic(self):
+      ffeat = ChemicalFeatures.FreeChemicalFeature()
+      ffeat.SetFamily("HBondDonor")
+      self.failUnless(ffeat.GetFamily() == "HBondDonor")
+      ffeat.SetPos(geom.Point3D(1.0, 2.0, 3.0))
+      pos = ffeat.GetPos()
+      self.failUnless(ptFeq(pos, geom.Point3D(1.0, 2.0, 3.0)))
+      
+      ffeat.SetType("HBondDonor1")
+      self.failUnless(ffeat.GetType() == "HBondDonor1")
+
+      ffeat = ChemicalFeatures.FreeChemicalFeature("HBondDonor", "HBondDonor1", geom.Point3D(1.0, 2.0, 3.0))
+      self.failUnless(ffeat.GetFamily() == "HBondDonor")
+      self.failUnless(ffeat.GetType() == "HBondDonor1")
+      pos = ffeat.GetPos()
+      self.failUnless(ptFeq(pos, geom.Point3D(1.0, 2.0, 3.0)))
+
+      ffeat = ChemicalFeatures.FreeChemicalFeature(type="HBondDonor1", family="HBondDonor",
+                                       loc=geom.Point3D(1.0, 2.0, 3.0))
+      self.failUnless(ffeat.GetFamily() == "HBondDonor")
+      self.failUnless(ffeat.GetType() == "HBondDonor1")
+      pos = ffeat.GetPos()
+      self.failUnless(ptFeq(pos, geom.Point3D(1.0, 2.0, 3.0)))
+      
+    def testPickle(self):
+      ffeat = ChemicalFeatures.FreeChemicalFeature("HBondDonor", "HBondDonor1", geom.Point3D(1.0, 2.0, 3.0))
+      pkl = cPickle.dumps(ffeat)
+      ffeat2 = cPickle.loads(pkl)
+      self.failUnless(ffeat2.GetFamily()==ffeat.GetFamily());
+      self.failUnless(ffeat2.GetType()==ffeat.GetType());
+      self.failUnless(ptFeq(ffeat2.GetPos(),ffeat.GetPos()))
+      
+if __name__ == '__main__':
+    print "Testing ChemicalFeatures Wrapper code:"
+    unittest.main()
+    

Code/ChemicalFeatures/Wrap/test_list.py

@@ -0,0 +1,14 @@
+
+tests=[
+  ("python","testFeatures.py",{})
+  ]
+
+
+
+longTests=[]
+
+if __name__=='__main__':
+  import sys
+  import TestRunner
+  failed,tests = TestRunner.RunScript('test_list.py',0,1)
+  sys.exit(len(failed))

Code/ChemicalFeatures/Wrap/wrapChemicalFeatures.vcproj

@@ -0,0 +1,252 @@
+<?xml version="1.0" encoding="Windows-1252"?>
+<VisualStudioProject
+	ProjectType="Visual C++"
+	Version="7.10"
+	Name="wrapChemicalFeatures"
+	ProjectGUID="{1D23BB8D-2E2E-4FBE-88B3-986B13576972}"
+	SccProjectName="wrapChemicalFeatures"
+	SccLocalPath=".">
+	<Platforms>
+		<Platform
+			Name="Win32"/>
+	</Platforms>
+	<Configurations>
+		<Configuration
+			Name="DebugPython|Win32"
+			OutputDirectory=".\wrapChemicalFeatures_Win32_DebugPython"
+			IntermediateDirectory=".\wrapChemicalFeatures_Win32_DebugPython"
+			ConfigurationType="2"
+			UseOfMFC="0"
+			ATLMinimizesCRunTimeLibraryUsage="FALSE"
+			CharacterSet="2">
+			<Tool
+				Name="VCCLCompilerTool"
+				Optimization="0"
+				AdditionalIncludeDirectories="$(RDBASE)/Code,$(PYTHONHOME)\include,$(RDBASE)/External/boost/include/$(BOOSTBASE),$(RDBASE)/External/vflib-2.0/include"
+				PreprocessorDefinitions="WIN32;_DEBUG;_WINDOWS;_USRDLL;TEST_EXPORTS;BOOST_DEBUG_PYTHON"
+				BasicRuntimeChecks="3"
+				RuntimeLibrary="3"
+				RuntimeTypeInfo="TRUE"
+				PrecompiledHeaderFile=".\wrapChemicalFeatures_Win32_DebugPython/wrapChemicalFeatures.pch"
+				AssemblerListingLocation=".\wrapChemicalFeatures_Win32_DebugPython/"
+				ObjectFile=".\wrapChemicalFeatures_Win32_DebugPython/"
+				ProgramDataBaseFileName=".\wrapChemicalFeatures_Win32_DebugPython/"
+				WarningLevel="3"
+				SuppressStartupBanner="TRUE"
+				DebugInformationFormat="3"
+				CompileAs="0"/>
+			<Tool
+				Name="VCCustomBuildTool"/>
+			<Tool
+				Name="VCLinkerTool"
+				IgnoreImportLibrary="TRUE"
+				AdditionalDependencies="boost_python.lib; vflib.lib;libDatastructs.lib odbc32.lib odbccp32.lib $(PYTHONVERS).lib BLAS.lib LAPACK.lib boost_python.lib"
+				OutputFile="DebugPython/rdChemicalFeatures_d.dll"
+				LinkIncremental="1"
+				SuppressStartupBanner="TRUE"
+				AdditionalLibraryDirectories="$(PYTHONHOME)\libs,$(RDBASE)\External\Lapack\win32,$(RDBASE)/External/boost/lib"
+				IgnoreDefaultLibraryNames="msvcprtdlib.lib"
+				GenerateDebugInformation="TRUE"
+				ProgramDatabaseFile=".\wrapChemicalFeatures_Win32_DebugPython/rdChemicalFeatures_new_d.pdb"
+				SubSystem="2"
+				ImportLibrary=".\wrapChemicalFeatures_Win32_DebugPython/rdChemicalFeatures_new_d.lib"
+				TargetMachine="1"/>
+			<Tool
+				Name="VCMIDLTool"
+				PreprocessorDefinitions="_DEBUG"
+				MkTypLibCompatible="TRUE"
+				SuppressStartupBanner="TRUE"
+				TargetEnvironment="1"
+				TypeLibraryName=".\wrapChemicalFeatures_Win32_DebugPython/wrapChemicalFeatures.tlb"
+				HeaderFileName=""/>
+			<Tool
+				Name="VCPostBuildEventTool"
+				Description="copy dll"
+				CommandLine="copy DebugPython\rdChemicalFeatures_new_d.dll &quot;$(RDBASE)&quot;\Python\Chem"/>
+			<Tool
+				Name="VCPreBuildEventTool"/>
+			<Tool
+				Name="VCPreLinkEventTool"/>
+			<Tool
+				Name="VCResourceCompilerTool"
+				PreprocessorDefinitions="_DEBUG"
+				Culture="1033"/>
+			<Tool
+				Name="VCWebServiceProxyGeneratorTool"/>
+			<Tool
+				Name="VCXMLDataGeneratorTool"/>
+			<Tool
+				Name="VCWebDeploymentTool"/>
+			<Tool
+				Name="VCManagedWrapperGeneratorTool"/>
+			<Tool
+				Name="VCAuxiliaryManagedWrapperGeneratorTool"/>
+		</Configuration>
+		<Configuration
+			Name="Debug|Win32"
+			OutputDirectory=".\Debug"
+			IntermediateDirectory=".\Debug"
+			ConfigurationType="2"
+			UseOfMFC="0"
+			ATLMinimizesCRunTimeLibraryUsage="FALSE">
+			<Tool
+				Name="VCCLCompilerTool"
+				AdditionalOptions="/Zm400 "
+				Optimization="0"
+				AdditionalIncludeDirectories="$(RDBASE)/Code,$(PYTHONHOME)\include,$(RDBASE)/External/boost/include/$(BOOSTBASE),$(RDBASE)/External/vflib-2.0/include"
+				PreprocessorDefinitions="WIN32;_DEBUG;_WINDOWS"
+				BasicRuntimeChecks="3"
+				RuntimeLibrary="3"
+				RuntimeTypeInfo="TRUE"
+				PrecompiledHeaderFile=".\Debug/wrapChemicalFeatures.pch"
+				AssemblerListingLocation=".\Debug/"
+				ObjectFile=".\Debug/"
+				ProgramDataBaseFileName=".\Debug/"
+				WarningLevel="3"
+				SuppressStartupBanner="TRUE"
+				DebugInformationFormat="3"
+				CompileAs="0"/>
+			<Tool
+				Name="VCCustomBuildTool"/>
+			<Tool
+				Name="VCLinkerTool"
+				IgnoreImportLibrary="TRUE"
+				AdditionalDependencies="boost_log-vc71-mt-gd-$(BOOSTVERSION).lib boost_python-vc71-mt-gd-$(BOOSTVERSION).lib odbc32.lib odbccp32.lib $(PYTHONVERS).lib BLAS.lib LAPACK.lib"
+				OutputFile="Debug/rdChemicalFeatures.dll"
+				LinkIncremental="1"
+				SuppressStartupBanner="TRUE"
+				AdditionalLibraryDirectories="$(PYTHONHOME)\libs,$(RDBASE)\External\Lapack\win32,$(RDBASE)/External/boost/lib"
+				IgnoreDefaultLibraryNames="msvcprtdlib.lib"
+				GenerateDebugInformation="TRUE"
+				ProgramDatabaseFile=".\Debug/rdChemicalFeatures.pdb"
+				SubSystem="2"
+				ImportLibrary=".\Debug/rdChemicalFeatures.lib"
+				TargetMachine="1"/>
+			<Tool
+				Name="VCMIDLTool"
+				PreprocessorDefinitions="_DEBUG"
+				MkTypLibCompatible="TRUE"
+				SuppressStartupBanner="TRUE"
+				TargetEnvironment="1"
+				TypeLibraryName=".\Debug/wrapChemicalFeatures.tlb"
+				HeaderFileName=""/>
+			<Tool
+				Name="VCPostBuildEventTool"
+				Description="copy dll"
+				CommandLine="copy Debug\rdChemicalFeatures.dll &quot;$(RDBASE)&quot;\Python\Chem"/>
+			<Tool
+				Name="VCPreBuildEventTool"/>
+			<Tool
+				Name="VCPreLinkEventTool"/>
+			<Tool
+				Name="VCResourceCompilerTool"
+				PreprocessorDefinitions="_DEBUG"
+				Culture="1033"/>
+			<Tool
+				Name="VCWebServiceProxyGeneratorTool"/>
+			<Tool
+				Name="VCXMLDataGeneratorTool"/>
+			<Tool
+				Name="VCWebDeploymentTool"/>
+			<Tool
+				Name="VCManagedWrapperGeneratorTool"/>
+			<Tool
+				Name="VCAuxiliaryManagedWrapperGeneratorTool"/>
+		</Configuration>
+		<Configuration
+			Name="Release|Win32"
+			OutputDirectory=".\Release"
+			IntermediateDirectory=".\Release"
+			ConfigurationType="2"
+			UseOfMFC="0"
+			ATLMinimizesCRunTimeLibraryUsage="FALSE">
+			<Tool
+				Name="VCCLCompilerTool"
+				AdditionalOptions="/Zm400 "
+				Optimization="2"
+				InlineFunctionExpansion="1"
+				AdditionalIncludeDirectories="$(RDBASE)/Code,$(PYTHONHOME)\include,$(RDBASE)/External/boost/include/$(BOOSTBASE),$(RDBASE)/External/vflib-2.0/include"
+				PreprocessorDefinitions="WIN32;NDEBUG;_WINDOWS"
+				StringPooling="TRUE"
+				RuntimeLibrary="2"
+				EnableFunctionLevelLinking="TRUE"
+				RuntimeTypeInfo="TRUE"
+				PrecompiledHeaderFile=".\Release/wrapChemicalFeatures.pch"
+				AssemblerListingLocation=".\Release/"
+				ObjectFile=".\Release/"
+				ProgramDataBaseFileName=".\Release/"
+				WarningLevel="3"
+				SuppressStartupBanner="TRUE"
+				CompileAs="0"/>
+			<Tool
+				Name="VCCustomBuildTool"/>
+			<Tool
+				Name="VCLinkerTool"
+				IgnoreImportLibrary="TRUE"
+				AdditionalDependencies="boost_log-vc71-mt-$(BOOSTVERSION).lib boost_python-vc71-mt-$(BOOSTVERSION).lib odbc32.lib odbccp32.lib $(PYTHONVERS).lib BLAS.lib LAPACK.lib"
+				OutputFile="Release/rdChemicalFeatures.dll"
+				LinkIncremental="1"
+				SuppressStartupBanner="TRUE"
+				AdditionalLibraryDirectories="$(PYTHONHOME)\libs,$(RDBASE)\External\Lapack\win32,$(RDBASE)/External/boost/lib"
+				IgnoreDefaultLibraryNames="msvcprtdlib.lib"
+				ProgramDatabaseFile=".\Release/rdChemicalFeatures.pdb"
+				SubSystem="2"
+				ImportLibrary=".\Release/rdChemicalFeatures.lib"
+				TargetMachine="1"/>
+			<Tool
+				Name="VCMIDLTool"
+				PreprocessorDefinitions="NDEBUG"
+				MkTypLibCompatible="TRUE"
+				SuppressStartupBanner="TRUE"
+				TargetEnvironment="1"
+				TypeLibraryName=".\Release/wrapChemicalFeatures.tlb"
+				HeaderFileName=""/>
+			<Tool
+				Name="VCPostBuildEventTool"
+				Description="copy dll"
+				CommandLine="copy        Release\rdChemicalFeatures.dll      &quot;$(RDBASE)&quot;\Python\Chem"/>
+			<Tool
+				Name="VCPreBuildEventTool"/>
+			<Tool
+				Name="VCPreLinkEventTool"/>
+			<Tool
+				Name="VCResourceCompilerTool"
+				PreprocessorDefinitions="NDEBUG"
+				Culture="1033"/>
+			<Tool
+				Name="VCWebServiceProxyGeneratorTool"/>
+			<Tool
+				Name="VCXMLDataGeneratorTool"/>
+			<Tool
+				Name="VCWebDeploymentTool"/>
+			<Tool
+				Name="VCManagedWrapperGeneratorTool"/>
+			<Tool
+				Name="VCAuxiliaryManagedWrapperGeneratorTool"/>
+		</Configuration>
+	</Configurations>
+	<References>
+	</References>
+	<Files>
+		<Filter
+			Name="Source Files"
+			Filter="cpp;c;cxx;rc;def;r;odl;idl;hpj;bat">
+			<File
+				RelativePath=".\FreeChemicalFeature.cpp">
+			</File>
+			<File
+				RelativePath=".\rdChemicalFeatures.cpp">
+			</File>
+		</Filter>
+		<Filter
+			Name="Header Files"
+			Filter="h;hpp;hxx;hm;inl">
+		</Filter>
+		<Filter
+			Name="Resource Files"
+			Filter="ico;cur;bmp;dlg;rc2;rct;bin;rgs;gif;jpg;jpeg;jpe">
+		</Filter>
+	</Files>
+	<Globals>
+	</Globals>
+</VisualStudioProject>

Code/ChemicalFeatures/libChemicalFeatures.vcproj

@@ -0,0 +1,137 @@
+<?xml version="1.0" encoding="Windows-1252"?>
+<VisualStudioProject
+	ProjectType="Visual C++"
+	Version="7.10"
+	Name="libChemicalFeatures"
+	ProjectGUID="{636B9719-70AC-4074-883E-8DAE1BD0F684}"
+	SccProjectName=""
+	SccLocalPath="">
+	<Platforms>
+		<Platform
+			Name="Win32"/>
+	</Platforms>
+	<Configurations>
+		<Configuration
+			Name="Debug|Win32"
+			OutputDirectory=".\libChemicalFeatures___Win32_Debug0"
+			IntermediateDirectory=".\libChemicalFeatures___Win32_Debug0"
+			ConfigurationType="4"
+			UseOfMFC="0"
+			ATLMinimizesCRunTimeLibraryUsage="FALSE"
+			CharacterSet="2">
+			<Tool
+				Name="VCCLCompilerTool"
+				Optimization="0"
+				AdditionalIncludeDirectories=".,$(RDBASE)/code,$(RDBASE)/External/boost/include/$(BOOSTBASE)"
+				PreprocessorDefinitions="WIN32;_DEBUG;_LIB"
+				BasicRuntimeChecks="3"
+				RuntimeLibrary="3"
+				RuntimeTypeInfo="TRUE"
+				UsePrecompiledHeader="2"
+				PrecompiledHeaderFile=".\libChemicalFeatures___Win32_Debug0/libChemicalFeatures.pch"
+				AssemblerListingLocation=".\libChemicalFeatures___Win32_Debug0/"
+				ObjectFile=".\libChemicalFeatures___Win32_Debug0/"
+				ProgramDataBaseFileName=".\libChemicalFeatures___Win32_Debug0/"
+				WarningLevel="3"
+				SuppressStartupBanner="TRUE"
+				DebugInformationFormat="4"
+				CompileAs="0"/>
+			<Tool
+				Name="VCCustomBuildTool"/>
+			<Tool
+				Name="VCLibrarianTool"
+				OutputFile=".\libChemicalFeatures___Win32_Debug0\libChemicalFeatures.lib"
+				SuppressStartupBanner="TRUE"/>
+			<Tool
+				Name="VCMIDLTool"/>
+			<Tool
+				Name="VCPostBuildEventTool"/>
+			<Tool
+				Name="VCPreBuildEventTool"/>
+			<Tool
+				Name="VCPreLinkEventTool"/>
+			<Tool
+				Name="VCResourceCompilerTool"
+				PreprocessorDefinitions="_DEBUG"
+				Culture="1033"/>
+			<Tool
+				Name="VCWebServiceProxyGeneratorTool"/>
+			<Tool
+				Name="VCXMLDataGeneratorTool"/>
+			<Tool
+				Name="VCManagedWrapperGeneratorTool"/>
+			<Tool
+				Name="VCAuxiliaryManagedWrapperGeneratorTool"/>
+		</Configuration>
+		<Configuration
+			Name="Release|Win32"
+			OutputDirectory=".\libChemicalFeatures___Win32_Release"
+			IntermediateDirectory=".\libChemicalFeatures___Win32_Release"
+			ConfigurationType="4"
+			UseOfMFC="0"
+			ATLMinimizesCRunTimeLibraryUsage="FALSE"
+			CharacterSet="2">
+			<Tool
+				Name="VCCLCompilerTool"
+				Optimization="2"
+				InlineFunctionExpansion="1"
+				AdditionalIncludeDirectories=".,$(RDBASE)/code,$(RDBASE)/External/boost/include/$(BOOSTBASE)"
+				PreprocessorDefinitions="WIN32;NDEBUG;_LIB"
+				StringPooling="TRUE"
+				RuntimeLibrary="2"
+				EnableFunctionLevelLinking="TRUE"
+				RuntimeTypeInfo="TRUE"
+				UsePrecompiledHeader="2"
+				PrecompiledHeaderFile=".\libChemicalFeatures___Win32_Release/libChemicalFeatures.pch"
+				AssemblerListingLocation=".\libChemicalFeatures___Win32_Release/"
+				ObjectFile=".\libChemicalFeatures___Win32_Release/"
+				ProgramDataBaseFileName=".\libChemicalFeatures___Win32_Release/"
+				WarningLevel="3"
+				SuppressStartupBanner="TRUE"
+				CompileAs="0"/>
+			<Tool
+				Name="VCCustomBuildTool"/>
+			<Tool
+				Name="VCLibrarianTool"
+				OutputFile=".\libChemicalFeatures___Win32_Release\libChemicalFeatures.lib"
+				SuppressStartupBanner="TRUE"/>
+			<Tool
+				Name="VCMIDLTool"/>
+			<Tool
+				Name="VCPostBuildEventTool"/>
+			<Tool
+				Name="VCPreBuildEventTool"/>
+			<Tool
+				Name="VCPreLinkEventTool"/>
+			<Tool
+				Name="VCResourceCompilerTool"
+				PreprocessorDefinitions="NDEBUG"
+				Culture="1033"/>
+			<Tool
+				Name="VCWebServiceProxyGeneratorTool"/>
+			<Tool
+				Name="VCXMLDataGeneratorTool"/>
+			<Tool
+				Name="VCManagedWrapperGeneratorTool"/>
+			<Tool
+				Name="VCAuxiliaryManagedWrapperGeneratorTool"/>
+		</Configuration>
+	</Configurations>
+	<References>
+	</References>
+	<Files>
+		<Filter
+			Name="Source Files"
+			Filter="cpp;c;cxx;rc;def;r;odl;idl;hpj;bat">
+			<File
+				RelativePath=".\FreeChemicalFeature.cpp">
+			</File>
+		</Filter>
+		<Filter
+			Name="Header Files"
+			Filter="h;hpp;hxx;hm;inl">
+		</Filter>
+	</Files>
+	<Globals>
+	</Globals>
+</VisualStudioProject>

Code/ChemicalFeatures/testChemicalFeatures.cpp

@@ -0,0 +1,43 @@
+// $Id: testChemicalFeatures.cpp 4943 2006-02-17 01:21:27Z glandrum $
+//
+//  Copyright (C) 2005-2006 Rational Discovery LLC
+//
+//  @@ All Rights Reserved @@
+//
+//
+
+#include "FreeChemicalFeature.h"
+#include <Geometry/point.h>
+#include <iostream>
+#include <RDGeneral/Invariant.h>
+
+using namespace ChemicalFeatures;
+
+
+void test1() {
+  std::cout << "-----------------------------------------" << std::endl;
+  std::cout << "Test1" << std::endl;
+
+  FreeChemicalFeature f1("foo","bar",RDGeom::Point3D(0,0,0));
+  TEST_ASSERT(f1.getFamily()=="foo");
+  TEST_ASSERT(f1.getType()=="bar");
+
+  FreeChemicalFeature f2;
+  f2.initFromString(f1.toString());
+  TEST_ASSERT(f2.getFamily()=="foo");
+  TEST_ASSERT(f2.getType()=="bar");
+
+  FreeChemicalFeature f3(f1.toString());
+  TEST_ASSERT(f3.getFamily()=="foo");
+  TEST_ASSERT(f3.getType()=="bar");
+
+  
+  std::cout << "Done" << std::endl;
+
+}
+
+int main() {
+  test1();
+  return 0;
+}
+

Code/ChemicalFeatures/testChemicalFeatures.vcproj

@@ -0,0 +1,156 @@
+<?xml version="1.0" encoding="Windows-1252"?>
+<VisualStudioProject
+	ProjectType="Visual C++"
+	Version="7.10"
+	Name="testChemicalFeatures"
+	ProjectGUID="{4559772E-98D5-431C-9323-657ABE1EF042}"
+	SccProjectName=""
+	SccLocalPath="">
+	<Platforms>
+		<Platform
+			Name="Win32"/>
+	</Platforms>
+	<Configurations>
+		<Configuration
+			Name="Debug|Win32"
+			OutputDirectory=".\Debug"
+			IntermediateDirectory=".\Debug"
+			ConfigurationType="1"
+			UseOfMFC="0"
+			ATLMinimizesCRunTimeLibraryUsage="FALSE"
+			CharacterSet="2">
+			<Tool
+				Name="VCCLCompilerTool"
+				Optimization="0"
+				AdditionalIncludeDirectories="$(RDBASE)/External/boost/include/$(BOOSTBASE),$(RDBASE)/Code"
+				PreprocessorDefinitions="WIN32;_DEBUG;_CONSOLE"
+				BasicRuntimeChecks="3"
+				RuntimeLibrary="3"
+				PrecompiledHeaderFile=".\Debug/testChemicalFeatures.pch"
+				AssemblerListingLocation=".\Debug/"
+				ObjectFile=".\Debug/"
+				ProgramDataBaseFileName=".\Debug/"
+				WarningLevel="3"
+				SuppressStartupBanner="TRUE"
+				DebugInformationFormat="4"/>
+			<Tool
+				Name="VCCustomBuildTool"/>
+			<Tool
+				Name="VCLinkerTool"
+				AdditionalDependencies="boost_log-vc71-mt-gd-$(BOOSTVERSION).lib "
+				OutputFile="./testExecs/main.exe"
+				LinkIncremental="1"
+				SuppressStartupBanner="TRUE"
+				AdditionalLibraryDirectories="$(RDBASE)\External\boost\lib"
+				GenerateDebugInformation="TRUE"
+				ProgramDatabaseFile=".\Debug/test.pdb"
+				SubSystem="1"
+				TargetMachine="1"/>
+			<Tool
+				Name="VCMIDLTool"
+				TypeLibraryName=".\Debug/testChemicalFeatures.tlb"
+				HeaderFileName=""/>
+			<Tool
+				Name="VCPostBuildEventTool"/>
+			<Tool
+				Name="VCPreBuildEventTool"/>
+			<Tool
+				Name="VCPreLinkEventTool"/>
+			<Tool
+				Name="VCResourceCompilerTool"
+				PreprocessorDefinitions="_DEBUG"
+				Culture="1033"/>
+			<Tool
+				Name="VCWebServiceProxyGeneratorTool"/>
+			<Tool
+				Name="VCXMLDataGeneratorTool"/>
+			<Tool
+				Name="VCWebDeploymentTool"/>
+			<Tool
+				Name="VCManagedWrapperGeneratorTool"/>
+			<Tool
+				Name="VCAuxiliaryManagedWrapperGeneratorTool"/>
+		</Configuration>
+		<Configuration
+			Name="Release|Win32"
+			OutputDirectory=".\testExecs\"
+			IntermediateDirectory=".\Release"
+			ConfigurationType="1"
+			UseOfMFC="0"
+			ATLMinimizesCRunTimeLibraryUsage="FALSE"
+			CharacterSet="2">
+			<Tool
+				Name="VCCLCompilerTool"
+				Optimization="2"
+				InlineFunctionExpansion="1"
+				AdditionalIncludeDirectories="$(RDBASE)/External/boost/include/$(BOOSTBASE),$(RDBASE)/Code"
+				PreprocessorDefinitions="WIN32;NDEBUG;_CONSOLE"
+				StringPooling="TRUE"
+				RuntimeLibrary="2"
+				EnableFunctionLevelLinking="TRUE"
+				PrecompiledHeaderFile=".\Release/testChemicalFeatures.pch"
+				AssemblerListingLocation=".\Release/"
+				ObjectFile=".\Release/"
+				ProgramDataBaseFileName=".\Release/"
+				WarningLevel="3"
+				SuppressStartupBanner="TRUE"/>
+			<Tool
+				Name="VCCustomBuildTool"/>
+			<Tool
+				Name="VCLinkerTool"
+				AdditionalDependencies="boost_log-vc71-mt-$(BOOSTVERSION).lib "
+				OutputFile="./testExecs/main.exe"
+				LinkIncremental="1"
+				SuppressStartupBanner="TRUE"
+				AdditionalLibraryDirectories="$(RDBASE)\External\boost\lib"
+				ProgramDatabaseFile=".\Release/test.pdb"
+				SubSystem="1"
+				TargetMachine="1"/>
+			<Tool
+				Name="VCMIDLTool"
+				TypeLibraryName=".\Release/testChemicalFeatures.tlb"
+				HeaderFileName=""/>
+			<Tool
+				Name="VCPostBuildEventTool"/>
+			<Tool
+				Name="VCPreBuildEventTool"/>
+			<Tool
+				Name="VCPreLinkEventTool"/>
+			<Tool
+				Name="VCResourceCompilerTool"
+				PreprocessorDefinitions="NDEBUG"
+				Culture="1033"/>
+			<Tool
+				Name="VCWebServiceProxyGeneratorTool"/>
+			<Tool
+				Name="VCXMLDataGeneratorTool"/>
+			<Tool
+				Name="VCWebDeploymentTool"/>
+			<Tool
+				Name="VCManagedWrapperGeneratorTool"/>
+			<Tool
+				Name="VCAuxiliaryManagedWrapperGeneratorTool"/>
+		</Configuration>
+	</Configurations>
+	<References>
+	</References>
+	<Files>
+		<Filter
+			Name="Source Files"
+			Filter="cpp;c;cxx;rc;def;r;odl;idl;hpj;bat">
+			<File
+				RelativePath=".\testChemicalFeatures.cpp">
+			</File>
+		</Filter>
+		<Filter
+			Name="Header Files"
+			Filter="h;hpp;hxx;hm;inl">
+		</Filter>
+		<Filter
+			Name="Resource Files"
+			Filter="ico;cur;bmp;dlg;rc2;rct;bin;rgs;gif;jpg;jpeg;jpe">
+		</Filter>
+	</Files>
+	<Globals>
+	</Globals>
+</VisualStudioProject>

Code/ChemicalFeatures/test_list.py

@@ -0,0 +1,12 @@
+
+tests=[
+  ("testExecs/main.exe","",{}),
+
+  ]
+
+
+if __name__=='__main__':
+  import sys
+  import TestRunner
+  failed,tests = TestRunner.RunScript('test_list.py',0,1)
+  sys.exit(len(failed))

Code/DataManip/MetricMatrixCalc/Makefile

@@ -0,0 +1,13 @@
+include $(RDBASE)/Code/rdvars.make
+include $(RDBASE)/Code/rdrules.make
+CXXFLAGS=$(RDOPTFLAGS) $(BOOSTINC) -I$(RDCODEDIR)
+
+regrs: testExecs/testMatCalc.exe
+
+testExecs/testMatCalc.exe: testMatCalc.o
+	g++ -o $@ $(CXXFLAGS) $^ $(RDGENERAL)
+
+clean:
+	rm -f  testMatCalc.o testExecs/testMatCalc.exe $(DEPENDS)
+
+include $(DEPENDS)

Code/DataManip/MetricMatrixCalc/MetricFuncs.h

@@ -0,0 +1,58 @@
+//
+//  Copyright (C) 2003-2006 Rational Discovery LLC
+//
+//  @@ All Rights Reserved @@
+//
+#ifndef __RD_METRICFUNCS_H__
+#define __RD_METRICFUNCS_H__
+#include <cmath>
+#include <DataStructs/BitOps.h>
+
+namespace RDDataManip {
+  
+  template <typename T1, typename T2> double EuclideanDistance(const T1 &v1, const T2 &v2, int dim) 
+    {
+      int i;
+      double diff, dist = 0.0;
+      for (i = 0; i < dim; i++) {
+        diff = (double)v1[i] - (double)v2[i];
+        dist += (diff*diff);
+      }
+      return sqrt(dist);
+    };
+
+  template <typename T1, typename T2> double TanimotoDistance(const T1 &bv1, const T2 &bv2, int dim) 
+    {
+      // the dim parameter is actually irrelevant here but we have to include it to deal with 
+      // template version of setMetricFunc in MetricMatricCalc
+      return (1.0 - TanimotoSimilarity(bv1, bv2));
+    }
+
+  template <typename T1, typename T2> double TanimotoSimilarity(const T1 &bv1, const T2 &bv2, int dim)
+    {
+      double res;
+      if(bv1.GetNumBits()!=bv2.GetNumBits()){
+        // fold down automatically:
+        unsigned int nb1=bv1.GetNumBits();
+        unsigned int nb2=bv2.GetNumBits();
+    	
+    	if(nb1 < nb2){
+    	  T2 *bv3=FoldFingerprint(bv2,nb2/nb1);
+    	  res = TanimotoSimilarity(bv1,*bv3);
+    	  delete bv3;
+    	} else {
+    	  T2 *bv3=FoldFingerprint(bv1,nb1/nb2);
+    	  res = TanimotoSimilarity(*bv3,bv2);
+    	  delete bv3;
+    	}
+          } else {
+    	res = TanimotoSimilarity(bv1, bv2);
+      }
+      return res;
+    }
+
+}
+
+#endif
+    
+    

Code/DataManip/MetricMatrixCalc/MetricMatrixCalc.h

@@ -0,0 +1,97 @@
+// $Id: MetricMatrixCalc.h 4945 2006-02-17 01:28:12Z glandrum $
+//
+//  Copyright (C) 2003-2006 Rational Discovery LLC
+//
+//  @@ All Rights Reserved @@
+//
+#ifndef __RD_METRICMATRIXCAL_H__
+#define __RD_METRICMATRIXCAL_H__
+
+#include "MetricFuncs.h"
+#include <RDGeneral/Invariant.h>
+
+namespace RDDataManip {
+  
+  /*! \brief A generic metric matrix calculator (e.g simialrity matrix or
+   *         ditance matrix) 
+   *
+   *  This templated class needs some explanation\n
+   *    vectType is a container that can support [] operator \n
+   *    entryType is the type of entry that is returned by the [] operator\n
+   *  Examples of the container include PySequenceHolder which is wrapper around 
+   *  a python sequence objects like lists and tuples. \n
+   *  Examples of the entryType include a sequence of double, floats, and Explicit Bit Vectors 
+   *
+   */
+  template <class vectType, class entryType> class MetricMatrixCalc {
+  public:
+    /*! \brief Default Constructor
+     *
+     */
+    MetricMatrixCalc() {};
+    
+    /*! \brief Set the metric function
+     *
+     * Set the pointer to the mertic funvtion to be used by the metric calculator
+     *
+     * ARGUMENTS:
+     *
+     *  mFunc - pointer to the metric funtion
+     */
+    void setMetricFunc(double (*mFunc)(const entryType &, const entryType &, int)) {
+      dp_metricFunc = mFunc;
+    }
+
+    /*! \brief The calculator function
+     *
+     * ARGUMENTS:
+     *
+     *  descrips - vectType container with a entryType for each item\n
+     *  nItems - the number of item in the descripts.
+     *           In several cases this argument is irrelvant since vectType probably supports
+     *           a size() member function, But we would like this interface to take for example 
+     *           a double** as the and correctly parse the row and columns. \n
+     *  dim - the dimension of the 
+     *  distMat - pointer to an array to write the distance matrix to
+     *            it is assumed that the right sized array has already be allocated.
+     *
+     * FIX: we can probably make this function create the correct sized distMat and return
+     * it to the caller, but when pushing he result out to a python array not sure how to
+     * avoid copy the entire distance matrix in that case
+     *
+     * RETURNS:
+     * 
+     *  pointer to a 1D array of doubles. Only the lower triangle elements are
+     *  included in the array
+     */
+    void calcMetricMatrix(const vectType &descripts, int nItems, int dim,
+                          double *distMat) {
+      int i, j, itab, id;
+      CHECK_INVARIANT(distMat, "invalid pointer to a distance matix");
+      
+      for (i = 1; i < nItems; i++) {
+        //itab = nItems*i - (i+1)*(i+2)/2;
+        itab = i*(i-1)/2;
+        for (j = 0; j < i; j++) {
+          id = itab + j;
+          distMat[id] = dp_metricFunc(descripts[i], descripts[j], dim);
+        }
+      }
+    };
+    
+  private:
+    // pointer to the metric function
+    /*! \brief pointer to the metric function
+     *
+     * In several cases the last argument 'dim' should be irrelevant, 
+     * For example when entryType is a bit vector the size is of the vector
+     * or the dimension can be obtained by asking the bit vector itself. However
+     * we woul like this interface to support other containers lines double* 
+     * in which case the 'dim' value is useful in cumputing the metric.
+     */  
+    double (*dp_metricFunc)(const entryType &, const entryType &, int);
+    
+  };
+};
+
+#endif

Code/DataManip/MetricMatrixCalc/Wrap/Makefile

@@ -0,0 +1,7 @@
+
+$(RDBASE)/Python/DataManip/Metric/rdMetricMatrixCalc.so: rdMetricMatrixCalc.cpp
+	python setup.py install --install-lib=$(RDBASE)/Python
+
+clean:
+	if test -e $(RDBASE)/Python/DataManip/Metric/rdMetricMatrixCalc.so; then rm $(RDBASE)/Python/DataManip/Metric/rdMetricMatrixCalc.so; fi
+	if test -e build; then rm -rf build; fi

Code/DataManip/MetricMatrixCalc/Wrap/rdMetricMatrixCalc.cpp

@@ -0,0 +1,282 @@
+// $Id: rdMetricMatrixCalc.cpp 4945 2006-02-17 01:28:12Z glandrum $
+//
+//  Copyright (C) 2003-2006 Rational Discovery LLC
+//
+//  @@ All Rights Reserved @@
+//
+#define PY_ARRAY_UNIQUE_SYMBOL rdmetric_array_API
+#include <boost/python.hpp>
+#include <boost/python/numeric.hpp>
+#include "Numeric/arrayobject.h"
+
+#include <RDBoost/PySequenceHolder.h>
+#include <RDBoost/Wrap.h>
+
+#include <RDGeneral/types.h>
+
+#include <DataManip/MetricMatrixCalc/MetricMatrixCalc.h>
+#include <DataManip/MetricMatrixCalc/MetricFuncs.h>
+#include <DataStructs/BitVects.h>
+#include <string>
+
+using namespace RDDataManip;
+
+void wrap_MMcalc();
+
+namespace python = boost::python;
+namespace RDDataManip {
+  
+  PyObject *getEuclideanDistMat(python::object descripMat) {
+    // Bit of a pain involved here, we accept three types of PyObjects here
+    // 1. A Numeric Array 
+    //     - first find what 'type' of entry we have (float, double and int is all we recognize for now)
+    //     - then point to contiguous piece of memory from the array that contains the data with a type*
+    //     - then make a new type** pointer so that double index into this contiguous memory will work
+    //       and then pass it along to the distance calculator
+    // 2. A list of Numeric Vector (or 1D arrays) 
+    //     - in this case wrap descripMat with a PySequenceHolder<type*> where type is the 
+    //       type of entry in vector (accepted types are int, double and float
+    //     - Then pass the PySequenceHolder to the metrci calculator
+    // 3. A list (or tuple) of lists (or tuple)
+    //     - In this case other than wrapping descripMat with a PySequenceHolder
+    //       each of the indivual list in there are also wrapped by a PySequenceHolder
+    //     - so the distance calculator is passed in a "PySequenceHolder<PySequenceHolder<double>>"
+    //     - FIX: not that we always convert entry values to double here, even if we passed
+    //       in a list of list of ints (or floats). Given that lists can be heterogeneous, I do not
+    //       know how to ask a list what type of entries if contains.
+    //
+    //  OK my brain is going to explode now
+    
+    // first deal with situation where we have an Numeric Array
+    PyObject *descMatObj = descripMat.ptr();
+    PyArrayObject *distRes;
+    if (PyArray_Check(descMatObj)) {
+      // get the dimensions of the array
+      int nrows = ((PyArrayObject *)descMatObj)->dimensions[0];
+      int ncols = ((PyArrayObject *)descMatObj)->dimensions[1];
+      int i;
+      CHECK_INVARIANT((nrows > 0) && (ncols > 0), "");
+
+      int dMatLen = nrows*(nrows-1)/2;
+      
+      // now that we have the dimensions declare the distance matrix which is always a 
+      // 1D double array
+      distRes = (PyArrayObject *)PyArray_FromDims(1, &dMatLen, PyArray_DOUBLE);
+      
+      // grab a pointer to the data in the array so that we can directly put values in there
+      // and avoid copying (as I understand it PyArray_FromDimsAndData will do it here for us
+      // because python will never free the malloced memory this way)
+      double *dMat = (double *)distRes->data;
+
+      // if we have double array
+      PyArrayObject *copy;
+      copy = (PyArrayObject *)PyArray_ContiguousFromObject(descMatObj, 
+							   ((PyArrayObject *)descMatObj)->descr->type_num,
+							   2,2);
+      if (((PyArrayObject *)descMatObj)->descr->type_num == PyArray_DOUBLE) {
+        double *desc = (double *)copy->data;
+        
+	// REVIEW: create an adaptor object to hold a double * and support
+	//  operator[]() so that we don't have to do this stuff:
+
+        // here is the 2D array trick this so that when the distance calaculator
+        // asks for desc2D[i] we basically get the ith row as double*
+        double **desc2D = new double*[nrows];
+        for (i = 0; i < nrows; i++) {
+          desc2D[i] = desc;
+          desc += ncols;
+        }
+        MetricMatrixCalc<double**, double*> mmCalc;
+        mmCalc.setMetricFunc(&EuclideanDistance<double *, double *>);
+        mmCalc.calcMetricMatrix(desc2D, nrows, ncols, dMat);
+        
+        delete [] desc2D;
+        // we got the distance matrix we are happy so return
+        return PyArray_Return(distRes);
+      }
+      
+      // if we have a float array
+      else if (((PyArrayObject *)descMatObj)->descr->type_num == PyArray_FLOAT) {
+        float* desc = (float *)copy->data;
+        float **desc2D = new float*[nrows];
+        for (i = 0; i < nrows; i++) {
+          desc2D[i] = desc;
+          desc += ncols;
+        }
+        MetricMatrixCalc<float**, float*> mmCalc;
+        mmCalc.setMetricFunc(&EuclideanDistance<float *, float*>);
+        mmCalc.calcMetricMatrix(desc2D, nrows, ncols, dMat);
+        delete [] desc2D;
+        return PyArray_Return(distRes);
+      }
+
+      // if we have an interger array
+      else if (((PyArrayObject *)descMatObj)->descr->type_num == PyArray_INT) {
+        int *desc = (int *)copy->data;
+        int **desc2D = new int*[nrows];
+        for (i = 0; i < nrows; i++) {
+          desc2D[i] = desc;
+          desc += ncols;
+        }
+        MetricMatrixCalc<int**, int*> mmCalc;
+        mmCalc.setMetricFunc(&EuclideanDistance<int *, int*>);
+        mmCalc.calcMetricMatrix(desc2D, nrows, ncols, dMat);
+        delete [] desc2D;
+        return PyArray_Return(distRes);
+      }
+      else {
+        // unreconiged type for the matrix, throw up
+        throw_value_error("The array has to be of type int, float, or double for GetEuclideanDistMat");
+      }
+    } // done with an array input
+    else {
+      // REVIEW: removed a ton of code here
+
+      // we have probably have a list or a tuple
+      
+      int nrows, ncols, i;
+      ncols = 0;
+      nrows = python::extract<int>(descripMat.attr("__len__")());
+      CHECK_INVARIANT(nrows > 0, "Empty list passed in");
+
+      int dMatLen = nrows*(nrows-1)/2;
+      distRes = (PyArrayObject *)PyArray_FromDims(1, &dMatLen, PyArray_DOUBLE);
+      double *dMat = (double *)distRes->data;
+      
+      // assume that we a have a list of list of values (that can be extracted to double)
+      std::vector<PySequenceHolder<double> > dData;
+      dData.reserve(nrows);
+      for (i = 0; i < nrows; i++) {
+	//PySequenceHolder<double> row(seq[i]);
+        PySequenceHolder<double> row(descripMat[i]);
+        if(i==0){
+	  ncols = row.size();
+	} else if( row.size() != ncols ){
+	  throw_value_error("All subsequences must be the same length");
+	}
+	dData.push_back(row);
+      }
+      
+      MetricMatrixCalc< std::vector<PySequenceHolder<double> >, PySequenceHolder<double> > mmCalc;
+      mmCalc.setMetricFunc(&EuclideanDistance< PySequenceHolder<double>, PySequenceHolder<double> >);
+      mmCalc.calcMetricMatrix(dData, nrows, ncols, dMat);
+    }
+    return PyArray_Return(distRes);
+  }
+  
+  PyObject *getTanimotoDistMat(python::object bitVectList) {
+    // we will assume here that we have a either a list of ExplicitBitVectors or
+    // SparseBitVects
+    int nrows = python::extract<int>(bitVectList.attr("__len__")());
+    CHECK_INVARIANT(nrows > 1, "");
+
+    // First check what type of vector we have
+    python::object v1 = bitVectList[0];
+    python::extract<ExplicitBitVect> ebvWorks(v1);
+    python::extract<SparseBitVect> sbvWorks(v1);
+    if(!ebvWorks.check() && !sbvWorks.check()){
+      throw_value_error("GetTanimotoDistMat can only take a sequence of ExplicitBitVects or SparseBitvects");
+    }
+
+    int dMatLen = nrows*(nrows-1)/2;
+    PyArrayObject *simRes = (PyArrayObject *)PyArray_FromDims(1, &dMatLen, PyArray_DOUBLE);
+    double *sMat = (double *)simRes->data;
+    
+    if (ebvWorks.check()) {
+      PySequenceHolder<ExplicitBitVect> dData(bitVectList);
+      MetricMatrixCalc<PySequenceHolder<ExplicitBitVect>, ExplicitBitVect> mmCalc;
+      mmCalc.setMetricFunc(&TanimotoDistance<ExplicitBitVect, ExplicitBitVect>);
+      mmCalc.calcMetricMatrix(dData, nrows, 0, sMat);
+    }
+    else if (sbvWorks.check()) {
+      PySequenceHolder<SparseBitVect> dData(bitVectList);
+      MetricMatrixCalc<PySequenceHolder<SparseBitVect>, SparseBitVect> mmCalc;
+      mmCalc.setMetricFunc(&TanimotoDistance<SparseBitVect, SparseBitVect>);
+      mmCalc.calcMetricMatrix(dData, nrows, 0, sMat);
+    }
+    return PyArray_Return(simRes);
+  }
+
+  PyObject *getTanimotoSimMat(python::object bitVectList) {
+    // we will assume here that we have a either a list of ExplicitBitVectors or
+    // SparseBitVects
+    int nrows = python::extract<int>(bitVectList.attr("__len__")());
+    CHECK_INVARIANT(nrows > 1, "");
+
+    // First check what type of vector we have
+    python::object v1 = bitVectList[0];
+    python::extract<ExplicitBitVect> ebvWorks(v1);
+    python::extract<SparseBitVect> sbvWorks(v1);
+    if(!ebvWorks.check() && !sbvWorks.check()){
+      throw_value_error("GetTanimotoDistMat can only take a sequence of ExplicitBitVects or SparseBitvects");
+    }
+
+    int dMatLen = nrows*(nrows-1)/2;
+    PyArrayObject *simRes = (PyArrayObject *)PyArray_FromDims(1, &dMatLen, PyArray_DOUBLE);
+    double *sMat = (double *)simRes->data;
+    
+    if (ebvWorks.check()) {
+      PySequenceHolder<ExplicitBitVect> dData(bitVectList);
+      MetricMatrixCalc<PySequenceHolder<ExplicitBitVect>, ExplicitBitVect> mmCalc;
+      mmCalc.setMetricFunc(&TanimotoSimilarity<ExplicitBitVect, ExplicitBitVect>);
+      mmCalc.calcMetricMatrix(dData, nrows, 0, sMat);
+    }
+    else if (sbvWorks.check()) {
+      PySequenceHolder<SparseBitVect> dData(bitVectList);
+      MetricMatrixCalc<PySequenceHolder<SparseBitVect>, SparseBitVect> mmCalc;
+      mmCalc.setMetricFunc(&TanimotoSimilarity<SparseBitVect, SparseBitVect>);
+      mmCalc.calcMetricMatrix(dData, nrows, 0, sMat);
+    }
+    return PyArray_Return(simRes);
+  }
+}
+                                            
+BOOST_PYTHON_MODULE(rdMetricMatrixCalc) 
+{
+  python::scope().attr("__doc__") =
+    "Module containing the calculator for metric matrix calculation, \n"
+    "e.g. simialrity and distance matrices"
+    ;
+
+  import_array();
+  python::register_exception_translator<IndexErrorException>(&translate_index_error);
+  python::register_exception_translator<ValueErrorException>(&translate_value_error);
+  
+  std::string docString;
+  docString = "Compute the distance matrix from a descriptor matrix using Euclidean distance metric\n\n\
+  ARGUMENTS: \n\
+\n\
+    descripMat - A python object of any one of the folliwng type \n\
+                   1. A numeric array of dimensions n by m where n is the number of items in the data set \n\
+                       and m is the number of descriptors \n\
+                   2. A list of Numeric Vectors (or 1D arrays), each entry in the list corresponds \n\
+                       to descriptor vector for one item \n\
+                   3. A list (or tuple) of list (or tuple) of values, where the values can be extracted to \n\
+                       double. \n\n\
+  RETURNS: \n\
+    A numeric 1 dimensional array containing the lower triangle elements of the symmetric distance matrix\n\n";
+  
+  python::def("GetEuclideanDistMat", RDDataManip::getEuclideanDistMat, 
+              docString.c_str());
+
+  docString = "Compute the distance matrix from a list of BitVects \n\n\
+  ARGUMENTS: \n\
+\n\
+    bitVectList - a list of bit vectors. Currently this works only for a list of explicit bit vectors, \n\
+                  needs to be expanded to support a lsit of SparseBitVects\n\n\
+  RETURNS: \n\
+    A numeric 1 dimensional array containing the lower triangle elements of the\n\
+    symmetric distance matrix\n\n";
+  python::def("GetTanimotoDistMat", RDDataManip::getTanimotoDistMat,
+              docString.c_str());
+  
+  docString = "Compute the similarity matrix from a list of BitVects \n\n\
+  ARGUMENTS: \n\
+\n\
+    bitVectList - a list of bit vectors. Currently this works only for a list of explicit bit vectors, \n\
+                  needs to be expanded to support a lsit of SparseBitVects\n\n\
+  RETURNS: \n\
+    A numeric 1 dimensional array containing the lower triangle elements of the symmetric similarity matrix\n\n";
+  python::def("GetTanimotoSimMat", RDDataManip::getTanimotoSimMat,
+              docString.c_str());
+}

Code/DataManip/MetricMatrixCalc/Wrap/setup.py

@@ -0,0 +1,18 @@
+# Run this with:
+#  python setup.py install --install-lib=$RDBASE/Python
+from RDBuild import *
+from distutils.core import setup,Extension
+
+
+libDirs +=[
+  rdBitDir,
+  ]
+
+libraries += ["DataStructs", "RDGeneral", "RDBoost"]
+setup(name="DataManip.Metric.rdMetricMatrixCalc", version="2.0",
+      ext_modules=[Extension("DataManip.Metric.rdMetricMatrixCalc",
+                             ["rdMetricMatrixCalc.cpp"],
+                             library_dirs=libDirs,
+                             libraries=libraries,
+                             extra_link_args=linkArgs,
+                             extra_compile_args=compileArgs)])

Code/DataManip/MetricMatrixCalc/Wrap/testMatricCalc.py

@@ -0,0 +1,156 @@
+import RDConfig
+import unittest
+from DataManip.Metric import rdMetricMatrixCalc as rdmmc
+from Numeric import *
+import random
+import DataStructs
+
+def feq(v1,v2,tol2=1e-4):
+    return abs(v1-v2)<=tol2
+
+class TestCase(unittest.TestCase):
+
+    def setUp(self) :
+        pass
+
+    def test0DistsArray(self) :
+        exp = array([1., 1.414213, 1.0], 'd')
+
+        # initialize a double array and check if get back the expected distances
+        desc = zeros((3,2), 'd')
+        desc[1,0] = 1.0
+        desc[2,0] = 1.0
+        desc[2,1] = 1.0
+
+        dmat = rdmmc.GetEuclideanDistMat(desc)
+        for i in range(shape(dmat)[0]) :
+            assert feq(dmat[i], exp[i])
+
+        # repeat with an flaot array
+        desc = zeros((3,2), 'f')
+        desc[1,0] = 1.0
+        desc[2,0] = 1.0
+        desc[2,1] = 1.0
+
+        dmat = rdmmc.GetEuclideanDistMat(desc)
+        for i in range(shape(dmat)[0]) :
+            assert feq(dmat[i], exp[i])
+
+        # finally with an interger array
+        desc = zeros((3,2), 'i')
+        desc[1,0] = 1
+        desc[2,0] = 1
+        desc[2,1] = 1
+
+        dmat = rdmmc.GetEuclideanDistMat(desc)
+        for i in range(shape(dmat)[0]) :
+            assert feq(dmat[i], exp[i])
+
+    def ctest1DistsListArray(self):
+        exp = array([1., 1.414213, 1.0], 'd')
+
+        desc = [array([0.0, 0.0], 'd'),
+                array([1.0, 0.0], 'd'),
+                array([1.0, 1.0], 'd')]
+        dmat = rdmmc.GetEuclideanDistMat(desc)
+
+        for i in range(shape(dmat)[0]) :
+            assert feq(dmat[i], exp[i])
+
+        # repeat the test with a list of arrays of floats
+        desc = [array([0.0, 0.0], 'f'),
+                array([1.0, 0.0], 'f'),
+                array([1.0, 1.0], 'f')]
+        dmat = rdmmc.GetEuclideanDistMat(desc)
+        for i in range(shape(dmat)[0]) :
+            assert feq(dmat[i], exp[i])
+
+        # repeat the test with a list of arrays of ints
+        desc = [array([0, 0], 'i'),
+                array([1, 0], 'i'),
+                array([1, 1], 'i')]
+        dmat = rdmmc.GetEuclideanDistMat(desc)
+        for i in range(shape(dmat)[0]) :
+            assert feq(dmat[i], exp[i])
+
+    def test2DistListList(self) :
+        exp = array([1., 1.414213, 1.0], 'd')
+
+        desc = [[0.0, 0.0],
+                [1.0, 0.0],
+                [1.0, 1.0]]
+        dmat = rdmmc.GetEuclideanDistMat(desc)
+        for i in range(shape(dmat)[0]) :
+            assert feq(dmat[i], exp[i])
+
+        #test with ints
+        desc = [[0, 0],
+                [1, 0],
+                [1, 1]]
+        dmat = rdmmc.GetEuclideanDistMat(desc)
+        for i in range(shape(dmat)[0]) :
+            assert feq(dmat[i], exp[i])
+
+    def test3Compare(self) :
+        n = 30
+        m = 5
+
+        dscArr = zeros((n,m), 'd')
+        for i in range(n):
+            for j in range(m):
+                dscArr[i,j] = random.random()
+        dmatArr = rdmmc.GetEuclideanDistMat(dscArr)
+
+        dscLL = []
+        for i in range(n) :
+            row = []
+            for j in range(m):
+                row.append(dscArr[i,j])
+            dscLL.append(row)
+        dmatLL = rdmmc.GetEuclideanDistMat(dscLL)
+
+        assert shape(dmatArr) == shape(dmatLL)
+
+        for i in range(n*(n-1)/2):
+            assert feq(dmatArr[i], dmatLL[i])
+
+    def test4ebv(self) :
+
+        n = 30
+        m = 2048
+        dm = 800
+        lst = []
+        for i in range(n):
+            v = DataStructs.ExplicitBitVect(m)
+            for j in range(dm) :
+                v.SetBit(random.randrange(0, m))
+            lst.append(v)
+
+        dMat = rdmmc.GetTanimotoDistMat(lst)
+
+        sMat = rdmmc.GetTanimotoSimMat(lst)
+
+        for i in range(n*(n-1)/2) :
+            assert feq(sMat[i] + dMat[i], 1.0) 
+                        
+    def test5sbv(self) :
+
+        n = 30
+        m = 2048
+        dm = 800
+        lst = []
+        for i in range(n):
+            v = DataStructs.SparseBitVect(m)
+            for j in range(dm) :
+                v.SetBit(random.randrange(0, m))
+            lst.append(v)
+
+        dMat = rdmmc.GetTanimotoDistMat(lst)
+
+        sMat = rdmmc.GetTanimotoSimMat(lst)
+
+        for i in range(n*(n-1)/2) :
+            assert feq(sMat[i] + dMat[i], 1.0) 
+                        
+if __name__ == '__main__':
+    unittest.main()

Code/DataManip/MetricMatrixCalc/Wrap/test_list.py

@@ -0,0 +1,12 @@
+
+tests=[
+    ("python","testMatricCalc.py",{}),
+    ]
+
+longTests=[]
+
+if __name__=='__main__':
+  import sys
+  import TestRunner
+  failed,tests = TestRunner.RunScript('test_list.py',0,1)
+  sys.exit(len(failed))

Code/DataManip/MetricMatrixCalc/Wrap/wrapMetricMatrixCalc.vcproj

@@ -0,0 +1,250 @@
+<?xml version="1.0" encoding="Windows-1252"?>
+<VisualStudioProject
+	ProjectType="Visual C++"
+	Version="7.10"
+	Name="wrapMetricMatrixCalc"
+	ProjectGUID="{65160106-70A9-4BC1-A0FC-CC7740E5E210}"
+	RootNamespace="wrapMetricMatrixCalc"
+	SccProjectName="wrapMetricMatrixCalc"
+	SccLocalPath=".">
+	<Platforms>
+		<Platform
+			Name="Win32"/>
+	</Platforms>
+	<Configurations>
+		<Configuration
+			Name="DebugPython|Win32"
+			OutputDirectory=".\wrapMetricMatrixCalc_Win32_DebugPython"
+			IntermediateDirectory=".\wrapMetricMatrixCalc_Win32_DebugPython"
+			ConfigurationType="2"
+			UseOfMFC="0"
+			ATLMinimizesCRunTimeLibraryUsage="FALSE"
+			CharacterSet="2">
+			<Tool
+				Name="VCCLCompilerTool"
+				Optimization="0"
+				AdditionalIncludeDirectories="$(RDBASE)/Code,$(PYTHONHOME)\include,$(RDBASE)/External/boost/include/$(BOOSTBASE),$(RDBASE)/External/vflib-2.0/include"
+				PreprocessorDefinitions="WIN32;_DEBUG;_WINDOWS;_USRDLL;TEST_EXPORTS;BOOST_DEBUG_PYTHON"
+				BasicRuntimeChecks="3"
+				RuntimeLibrary="3"
+				RuntimeTypeInfo="TRUE"
+				PrecompiledHeaderFile=".\wrapMetricMatrixCalc_Win32_DebugPython/wrapMetricMatrixCalc.pch"
+				AssemblerListingLocation=".\wrapMetricMatrixCalc_Win32_DebugPython/"
+				ObjectFile=".\wrapMetricMatrixCalc_Win32_DebugPython/"
+				ProgramDataBaseFileName=".\wrapMetricMatrixCalc_Win32_DebugPython/"
+				WarningLevel="3"
+				SuppressStartupBanner="TRUE"
+				DebugInformationFormat="3"
+				CompileAs="0"/>
+			<Tool
+				Name="VCCustomBuildTool"/>
+			<Tool
+				Name="VCLinkerTool"
+				IgnoreImportLibrary="TRUE"
+				AdditionalDependencies="boost_python.lib; vflib.lib;libDatastructs.lib odbc32.lib odbccp32.lib $(PYTHONVERS).lib BLAS.lib LAPACK.lib boost_python.lib"
+				OutputFile="DebugPython/rdMetricMatrixCalc_d.dll"
+				LinkIncremental="1"
+				SuppressStartupBanner="TRUE"
+				AdditionalLibraryDirectories="$(PYTHONHOME)\libs,$(RDBASE)\External\Lapack\win32,$(RDBASE)/External/boost/lib"
+				IgnoreDefaultLibraryNames="msvcprtdlib.lib"
+				GenerateDebugInformation="TRUE"
+				ProgramDatabaseFile=".\wrapMetricMatrixCalc_Win32_DebugPython/rdMetricMatrixCalc_d.pdb"
+				SubSystem="2"
+				ImportLibrary=".\wrapMetricMatrixCalc_Win32_DebugPython/rdMetricMatrixCalc_d.lib"
+				TargetMachine="1"/>
+			<Tool
+				Name="VCMIDLTool"
+				PreprocessorDefinitions="_DEBUG"
+				MkTypLibCompatible="TRUE"
+				SuppressStartupBanner="TRUE"
+				TargetEnvironment="1"
+				TypeLibraryName=".\wrapMetricMatrixCalc_Win32_DebugPython/wrapMetricMatrixCalc.tlb"
+				HeaderFileName=""/>
+			<Tool
+				Name="VCPostBuildEventTool"
+				Description="copy dll"
+				CommandLine="copy DebugPython\rdMetricMatrixCalc_d.dll &quot;$(RDBASE)&quot;\Python\Chem"/>
+			<Tool
+				Name="VCPreBuildEventTool"/>
+			<Tool
+				Name="VCPreLinkEventTool"/>
+			<Tool
+				Name="VCResourceCompilerTool"
+				PreprocessorDefinitions="_DEBUG"
+				Culture="1033"/>
+			<Tool
+				Name="VCWebServiceProxyGeneratorTool"/>
+			<Tool
+				Name="VCXMLDataGeneratorTool"/>
+			<Tool
+				Name="VCWebDeploymentTool"/>
+			<Tool
+				Name="VCManagedWrapperGeneratorTool"/>
+			<Tool
+				Name="VCAuxiliaryManagedWrapperGeneratorTool"/>
+		</Configuration>
+		<Configuration
+			Name="Debug|Win32"
+			OutputDirectory=".\Debug"
+			IntermediateDirectory=".\Debug"
+			ConfigurationType="2"
+			UseOfMFC="0"
+			ATLMinimizesCRunTimeLibraryUsage="FALSE">
+			<Tool
+				Name="VCCLCompilerTool"
+				AdditionalOptions="/Zm400 "
+				Optimization="0"
+				AdditionalIncludeDirectories="$(RDBASE)/Code,$(PYTHONHOME)\include,$(RDBASE)/External/boost/include/$(BOOSTBASE),$(RDBASE)/External/vflib-2.0/include"
+				PreprocessorDefinitions="WIN32;_DEBUG;_WINDOWS"
+				BasicRuntimeChecks="3"
+				RuntimeLibrary="3"
+				RuntimeTypeInfo="TRUE"
+				PrecompiledHeaderFile=".\Debug/wrapMetricMatrixCalc.pch"
+				AssemblerListingLocation=".\Debug/"
+				ObjectFile=".\Debug/"
+				ProgramDataBaseFileName=".\Debug/"
+				WarningLevel="3"
+				SuppressStartupBanner="TRUE"
+				DebugInformationFormat="3"
+				CompileAs="0"/>
+			<Tool
+				Name="VCCustomBuildTool"/>
+			<Tool
+				Name="VCLinkerTool"
+				IgnoreImportLibrary="TRUE"
+				AdditionalDependencies="boost_log-vc71-mt-gd-$(BOOSTVERSION).lib boost_python-vc71-mt-gd-$(BOOSTVERSION).lib odbc32.lib odbccp32.lib $(PYTHONVERS).lib BLAS.lib LAPACK.lib"
+				OutputFile="Debug/rdMetricMatrixCalc.dll"
+				LinkIncremental="1"
+				SuppressStartupBanner="TRUE"
+				AdditionalLibraryDirectories="$(PYTHONHOME)\libs,$(RDBASE)\External\Lapack\win32,$(RDBASE)/External/boost/lib"
+				IgnoreDefaultLibraryNames="msvcprtdlib.lib"
+				GenerateDebugInformation="TRUE"
+				ProgramDatabaseFile=".\Debug/rdMetricMatrixCalc.pdb"
+				SubSystem="2"
+				ImportLibrary=".\Debug/rdMetricMatrixCalc.lib"
+				TargetMachine="1"/>
+			<Tool
+				Name="VCMIDLTool"
+				PreprocessorDefinitions="_DEBUG"
+				MkTypLibCompatible="TRUE"
+				SuppressStartupBanner="TRUE"
+				TargetEnvironment="1"
+				TypeLibraryName=".\Debug/wrapMetricMatrixCalc.tlb"
+				HeaderFileName=""/>
+			<Tool
+				Name="VCPostBuildEventTool"
+				Description="copy dll"
+				CommandLine="copy Debug\rdMetricMatrixCalc.dll &quot;$(RDBASE)&quot;\Python\DataManip\Metric"/>
+			<Tool
+				Name="VCPreBuildEventTool"/>
+			<Tool
+				Name="VCPreLinkEventTool"/>
+			<Tool
+				Name="VCResourceCompilerTool"
+				PreprocessorDefinitions="_DEBUG"
+				Culture="1033"/>
+			<Tool
+				Name="VCWebServiceProxyGeneratorTool"/>
+			<Tool
+				Name="VCXMLDataGeneratorTool"/>
+			<Tool
+				Name="VCWebDeploymentTool"/>
+			<Tool
+				Name="VCManagedWrapperGeneratorTool"/>
+			<Tool
+				Name="VCAuxiliaryManagedWrapperGeneratorTool"/>
+		</Configuration>
+		<Configuration
+			Name="Release|Win32"
+			OutputDirectory=".\Release"
+			IntermediateDirectory=".\Release"
+			ConfigurationType="2"
+			UseOfMFC="0"
+			ATLMinimizesCRunTimeLibraryUsage="FALSE">
+			<Tool
+				Name="VCCLCompilerTool"
+				AdditionalOptions="/Zm400 "
+				Optimization="2"
+				InlineFunctionExpansion="1"
+				AdditionalIncludeDirectories="$(RDBASE)/Code,$(PYTHONHOME)\include,$(RDBASE)/External/boost/include/$(BOOSTBASE),$(RDBASE)/External/vflib-2.0/include"
+				PreprocessorDefinitions="WIN32;NDEBUG;_WINDOWS"
+				StringPooling="TRUE"
+				RuntimeLibrary="2"
+				EnableFunctionLevelLinking="TRUE"
+				RuntimeTypeInfo="TRUE"
+				PrecompiledHeaderFile=".\Release/wrapMetricMatrixCalc.pch"
+				AssemblerListingLocation=".\Release/"
+				ObjectFile=".\Release/"
+				ProgramDataBaseFileName=".\Release/"
+				WarningLevel="3"
+				SuppressStartupBanner="TRUE"
+				CompileAs="0"/>
+			<Tool
+				Name="VCCustomBuildTool"/>
+			<Tool
+				Name="VCLinkerTool"
+				IgnoreImportLibrary="TRUE"
+				AdditionalDependencies="boost_log-vc71-mt-$(BOOSTVERSION).lib boost_python-vc71-mt-$(BOOSTVERSION).lib $(PYTHONVERS).lib BLAS.lib LAPACK.lib"
+				OutputFile="Release/rdMetricMatrixCalc.dll"
+				LinkIncremental="1"
+				SuppressStartupBanner="TRUE"
+				AdditionalLibraryDirectories="$(PYTHONHOME)\libs,$(RDBASE)\External\Lapack\win32,$(RDBASE)/External/boost/lib"
+				IgnoreDefaultLibraryNames="msvcprtdlib.lib"
+				ProgramDatabaseFile=".\Release/rdMetricMatrixCalc.pdb"
+				SubSystem="2"
+				ImportLibrary=".\Release/rdMetricMatrixCalc.lib"
+				TargetMachine="1"/>
+			<Tool
+				Name="VCMIDLTool"
+				PreprocessorDefinitions="NDEBUG"
+				MkTypLibCompatible="TRUE"
+				SuppressStartupBanner="TRUE"
+				TargetEnvironment="1"
+				TypeLibraryName=".\Release/wrapMetricMatrixCalc.tlb"
+				HeaderFileName=""/>
+			<Tool
+				Name="VCPostBuildEventTool"
+				Description="copy dll"
+				CommandLine="copy        Release\rdMetricMatrixCalc.dll      &quot;$(RDBASE)&quot;\Python\DataManip\Metric"/>
+			<Tool
+				Name="VCPreBuildEventTool"/>
+			<Tool
+				Name="VCPreLinkEventTool"/>
+			<Tool
+				Name="VCResourceCompilerTool"
+				PreprocessorDefinitions="NDEBUG"
+				Culture="1033"/>
+			<Tool
+				Name="VCWebServiceProxyGeneratorTool"/>
+			<Tool
+				Name="VCXMLDataGeneratorTool"/>
+			<Tool
+				Name="VCWebDeploymentTool"/>
+			<Tool
+				Name="VCManagedWrapperGeneratorTool"/>
+			<Tool
+				Name="VCAuxiliaryManagedWrapperGeneratorTool"/>
+		</Configuration>
+	</Configurations>
+	<References>
+	</References>
+	<Files>
+		<Filter
+			Name="Source Files"
+			Filter="cpp;c;cxx;rc;def;r;odl;idl;hpj;bat">
+			<File
+				RelativePath=".\rdMetricMatrixCalc.cpp">
+			</File>
+		</Filter>
+		<Filter
+			Name="Header Files"
+			Filter="h;hpp;hxx;hm;inl">
+		</Filter>
+		<Filter
+			Name="Resource Files"
+			Filter="ico;cur;bmp;dlg;rc2;rct;bin;rgs;gif;jpg;jpeg;jpe">
+		</Filter>
+	</Files>
+	<Globals>
+	</Globals>
+</VisualStudioProject>

Code/DataManip/MetricMatrixCalc/testMatCalc.cpp

@@ -0,0 +1,50 @@
+// $Id: testMatCalc.cpp 4945 2006-02-17 01:28:12Z glandrum $
+//
+//  Copyright (C) 2003-2006 Rational Discovery LLC
+//
+//  @@ All Rights Reserved @@
+//
+#include "MetricFuncs.h"
+#include "MetricMatrixCalc.h"
+
+#include <cstdlib>
+#include <time.h>
+
+using namespace RDDataManip;
+int main() {
+  
+  int n = 10;
+  int m = 3;
+  int dlen = n*(n-1)/2;
+  int i, j;
+  double *desc = new double[n*m];
+  double **desc2D = new double*[n];
+
+  for (i = 0; i < n; i++) {
+    desc2D[i] = desc;
+    desc += m;
+  }
+  desc = desc2D[0];
+
+  for (i = 0; i < n; i++) {
+    for (j = 0; j < m ; j++) {
+      desc[i*m + j] = ((double)rand())/10;
+    }
+  }
+
+  //double x = EuclideanDistance(desc2D[0], desc2D[1], m);
+  double *dmat = new double[dlen];
+  MetricMatrixCalc<double**, double*> mmCalc;
+  mmCalc.setMetricFunc(&EuclideanDistance<double *, double *>);
+  mmCalc.calcMetricMatrix(desc2D, n, m, dmat);
+
+  for (i = 0; i < dlen; i++) {
+    std::cout << dmat[i] << "\n";
+  }
+
+  delete [] desc2D;
+  delete [] desc;
+  delete [] dmat;
+  
+  exit(0);
+}

Code/DataManip/MetricMatrixCalc/testMatCalc.vcproj

@@ -0,0 +1,177 @@
+<?xml version="1.0" encoding="Windows-1252"?>
+<VisualStudioProject
+	ProjectType="Visual C++"
+	Version="7.10"
+	Name="testMatCalc"
+	ProjectGUID="{D9D29F03-FC1E-4B7D-AA08-DED741874D9A}"
+	SccProjectName=""
+	SccLocalPath="">
+	<Platforms>
+		<Platform
+			Name="Win32"/>
+	</Platforms>
+	<Configurations>
+		<Configuration
+			Name="Debug|Win32"
+			OutputDirectory=".\testMatCalc___Win32_Debug"
+			IntermediateDirectory=".\testMatCalc___Win32_Debug"
+			ConfigurationType="1"
+			UseOfMFC="0"
+			ATLMinimizesCRunTimeLibraryUsage="FALSE"
+			CharacterSet="2">
+			<Tool
+				Name="VCCLCompilerTool"
+				Optimization="0"
+				AdditionalIncludeDirectories="$(RDBASE)/External/boost/include/$(BOOSTBASE),$(RDBASE)/code"
+				PreprocessorDefinitions="WIN32;_DEBUG;_CONSOLE"
+				BasicRuntimeChecks="3"
+				RuntimeLibrary="3"
+				RuntimeTypeInfo="TRUE"
+				PrecompiledHeaderFile=".\testMatCalc___Win32_Debug/testMatCalc.pch"
+				AssemblerListingLocation=".\testMatCalc___Win32_Debug/"
+				ObjectFile=".\testMatCalc___Win32_Debug/"
+				ProgramDataBaseFileName=".\testMatCalc___Win32_Debug/"
+				WarningLevel="3"
+				SuppressStartupBanner="TRUE"
+				DebugInformationFormat="4"
+				CompileAs="0"/>
+			<Tool
+				Name="VCCustomBuildTool"/>
+			<Tool
+				Name="VCLinkerTool"
+				AdditionalDependencies="boost_log-vc71-mt-gd-$(BOOSTVERSION).lib "
+				ShowProgress="0"
+				OutputFile="./testExecs/testMatCalc.exe"
+				LinkIncremental="1"
+				SuppressStartupBanner="TRUE"
+				AdditionalLibraryDirectories="$(RDBASE)\External\boost\lib"
+				GenerateDebugInformation="TRUE"
+				ProgramDatabaseFile=".\testMatCalc___Win32_Debug/testMatCalc.pdb"
+				SubSystem="1"
+				TargetMachine="1"/>
+			<Tool
+				Name="VCMIDLTool"
+				TypeLibraryName=".\testMatCalc___Win32_Debug/testMatCalc.tlb"
+				HeaderFileName=""/>
+			<Tool
+				Name="VCPostBuildEventTool"/>
+			<Tool
+				Name="VCPreBuildEventTool"/>
+			<Tool
+				Name="VCPreLinkEventTool"/>
+			<Tool
+				Name="VCResourceCompilerTool"
+				PreprocessorDefinitions="_DEBUG"
+				Culture="1033"/>
+			<Tool
+				Name="VCWebServiceProxyGeneratorTool"/>
+			<Tool
+				Name="VCXMLDataGeneratorTool"/>
+			<Tool
+				Name="VCWebDeploymentTool"/>
+			<Tool
+				Name="VCManagedWrapperGeneratorTool"/>
+			<Tool
+				Name="VCAuxiliaryManagedWrapperGeneratorTool"/>
+		</Configuration>
+		<Configuration
+			Name="Release|Win32"
+			OutputDirectory=".\testExecs\"
+			IntermediateDirectory=".\Release"
+			ConfigurationType="1"
+			UseOfMFC="0"
+			ATLMinimizesCRunTimeLibraryUsage="FALSE"
+			CharacterSet="2">
+			<Tool
+				Name="VCCLCompilerTool"
+				Optimization="2"
+				InlineFunctionExpansion="1"
+				AdditionalIncludeDirectories="$(RDBASE)/External/boost/include/$(BOOSTBASE),$(RDBASE)/code"
+				PreprocessorDefinitions="WIN32;NDEBUG;_CONSOLE"
+				StringPooling="TRUE"
+				RuntimeLibrary="2"
+				EnableFunctionLevelLinking="TRUE"
+				PrecompiledHeaderFile=".\Release/testMatCalc.pch"
+				AssemblerListingLocation=".\Release/"
+				ObjectFile=".\Release/"
+				ProgramDataBaseFileName=".\Release/"
+				WarningLevel="3"
+				SuppressStartupBanner="TRUE"
+				CompileAs="0"/>
+			<Tool
+				Name="VCCustomBuildTool"/>
+			<Tool
+				Name="VCLinkerTool"
+				AdditionalDependencies="boost_log-vc71-mt-$(BOOSTVERSION).lib "
+				OutputFile=".\testExecs\testMatCalc.exe"
+				LinkIncremental="1"
+				SuppressStartupBanner="TRUE"
+				AdditionalLibraryDirectories="$(RDBASE)\External\boost\lib"
+				ProgramDatabaseFile=".\Release/testMatCalc.pdb"
+				SubSystem="1"
+				TargetMachine="1"/>
+			<Tool
+				Name="VCMIDLTool"
+				TypeLibraryName=".\Release/testMatCalc.tlb"
+				HeaderFileName=""/>
+			<Tool
+				Name="VCPostBuildEventTool"/>
+			<Tool
+				Name="VCPreBuildEventTool"/>
+			<Tool
+				Name="VCPreLinkEventTool"/>
+			<Tool
+				Name="VCResourceCompilerTool"
+				PreprocessorDefinitions="NDEBUG"
+				Culture="1033"/>
+			<Tool
+				Name="VCWebServiceProxyGeneratorTool"/>
+			<Tool
+				Name="VCXMLDataGeneratorTool"/>
+			<Tool
+				Name="VCWebDeploymentTool"/>
+			<Tool
+				Name="VCManagedWrapperGeneratorTool"/>
+			<Tool
+				Name="VCAuxiliaryManagedWrapperGeneratorTool"/>
+		</Configuration>
+	</Configurations>
+	<References>
+	</References>
+	<Files>
+		<Filter
+			Name="Source Files"
+			Filter="cpp;c;cxx;rc;def;r;odl;idl;hpj;bat">
+			<File
+				RelativePath="testMatCalc.cpp">
+				<FileConfiguration
+					Name="Debug|Win32">
+					<Tool
+						Name="VCCLCompilerTool"
+						Optimization="0"
+						AdditionalIncludeDirectories=""
+						PreprocessorDefinitions=""
+						BasicRuntimeChecks="3"/>
+				</FileConfiguration>
+				<FileConfiguration
+					Name="Release|Win32">
+					<Tool
+						Name="VCCLCompilerTool"
+						Optimization="2"
+						AdditionalIncludeDirectories=""
+						PreprocessorDefinitions=""/>
+				</FileConfiguration>
+			</File>
+		</Filter>
+		<Filter
+			Name="Header Files"
+			Filter="h;hpp;hxx;hm;inl">
+		</Filter>
+		<Filter
+			Name="Resource Files"
+			Filter="ico;cur;bmp;dlg;rc2;rct;bin;rgs;gif;jpg;jpeg;jpe">
+		</Filter>
+	</Files>
+	<Globals>
+	</Globals>
+</VisualStudioProject>

Code/DataManip/MetricMatrixCalc/test_list.py

@@ -0,0 +1,11 @@
+tests=[
+    ("testExecs/testMatCalc.exe","", {})
+    ]
+
+longTests=[]
+
+if __name__=='__main__':
+  import sys
+  import TestRunner
+  failed,tests = TestRunner.RunScript('test_list.py',0,1)
+  sys.exit(len(failed))

Code/DataStructs/BitOps.cpp

@@ -0,0 +1,660 @@
+// $Id: BitOps.cpp 5061 2006-03-08 00:36:29Z glandrum $
+//
+//  Copyright (C) 2003-2006 greg Landrum and Rational Discovery LLC
+//
+//  @@ All Rights Reserved @@
+//
+#include <RDBoost/Exceptions.h>
+#include "BitVects.h"
+#include "BitOps.h"
+#include <math.h>
+#include <string>
+#include <iostream>
+#include <RDGeneral/StreamOps.h>
+#include <RDGeneral/types.h>
+
+int getBitId(const char *&text,int format,int size,int curr){
+  PRECONDITION(text,"no text");
+  int res=-1;
+  if( (format==0) || 
+      ( (format == 1) && (size >= std::numeric_limits<unsigned short>::max()) ) ) {
+    int tmp;
+    tmp = *(int *)text;
+    text += sizeof(tmp);
+    res=tmp;
+  } else if (format == 1) { // version 16 and on bits sotred as short ints
+    unsigned short tmp;
+    tmp = *(unsigned short *)text;
+    text += sizeof(tmp);
+    res=tmp;
+  } else if (format == 2) { // run length encoded format
+    res = curr + RDKit::pullPackedIntFromString(text);
+  }
+  return res;
+}
+
+
+
+bool AllProbeBitsMatch(const std::string &probe,const std::string &ref){
+  return AllProbeBitsMatch(probe.c_str(),ref.c_str());
+}
+
+bool AllProbeBitsMatch(const char *probe,const char *ref){
+  PRECONDITION(probe,"no probe text");
+  PRECONDITION(ref,"no probe text");
+  int probeFormat=0;
+  int refFormat=0;
+  int version=0;
+
+  int probeSize = *(int *)probe;
+  probe+=sizeof(probeSize);
+  if(probeSize<0){
+    version = -1*probeSize;
+    if (version == 16) {
+      probeFormat=1;
+    }
+    else if (version == 32) {
+      probeFormat=2;
+    }
+    else {
+      throw("Unknown version type for the encode bit vect");
+    }
+    probeSize = *(int *)probe;
+    probe+=sizeof(probeSize);
+  }
+
+  int refSize = *(int *)ref;
+  ref+=sizeof(refSize);
+  if(refSize<0){
+    version = -1*refSize;
+    if (version == 16) {
+      refFormat=1;
+    }
+    else if (version == 32) {
+      refFormat=2;
+    }
+    else {
+      throw("Unknown version type for the encode bit vect");
+    }
+    refSize = *(int *)ref;
+    ref+=sizeof(refSize);
+  }
+
+
+  int nProbeOn = *(int *)probe;
+  probe+=sizeof(nProbeOn);
+  int nRefOn = *(int *)ref;
+  ref+=sizeof(nRefOn);
+
+  int currProbeBit=0;
+  currProbeBit=getBitId(probe,probeFormat,probeSize,currProbeBit);
+  nProbeOn--;
+
+  int currRefBit=0;
+  currRefBit=getBitId(ref,refFormat,refSize,currRefBit);
+  nRefOn--;
+
+  while(nProbeOn){
+    while(currRefBit<currProbeBit && nRefOn>0){
+      if(refFormat==2) currRefBit++;
+      currRefBit=getBitId(ref,refFormat,refSize,currRefBit);
+      nRefOn--;
+    }
+    if(currRefBit!=currProbeBit) return false;
+    if(probeFormat==2) currProbeBit++;
+    currProbeBit=getBitId(probe,probeFormat,probeSize,currProbeBit);
+    nProbeOn--;
+  }
+  return true;
+}
+
+template <typename T1>
+bool AllProbeBitsMatch(const T1 &probe,const std::string &pkl){
+  const char *text=pkl.c_str();
+  int format=0;
+  int nOn=0,size,version=0;
+  size = *(int *)text;
+  text+=sizeof(size);
+  if(size<0){
+    version = -1*size;
+    if (version == 16) {
+      format=1;
+    }
+    else if (version == 32) {
+      format=2;
+    }
+    else {
+      throw("Unknown version type for the encode bit vect");
+    }
+    size = *(int *)text;
+    text+=sizeof(size);
+  }
+  nOn = *(int *)text;
+  text+=sizeof(nOn);
+
+  int currBit=0;
+  currBit=getBitId(text,format,size,currBit);
+  nOn--;
+  std::vector<int> obl;
+  probe.GetOnBits(obl);
+  
+
+  //for(int i=0;i<probe.GetNumBits();i++){
+  //  if(probe.GetBit(i)){
+  for(std::vector<int>::const_iterator i=obl.begin();i!=obl.end();i++){
+    while(currBit<*i && nOn>0){
+	if(format==2) currBit++;
+	currBit=getBitId(text,format,size,currBit);
+	nOn--;
+      }
+      if(currBit!=*i) return false;
+      //}
+  }
+  return true;
+}
+template bool AllProbeBitsMatch(const SparseBitVect& bv1,const std::string &pkl);
+template bool AllProbeBitsMatch(const ExplicitBitVect& bv1,const std::string &pkl);
+
+// """ -------------------------------------------------------
+//
+//  NumOnBitsInCommon(T1,T2)
+//  Returns the number of on bits which are set in both T1 and T2.
+//
+// """ -------------------------------------------------------
+template <typename T1, typename T2>
+int
+NumOnBitsInCommon(const T1& bv1,
+		const T2& bv2)
+{
+  return OnBitsInCommon(bv1,bv2).size();
+}
+
+int
+NumOnBitsInCommon(const ExplicitBitVect& bv1,
+		  const ExplicitBitVect& bv2)
+{
+  //std::cout << "nobic" << std::endl;
+  int res = 0;
+  unsigned int _sz = bv1.GetNumBits()<bv2.GetNumBits()?bv1.GetNumBits():bv2.GetNumBits();
+  for(unsigned int i=0;i<_sz;i++) {
+    if((*bv1.dp_bits)[i] && (*bv2.dp_bits)[i]) res+=1;
+  }
+  return res;
+}
+
+
+// In all these similarity metrics the notation is selected to be
+//   consistent with J.W. Raymond and P. Willett, JCAMD _16_ 59-71 (2002)
+// """ -------------------------------------------------------
+//
+//  TanimotoSimilarity(T1,T2)
+//   returns the Tanamoto similarity between T1 and T2, a double.
+//
+//  T1 and T2 should be the same length.
+//
+//  C++ Notes: T1 and T2 must support operator&, GetNumBits()
+//  and GetOnBits().
+//
+//  Python Notes: T1 and T2 are BitVects.
+//
+// """ -------------------------------------------------------
+template <typename T1, typename T2>
+const double
+TanimotoSimilarity(const T1& bv1,
+		   const T2& bv2)
+{
+  if(bv1.GetNumBits()!=bv2.GetNumBits())
+    throw ValueErrorException("BitVects must be same length");
+  double x = NumOnBitsInCommon(bv1,bv2);
+  double y = bv1.GetNumOnBits();
+  double z = bv2.GetNumOnBits();
+  if((y+z-x)==0.0) return 1.0;
+  else return x / (y+z-x);
+}
+
+
+template <typename T1, typename T2>
+const double
+CosineSimilarity(const T1& bv1,
+		   const T2& bv2)
+{
+  if(bv1.GetNumBits()!=bv2.GetNumBits())
+    throw ValueErrorException("BitVects must be same length");
+  double x = NumOnBitsInCommon(bv1,bv2);
+  double y = bv1.GetNumOnBits();
+  double z = bv2.GetNumOnBits();
+
+  if(y*z>0.0){
+    return x / sqrt(y*z);
+  } else {
+    return 0.0;
+  }
+}
+
+template <typename T1, typename T2>
+const double
+KulczynskiSimilarity(const T1& bv1,
+		   const T2& bv2)
+{
+  if(bv1.GetNumBits()!=bv2.GetNumBits())
+    throw ValueErrorException("BitVects must be same length");
+  double x = NumOnBitsInCommon(bv1,bv2);
+  double y = bv1.GetNumOnBits();
+  double z = bv2.GetNumOnBits();
+
+  if(y*z>0.0){
+    return x*(y+z)/(2*y*z);
+  } else {
+    return 0.0;
+  }
+}
+
+
+template <typename T1, typename T2>
+const double
+DiceSimilarity(const T1& bv1,
+	      const T2& bv2)
+{
+  if(bv1.GetNumBits()!=bv2.GetNumBits())
+    throw ValueErrorException("BitVects must be same length");
+  double x = NumOnBitsInCommon(bv1,bv2);
+  double y = bv1.GetNumOnBits();
+  double z = bv2.GetNumOnBits();
+
+  if(y+z>0.0){
+    return 2*x/(y+z);
+  } else {
+    return 0.0;
+  }
+}
+
+template <typename T1, typename T2>
+const double
+SokalSimilarity(const T1& bv1,
+	      const T2& bv2)
+{
+  if(bv1.GetNumBits()!=bv2.GetNumBits())
+    throw ValueErrorException("BitVects must be same length");
+  double x = NumOnBitsInCommon(bv1,bv2);
+  double y = bv1.GetNumOnBits();
+  double z = bv2.GetNumOnBits();
+
+  return x/(2*y+2*z-3*x);
+}
+
+template <typename T1, typename T2>
+const double
+McConnaugheySimilarity(const T1& bv1,
+		       const T2& bv2)
+{
+  if(bv1.GetNumBits()!=bv2.GetNumBits())
+    throw ValueErrorException("BitVects must be same length");
+  double x = NumOnBitsInCommon(bv1,bv2);
+  double y = bv1.GetNumOnBits();
+  double z = bv2.GetNumOnBits();
+
+  if(y*z>0.0){
+    return (x*(y+z)-(y*z))/(y*z);
+  } else {
+    return 0.0;
+  }
+}
+
+template <typename T>
+inline T tmin(T v1,T v2) {
+  if(v1<v2) return v1;
+  return v2;
+}
+
+template <typename T>
+inline T tmax(T v1,T v2) {
+  if(v1>v2) return v1;
+  return v2;
+}
+
+template <typename T1, typename T2>
+const double
+AsymmetricSimilarity(const T1& bv1,
+		     const T2& bv2)
+{
+  if(bv1.GetNumBits()!=bv2.GetNumBits())
+    throw ValueErrorException("BitVects must be same length");
+  double x = NumOnBitsInCommon(bv1,bv2);
+  double y = bv1.GetNumOnBits();
+  double z = bv2.GetNumOnBits();
+  
+  if(tmin(y,z)>0){
+    return x/tmin(y,z);
+  } else {
+    return 0.0;
+  }
+}
+
+template <typename T1, typename T2>
+const double
+BraunBlanquetSimilarity(const T1& bv1,
+		     const T2& bv2)
+{
+  if(bv1.GetNumBits()!=bv2.GetNumBits())
+    throw ValueErrorException("BitVects must be same length");
+  double x = NumOnBitsInCommon(bv1,bv2);
+  double y = bv1.GetNumOnBits();
+  double z = bv2.GetNumOnBits();
+
+  if(tmax(y,z)>0){
+    return x/tmax(y,z);
+  } else {
+    return 0.0;
+  }
+}
+
+template <typename T1, typename T2>
+const double
+RusselSimilarity(const T1& bv1,
+		     const T2& bv2)
+{
+  if(bv1.GetNumBits()!=bv2.GetNumBits())
+    throw ValueErrorException("BitVects must be same length");
+  double x = NumOnBitsInCommon(bv1,bv2);
+  return x/bv1.GetNumBits();
+}
+
+
+
+
+// """ -------------------------------------------------------
+//
+//  OnBitSimilarity(T1,T2)
+//  Returns the percentage of possible on bits in common
+//  between T1 and T2 (a double)
+//
+//  C++ Notes: T1 and T2 must support operator|, operator&
+//  and GetOnBits().
+//
+//  Python Notes: T1 and T2 are BitVects.
+//
+// """ -------------------------------------------------------
+template <typename T1, typename T2>
+const double
+OnBitSimilarity(const T1& bv1,
+		const T2& bv2)
+{
+  if(bv1.GetNumBits()!=bv2.GetNumBits())
+    throw ValueErrorException("BitVects must be same length");
+
+  double num = NumOnBitsInCommon(bv1,bv2);
+  double denom=(bv1|bv2).GetNumOnBits();
+
+  if(denom>0){
+    return num/denom;
+  } else {
+    return 0;
+  }
+}
+
+// """ -------------------------------------------------------
+//
+//  NumBitsInCommon(T1,T2)
+//  Returns the number of bits in common (on and off)
+//  between T1 and T2 (an int)
+//
+//  T1 and T2 should be the same length.
+//
+//  C++ Notes: T1 and T2 must support operator^, GetNumBits().
+//
+//  Python Notes: T1 and T2 are BitVects.
+//
+// """ -------------------------------------------------------
+template <typename T1, typename T2>
+const int
+NumBitsInCommon(const T1& bv1,
+		const T2& bv2)
+{
+  if(bv1.GetNumBits()!=bv2.GetNumBits())
+    throw ValueErrorException("BitVects must be same length");
+
+  return bv1.GetNumBits() - (bv1^bv2).GetNumOnBits();
+}
+
+
+// """ -------------------------------------------------------
+//
+//  AllBitSimilarity(T1,T2)
+//  Returns the percentage of bits in common (on and off)
+//  between T1 and T2 (a double)
+//
+//  T1 and T2 should be the same length.
+//
+//  C++ Notes: T1 and T2 must support operator^, GetNumBits()
+//  and GetNumOnBits().
+//
+//  Python Notes: T1 and T2 are BitVects.
+//
+// """ -------------------------------------------------------
+template <typename T1, typename T2>
+const double
+AllBitSimilarity(const T1& bv1,
+		const T2& bv2)
+{
+  if(bv1.GetNumBits()!=bv2.GetNumBits())
+    throw ValueErrorException("BitVects must be same length");
+
+  return double(NumBitsInCommon(bv1,bv2))/bv1.GetNumBits();
+}
+
+
+
+
+// """ -------------------------------------------------------
+//
+//  OnBitsInCommon(T1,T2)
+//  Returns the on bits which are set in both T1 and T2.
+//
+//  T1 and T2 should be the same length.
+//
+//  C++ Notes: T1 and T2 must support operator&, GetNumBits()
+//  and GetOnBits(), the return value is an IntVect.
+//
+//  Python Notes: T1 and T2 are BitVects, the return value
+//  is a tuple of ints.
+//
+// """ -------------------------------------------------------
+template <typename T1, typename T2>
+IntVect
+OnBitsInCommon(const T1& bv1,
+		const T2& bv2)
+{
+  if(bv1.GetNumBits()!=bv2.GetNumBits())
+    throw ValueErrorException("BitVects must be same length");
+  IntVect res;
+  (bv1&bv2).GetOnBits(res);
+  return res;
+}
+
+// """ -------------------------------------------------------
+//
+//  OffBitsInCommon(T1,T2)
+//  Returns the off bits which are set in both T1 and T2.
+//
+//  T1 and T2 should be the same length.
+//
+//  C++ Notes: T1 and T2 must support operator|, operator~,
+// GetNumBits() and GetOnBits(), the return value is an IntVect.
+//
+//  Python Notes: T1 and T2 are BitVects, the return value
+//  is a tuple of ints.
+//
+// """ -------------------------------------------------------
+template <typename T1, typename T2>
+IntVect
+OffBitsInCommon(const T1& bv1,
+		const T2& bv2)
+{
+  if(bv1.GetNumBits()!=bv2.GetNumBits())
+    throw ValueErrorException("BitVects must be same length");
+  IntVect res;
+  (~(bv1|bv2)).GetOnBits(res);
+  return res;
+}
+
+// """ -------------------------------------------------------
+//
+//  OnBitProjSimilarity(T1,T2)
+//  Returns the projected similarity between the on bits of
+//  T1 and T2.
+//
+//  The on bit projected similarity of T1 onto T2 is the
+//  percentage of T1's on bits which are on in T2.
+//
+//  This type of measure may be useful for substructure-type
+//  searches.
+//
+//  Two values are returned, the projection of T1 onto T2
+//  and the projection of T2 onto T1
+//
+//  T1 and T2 should be the same length.
+//
+//  C++ Notes: T1 and T2 must support operator&, GetNumBits()
+//  and GetNumOnBits(), the return value is an DoubleVect with
+//  two elements.
+//
+//  Python Notes: T1 and T2 are BitVects, the return value
+//  is a 2-tuple of doubles.
+//
+// """ -------------------------------------------------------
+template <typename T1, typename T2>
+DoubleVect
+OnBitProjSimilarity(const T1& bv1,
+		     const T2& bv2)
+{
+  if(bv1.GetNumBits()!=bv2.GetNumBits())
+    throw ValueErrorException("BitVects must be same length");
+  DoubleVect res(2,0.0);
+  double num=NumOnBitsInCommon(bv1,bv2);
+  if(num){
+    res[0] = num/bv1.GetNumOnBits();
+    res[1] = num/bv2.GetNumOnBits();
+  }
+  return res;
+}
+
+// """ -------------------------------------------------------
+//
+//  OffBitProjSimilarity(T1,T2)
+//  Returns the projected similarity between the off bits of
+//  T1 and T2.
+//
+//  The off bit projected similarity of T1 onto T2 is the
+//  percentage of T1's off bits which are off in T2.
+//
+//  This type of measure may be useful for substructure-type
+//  searches.
+//
+//  Two values are returned, the projection of T1 onto T2
+//  and the projection of T2 onto T1
+//
+//  T1 and T2 should be the same length.
+//
+//  C++ Notes: T1 and T2 must support operator|, GetNumBits()
+//  and GetNumOffBits(), the return value is an DoubleVect with
+//  two elements.
+//
+//  Python Notes: T1 and T2 are BitVects, the return value
+//  is a 2-tuple of doubles.
+//
+// """ -------------------------------------------------------
+template <typename T1, typename T2>
+DoubleVect
+OffBitProjSimilarity(const T1& bv1,
+		     const T2& bv2)
+{
+  if(bv1.GetNumBits()!=bv2.GetNumBits())
+    throw ValueErrorException("BitVects must be same length");
+  DoubleVect res(2,0.0);
+  double num=(bv1|bv2).GetNumOffBits();
+  if(num){
+    res[0] = num/bv1.GetNumOffBits();
+    res[1] = num/bv2.GetNumOffBits();
+  }
+  return res;
+}
+
+
+
+
+template <typename T1>
+T1 *
+FoldFingerprint(const T1 &bv1,unsigned int factor)
+{
+  if(factor <=0 || factor >= bv1.GetNumBits())
+    throw ValueErrorException("invalid fold factor");
+
+  int initSize = bv1.GetNumBits();
+  int resSize = initSize/factor;
+  T1 *res = new T1(resSize);
+
+  IntVect onBits;
+  bv1.GetOnBits(onBits);
+  for(IntVectIter iv=onBits.begin();iv!=onBits.end();iv++){
+    int pos = (*iv) % resSize;
+    res->SetBit(pos);
+  }
+  return res;
+}
+
+template <typename T1>
+std::string
+BitVectToText(const T1& bv1){
+  std::string res(bv1.GetNumBits(),'0');
+  for(unsigned int i=0;i<bv1.GetNumBits();i++){
+    if(bv1.GetBit(i)) res[i] = '1';
+  }
+  return res;
+}
+
+
+
+template const double TanimotoSimilarity(const SparseBitVect& bv1,const SparseBitVect& bv2);
+template const double CosineSimilarity(const SparseBitVect& bv1,const SparseBitVect& bv2);
+template const double KulczynskiSimilarity(const SparseBitVect& bv1,const SparseBitVect& bv2);
+template const double DiceSimilarity(const SparseBitVect& bv1,const SparseBitVect& bv2);
+template const double SokalSimilarity(const SparseBitVect& bv1,const SparseBitVect& bv2);
+template const double McConnaugheySimilarity(const SparseBitVect& bv1,const SparseBitVect& bv2);
+template const double AsymmetricSimilarity(const SparseBitVect& bv1,const SparseBitVect& bv2);
+template const double BraunBlanquetSimilarity(const SparseBitVect& bv1,const SparseBitVect& bv2);
+template const double RusselSimilarity(const SparseBitVect& bv1,const SparseBitVect& bv2);
+template const double OnBitSimilarity(const SparseBitVect& bv1,const SparseBitVect& bv2);
+template const int NumBitsInCommon(const SparseBitVect& bv1,const SparseBitVect& bv2);
+template const double AllBitSimilarity(const SparseBitVect& bv1,const SparseBitVect& bv2);
+template int NumOnBitsInCommon(const SparseBitVect& bv1,const SparseBitVect& bv2);
+template IntVect OnBitsInCommon(const SparseBitVect& bv1,const SparseBitVect& bv2);
+template IntVect OffBitsInCommon(const SparseBitVect& bv1,const SparseBitVect& bv2);
+template DoubleVect OnBitProjSimilarity(const SparseBitVect& bv1,const SparseBitVect& bv2);
+template DoubleVect OffBitProjSimilarity(const SparseBitVect& bv1,const SparseBitVect& bv2);
+
+template const double TanimotoSimilarity(const ExplicitBitVect& bv1,const ExplicitBitVect& bv2);
+template const double CosineSimilarity(const ExplicitBitVect& bv1,const ExplicitBitVect& bv2);
+template const double KulczynskiSimilarity(const ExplicitBitVect& bv1,const ExplicitBitVect& bv2);
+template const double DiceSimilarity(const ExplicitBitVect& bv1,const ExplicitBitVect& bv2);
+template const double SokalSimilarity(const ExplicitBitVect& bv1,const ExplicitBitVect& bv2);
+template const double McConnaugheySimilarity(const ExplicitBitVect& bv1,const ExplicitBitVect& bv2);
+template const double AsymmetricSimilarity(const ExplicitBitVect& bv1,const ExplicitBitVect& bv2);
+template const double BraunBlanquetSimilarity(const ExplicitBitVect& bv1,const ExplicitBitVect& bv2);
+template const double RusselSimilarity(const ExplicitBitVect& bv1,const ExplicitBitVect& bv2);
+template const double OnBitSimilarity(const ExplicitBitVect& bv1,const ExplicitBitVect& bv2);
+template const int NumBitsInCommon(const ExplicitBitVect& bv1,const ExplicitBitVect& bv2);
+template const double AllBitSimilarity(const ExplicitBitVect& bv1,const ExplicitBitVect& bv2);
+template IntVect OnBitsInCommon(const ExplicitBitVect& bv1,const ExplicitBitVect& bv2);
+template IntVect OffBitsInCommon(const ExplicitBitVect& bv1,const ExplicitBitVect& bv2);
+template DoubleVect OnBitProjSimilarity(const ExplicitBitVect& bv1,const ExplicitBitVect& bv2);
+template DoubleVect OffBitProjSimilarity(const ExplicitBitVect& bv1,const ExplicitBitVect& bv2);
+
+template SparseBitVect *FoldFingerprint(const SparseBitVect &,unsigned int);
+template ExplicitBitVect *FoldFingerprint(const ExplicitBitVect &,unsigned int);
+
+template std::string BitVectToText(const SparseBitVect &);
+template std::string BitVectToText(const ExplicitBitVect &);
+
+
+
+

Code/DataStructs/BitOps.h

@@ -0,0 +1,211 @@
+//
+//  Copyright (C) 2003-2006 greg Landrum and Rational Discovery LLC
+//
+//  @@ All Rights Reserved @@
+//
+#ifndef __RD_BITOPS_H__
+#define __RD_BITOPS_H__
+/*! \file BitOps.h
+
+  \brief Contains general bit-comparison and similarity operations.
+
+  The notation used to document the similarity metrics is:
+    - \c V1_n: number of bits in vector 1
+    - \c V1_o: number of on bits in vector 1
+    - <tt>(V1&V2)_o</tt>: number of on bits in the intersection of vectors 1 and 2
+  
+ */
+
+#include "BitVects.h"
+#include <sstream>
+
+bool AllProbeBitsMatch(const char *probe,const char *ref);
+bool AllProbeBitsMatch(const std::string &probe,const std::string &ref);
+
+  
+template <typename T1>
+bool AllProbeBitsMatch(const T1 &probe,const std::string &pkl);
+
+
+//! returns the number of on bits in common between two bit vectors
+/*!
+  \return (bv1&bv2)_o
+*/
+template <typename T1, typename T2>
+int
+NumOnBitsInCommon(const T1& bv1,const T2& bv2);
+
+int
+NumOnBitsInCommon(const ExplicitBitVect & bv1,const ExplicitBitVect & bv2);
+
+//! returns the Tanimoto similarity between two bit vects
+/*!
+  \return <tt>(bv1&bv2)_o / [bv1_o + bv2_o - (bv1&bv2)_o]</tt>
+*/
+template <typename T1, typename T2>
+const double
+TanimotoSimilarity(const T1& bv1,const T2& bv2);
+
+//! returns the Cosine similarity between two bit vects
+/*!
+  \return <tt>(bv1&bv2)_o / sqrt(bv1_o + bv2_o)</tt>
+*/
+template <typename T1, typename T2>
+const double
+CosineSimilarity(const T1& bv1,
+		 const T2& bv2);
+
+//! returns the Kulczynski similarity between two bit vects
+/*!
+  \return <tt>(bv1&bv2)_o * [bv1_o + bv2_o] / [2 * bv1_o * bv2_o]</tt>
+*/
+template <typename T1, typename T2>
+const double
+KulczynskiSimilarity(const T1& bv1,
+		     const T2& bv2);
+
+//! returns the Dice similarity between two bit vects
+/*!
+  \return <tt>2*(bv1&bv2)_o / [bv1_o + bv2_o]</tt>
+*/
+template <typename T1, typename T2>
+const double
+DiceSimilarity(const T1& bv1,
+	       const T2& bv2);
+
+//! returns the Sokal similarity between two bit vects
+/*!
+  \return <tt>(bv1&bv2)_o / [2*bv1_o + 2*bv2_o - 3*(bv1&bv2)_o]</tt>
+*/
+template <typename T1, typename T2>
+const double
+SokalSimilarity(const T1& bv1,
+		const T2& bv2);
+
+//! returns the McConnaughey similarity between two bit vects
+/*!
+  \return <tt>[(bv1&bv2)_o * (bv1_o + bv2_o) - (bv1_o * bv2_o)] / (bv1_o * bv2_o)</tt>
+*/
+template <typename T1, typename T2>
+const double
+McConnaugheySimilarity(const T1& bv1,
+		       const T2& bv2);
+
+//! returns the Asymmetric similarity between two bit vects
+/*!
+  \return <tt>(bv1&bv2)_o / min(bv1_o,bv2_o)</tt>
+*/
+template <typename T1, typename T2>
+const double
+AsymmetricSimilarity(const T1& bv1,
+		     const T2& bv2);
+
+//! returns the Braun-Blanquet similarity between two bit vects
+/*!
+  \return <tt>(bv1&bv2)_o / max(bv1_o,bv2_o)</tt>
+*/
+template <typename T1, typename T2>
+const double
+BraunBlanquetSimilarity(const T1& bv1,
+			const T2& bv2);
+
+//! returns the Russel similarity between two bit vects
+/*!
+  \return <tt>(bv1&bv2)_o / bv1_o</tt>
+
+  <b>Note:</b> that this operation is non-commutative:
+    RusselSimilarity(bv1,bv2) != RusselSimilarity(bv2,bv1)
+
+*/
+template <typename T1, typename T2>
+const double
+RusselSimilarity(const T1& bv1,
+		 const T2& bv2);
+
+
+//! returns the on bit similarity between two bit vects
+/*!
+  \return <tt>(bv1&bv2)_o / (bv1|bv2)_o </tt>
+*/
+template <typename T1, typename T2>
+const double
+OnBitSimilarity(const T1& bv1,const T2& bv2);
+
+//! returns the number of common bits (on and off) between two bit vects
+/*!
+  \return <tt>bv1_n - (bv1^bv2)_o</tt>
+*/
+template <typename T1, typename T2>
+const int
+NumBitsInCommon(const T1& bv1,const T2& bv2);
+
+//! returns the commong-bit similarity (on and off) between two bit vects
+/*!
+  \return <tt>[bv1_n - (bv1^bv2)_o] / bv1_n</tt>
+*/
+template <typename T1, typename T2>
+const double
+AllBitSimilarity(const T1& bv1,const T2& bv2);
+
+//! returns an IntVect with indices of all on bits in common between two bit vects
+template <typename T1, typename T2>
+IntVect
+OnBitsInCommon(const T1& bv1,const T2& bv2);
+
+//! returns an IntVect with indices of all off bits in common between two bit vects
+template <typename T1, typename T2>
+IntVect
+OffBitsInCommon(const T1& bv1,const T2& bv2);
+
+//! returns the on-bit projected similarities between two bit vects
+/*!
+  \return two values, as a DoubleVect:
+      - <tt>(bv1&bv2)_o / bv1_o</tt> 
+      - <tt>(bv1&bv2)_o / bv2_o</tt> 
+*/
+template <typename T1, typename T2>
+DoubleVect
+OnBitProjSimilarity(const T1& bv1,const T2& bv2);
+
+//! returns the on-bit projected similarities between two bit vects
+/*!
+  \return two values, as a DoubleVect:
+     - <tt>[bv1_n - (bv1|bv2)_o] / [bv1_n - bv1_o]</tt> 
+     - <tt>[bv2_n - (bv1|bv2)_o] / [bv2_n - bv2_o]</tt> 
+
+   <b>Note:</b> <tt>bv1_n = bv2_n</tt>
+      
+*/
+template <typename T1, typename T2>
+DoubleVect
+OffBitProjSimilarity(const T1& bv1,const T2& bv2);
+
+
+//! folds a bit vector \c factor times and returns the result
+/*!
+  \param bv1    the vector to be folded
+  \param factor (optional) the number of times to fold it
+  
+  \return a pointer to the folded fingerprint, which is
+     <tt>bv1_n/factor</tt> long.
+     
+   <b>Note:</b> The caller is responsible for <tt>delete</tt>ing the result.
+ */
+template <typename T1>
+T1 *
+FoldFingerprint(const T1& bv1,unsigned int factor=2);
+
+//! returns a text representation of a bit vector (a string of 0s and 1s)
+/*!
+  \param bv1    the vector to be folded
+  
+  \return an std::string
+
+ */
+template <typename T1>
+std::string
+BitVectToText(const T1& bv1);
+
+
+
+#endif

Code/DataStructs/BitVect.cpp

@@ -0,0 +1,81 @@
+// $Id: BitVect.cpp 5062 2006-03-08 01:43:55Z glandrum $
+//
+// Copyright (c) 2003-2006 greg Landrum and Rational Discovery LLC
+//
+//  @@ All Rights Reserved @@
+//
+#include "BitVect.h"
+#include <sstream>
+#include <limits>
+#include <RDGeneral/StreamOps.h>
+#include "base64.h"
+#ifdef WIN32
+#include <ios>
+#endif
+
+BitVect::~BitVect() {}; // must always implement virtual destructors
+
+void BitVect::InitFromText(const char *data,const unsigned int dataLen,
+                   bool isBase64,bool allowOldFormat){
+  std::stringstream ss(std::ios_base::binary|std::ios_base::in|std::ios_base::out);
+  if(isBase64){
+    unsigned int actualLen;
+    char *decoded;
+    decoded = Base64Decode((const char *)data,&actualLen);
+    ss.write(decoded,actualLen);
+    free(decoded);
+  } else {
+    ss.write(data,dataLen);
+  }
+
+  int format=0;
+  unsigned int nOn=0;
+  int size;
+  int version=0;
+  
+  // earlier versions of the code did not have the version number encoded, so
+  //  we'll use that to distinguish version 0
+  ss.read((char *)&size,sizeof(size));
+  if(size<0){
+    version = -1*size;
+    if (version == 16) {
+      format=1;
+    }
+    else if (version == 32) {
+      format=2;
+    }
+    else {
+      throw ValueErrorException("bad version in BitVect pickle");
+    }
+
+    ss.read((char *)&size,sizeof(size));
+  } else if( !allowOldFormat ) {
+    throw ValueErrorException("invalid BitVect pickle");
+  }
+  ss.read((char *)&nOn,sizeof(nOn));
+  _InitForSize(static_cast<int>(size));
+
+  // if the either have older version or or version 16 with ints for on bits
+  if( (format==0) || 
+      ( (format == 1) && (size >= std::numeric_limits<unsigned short>::max()) ) ) {
+    unsigned int tmp;
+    for(unsigned int i=0; i<nOn; i++){
+      ss.read((char *)&tmp,sizeof(tmp));
+      SetBit(tmp);
+    }
+  } else if (format == 1) { // version 16 and on bits sotred as short ints
+    unsigned short tmp;
+    for(unsigned int i=0; i<nOn; i++){
+      ss.read((char *)&tmp,sizeof(tmp));
+      SetBit(tmp);
+    }
+  } else if (format == 2) { // run length encoded format
+    unsigned int curr=0;
+    for (unsigned int i=0; i<nOn; i++) {
+      curr += RDKit::readPackedIntFromStream(ss);
+      SetBit(curr);
+      curr++;
+    }
+  }
+
+}

Code/DataStructs/BitVect.h

@@ -0,0 +1,62 @@
+//
+// Copyright (c) 2003-2006 greg Landrum and Rational Discovery LLC
+//
+//  @@ All Rights Reserved @@
+//
+#ifndef __RD_BITVECT_H__
+#define __RD_BITVECT_H__
+
+#include <vector>
+using std::vector;
+typedef vector<int> IntVect;
+typedef IntVect::iterator IntVectIter;
+typedef vector<double> DoubleVect;
+typedef DoubleVect::iterator DoubleVectIter;
+const int ci_BITVECT_VERSION=0x0020; //!< version number to use in pickles
+
+//! Abstract base class for storing BitVectors
+class BitVect{
+public:
+  virtual ~BitVect() = 0;
+  //! sets a particular bit and returns its original value
+  virtual bool SetBit(const unsigned int which) = 0;
+  //! unsets a particular bit and returns its original value
+  virtual bool UnSetBit(const unsigned int which) = 0;
+  //! returns the value of a particular bit
+  virtual bool GetBit(const unsigned int which) const = 0;
+  //! returns the number of bits (the length of the BitVect)
+  virtual const unsigned int GetNumBits() const = 0;
+  //! returns the number of on bits
+  virtual const unsigned int GetNumOnBits() const = 0;
+  //! returns the number of off bits
+  virtual const unsigned int GetNumOffBits() const =0;
+  //! replaces the contents of \c v with indices of our on bits
+  virtual void GetOnBits (IntVect& v) const = 0;
+  //! clears (sets to off) all of our bits
+  virtual void ClearBits() = 0;
+
+  //! initializes this BitVect from a pickle
+  /*!
+    \param data     the raw pickle data
+    \param dataLen  the length of \c data 
+    \param isBase64 (optional) if this is set, \c data is assumed to
+         be base64 encoded.
+    \param allowOldFormat (optional) allows a very old form of the BitVect
+         representation to be recognized. This argument disables a large
+	 amount of error checking and it is strongly suggested that it not
+	 be used in client code.
+   */
+  void InitFromText(const char *data,const unsigned int dataLen,
+                    bool isBase64=false,bool allowOldFormat=false);
+                    
+  //! returns a serialized (pickled) version of this BitVect
+  virtual std::string ToString() const = 0;
+
+  virtual bool operator[] (const unsigned int which) const = 0;
+
+private:
+  virtual void _InitForSize(const unsigned int size) = 0;
+};
+
+
+#endif

Code/DataStructs/BitVectUtils.h

@@ -0,0 +1,30 @@
+//
+// Copyright (c) 2002-2006 greg Landrum, Rational Discovery LLC
+//
+//  @@ All Rights Reserved @@
+//
+#ifndef __RD_BITVECTS_UTILS_H__
+#define __RD_BITVECTS_UTILS_H__
+
+#include "BitVects.h"
+#include <string>
+
+//! \brief Construct a BitVect from the ASCII representation of a
+//! Daylight fingerprint string
+template <typename T>
+void FromDaylightString(T &sbv,std::string s);
+
+//! \brief Construct a BitVect from the ASCII representation of a
+//! bit string (i.e. a bunch of zeros and ones)
+template <typename T>
+void FromBitString(T &sbv,const std::string &s);
+
+
+//! Convert a SparseBitVector to an ExplicitBitVector
+/*!
+  \return a pointer to an ExplicitBitVector
+  <b>Note:</b> the caller is responsible for <tt>delete</tt>ing this.
+
+ */
+ExplicitBitVect *convertToExplicit(const SparseBitVect *sbv);
+#endif

Code/DataStructs/BitVects.h

@@ -0,0 +1,20 @@
+//
+// Copyright (c) 2001-2006 greg Landrum and Rational Discovery LLC
+//
+//  @@ All Rights Reserved @@
+//
+/*! \file BitVects.h
+
+  \brief Pulls in all the BitVect classes
+
+*/
+#ifndef __BITVECTS_H__
+#define __BITVECTS_H__
+
+#include "BitVect.h"
+#include "ExplicitBitVect.h"
+#include "SparseBitVect.h"
+typedef SparseBitVect SBV;
+typedef ExplicitBitVect EBV;
+
+#endif

Code/DataStructs/BitVectsTest.vcproj

@@ -0,0 +1,156 @@
+<?xml version="1.0" encoding="Windows-1252"?>
+<VisualStudioProject
+	ProjectType="Visual C++"
+	Version="7.10"
+	Name="testDatastructs"
+	ProjectGUID="{219B86E8-EEC8-4C8C-AB3C-5795CCE4D212}"
+	SccProjectName=""
+	SccLocalPath="">
+	<Platforms>
+		<Platform
+			Name="Win32"/>
+	</Platforms>
+	<Configurations>
+		<Configuration
+			Name="Debug|Win32"
+			OutputDirectory=".\datastructs_test___Win32_Debug"
+			IntermediateDirectory=".\datastructs_test___Win32_Debug"
+			ConfigurationType="1"
+			UseOfMFC="0"
+			ATLMinimizesCRunTimeLibraryUsage="FALSE"
+			CharacterSet="2">
+			<Tool
+				Name="VCCLCompilerTool"
+				Optimization="0"
+				AdditionalIncludeDirectories="$(RDBASE)/Code,$(RDBASE)\external\boost\include\$(BOOSTBASE)"
+				PreprocessorDefinitions="WIN32;_DEBUG;_CONSOLE"
+				BasicRuntimeChecks="3"
+				RuntimeLibrary="3"
+				PrecompiledHeaderFile=".\datastructs_test___Win32_Debug/BitVectsTest.pch"
+				AssemblerListingLocation=".\datastructs_test___Win32_Debug/"
+				ObjectFile=".\datastructs_test___Win32_Debug/"
+				ProgramDataBaseFileName=".\datastructs_test___Win32_Debug/"
+				WarningLevel="3"
+				SuppressStartupBanner="TRUE"
+				DebugInformationFormat="4"/>
+			<Tool
+				Name="VCCustomBuildTool"/>
+			<Tool
+				Name="VCLinkerTool"
+				AdditionalDependencies="boost_log-vc71-mt-gd-$(BOOSTVERSION).lib "
+				OutputFile="./testExecs/test.exe"
+				LinkIncremental="1"
+				SuppressStartupBanner="TRUE"
+				AdditionalLibraryDirectories="$(RDBASE)\External\boost\lib"
+				GenerateDebugInformation="TRUE"
+				ProgramDatabaseFile=".\datastructs_test___Win32_Debug/test.pdb"
+				SubSystem="1"
+				TargetMachine="1"/>
+			<Tool
+				Name="VCMIDLTool"
+				TypeLibraryName=".\datastructs_test___Win32_Debug/BitVectsTest.tlb"
+				HeaderFileName=""/>
+			<Tool
+				Name="VCPostBuildEventTool"/>
+			<Tool
+				Name="VCPreBuildEventTool"/>
+			<Tool
+				Name="VCPreLinkEventTool"/>
+			<Tool
+				Name="VCResourceCompilerTool"
+				PreprocessorDefinitions="_DEBUG"
+				Culture="1033"/>
+			<Tool
+				Name="VCWebServiceProxyGeneratorTool"/>
+			<Tool
+				Name="VCXMLDataGeneratorTool"/>
+			<Tool
+				Name="VCWebDeploymentTool"/>
+			<Tool
+				Name="VCManagedWrapperGeneratorTool"/>
+			<Tool
+				Name="VCAuxiliaryManagedWrapperGeneratorTool"/>
+		</Configuration>
+		<Configuration
+			Name="Release|Win32"
+			OutputDirectory=".\Release"
+			IntermediateDirectory=".\Release"
+			ConfigurationType="1"
+			UseOfMFC="0"
+			ATLMinimizesCRunTimeLibraryUsage="FALSE"
+			CharacterSet="2">
+			<Tool
+				Name="VCCLCompilerTool"
+				Optimization="2"
+				InlineFunctionExpansion="1"
+				AdditionalIncludeDirectories="$(RDBASE)/Code,$(RDBASE)\external\boost\include\$(BOOSTBASE)"
+				PreprocessorDefinitions="WIN32;NDEBUG;_CONSOLE"
+				StringPooling="TRUE"
+				RuntimeLibrary="2"
+				EnableFunctionLevelLinking="TRUE"
+				PrecompiledHeaderFile=".\Release/BitVectsTest.pch"
+				AssemblerListingLocation=".\Release/"
+				ObjectFile=".\Release/"
+				ProgramDataBaseFileName=".\Release/"
+				WarningLevel="3"
+				SuppressStartupBanner="TRUE"/>
+			<Tool
+				Name="VCCustomBuildTool"/>
+			<Tool
+				Name="VCLinkerTool"
+				AdditionalDependencies="boost_log-vc71-mt-$(BOOSTVERSION).lib "
+				OutputFile="testExecs/test.exe"
+				LinkIncremental="1"
+				SuppressStartupBanner="TRUE"
+				AdditionalLibraryDirectories="$(RDBASE)\External\boost\lib"
+				ProgramDatabaseFile=".\Release/test.pdb"
+				SubSystem="1"
+				TargetMachine="1"/>
+			<Tool
+				Name="VCMIDLTool"
+				TypeLibraryName=".\Release/BitVectsTest.tlb"
+				HeaderFileName=""/>
+			<Tool
+				Name="VCPostBuildEventTool"/>
+			<Tool
+				Name="VCPreBuildEventTool"/>
+			<Tool
+				Name="VCPreLinkEventTool"/>
+			<Tool
+				Name="VCResourceCompilerTool"
+				PreprocessorDefinitions="NDEBUG"
+				Culture="1033"/>
+			<Tool
+				Name="VCWebServiceProxyGeneratorTool"/>
+			<Tool
+				Name="VCXMLDataGeneratorTool"/>
+			<Tool
+				Name="VCWebDeploymentTool"/>
+			<Tool
+				Name="VCManagedWrapperGeneratorTool"/>
+			<Tool
+				Name="VCAuxiliaryManagedWrapperGeneratorTool"/>
+		</Configuration>
+	</Configurations>
+	<References>
+	</References>
+	<Files>
+		<Filter
+			Name="Source Files"
+			Filter="cpp;c;cxx;rc;def;r;odl;idl;hpj;bat">
+			<File
+				RelativePath=".\testDatastructs.cpp">
+			</File>
+		</Filter>
+		<Filter
+			Name="Header Files"
+			Filter="h;hpp;hxx;hm;inl">
+		</Filter>
+		<Filter
+			Name="Resource Files"
+			Filter="ico;cur;bmp;dlg;rc2;rct;bin;rgs;gif;jpg;jpeg;jpe">
+		</Filter>
+	</Files>
+	<Globals>
+	</Globals>
+</VisualStudioProject>

Code/DataStructs/DatastructsException.h

@@ -0,0 +1,23 @@
+//
+//  Copyright (C) 2005-2006 Rational Discovery LLC
+//
+//  @@ All Rights Reserved @@
+//
+
+#ifndef _DATASTRUCTS_EXCEPTION_H_20050126
+#define _DATASTRUCTS_EXCEPTION_H_20050126
+
+class DatastructsException : public std::exception {
+ public:
+  //! construct with an error message
+  DatastructsException(const char *msg) : _msg(msg) {};
+  //! construct with an error message
+  DatastructsException(const std::string msg) : _msg(msg) {};
+  //! get the error message
+  const char *message () const { return _msg.c_str(); };
+  ~DatastructsException () throw () {};
+  private:
+  std::string _msg;
+};
+
+#endif

Code/DataStructs/DiscreteDistMat.cpp

@@ -0,0 +1,87 @@
+// $Id: DiscreteDistMat.cpp 4946 2006-02-17 01:44:04Z glandrum $
+//
+//  Copyright (C) 2004-2006 Rational Discovery LLC
+//
+//  @@ All Rights Reserved @@
+//
+#include "DiscreteDistMat.h"
+#include "DiscreteValueVect.h"
+#include <iostream>
+#include "DatastructsException.h"
+
+void _fillDistMat(unsigned int dmat[], unsigned int nBits) {
+  unsigned int i,j, a, b, ta, tb, dist;
+  int temp;
+  unsigned int mask = ((1<<nBits) -1);
+  for (i = 0; i < 256; ++i) {
+    for (j = 0; j < 256; ++j) {
+      dist = 0;
+      a = i;
+      b = j;
+      while (a || b) {
+        ta = a&mask;
+        tb = b&mask;
+        temp = ta-tb;
+        if (temp > 0) {
+          dist += temp;
+        } else {
+          dist -= temp;
+        }
+        a >>= nBits;
+        b >>= nBits;
+      }
+      dmat[i*256 + j] = dist;
+    }
+  }
+}
+
+DiscreteDistMat::DiscreteDistMat() {
+  // fill in the distance matrix table
+
+  // one bit per value table
+  _fillDistMat(d_oneBitTab, 1);
+
+  // two bits per value table
+  _fillDistMat(d_twoBitTab, 2);
+
+  // four bits per value table
+  _fillDistMat(d_fourBitTab, 4);
+}
+
+unsigned int DiscreteDistMat::getDist(unsigned char v1, 
+                                     unsigned char v2, 
+                                     DiscreteValueVect::DiscreteValueType type) {
+  unsigned int res=0;
+  int temp;
+  unsigned int id = static_cast<unsigned int>(v1)*256 + static_cast<unsigned int>(v2);
+  switch(type) {
+  case DiscreteValueVect::ONEBITVALUE :
+    res = d_oneBitTab[id];
+    break;
+  case DiscreteValueVect::TWOBITVALUE :
+    res = d_twoBitTab[id];
+    break;
+  case DiscreteValueVect::FOURBITVALUE :
+    res = d_fourBitTab[id];
+    break;
+  case DiscreteValueVect::EIGHTBITVALUE :
+    temp = static_cast<unsigned int>(v1) - static_cast<unsigned int>(v2);
+    if (temp < 0) {
+      res -= temp;
+    } else {
+      res += temp;
+    }
+    break;
+  default:
+    // ummm.. we shouldn't have come here
+    throw DatastructsException("We shouldn't be here");
+  }
+  return res;
+}
+
+static DiscreteDistMat discreteDMat;
+DiscreteDistMat *getDiscreteDistMat() {
+  return &discreteDMat;
+}
+
+  

Code/DataStructs/DiscreteDistMat.h

@@ -0,0 +1,26 @@
+//
+//  Copyright (C) 2004-2006 Rational Discovery LLC
+//
+//  @@ All Rights Reserved @@
+//
+#ifndef __RD_DISCRETEDISTMAT_H__
+#define __RD_DISCRETEDISTMAT_H__
+#include "DiscreteValueVect.h"
+
+class DiscreteDistMat {
+ public:
+  DiscreteDistMat();
+  ~DiscreteDistMat(){};
+  unsigned int getDist(unsigned char v1, 
+                       unsigned char v2, 
+                       DiscreteValueVect::DiscreteValueType type);
+
+ private:
+  unsigned int d_oneBitTab[256*256];
+  unsigned int d_twoBitTab[256*256];
+  unsigned int d_fourBitTab[256*256];
+  
+};
+
+extern DiscreteDistMat *getDiscreteDistMat();
+#endif

Code/DataStructs/DiscreteValueVect.cpp

@@ -0,0 +1,116 @@
+//
+//  Copyright (C) 2004-2006 Rational Discovery LLC
+//
+//  @@ All Rights Reserved @@
+//
+#include "DiscreteValueVect.h"
+#include <RDGeneral/Invariant.h>
+#include "DatastructsException.h"
+#include "DiscreteDistMat.h"
+#include <RDBoost/Exceptions.h>
+
+DiscreteValueVect::DiscreteValueVect(const DiscreteValueVect &other) {
+  d_type = other.getValueType();
+  d_bitsPerVal = other.getNumBitsPerVal();
+  d_numInts = other.getNumInts();
+  d_length = other.getLength();
+  d_valsPerInt = BITS_PER_INT/d_bitsPerVal;
+  const unsigned int *odata = other.getData();
+  unsigned int *data = new unsigned int[d_numInts];
+  memcpy(static_cast<void *>(data), static_cast<const void *>(odata),
+         d_numInts*sizeof(unsigned int));
+  d_data.reset(data);
+}
+
+unsigned int DiscreteValueVect::getVal(unsigned int i) const {
+  RANGE_CHECK(0, i, d_length-1);
+  unsigned int shift = d_bitsPerVal*(i%d_valsPerInt);
+  unsigned int intId = i/d_valsPerInt;
+  return ( (d_data[intId] >> shift) & d_mask);
+}
+
+void DiscreteValueVect::setVal(unsigned int i, unsigned int val) {
+  RANGE_CHECK(0, i, d_length-1);
+  if ((val & d_mask) != val) {
+    throw ValueErrorException("Value out of range");
+  }
+  unsigned int shift = d_bitsPerVal*(i%d_valsPerInt);
+  unsigned int intId = i/d_valsPerInt;
+  unsigned int mask = ((1<<d_bitsPerVal) -1) << shift;
+  mask = ~mask;
+  d_data[intId] = (d_data[intId]&mask)|(val << shift);
+}
+
+unsigned int DiscreteValueVect::getTotalVal() const {
+  unsigned int i, j, res = 0;
+  
+  for (i = 0; i < d_numInts; ++i) {
+    for (j = 0; j < d_valsPerInt; ++j) {
+      res += ((d_data[i] >> (j*d_bitsPerVal)) & d_mask);
+    }
+  }
+  return res;
+}
+
+unsigned int DiscreteValueVect::getLength() const {
+  return d_length;
+}
+
+const unsigned int *DiscreteValueVect::getData() const {
+  return d_data.get();
+}
+  
+unsigned int computeL1Norm(const DiscreteValueVect &v1, const DiscreteValueVect &v2) {
+  if (v1.getLength() != v2.getLength()) {
+    throw ValueErrorException("Comparing vectors of different lengths");
+  }
+
+  DiscreteValueVect::DiscreteValueType valType = v1.getValueType();
+
+  if (valType != v2.getValueType()) {
+    throw ValueErrorException("Comparing vector of different value types");
+  }
+
+  const unsigned int* data1 = v1.getData();
+  const unsigned int* data2 = v2.getData();
+
+  unsigned int res = 0;
+  if (valType <= DiscreteValueVect::EIGHTBITVALUE) {
+    DiscreteDistMat *dmat = getDiscreteDistMat();
+    
+    unsigned char *cd1 = (unsigned char *)(data1);
+    unsigned char *cd2 = (unsigned char *)(data2);
+    const unsigned char *cend = cd1 + (v1.getNumInts()*4);
+    while (cd1 != cend) {
+      if (*cd1 == *cd2) {
+        cd1++;
+        cd2++;
+        continue;
+      }
+      res += dmat->getDist(*cd1, *cd2, valType);
+      cd1++;
+      cd2++;
+    }
+  } else {
+    // we have a sixteen bits per value type
+    // REVIEW: we are making an assumption here that a short 
+    // is 16 bit - may fail on a different compiler
+    const unsigned short int *sd1 = (unsigned short int *)(data1);
+    const unsigned short int *sd2 = (unsigned short int *)(data2);
+    
+    const unsigned short int *send = sd1 + (v1.getNumInts()*2);
+    while (sd1 != send) {
+      if (*sd1 == *sd2) {
+        sd1++;
+        sd2++;
+        continue;
+      }
+      res += abs((*sd1) - (*sd2));
+      sd1++;
+      sd2++;
+    }
+  }
+  return res;
+}
+
+

Code/DataStructs/DiscreteValueVect.h

@@ -0,0 +1,72 @@
+//
+//  Copyright (C) 2004-2006 Rational Discovery LLC
+//
+//  @@ All Rights Reserved @@
+//
+#ifndef __RD_DISCRETE_VALUE_VECT_20050124__
+#define __RD_DISCRETE_VALUE_VECT_20050124__
+
+#include <boost/smart_ptr.hpp>
+
+// we are making an assumption here that and unsigned int is 32 bits long
+const unsigned int BITS_PER_INT=32;
+
+class DiscreteValueVect {
+  public:
+    typedef boost::shared_array<unsigned int> DATA_SPTR;
+
+    typedef enum {
+      ONEBITVALUE=0,
+      TWOBITVALUE,
+      FOURBITVALUE,
+      EIGHTBITVALUE,
+      SIXTEENBITVALUE,
+    } DiscreteValueType;
+
+    DiscreteValueVect(DiscreteValueType valType, unsigned length) : d_type(valType), d_length(length) {
+      d_bitsPerVal = (1 << static_cast<unsigned int>(valType));
+      d_valsPerInt = BITS_PER_INT/d_bitsPerVal;
+      d_numInts = (length + d_valsPerInt -1)/d_valsPerInt;
+      d_mask = ((1<<d_bitsPerVal) -1);
+      unsigned int *data = new unsigned int[d_numInts];
+      memset(static_cast<void *>(data),0,d_numInts*sizeof(unsigned int));
+      d_data.reset(data);
+    }
+
+    //! Copy constructor
+    DiscreteValueVect(const DiscreteValueVect& other);
+
+    ~DiscreteValueVect() {}
+
+    unsigned int getVal(unsigned int i) const;
+    void setVal(unsigned int i, unsigned int val);
+    unsigned int getTotalVal() const;
+
+    unsigned int getLength() const;
+
+    const unsigned int *getData() const;
+    unsigned int getNumBitsPerVal() const {
+      return d_bitsPerVal;
+    }
+
+    DiscreteValueType getValueType() const {
+      return d_type;
+    }
+
+    unsigned int getNumInts() const {
+      return d_numInts;
+    }
+
+  private:
+    DiscreteValueType d_type;
+    unsigned int d_bitsPerVal;
+    unsigned int d_valsPerInt;
+    unsigned int d_numInts;
+    unsigned int d_length;
+    unsigned int d_mask;
+    DATA_SPTR d_data;
+};
+
+unsigned int computeL1Norm(const DiscreteValueVect &v1, const DiscreteValueVect &v2);
+
+#endif

Code/DataStructs/ExplicitBitVect.cpp

@@ -0,0 +1,166 @@
+// $Id: ExplicitBitVect.cpp 5062 2006-03-08 01:43:55Z glandrum $
+//
+// Copyright (c) 2001-2006 greg Landrum and Rational Discovery LLC
+//
+//  @@ All Rights Reserved @@
+//
+#include <iostream>
+#include <RDBoost/Exceptions.h>
+#include "ExplicitBitVect.h"
+#include <RDGeneral/StreamOps.h>
+#include "base64.h"
+#include <sstream>
+#include <limits>
+#ifdef WIN32
+#include <ios>
+#endif
+
+
+ExplicitBitVect::ExplicitBitVect(const std::string s)
+{
+  d_size=0;dp_bits = 0;
+  InitFromText(s.c_str(),s.length());
+}
+ExplicitBitVect::ExplicitBitVect(const char *data,const unsigned int dataLen)
+{
+  d_size=0;dp_bits = 0;
+  InitFromText(data,dataLen);
+}
+
+  ExplicitBitVect::ExplicitBitVect(const ExplicitBitVect& other){
+    d_size = other.d_size;
+    dp_bits = new boost::dynamic_bitset<>(*(other.dp_bits));
+  };
+
+  ExplicitBitVect& ExplicitBitVect::operator=(const ExplicitBitVect& other){
+    d_size = other.d_size;
+    dp_bits = new boost::dynamic_bitset<>(*(other.dp_bits));
+    return *this;
+  };
+  bool ExplicitBitVect::operator[] (const unsigned int which) const {
+    if(which < 0 || which >= d_size){
+      throw IndexErrorException(which);
+    }
+    return (bool)(*dp_bits)[which];
+  };
+  bool ExplicitBitVect::SetBit(const unsigned int which){
+    if(which < 0 || which >= d_size){
+      throw IndexErrorException(which);
+    }
+    if((bool)(*dp_bits)[which]){
+      return true;
+    } else {
+      (*dp_bits)[which] = 1;
+      return false;
+    }
+  };
+  bool ExplicitBitVect::UnSetBit(const unsigned int which){
+    if(which < 0 || which >= d_size){
+      throw IndexErrorException(which);
+    }
+    if((bool)(*dp_bits)[which]){
+      (*dp_bits)[which] = 0;
+      return true;
+    } else {
+      return false;
+    }
+  };
+  bool ExplicitBitVect::GetBit(const unsigned int which) const {
+    if(which < 0 || which >= d_size){
+      throw IndexErrorException(which);
+    }
+    return((bool)(*dp_bits)[which]);
+  };
+
+  ExplicitBitVect ExplicitBitVect::operator^ (const ExplicitBitVect &other) const {
+    ExplicitBitVect ans(d_size);
+    *(ans.dp_bits) = (*dp_bits) ^ *(other.dp_bits);
+    return(ans);
+  };
+
+  ExplicitBitVect ExplicitBitVect::operator& (const ExplicitBitVect &other) const {
+    ExplicitBitVect ans(d_size);
+    *(ans.dp_bits) = (*dp_bits) & *(other.dp_bits);
+    return(ans);
+  };
+
+  ExplicitBitVect ExplicitBitVect::operator| (const ExplicitBitVect &other) const {
+    ExplicitBitVect ans(d_size);
+    *(ans.dp_bits) = (*dp_bits) | *(other.dp_bits);
+    return(ans);
+  };
+  
+  ExplicitBitVect ExplicitBitVect::operator~ () const {
+    ExplicitBitVect ans(d_size);
+    *(ans.dp_bits) = ~(*dp_bits);
+    return(ans);
+  };
+
+  const unsigned int ExplicitBitVect::GetNumBits() const {
+    return d_size;
+  };
+  const unsigned int ExplicitBitVect::GetNumOnBits() const {
+    return dp_bits->count();
+  };
+  const unsigned int ExplicitBitVect::GetNumOffBits() const {
+    return d_size - dp_bits->count();
+  };
+
+  // the contents of v are blown out
+  void ExplicitBitVect::GetOnBits (IntVect& v) const {
+    unsigned int nOn = GetNumOnBits();
+    if(!v.empty()) IntVect().swap(v);
+    v.reserve(nOn);
+    for(unsigned int i=0;i<d_size;i++){
+      if((bool)(*dp_bits)[i]) v.push_back(i);
+    }
+  };
+
+  void ExplicitBitVect::_InitForSize(unsigned int size) {
+    d_size = size;
+    if(dp_bits) delete dp_bits;
+    dp_bits = new boost::dynamic_bitset<>(size);
+  };
+
+
+  ExplicitBitVect::~ExplicitBitVect() {
+    if(dp_bits) delete dp_bits;
+  };
+
+std::string
+ExplicitBitVect::ToString() const
+{
+  // This Function replaces the older version (version 16) of writing the onbits to
+  // a string
+  // the old version does not perform any run length encoding, it only checks to see if 
+  // the length of the bitvect can be short ints and writes the on bits as shorts 
+  // other wise the onbits are all written as ints
+
+  // here we do run length encoding and the version number has been bumped to 32 as well. 
+  // only the reader needs to take care of readinf all legacy versions
+  // also in this scheme each bit number written to the string is checked to see how many 
+  // bytes it needs
+  std::stringstream ss(std::ios_base::binary|std::ios_base::out|std::ios_base::in);
+
+  unsigned int nOnBits=GetNumOnBits();
+  int tVers = ci_BITVECT_VERSION*-1;
+  ss.write((const char *)&(tVers),sizeof(tVers));
+  ss.write((const char *)&d_size,sizeof(d_size));
+  ss.write((const char *)&nOnBits,sizeof(nOnBits));
+  
+  int prev = -1;
+  unsigned int zeroes;
+  for(unsigned int i=0;i<d_size;i++){
+    if( (bool)(*dp_bits)[i] ){
+      zeroes = i - prev -1;
+      RDKit::appendPackedIntToStream(ss, zeroes);
+      prev = i;
+    }
+  }
+  zeroes = d_size - prev -1;
+  RDKit::appendPackedIntToStream(ss, zeroes);
+  std::string res(ss.str());
+  return res;
+}
+
+

Code/DataStructs/ExplicitBitVect.h

@@ -0,0 +1,61 @@
+//
+// Copyright (c) 2003-2006 greg Landrum and Rational Discovery LLC
+//
+//  @@ All Rights Reserved @@
+//
+#ifndef __RD_EXPLICITBITVECTS_H__
+#define __RD_EXPLICITBITVECTS_H__
+
+#include <boost/dynamic_bitset.hpp>
+#include "BitVect.h"
+
+//! a class for bit vectors that are densely occupied
+/*!
+    ExplicitBitVect objects store all of their bits, using
+    a boost::dynamic_bitset
+
+    These are very fast, but can require large amounts of memory for large,
+    sparsely occupied vectors.
+
+ */
+class ExplicitBitVect : public BitVect {
+public:
+  ExplicitBitVect() : dp_bits(0), d_size(0) {};
+  //! initialize with a particular size;
+  explicit ExplicitBitVect(unsigned int size) : dp_bits(0), d_size(0) {_InitForSize(size);};
+  ExplicitBitVect(const ExplicitBitVect& other);
+  //! construct from a string pickle
+  ExplicitBitVect(const std::string);
+  //! construct from a text pickle
+  ExplicitBitVect(const char *,const unsigned int);
+  
+  ~ExplicitBitVect();
+
+  ExplicitBitVect& operator=(const ExplicitBitVect& other);
+  bool operator[] (const unsigned int which) const;
+  bool SetBit(const unsigned int which);
+  bool UnSetBit(const unsigned int which);
+  bool GetBit(const unsigned int which) const;
+
+  ExplicitBitVect operator^ (const ExplicitBitVect &other) const;
+  ExplicitBitVect operator& (const ExplicitBitVect &other) const;
+  ExplicitBitVect operator| (const ExplicitBitVect &other) const;
+  ExplicitBitVect operator~ () const;
+  const unsigned int GetNumBits() const;
+  const unsigned int GetNumOnBits() const;
+  const unsigned int GetNumOffBits() const;
+
+  void GetOnBits (IntVect& v) const;
+
+  // FIX: complete these
+  void ClearBits() { ; };
+  std::string ToString() const;
+  
+  boost::dynamic_bitset<> *dp_bits; //!< our raw storage
+private:
+  unsigned int d_size;
+  void _InitForSize(const unsigned int size);
+};
+
+
+#endif

Code/DataStructs/Makefile

@@ -0,0 +1,23 @@
+include $(RDBASE)/Code/rdvars.make
+include $(RDBASE)/Code/rdrules.make
+
+CXXFLAGS=$(RDOPTFLAGS) -I$(RDBASE)/Code/DataStructs -I$(RDBASE)/Code $(BOOSTINC) -Wall
+SOURCES=BitVect.cpp SparseBitVect.cpp ExplicitBitVect.cpp Utils.cpp \
+	base64.cpp BitOps.cpp DiscreteDistMat.cpp DiscreteValueVect.cpp
+LIB=libDataStructs.a
+
+$(LIB): $(OBJS)
+	ar -rv $@ $^
+
+testExecs/test.exe: testDatastructs.o $(LIB) 
+	g++ $(CXXFLAGS) -o $@ $^ $(RDGENERAL)
+
+clean:
+	rm -f $(OBJS) $(LIB) testDatastructs.o testExecs/test.exe $(DEPENDS)
+
+regrs: testExecs/test.exe
+
+testExecs/bench.exe: bench.o $(LIB)
+	g++ $(CXXFLAGS) -o $@ $^ $(RDGENERAL)
+
+include $(DEPENDS)

Code/DataStructs/SparseBitVect.cpp

@@ -0,0 +1,337 @@
+// $Id: SparseBitVect.cpp 5062 2006-03-08 01:43:55Z glandrum $
+//
+// Copyright (c) 2001-2006 greg Landrum and Rational Discovery LLC
+//
+//  @@ All Rights Reserved @@
+//
+#include "SparseBitVect.h"
+#include <RDBoost/Exceptions.h>
+
+#include "base64.h"
+#include <RDGeneral/StreamOps.h>
+#include <sstream>
+#include <limits>
+
+#ifdef WIN32
+#include <ios>
+#endif
+
+
+// """ -------------------------------------------------------
+//
+// Construct a SparseBitVect from a binary string.
+//   The format of the string should be
+//   the format produced by SparseBitVect::ToString
+//
+// """ -------------------------------------------------------
+SparseBitVect::SparseBitVect(const std::string s)
+{
+  d_size=0;dp_bits = 0;
+  InitFromText(s.c_str(),s.length());
+}
+
+
+// """ -------------------------------------------------------
+//
+// Construct a SparseBitVect from a binary string stored as a char *.
+//   The format of the string should be
+//   the format produced by SparseBitVect::ToString
+//
+// """ -------------------------------------------------------
+SparseBitVect::SparseBitVect(const char *data,const unsigned int dataLen)
+{
+  d_size=0;dp_bits = 0;
+  InitFromText(data,dataLen);
+}
+
+// """ -------------------------------------------------------
+//
+//  Operator[]
+//   Returns the state of the ith bit.
+//
+//   **C++ NOTE** The state of BitVects cannot be changed using
+//    operator&.  So this will not work:
+//     SBV[i] = 0;
+//    In Python this type of assignment **is** valid.
+//
+// """ -------------------------------------------------------
+bool
+SparseBitVect::operator[](const unsigned int which) const
+{
+  if(which < 0 || which >= d_size){
+    throw IndexErrorException(which);
+  }
+  if(dp_bits->count(which)) return true;
+  else return false;
+}
+
+// """ -------------------------------------------------------
+//
+//  Assignment operator
+//    The bits of the other SBV are copied.
+//
+// """ -------------------------------------------------------
+SparseBitVect&
+SparseBitVect::operator=(const SparseBitVect& other)
+{
+  IntSet *bv=other.dp_bits;
+  if(dp_bits) delete dp_bits;
+  d_size = other.GetNumBits();
+  dp_bits = new IntSet;
+  std::copy(bv->begin(),bv->end(),std::inserter(*dp_bits,dp_bits->end()));
+
+  return *this;
+}
+
+
+// -------------------------------------------------------
+//
+//  Operator|
+//   allows SBV3 = SBV1|SBV2;
+//
+// -------------------------------------------------------
+SparseBitVect
+SparseBitVect::operator| (const SparseBitVect &other) const
+{
+  SparseBitVect ans(d_size);
+  std::set_union(dp_bits->begin(),dp_bits->end(),
+		 other.dp_bits->begin(),other.dp_bits->end(),
+		 std::inserter(*(ans.dp_bits),ans.dp_bits->end()));
+  return ans;
+}
+
+// """ -------------------------------------------------------
+//
+//  Operator&
+//   allows SBV3 = SBV1&SBV2;
+//
+// """ -------------------------------------------------------
+SparseBitVect
+SparseBitVect::operator& (const SparseBitVect &other) const
+{
+  SparseBitVect ans(d_size);
+  std::set_intersection(dp_bits->begin(),dp_bits->end(),
+			other.dp_bits->begin(),other.dp_bits->end(),
+			std::inserter(*(ans.dp_bits),ans.dp_bits->end()));
+  return ans;
+}
+
+// """ -------------------------------------------------------
+//
+//  Operator^
+//   allows SBV3 = SBV1^SBV2;
+//
+// """ -------------------------------------------------------
+SparseBitVect
+SparseBitVect::operator^ (const SparseBitVect &other) const
+{
+  SparseBitVect ans(d_size);
+  std::set_symmetric_difference(dp_bits->begin(),dp_bits->end(),
+				other.dp_bits->begin(),other.dp_bits->end(),
+				std::inserter(*(ans.dp_bits),ans.dp_bits->end()));
+  return(ans);
+}
+
+// """ -------------------------------------------------------
+//
+//  Operator~  (the negation operator)
+//   allows SBV2 = ~SBV1;
+//
+// """ -------------------------------------------------------
+SparseBitVect
+SparseBitVect::operator~ () const
+{
+  SparseBitVect ans(d_size);
+  for(unsigned int i=0;i<d_size;i++){
+    if(!GetBit(i)) ans.SetBit(i);
+  }
+  
+  return(ans);
+}
+
+// """ -------------------------------------------------------
+//
+// GetBit(int which)
+//   Returns the state of bit which
+//
+// """ -------------------------------------------------------
+bool
+SparseBitVect::GetBit(const unsigned int which) const
+{
+  if(which < 0 || which >= d_size){
+    throw IndexErrorException(which);
+  }
+  if(dp_bits->count(which)) return true;
+  else return false;
+}
+
+
+// """ -------------------------------------------------------
+//
+// GetBit(const IntVectIter which)  (C++ SPECIFIC)
+//   Returns the state of bit which
+//
+// """ -------------------------------------------------------
+bool
+SparseBitVect::GetBit (const IntVectIter which) const
+{
+  if(*which < 0 || static_cast<unsigned int>(*which) >= d_size){
+    throw IndexErrorException(*which);
+  }
+  if(dp_bits->count(*which)) return true;
+  else return false;
+
+}
+
+// """ -------------------------------------------------------
+//
+// GetBit(const IntSetIter which)  (C++ SPECIFIC)
+//   Returns the state of bit which
+//
+// """ -------------------------------------------------------
+bool
+SparseBitVect::GetBit (const IntSetIter which) const
+{
+  if(*which < 0 || static_cast<unsigned int>(*which) >= d_size){
+    throw IndexErrorException(*which);
+  }
+  if(dp_bits->count(*which)) return true;
+  else return false;
+
+}
+
+// """ -------------------------------------------------------
+//
+//  Sets bit which to be on.
+//
+//  Returns the original state of the bit
+//
+// """ -------------------------------------------------------
+bool
+SparseBitVect::SetBit(const unsigned int which)
+{
+  if(!dp_bits){
+    throw ValueErrorException("BitVect not properly initialized.");
+  }
+  std::pair<IntSetIter,bool> res;
+  if(which < 0 || which >= d_size){
+    throw IndexErrorException(which);
+  }
+  res = dp_bits->insert(which);
+  return !(res.second);
+}
+
+// """ -------------------------------------------------------
+//
+// SetBit(const IntSetIter which)  (C++ SPECIFIC)
+//  Sets bit which to be on.
+//
+//  Returns the original state of the bit
+//
+// """ -------------------------------------------------------
+bool
+SparseBitVect::SetBit(const IntSetIter which)
+{
+  if(!dp_bits){
+    throw ValueErrorException("BitVect not properly initialized.");
+  }
+  std::pair<IntSetIter,bool> res;
+  if(*which < 0 || static_cast<unsigned int>(*which) >= d_size){
+    throw IndexErrorException(*which);
+  }
+  res = dp_bits->insert(*which);
+  return !(res.second);
+}
+
+// """ -------------------------------------------------------
+//
+//  Sets bit which to be off.
+//
+//  Returns the original state of the bit
+//
+// """ -------------------------------------------------------
+bool
+SparseBitVect::UnSetBit(const unsigned int which)
+{
+  if(!dp_bits){
+    throw ValueErrorException("BitVect not properly initialized.");
+  }
+  if(which < 0 || which >= d_size){
+    throw IndexErrorException(which);
+  }
+
+  if(dp_bits->count(which)){
+    dp_bits->erase(dp_bits->find(which));
+    return true;
+  }
+  else{
+    return false;
+  }
+}
+
+// """ -------------------------------------------------------
+//
+// GetOnBits(IntVect &which)
+//  C++: Passes the set of on bits out in the IntVect passed in.
+//   The contents of IntVect are destroyed.
+//
+//  Python: Returns the tuple of on bits
+//
+// """ -------------------------------------------------------
+void
+SparseBitVect::GetOnBits(IntVect& v) const
+{
+  if(!dp_bits){
+    throw ValueErrorException("BitVect not properly initialized.");
+  }
+  unsigned int nOn = GetNumOnBits();
+  if(!v.empty()) IntVect().swap(v);
+  v.reserve(nOn);
+  v.resize(nOn);
+  std::copy(dp_bits->begin(),dp_bits->end(),v.begin());
+};
+
+// """ -------------------------------------------------------
+//
+// ToString()
+//  Returns a binary string with the contents of the BitVector
+//
+// """ -------------------------------------------------------
+std::string SparseBitVect::ToString() const {
+  // This Function replaces the older version (version 16) of writing the onbits to
+  // a string
+  // the old version does not perform any run length encoding, it only checks to see if 
+  // the length of the bitvect can be short ints and writes the on bits as shorts 
+  // other wise the onbits are all written as ints
+
+  // here we do run length encoding and the version number has been bumped to 32 as well. 
+  // only the reader needs to take care of readinf all legacy versions
+  // also in this scheme each bit number written to the string is checked to see how many 
+  // bytes it needs
+  std::stringstream ss(std::ios_base::binary|std::ios_base::out|std::ios_base::in);
+
+  unsigned int nOnBits=GetNumOnBits();
+  int tVers =ci_BITVECT_VERSION*-1;
+  
+  ss.write((const char *)&(tVers),sizeof(tVers));
+  ss.write((const char *)&d_size,sizeof(d_size));
+  ss.write((const char *)&nOnBits,sizeof(nOnBits));
+  int prev = -1;
+  unsigned int zeroes;
+  for (IntSetIter i=dp_bits->begin(); i!=dp_bits->end(); i++) {
+    zeroes = *i - prev -1;
+    RDKit::appendPackedIntToStream(ss, zeroes);
+    prev = *i;
+  }
+  zeroes = d_size - prev -1;
+  RDKit::appendPackedIntToStream(ss, zeroes);
+  
+  std::string res(ss.str());
+  return res;
+  }
+
+void SparseBitVect::_InitForSize(unsigned int size){
+  d_size=size;
+  if(dp_bits) delete dp_bits;
+  dp_bits=new IntSet;
+};

Code/DataStructs/SparseBitVect.h

@@ -0,0 +1,82 @@
+//
+// Copyright (c) 2003-2006 greg Landrum and Rational Discovery LLC
+//
+//  @@ All Rights Reserved @@
+//
+#ifndef __RD_SPARSEBITVECTS_H__
+#define __RD_SPARSEBITVECTS_H__
+
+#include "BitVect.h"
+
+#include <set>
+using std::set;
+#include <iterator>
+#include <algorithm>
+
+
+
+typedef set<int> IntSet;
+typedef IntSet::iterator IntSetIter;
+typedef IntSet::const_iterator IntSetConstIter;
+
+//! a class for bit vectors that are sparsely occupied.
+/*!
+    SparseBitVect objects store only their on bits, in an
+    std::set.
+
+    They are, as you might expect, quite memory efficient for sparsely populated
+    vectors but become rather a nightmare if they need to be negated.
+
+ */
+class SparseBitVect : public BitVect{
+public:
+  SparseBitVect() : dp_bits(0), d_size(0) {};
+  //! initialize with a particular size;
+  explicit SparseBitVect(unsigned int size): dp_bits(0), d_size(0) {_InitForSize(size); };
+
+  //! copy constructor
+  SparseBitVect(const SparseBitVect& other){
+    d_size=0;dp_bits = 0;
+    _InitForSize(other.GetNumBits());
+    IntSet *bv=other.dp_bits;
+    std::copy(bv->begin(),bv->end(),std::inserter(*dp_bits,dp_bits->end()));
+  }
+  //! construct from a string pickle
+  SparseBitVect(const std::string);
+  //! construct from a text pickle
+  SparseBitVect(const char *data,const unsigned int dataLen);
+
+  SparseBitVect& operator=(const SparseBitVect&);
+  ~SparseBitVect(){ delete dp_bits; };
+
+  bool operator[](const unsigned int which) const;
+  SparseBitVect operator| (const SparseBitVect&) const;
+  SparseBitVect operator& (const SparseBitVect&) const;
+  SparseBitVect operator^ (const SparseBitVect&) const;
+  SparseBitVect operator~ () const;
+
+  //! returns a (const) pointer to our raw storage
+  const IntSet *GetBitSet() const { return dp_bits;}
+
+  const unsigned int GetNumBits() const { return d_size; };
+  bool SetBit(const unsigned int which);
+  bool SetBit(const IntSetIter which);
+  bool UnSetBit(const unsigned int which);
+  bool GetBit (const unsigned int which) const;
+  bool GetBit(const IntVectIter which) const;
+  bool GetBit(const IntSetIter which) const;
+
+  const unsigned int GetNumOnBits() const { return dp_bits->size(); };
+  const unsigned int GetNumOffBits() const { return d_size - dp_bits->size(); };
+
+  std::string ToString() const;
+
+  void GetOnBits (IntVect& v) const;
+  void ClearBits() { dp_bits->clear(); };
+  IntSet *dp_bits; //!< our raw data, exposed for the sake of efficiency
+private:
+  unsigned int d_size;
+  void _InitForSize(const unsigned int size);
+};
+
+#endif

Code/DataStructs/Utils.cpp

@@ -0,0 +1,217 @@
+// $Id: Utils.cpp 5061 2006-03-08 00:36:29Z glandrum $
+//
+// Copyright (c) 2002-2006  greg Landrum, Rational Discovery LLC
+//
+//  @@ All Rights Reserved @@
+//
+#include "BitVects.h"
+#include "BitVectUtils.h"
+#include <RDGeneral/Invariant.h>
+#include <iostream>
+
+//! Convert a SparseBitVector to an ExplicitBitVector
+ExplicitBitVect *convertToExplicit(const SparseBitVect *sbv) {
+  unsigned int sl = sbv->GetNumBits();
+  ExplicitBitVect *ebv = new ExplicitBitVect(sl);
+  const IntSet *bset = sbv->GetBitSet();
+  for (IntSetConstIter it = bset->begin(); it != bset->end(); it++) {
+    ebv->SetBit(*it);
+  }
+  return ebv;
+}
+
+void a2b(const char *,char *);
+
+//! \brief Construct a BitVect from the ASCII representation of a
+//! Daylight fingerprint string
+template <typename T>
+void FromDaylightString(T &sbv,std::string s)
+{
+  sbv.ClearBits();
+  int length = s.length();
+  int nBits;
+
+  if(s[length-1] == '\n') length -= 1;
+
+  // 4 bytes in the ascii correspond to 3 bytes in the binary
+  //  plus there's one extra ascii byte for the pad marker
+  length -= 1;
+  nBits = (3*length/4)*8;
+  
+  switch(s[length]){
+  case '1': nBits -= 16;break;
+  case '2': nBits -= 8;break;
+  case '3': break;
+  default:  throw "ValueError bad daylight fingerprint string";
+  }
+  int i=0,nBitsDone=0;
+  while(i < length){
+    char bytes[3];
+    a2b(s.c_str()+i,bytes);
+    for(int j=0;j<3 && nBitsDone < nBits;j++){
+      unsigned char query=0x80;
+      for(int k=0;k<8;k++) {
+	if(bytes[j]&query){
+	  sbv.SetBit(nBitsDone);
+	}
+	query >>= 1;
+	nBitsDone++;
+      }
+    }
+    i += 4;
+  }
+}
+
+template void FromDaylightString(SparseBitVect &sbv,std::string s);
+template void FromDaylightString(ExplicitBitVect &sbv,std::string s);
+
+//! \brief Construct a BitVect from the ASCII representation of a
+//! BitString
+template <typename T>
+void FromBitString(T &sbv,const std::string &s)
+{
+  PRECONDITION(s.length()<=sbv.GetNumBits(),"bad bitvect length");
+  sbv.ClearBits();
+  for(unsigned int i=0;i<sbv.GetNumBits();++i){
+    if(s[i]=='1') sbv.SetBit(i);
+  }
+}
+
+template void FromBitString(SparseBitVect &sbv,const std::string &s);
+template void FromBitString(ExplicitBitVect &sbv,const std::string &s);
+
+
+//! converts 4 ascii bytes at a4 to 3 binary bytes
+/*!
+ THE FOLLOWING IS TAKEN FROM THE DAYLIGHT CONTRIB PROGRAM
+   ascii2bits.c
+*********************************************************************
+*** a2b - converts 4 ascii bytes at a4 to 3 binary
+***       bytes at b3.
+***
+***  ASCII:    |=======+=======+=======+=======| etc.
+***                                            ^
+***    becomes...                      3  <->  4
+***                                    v        
+***  BINARY:   |=====+=====+=====+=====| etc.
+********************************************************************
+*/
+void a2b(const char *a4, char *b3)
+{
+  int i;
+  char byte=0x00, b=0x00;
+
+  /*********************************************
+  *** Use the Daylight mapping to convert each
+  *** ascii char to its 6-bit code.
+  ***
+  *** a4: |xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx (printable)
+  ***     |=======+=======+=======+=======|
+  ***   becomes...
+  *** a4: |00xxxxxx00xxxxxx00xxxxxx00xxxxxx
+  ***     |=======+=======+=======+=======|
+  *********************************************/
+  for (i = 0; i < 4; ++i) {
+    switch (a4[i]) {
+      case '.': byte = 0x00; break;      /* 00 = __000000 */
+      case '+': byte = 0x01; break;      /* 01 = __000001 */
+      case '0': byte = 0x02; break;      /* 02 = __000010 */
+      case '1': byte = 0x03; break;      /* 03 = __000011 */
+      case '2': byte = 0x04; break;      /* 04 = __000100 */
+      case '3': byte = 0x05; break;      /* 05 = __000101 */
+      case '4': byte = 0x06; break;      /* 06 = __000110 */
+      case '5': byte = 0x07; break;      /* 07 = __000111 */
+      case '6': byte = 0x08; break;      /* 08 = __001000 */
+      case '7': byte = 0x09; break;      /* 09 = __001001 */
+      case '8': byte = 0x0a; break;      /* 10 = __001010 */
+      case '9': byte = 0x0b; break;      /* 11 = __001011 */
+      case 'A': byte = 0x0c; break;      /* 12 = __001100 */
+      case 'B': byte = 0x0d; break;      /* 13 = __001101 */
+      case 'C': byte = 0x0e; break;      /* 14 = __001110 */
+      case 'D': byte = 0x0f; break;      /* 15 = __001111 */
+      case 'E': byte = 0x10; break;      /* 16 = __010000 */
+      case 'F': byte = 0x11; break;      /* 17 = __010001 */
+      case 'G': byte = 0x12; break;      /* 18 = __010010 */
+      case 'H': byte = 0x13; break;      /* 19 = __010011 */
+      case 'I': byte = 0x14; break;      /* 20 = __010100 */
+      case 'J': byte = 0x15; break;      /* 21 = __010101 */
+      case 'K': byte = 0x16; break;      /* 22 = __010110 */
+      case 'L': byte = 0x17; break;      /* 23 = __010111 */
+      case 'M': byte = 0x18; break;      /* 24 = __011000 */
+      case 'N': byte = 0x19; break;      /* 25 = __011001 */
+      case 'O': byte = 0x1a; break;      /* 26 = __011010 */
+      case 'P': byte = 0x1b; break;      /* 27 = __011011 */
+      case 'Q': byte = 0x1c; break;      /* 28 = __011100 */
+      case 'R': byte = 0x1d; break;      /* 29 = __011101 */
+      case 'S': byte = 0x1e; break;      /* 30 = __011110 */
+      case 'T': byte = 0x1f; break;      /* 31 = __011111 */
+      case 'U': byte = 0x20; break;      /* 32 = __100000 */
+      case 'V': byte = 0x21; break;      /* 33 = __100001 */
+      case 'W': byte = 0x22; break;      /* 34 = __100010 */
+      case 'X': byte = 0x23; break;      /* 35 = __100011 */
+      case 'Y': byte = 0x24; break;      /* 36 = __100100 */
+      case 'Z': byte = 0x25; break;      /* 37 = __100101 */
+      case 'a': byte = 0x26; break;      /* 38 = __100110 */
+      case 'b': byte = 0x27; break;      /* 39 = __100111 */
+      case 'c': byte = 0x28; break;      /* 40 = __101000 */
+      case 'd': byte = 0x29; break;      /* 41 = __101001 */
+      case 'e': byte = 0x2a; break;      /* 42 = __101010 */
+      case 'f': byte = 0x2b; break;      /* 43 = __101011 */
+      case 'g': byte = 0x2c; break;      /* 44 = __101100 */
+      case 'h': byte = 0x2d; break;      /* 45 = __101101 */
+      case 'i': byte = 0x2e; break;      /* 46 = __101110 */
+      case 'j': byte = 0x2f; break;      /* 47 = __101111 */
+      case 'k': byte = 0x30; break;      /* 48 = __110000 */
+      case 'l': byte = 0x31; break;      /* 49 = __110001 */
+      case 'm': byte = 0x32; break;      /* 50 = __110010 */
+      case 'n': byte = 0x33; break;      /* 51 = __110011 */
+      case 'o': byte = 0x34; break;      /* 52 = __110100 */
+      case 'p': byte = 0x35; break;      /* 53 = __110101 */
+      case 'q': byte = 0x36; break;      /* 54 = __110110 */
+      case 'r': byte = 0x37; break;      /* 55 = __110111 */
+      case 's': byte = 0x38; break;      /* 56 = __111000 */
+      case 't': byte = 0x39; break;      /* 57 = __111001 */
+      case 'u': byte = 0x3a; break;      /* 58 = __111010 */
+      case 'v': byte = 0x3b; break;      /* 59 = __111011 */
+      case 'w': byte = 0x3c; break;      /* 60 = __111100 */
+      case 'x': byte = 0x3d; break;      /* 61 = __111101 */
+      case 'y': byte = 0x3e; break;      /* 62 = __111110 */
+      case 'z': byte = 0x3f; break;      /* 63 = __111111 */
+    }
+
+    /*********************************************
+    *** Now copy the 4x6=24 bits from a4 to b3. 
+    ***
+    *** a4: |--000000--111111--222222--333333
+    ***     |=======+=======+=======+=======|
+    ***
+    *** b3: |000000111111222222333333
+    ***     |=====+=====+=====+=====|
+    *********************************************/
+    if (i == 0)
+      b3[0] = (byte << 2);             /*** 6 bits into 1st byte ***/
+    else if (i == 1) {
+      b3[0] |= ((b = byte) >> 4);      /*** 2 bits into 1st byte ***/
+      b3[1] = ((b = byte) << 4);       /*** 4 bits into 2nd byte ***/
+    } else if (i == 2) {
+      b3[1] |= ((b = byte) >> 2);      /*** 4 bits into 2nd byte ***/
+      b3[2] = ((b = byte) << 6);       /*** 2 bits into 3rd byte ***/
+    } else if (i == 3)
+      b3[2] |= byte;                   /*** 6 bits into 3rd byte ***/
+  }
+  return;
+}
+
+
+// Demo Data:
+// 256 bits:
+//.b7HEa..ccc+gWEIr89.8lV8gOF3aXFFR.+Ps.mZ6lg.2
+//
+// 00000010 01110010 01010011 01000010 01100000
+// 00000000 10100010 10001010 00000001 10110010
+// 00100100 00010100 11011100 10100010 11000000
+// 00101011 00011000 01001010 10110001 10100100
+// 01000101 10011010 00110100 01010001 01110100
+// 00000000 01011011 11100000 00001100 10100101
+// 00100011 00011011 
+

Code/DataStructs/Wrap/DataStructs.cpp

@@ -0,0 +1,40 @@
+// $Id: DataStructs.cpp 4946 2006-02-17 01:44:04Z glandrum $
+//
+// Copyright (c) 2001-2006 greg Landrum and Rational Discovery LLC
+//
+//  @@ All Rights Reserved @@
+//
+
+#include <boost/python.hpp>
+#include <RDBoost/Wrap.h>
+#include "DataStructs.h"
+
+namespace python = boost::python;
+
+void wrap_SBV();
+void wrap_EBV();
+void wrap_BitOps();
+void wrap_Utils();
+void wrap_discreteValVect();
+
+
+BOOST_PYTHON_MODULE(cDataStructs)
+{
+  python::scope().attr("__doc__") =
+    "Module containing an assortment of functionality for basic data structures.\n"
+    "\n"
+    "At the moment the data structures defined are:\n"
+    "  Bit Vector classes (for storing signatures, fingerprints and the like:\n"
+    "    - ExplicitBitVect:  class for relatively small (10s of thousands of bits) or\n"
+    "                        dense bit vectors.\n"
+    "    - SparseBitVect:  class for large, sparse bit vectors\n"
+    ;
+  
+  python::register_exception_translator<IndexErrorException>(&translate_index_error);
+  python::register_exception_translator<ValueErrorException>(&translate_value_error);
+  wrap_Utils();
+  wrap_SBV();
+  wrap_EBV();
+  wrap_BitOps();
+  wrap_discreteValVect();
+}

Code/DataStructs/Wrap/DataStructs.h

@@ -0,0 +1,6 @@
+//
+// Copyright (c) 2001-2006 greg Landrum and Rational Discovery LLC
+//
+//  @@ All Rights Reserved @@
+//
+

Code/DataStructs/Wrap/DiscreteValueVect.cpp

@@ -0,0 +1,49 @@
+// $Id: DiscreteValueVect.cpp 4946 2006-02-17 01:44:04Z glandrum $
+//
+//  Copyright (C) 2005-2006 Rational Discovery LLC
+//
+//  @@ All Rights Reserved @@
+//
+#include <boost/python.hpp>
+
+#include <RDGeneral/types.h>
+#include<RDGeneral/Invariant.h>
+#include <RDBoost/PySequenceHolder.h>
+#include <DataStructs/DiscreteValueVect.h>
+
+std::string disValVectDoc = "A container class for storing discrete integer values\n";
+
+struct discreteValVec_wrapper {
+  static void wrap() {
+    python::enum_<DiscreteValueVect::DiscreteValueType>("DiscreteValueType")
+      .value("ONEBITVALUE", DiscreteValueVect::ONEBITVALUE)
+      .value("TWOBITVALUE", DiscreteValueVect::TWOBITVALUE)
+      .value("FOURBITVALUE", DiscreteValueVect::FOURBITVALUE)
+      .value("EIGHTBITVALUE", DiscreteValueVect::EIGHTBITVALUE)
+      .value("SIXTEENBITVALUE", DiscreteValueVect::SIXTEENBITVALUE)
+      ;
+
+    python::class_<DiscreteValueVect>("DiscreteValueVect", 
+                                      disValVectDoc.c_str(),
+                                      python::init<DiscreteValueVect::DiscreteValueType, unsigned int>("Constructor"))
+      .def("__len__", &DiscreteValueVect::getLength,
+           "Get the number of entries in the vector")
+      .def("__setitem__", &DiscreteValueVect::setVal,
+           "Set the value at a specified location")
+      .def("__getitem__", &DiscreteValueVect::getVal,
+           "Get the value at a specified location")
+      .def("GetValueType", &DiscreteValueVect::getValueType,
+           "Get the type of value stored in the vector")
+      .def("GetTotalVal", &DiscreteValueVect::getTotalVal,
+           "Get the sum of the values in the vector, basically L1 norm")
+      ;
+
+    python::def("ComputeL1Norm", computeL1Norm,
+                "Compute the distance between two discrete vector values\n");
+  }
+};
+
+void wrap_discreteValVect() {
+  discreteValVec_wrapper::wrap();
+}
+

Code/DataStructs/Wrap/Makefile

@@ -0,0 +1,10 @@
+
+SOURCES=DataStructs.cpp DataStructs.h wrap_BitOps.cpp wrap_ExplicitBV.cpp wrap_helpers.h \
+	wrap_SparseBV.cpp wrap_Utils.cpp
+
+$(RDBASE)/Python/DataStructs/cDataStructs.so: $(SOURCES) ../libDataStructs.a
+	python setup.py install --install-lib=$(RDBASE)/Python
+
+clean:
+	if test -e $(RDBASE)/Python/DataStructs/cDataStructs.so; then rm $(RDBASE)/Python/DataStructs/cDataStructs.so; fi
+	if test -e build; then rm -rf build; fi

Code/DataStructs/Wrap/datastructs test.dsp

@@ -0,0 +1,116 @@
+# Microsoft Developer Studio Project File - Name="datastructs test" - Package Owner=<4>
+# Microsoft Developer Studio Generated Build File, Format Version 6.00
+# ** DO NOT EDIT **
+
+# TARGTYPE "Win32 (x86) Console Application" 0x0103
+
+CFG=datastructs test - Win32 Debug
+!MESSAGE This is not a valid makefile. To build this project using NMAKE,
+!MESSAGE use the Export Makefile command and run
+!MESSAGE 
+!MESSAGE NMAKE /f "datastructs test.mak".
+!MESSAGE 
+!MESSAGE You can specify a configuration when running NMAKE
+!MESSAGE by defining the macro CFG on the command line. For example:
+!MESSAGE 
+!MESSAGE NMAKE /f "datastructs test.mak" CFG="datastructs test - Win32 Debug"
+!MESSAGE 
+!MESSAGE Possible choices for configuration are:
+!MESSAGE 
+!MESSAGE "datastructs test - Win32 Release" (based on "Win32 (x86) Console Application")
+!MESSAGE "datastructs test - Win32 Debug" (based on "Win32 (x86) Console Application")
+!MESSAGE 
+
+# Begin Project
+# PROP AllowPerConfigDependencies 0
+# PROP Scc_ProjName ""
+# PROP Scc_LocalPath ""
+CPP=cl.exe
+RSC=rc.exe
+
+!IF  "$(CFG)" == "datastructs test - Win32 Release"
+
+# PROP BASE Use_MFC 0
+# PROP BASE Use_Debug_Libraries 0
+# PROP BASE Output_Dir "Release"
+# PROP BASE Intermediate_Dir "Release"
+# PROP BASE Target_Dir ""
+# PROP Use_MFC 0
+# PROP Use_Debug_Libraries 0
+# PROP Output_Dir "Release"
+# PROP Intermediate_Dir "Release"
+# PROP Ignore_Export_Lib 0
+# PROP Target_Dir ""
+# ADD BASE CPP /nologo /W3 /GX /O2 /D "WIN32" /D "NDEBUG" /D "_CONSOLE" /D "_MBCS" /YX /FD /c
+# ADD CPP /nologo /W3 /GX /O2 /D "WIN32" /D "NDEBUG" /D "_CONSOLE" /D "_MBCS" /FD /c
+# SUBTRACT CPP /YX
+# ADD BASE RSC /l 0x409 /d "NDEBUG"
+# ADD RSC /l 0x409 /d "NDEBUG"
+BSC32=bscmake.exe
+# ADD BASE BSC32 /nologo
+# ADD BSC32 /nologo
+LINK32=link.exe
+# ADD BASE LINK32 kernel32.lib user32.lib gdi32.lib winspool.lib comdlg32.lib advapi32.lib shell32.lib ole32.lib oleaut32.lib uuid.lib odbc32.lib odbccp32.lib kernel32.lib user32.lib gdi32.lib winspool.lib comdlg32.lib advapi32.lib shell32.lib ole32.lib oleaut32.lib uuid.lib odbc32.lib odbccp32.lib /nologo /subsystem:console /machine:I386
+# ADD LINK32 kernel32.lib user32.lib gdi32.lib winspool.lib comdlg32.lib advapi32.lib shell32.lib ole32.lib oleaut32.lib uuid.lib odbc32.lib odbccp32.lib kernel32.lib user32.lib gdi32.lib winspool.lib comdlg32.lib advapi32.lib shell32.lib ole32.lib oleaut32.lib uuid.lib odbc32.lib odbccp32.lib /nologo /subsystem:console /machine:I386 /out:"test.exe"
+
+!ELSEIF  "$(CFG)" == "datastructs test - Win32 Debug"
+
+# PROP BASE Use_MFC 0
+# PROP BASE Use_Debug_Libraries 1
+# PROP BASE Output_Dir "datastructs_test___Win32_Debug"
+# PROP BASE Intermediate_Dir "datastructs_test___Win32_Debug"
+# PROP BASE Target_Dir ""
+# PROP Use_MFC 0
+# PROP Use_Debug_Libraries 1
+# PROP Output_Dir "datastructs_test___Win32_Debug"
+# PROP Intermediate_Dir "datastructs_test___Win32_Debug"
+# PROP Ignore_Export_Lib 0
+# PROP Target_Dir ""
+# ADD BASE CPP /nologo /W3 /Gm /GX /ZI /Od /D "WIN32" /D "_DEBUG" /D "_CONSOLE" /D "_MBCS" /YX /FD /GZ /c
+# ADD CPP /nologo /W3 /Gm /GX /ZI /Od /D "WIN32" /D "_DEBUG" /D "_CONSOLE" /D "_MBCS" /FD /GZ /c
+# SUBTRACT CPP /YX
+# ADD BASE RSC /l 0x409 /d "_DEBUG"
+# ADD RSC /l 0x409 /d "_DEBUG"
+BSC32=bscmake.exe
+# ADD BASE BSC32 /nologo
+# ADD BSC32 /nologo
+LINK32=link.exe
+# ADD BASE LINK32 kernel32.lib user32.lib gdi32.lib winspool.lib comdlg32.lib advapi32.lib shell32.lib ole32.lib oleaut32.lib uuid.lib odbc32.lib odbccp32.lib kernel32.lib user32.lib gdi32.lib winspool.lib comdlg32.lib advapi32.lib shell32.lib ole32.lib oleaut32.lib uuid.lib odbc32.lib odbccp32.lib /nologo /subsystem:console /debug /machine:I386 /pdbtype:sept
+# ADD LINK32 kernel32.lib user32.lib gdi32.lib winspool.lib comdlg32.lib advapi32.lib shell32.lib ole32.lib oleaut32.lib uuid.lib odbc32.lib odbccp32.lib kernel32.lib user32.lib gdi32.lib winspool.lib comdlg32.lib advapi32.lib shell32.lib ole32.lib oleaut32.lib uuid.lib odbc32.lib odbccp32.lib /nologo /subsystem:console /debug /machine:I386 /out:"test.exe" /pdbtype:sept
+
+!ENDIF 
+
+# Begin Target
+
+# Name "datastructs test - Win32 Release"
+# Name "datastructs test - Win32 Debug"
+# Begin Group "Source Files"
+
+# PROP Default_Filter "cpp;c;cxx;rc;def;r;odl;idl;hpj;bat"
+# Begin Source File
+
+SOURCE=.\main.cpp
+# End Source File
+# Begin Source File
+
+SOURCE=.\test.cpp
+# End Source File
+# End Group
+# Begin Group "Header Files"
+
+# PROP Default_Filter "h;hpp;hxx;hm;inl"
+# End Group
+# Begin Group "Resource Files"
+
+# PROP Default_Filter "ico;cur;bmp;dlg;rc2;rct;bin;rgs;gif;jpg;jpeg;jpe"
+# End Group
+# Begin Group "external"
+
+# PROP Default_Filter ""
+# Begin Source File
+
+SOURCE=.\BitVects.cpp
+# End Source File
+# End Group
+# End Target
+# End Project

Code/DataStructs/Wrap/datastructs test.vcproj

@@ -0,0 +1,150 @@
+<?xml version="1.0" encoding="Windows-1252"?>
+<VisualStudioProject
+	ProjectType="Visual C++"
+	Version="7.10"
+	Name="datastructs test"
+	SccProjectName=""
+	SccLocalPath="">
+	<Platforms>
+		<Platform
+			Name="Win32"/>
+	</Platforms>
+	<Configurations>
+		<Configuration
+			Name="Debug|Win32"
+			OutputDirectory=".\datastructs_test___Win32_Debug"
+			IntermediateDirectory=".\datastructs_test___Win32_Debug"
+			ConfigurationType="1"
+			UseOfMFC="0"
+			ATLMinimizesCRunTimeLibraryUsage="FALSE"
+			CharacterSet="2">
+			<Tool
+				Name="VCCLCompilerTool"
+				Optimization="0"
+				PreprocessorDefinitions="WIN32;_DEBUG;_CONSOLE"
+				BasicRuntimeChecks="3"
+				RuntimeLibrary="5"
+				PrecompiledHeaderFile=".\datastructs_test___Win32_Debug/datastructs test.pch"
+				AssemblerListingLocation=".\datastructs_test___Win32_Debug/"
+				ObjectFile=".\datastructs_test___Win32_Debug/"
+				ProgramDataBaseFileName=".\datastructs_test___Win32_Debug/"
+				WarningLevel="3"
+				SuppressStartupBanner="TRUE"
+				DebugInformationFormat="4"/>
+			<Tool
+				Name="VCCustomBuildTool"/>
+			<Tool
+				Name="VCLinkerTool"
+				OutputFile="test.exe"
+				LinkIncremental="1"
+				SuppressStartupBanner="TRUE"
+				GenerateDebugInformation="TRUE"
+				ProgramDatabaseFile=".\datastructs_test___Win32_Debug/test.pdb"
+				SubSystem="1"
+				TargetMachine="1"/>
+			<Tool
+				Name="VCMIDLTool"
+				TypeLibraryName=".\datastructs_test___Win32_Debug/datastructs test.tlb"
+				HeaderFileName=""/>
+			<Tool
+				Name="VCPostBuildEventTool"/>
+			<Tool
+				Name="VCPreBuildEventTool"/>
+			<Tool
+				Name="VCPreLinkEventTool"/>
+			<Tool
+				Name="VCResourceCompilerTool"
+				PreprocessorDefinitions="_DEBUG"
+				Culture="1033"/>
+			<Tool
+				Name="VCWebServiceProxyGeneratorTool"/>
+			<Tool
+				Name="VCXMLDataGeneratorTool"/>
+			<Tool
+				Name="VCWebDeploymentTool"/>
+			<Tool
+				Name="VCManagedWrapperGeneratorTool"/>
+			<Tool
+				Name="VCAuxiliaryManagedWrapperGeneratorTool"/>
+		</Configuration>
+		<Configuration
+			Name="Release|Win32"
+			OutputDirectory=".\testExecs\"
+			IntermediateDirectory=".\Release"
+			ConfigurationType="1"
+			UseOfMFC="0"
+			ATLMinimizesCRunTimeLibraryUsage="FALSE"
+			CharacterSet="2">
+			<Tool
+				Name="VCCLCompilerTool"
+				Optimization="2"
+				InlineFunctionExpansion="1"
+				AdditionalIncludeDirectories="$(RDBASE)/Code,$(RDBASE)/Code/GraphMol/,$(RDBASE)/external/boost_1_30_0"
+				PreprocessorDefinitions="WIN32;NDEBUG;_CONSOLE"
+				StringPooling="TRUE"
+				RuntimeLibrary="2"
+				EnableFunctionLevelLinking="TRUE"
+				PrecompiledHeaderFile=".\Release/datastructs test.pch"
+				AssemblerListingLocation=".\Release/"
+				ObjectFile=".\Release/"
+				ProgramDataBaseFileName=".\Release/"
+				WarningLevel="3"
+				SuppressStartupBanner="TRUE"/>
+			<Tool
+				Name="VCCustomBuildTool"/>
+			<Tool
+				Name="VCLinkerTool"
+				OutputFile="./testExecs/main.exe"
+				LinkIncremental="1"
+				SuppressStartupBanner="TRUE"
+				ProgramDatabaseFile=".\Release/test.pdb"
+				SubSystem="1"
+				TargetMachine="1"/>
+			<Tool
+				Name="VCMIDLTool"
+				TypeLibraryName=".\Release/datastructs test.tlb"
+				HeaderFileName=""/>
+			<Tool
+				Name="VCPostBuildEventTool"/>
+			<Tool
+				Name="VCPreBuildEventTool"/>
+			<Tool
+				Name="VCPreLinkEventTool"/>
+			<Tool
+				Name="VCResourceCompilerTool"
+				PreprocessorDefinitions="NDEBUG"
+				Culture="1033"/>
+			<Tool
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Code/DataStructs/Wrap/datastructs.dsp

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Code/DataStructs/Wrap/datastructs.vcproj

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+						Optimization="2"
+						AdditionalIncludeDirectories=""
+						PreprocessorDefinitions="WIN32;NDEBUG;_WINDOWS;$(NoInherit)"/>
+				</FileConfiguration>
+			</File>
+			<File
+				RelativePath="wrap_Utils.cpp">
+				<FileConfiguration
+					Name="Debug|Win32">
+					<Tool
+						Name="VCCLCompilerTool"
+						Optimization="0"
+						AdditionalIncludeDirectories=""
+						PreprocessorDefinitions="WIN32;_DEBUG;_WINDOWS;$(NoInherit)"
+						BasicRuntimeChecks="3"/>
+				</FileConfiguration>
+				<FileConfiguration
+					Name="DebugPython|Win32">
+					<Tool
+						Name="VCCLCompilerTool"
+						Optimization="0"
+						AdditionalIncludeDirectories=""
+						PreprocessorDefinitions="WIN32;_DEBUG;_WINDOWS;_MBCS;_USRDLL;TEST_EXPORTS;BOOST_DEBUG_PYTHON;$(NoInherit)"
+						BasicRuntimeChecks="3"/>
+				</FileConfiguration>
+				<FileConfiguration
+					Name="Release|Win32">
+					<Tool
+						Name="VCCLCompilerTool"
+						Optimization="2"
+						AdditionalIncludeDirectories=""
+						PreprocessorDefinitions="WIN32;NDEBUG;_WINDOWS;$(NoInherit)"/>
+				</FileConfiguration>
+			</File>
+		</Filter>
+		<Filter
+			Name="Header Files"
+			Filter="h;hpp;hxx;hm;inl">
+			<File
+				RelativePath="BitUtils.h">
+			</File>
+			<File
+				RelativePath="bitvects.h">
+			</File>
+		</Filter>
+		<Filter
+			Name="Resource Files"
+			Filter="ico;cur;bmp;dlg;rc2;rct;bin;rgs;gif;jpg;jpeg;jpe">
+		</Filter>
+	</Files>
+	<Globals>
+	</Globals>
+</VisualStudioProject>

Code/DataStructs/Wrap/setup.py

@@ -0,0 +1,26 @@
+# Run this with:
+#  python setup.py install --install-lib=$RDBASE/Python
+from RDBuild import *
+from distutils.core import setup,Extension
+
+
+libDirs += [
+  os.path.join(RDConfig.RDBaseDir,'Code','DataStructs'),
+  ]
+
+libraries += ["DataStructs","RDBoost",'RDGeneral']
+
+setup(name="DataStructs.cDataStructs",version="2.0",
+  ext_modules=[Extension("DataStructs.cDataStructs",
+                         ["DataStructs.cpp",
+                          "DiscreteValueVect.cpp",
+                          "wrap_SparseBV.cpp",
+                          "wrap_ExplicitBV.cpp",
+                          'wrap_BitOps.cpp',
+                          'wrap_Utils.cpp',
+                          ],
+                         library_dirs=libDirs,
+                         libraries=libraries,
+                         extra_link_args=linkArgs,
+                         extra_compile_args=compileArgs)])
+

Code/DataStructs/Wrap/testBV.py

@@ -0,0 +1,94 @@
+import DataStructs
+import RDConfig
+import unittest
+import cPickle as pickle
+import random
+
+class TestCase(unittest.TestCase):
+   def setUp(self) :
+      pass
+
+   def test0FromList(self) :
+      bv1 = DataStructs.SparseBitVect(1000)
+      bv2 = DataStructs.SparseBitVect(1000)
+      obits = range(0,1000, 3)
+      
+      for bit in obits :
+         bv1.SetBit(bit)
+         
+      bv2.SetBitsFromList(obits)
+         
+      for i in range(1000) :
+         assert bv1.GetBit(i) == bv2.GetBit(i)
+
+
+      bv1 = DataStructs.ExplicitBitVect(1000)
+      bv2 = DataStructs.ExplicitBitVect(1000)
+      obits = range(0,1000, 3)
+
+      for bit in obits :
+         bv1.SetBit(bit)
+
+      bv2.SetBitsFromList(obits)
+
+      for i in range(1000) :
+         assert bv1.GetBit(i) == bv2.GetBit(i)
+
+   def test1SparsePickle(self) :
+      nbits = 10000
+      bv1 = DataStructs.SparseBitVect(nbits)
+      for i in range(1000) :
+         x = random.randrange(0,nbits)
+         bv1.SetBit(x)
+         
+      pkl = pickle.dumps(bv1,1)
+      bv2 = pickle.loads(pkl)
+      for i in range(nbits) :
+         assert bv1[i] == bv2[i]
+
+   def test2ExplicitPickle(self):
+      nbits = 10000
+      bv1 = DataStructs.ExplicitBitVect(nbits)
+      for i in range(1000) :
+         x = random.randrange(0,nbits)
+         bv1.SetBit(x)
+      
+      pkl = pickle.dumps(bv1,1)
+      bv2 = pickle.loads(pkl)
+      for i in range(nbits) :
+         assert bv1[i] == bv2[i]
+
+   def test3Bounds(self) :
+      nbits = 10
+      bv1 = DataStructs.ExplicitBitVect(nbits)
+      bv1[0]
+      try:
+         bv1[11]
+      except IndexError:
+         ok = 1
+      except:
+         ok = -1
+      else:
+         ok = 0
+      assert ok>0,ok  
+      
+   def test4OnBitsInCommon(self) :
+      sz=100
+      bv1 = DataStructs.ExplicitBitVect(sz)
+      bv2 = DataStructs.ExplicitBitVect(sz)
+      for i in range(0,sz,2):
+         bv1.SetBit(i)
+         if i < 3*sz/4:
+            bv2.SetBit(i)
+      self.failUnless(DataStructs.AllProbeBitsMatch(bv1,bv1.ToBinary()))
+      self.failUnless(DataStructs.AllProbeBitsMatch(bv2,bv1.ToBinary()))
+      self.failIf(DataStructs.AllProbeBitsMatch(bv1,bv2.ToBinary()))
+      self.failUnless(DataStructs.AllProbeBitsMatch(bv2,bv2.ToBinary()))
+
+   def test5FromBitString(self):
+      s1 = '1010'
+      bv = DataStructs.CreateFromBitString(s1)
+      self.failUnless(len(bv)==4)
+      self.failUnless(list(bv.GetOnBits())==[0,2])
+if __name__ == '__main__':
+   unittest.main()

Code/DataStructs/Wrap/testDiscreteValueVect.py

@@ -0,0 +1,120 @@
+import RDConfig
+import os,sys
+import unittest
+import DataStructs as ds
+
+class TestCase(unittest.TestCase):
+    def setUp(self) :
+        pass
+
+    def test1Discrete(self):
+        v1 = ds.DiscreteValueVect(ds.DiscreteValueType.ONEBITVALUE, 30)
+        for i  in range(15):
+            v1[2*i] = 1;
+
+        self.failUnless(len(v1) == 30)
+        self.failUnless(v1.GetTotalVal() == 15)
+
+        for i in range(len(v1)):
+            self.failUnless(v1[i] == (i+1)%2)
+
+        self.failUnlessRaises(ValueError, lambda : v1.__setitem__(5, 2))   
+
+        v1 = ds.DiscreteValueVect(ds.DiscreteValueType.TWOBITVALUE, 30)
+        for i in range(len(v1)):
+            v1[i] = i%4;
+
+        self.failUnless(len(v1) == 30)
+        for i in range(len(v1)):
+            self.failUnless(v1[i] == i%4)
+
+        self.failUnlessRaises(ValueError, lambda : v1.__setitem__(10, 6))
+
+        v1 = ds.DiscreteValueVect(ds.DiscreteValueType.FOURBITVALUE, 30)
+        for i in range(len(v1)):
+            v1[i] = i%16;
+        
+        self.failUnless(len(v1) == 30)
+        self.failUnless(v1.GetTotalVal() == 211)
+        for i in range(len(v1)):
+            self.failUnless(v1[i] == i%16)
+
+        self.failUnlessRaises(ValueError, lambda : v1.__setitem__(10, 16))
+
+        v1 = ds.DiscreteValueVect(ds.DiscreteValueType.EIGHTBITVALUE, 32)
+        for i in range(len(v1)):
+            v1[i] = i%256;
+        
+        self.failUnless(len(v1) == 32)
+        self.failUnless(v1.GetTotalVal() == 496)
+        for i in range(len(v1)):
+            self.failUnless(v1[i] == i%256)
+
+        self.failUnlessRaises(ValueError, lambda : v1.__setitem__(10, 256))
+
+        v1 = ds.DiscreteValueVect(ds.DiscreteValueType.SIXTEENBITVALUE, 300)
+        for i in range(len(v1)):
+            v1[i] = i%300;
+        
+        self.failUnless(len(v1) == 300)
+        self.failUnless(v1.GetTotalVal() == 44850)
+        self.failUnlessRaises(ValueError, lambda : v1.__setitem__(10, 65536))
+
+    def test2VectDistances(self):
+        v1 = ds.DiscreteValueVect(ds.DiscreteValueType.ONEBITVALUE, 30)
+        v2 = ds.DiscreteValueVect(ds.DiscreteValueType.ONEBITVALUE, 30)
+        for i in range(15):
+            v1[2*i] = 1
+            v2[2*i] = 1
+        self.failUnless(ds.ComputeL1Norm(v1, v2) == 0)
+        for i in range(30):
+            if (i%3 == 0):
+                v2[i] = 1
+            else:
+                v2[i] = 0
+        self.failUnless(ds.ComputeL1Norm(v1, v2) == 15)
+
+        v1 = ds.DiscreteValueVect(ds.DiscreteValueType.TWOBITVALUE, 30)
+        v2 = ds.DiscreteValueVect(ds.DiscreteValueType.TWOBITVALUE, 30)
+        
+        for i in range(30):
+            v1[i] = i%4
+            v2[i] = (i+1)%4
+        
+        self.failUnless(ds.ComputeL1Norm(v1, v2) == 44)
+        
+        v1 = ds.DiscreteValueVect(ds.DiscreteValueType.FOURBITVALUE, 16)
+        v2 = ds.DiscreteValueVect(ds.DiscreteValueType.FOURBITVALUE, 16)
+        for i in range(16):
+            v1[i] = i%16
+            v2[i] = i%5
+        self.failUnless(ds.ComputeL1Norm(v1, v2) == 90)
+        
+        v1 = ds.DiscreteValueVect(ds.DiscreteValueType.EIGHTBITVALUE, 5)
+        v2 = ds.DiscreteValueVect(ds.DiscreteValueType.EIGHTBITVALUE, 5)
+        v1[0] = 34
+        v1[1] = 167
+        v1[2] = 3
+        v1[3] = 56
+        v1[4] = 128
+
+        v2[0] = 14
+        v2[1] = 67
+        v2[2] = 103
+        v2[3] = 6
+        v2[4] = 228
+        self.failUnless(ds.ComputeL1Norm(v1, v2) == 370)
+
+        v1 = ds.DiscreteValueVect(ds.DiscreteValueType.SIXTEENBITVALUE, 3)
+        v2 = ds.DiscreteValueVect(ds.DiscreteValueType.SIXTEENBITVALUE, 3)
+        v1[0] = 2345
+        v1[1] = 64578
+        v1[2] = 34
+
+        v2[0] = 1345
+        v2[1] = 54578
+        v2[2] = 10034
+        self.failUnless(ds.ComputeL1Norm(v1, v2) == 21000)
+        
+if __name__ == '__main__':
+    unittest.main()

Code/DataStructs/Wrap/test_list.py

@@ -0,0 +1,16 @@
+
+tests=[
+  ("python","testBV.py",{}),
+  ("python","testDiscreteValueVect.py",{}),
+  ]
+
+
+
+longTests=[]
+if __name__=='__main__':
+  import sys
+  import TestRunner
+  failed,tests = TestRunner.RunScript('test_list.py',0,1)
+  sys.exit(len(failed))
+
+

Code/DataStructs/Wrap/wrap_BitOps.cpp

@@ -0,0 +1,201 @@
+// $Id: wrap_BitOps.cpp 4946 2006-02-17 01:44:04Z glandrum $
+//
+//  Copyright (C) 2003-2006 greg Landrum and Rational Discovery LLC
+//
+//  @@ All Rights Reserved @@
+//
+#include <boost/python.hpp>
+#include <DataStructs/BitVects.h>
+#include <DataStructs/BitOps.h>
+
+
+namespace python = boost::python;
+
+// sometimes I <heart> C++ syntax:
+//   the following piece of grossness is, apparently, how
+//   you cast a pointer to a function that takes default
+//   arguments.  If you leave out the "=2" bit, you don't
+//   get the default arg values.
+//SBV *(*ff1)(const SBV&,int=2) = FoldFingerprint;
+// this is fi xfor VC++ which doesn't seem to like the "=2" passed in above
+SBV *ff1(const SBV &bv1, int factor=2) {
+  return FoldFingerprint(bv1,factor);
+}
+
+//ff1 = &FoldFingerprint(const SBV&, int=2);
+//EBV *(*ff2)(const EBV&,int) = FoldFingerprint;
+// same fix as above for VC 7.1
+EBV *ff2(const EBV &ev1, int factor=2) {
+  return FoldFingerprint(ev1,factor);
+}
+
+
+template <typename T>
+double SimilarityWrapper(const T &bv1,const std::string &pkl,
+			 const double (*metric)(const T &,const T &)){
+  double res=0.0;
+  T bv2(pkl);
+  if(bv1.GetNumBits()>bv2.GetNumBits()){
+    T *bv1tmp = FoldFingerprint(bv1,bv1.GetNumBits()/bv2.GetNumBits());
+    res = metric(*bv1tmp,bv2);
+    delete bv1tmp;
+  } else if(bv2.GetNumBits()>bv1.GetNumBits()){
+    T *bv2tmp = FoldFingerprint(bv2,bv2.GetNumBits()/bv1.GetNumBits());
+    res = metric(bv1,*bv2tmp);
+    delete bv2tmp;
+  } else {
+    res = metric(bv1,bv2);
+  }
+  return res;
+}
+
+template <typename T>
+double TanimotoSimilarity_w(const T &bv1,const std::string &pkl){
+  return SimilarityWrapper(bv1,pkl,
+			   (const double (*)(const T&,const T&))TanimotoSimilarity);
+}
+
+template <typename T>
+double CosineSimilarity_w(const T &bv1,const std::string &pkl){
+  return SimilarityWrapper(bv1,pkl,
+			   (const double (*)(const T&,const T&))CosineSimilarity);
+}
+
+template <typename T>
+double KulczynskiSimilarity_w(const T &bv1,const std::string &pkl){
+  return SimilarityWrapper(bv1,pkl,
+			   (const double (*)(const T&,const T&))KulczynskiSimilarity);
+}
+
+template <typename T>
+double DiceSimilarity_w(const T &bv1,const std::string &pkl){
+  return SimilarityWrapper(bv1,pkl,
+			   (const double (*)(const T&,const T&))DiceSimilarity);
+}
+
+template <typename T>
+double SokalSimilarity_w(const T &bv1,const std::string &pkl){
+  return SimilarityWrapper(bv1,pkl,
+			   (const double (*)(const T&,const T&))SokalSimilarity);
+}
+
+template <typename T>
+double McConnaugheySimilarity_w(const T &bv1,const std::string &pkl){
+  return SimilarityWrapper(bv1,pkl,
+			   (const double (*)(const T&,const T&))McConnaugheySimilarity);
+}
+
+template <typename T>
+double AsymmetricSimilarity_w(const T &bv1,const std::string &pkl){
+  return SimilarityWrapper(bv1,pkl,
+			   (const double (*)(const T&,const T&))AsymmetricSimilarity);
+}
+
+template <typename T>
+double BraunBlanquetSimilarity_w(const T &bv1,const std::string &pkl){
+  return SimilarityWrapper(bv1,pkl,
+			   (const double (*)(const T&,const T&))BraunBlanquetSimilarity);
+}
+
+template <typename T>
+double RusselSimilarity_w(const T &bv1,const std::string &pkl){
+  return SimilarityWrapper(bv1,pkl,
+			   (const double (*)(const T&,const T&))RusselSimilarity);
+}
+
+BOOST_PYTHON_FUNCTION_OVERLOADS(sbv_fold_overloads, ff1, 1, 2);
+BOOST_PYTHON_FUNCTION_OVERLOADS(ebv_fold_overloads, ff2, 1, 2);
+
+#define DBL_DEF(_name_,_fn_,_help_) \
+  python::def(_name_,(const double (*)(const SBV &,const SBV &))_fn_); \
+  python::def(_name_,(const double (*)(const EBV &,const EBV &))_fn_,_help_);\
+
+#define BIG_DEF(_name_,_fn_,_fn_w_,_help_) \
+  python::def(_name_,(const double (*)(const SBV &,const SBV &))_fn_); \
+  python::def(_name_,(const double (*)(const EBV &,const EBV &))_fn_,_help_);\
+  python::def(_name_,(double (*)(const SBV &,const std::string &))_fn_w_,_help_);\
+  python::def(_name_,(double (*)(const EBV &,const std::string &))_fn_w_,_help_);\
+
+struct BitOps_wrapper {
+  static void wrap(){
+    BIG_DEF("TanimotoSimilarity",TanimotoSimilarity,TanimotoSimilarity_w,
+	    "B(bv1&bv2) / (B(bv1) + B(bv2) - B(bv1&bv2))")
+    BIG_DEF("CosineSimilarity",CosineSimilarity,CosineSimilarity_w,
+	    "B(bv1&bv2) / sqrt(B(bv1) * B(bv2))")
+    BIG_DEF("KulczynskiSimilarity",KulczynskiSimilarity,KulczynskiSimilarity_w,
+	    "B(bv1&bv2)*(B(bv1) + B(bv2)) / (2 * B(bv1) * B(bv2))")
+    BIG_DEF("DiceSimilarity",DiceSimilarity,DiceSimilarity_w,
+	    "2*B(bv1&bv2) / (B(bv1) + B(bv2))")
+    BIG_DEF("SokalSimilarity",SokalSimilarity,SokalSimilarity_w,
+	    "B(bv1&bv2) / (2*B(bv1) + 2*B(bv2) - 3*B(bv1&bv2))")
+
+    BIG_DEF("McConnaugheySimilarity",McConnaugheySimilarity,McConnaugheySimilarity_w,
+	    "(B(bv1&bv2) * (B(bv1)+B(bv2)) - B(bv1)*B(bv2)) / (B(bv1) * B(bv2))")
+    BIG_DEF("AsymmetricSimilarity",AsymmetricSimilarity,AsymmetricSimilarity_w,
+	    "B(bv1&bv2) / min(B(bv1),B(bv2))")
+    BIG_DEF("BraunBlanquetSimilarity",BraunBlanquetSimilarity,BraunBlanquetSimilarity_w,
+	    "B(bv1&bv2) / max(B(bv1),B(bv2))")
+    BIG_DEF("RusselSimilarity",RusselSimilarity,RusselSimilarity_w,
+	    "B(bv1&bv2) / B(bv1)")
+
+    DBL_DEF("OnBitSimilarity",OnBitSimilarity,
+	    "B(bv1&bv2) / B(bv1|bv2)")
+    DBL_DEF("AllBitSimilarity",AllBitSimilarity,
+	    "(B(bv1) - B(bv1^bv2)) / B(bv1)")
+    python::def("OnBitProjSimilarity",
+		(DoubleVect (*)(const SBV&,const SBV&))OnBitProjSimilarity);
+    python::def("OnBitProjSimilarity",
+		(DoubleVect (*)(const EBV&,const EBV&))OnBitProjSimilarity,
+		"Returns a 2-tuple: (B(bv1&bv2) / B(bv1), B(bv1&bv2) / B(bv2))");
+    python::def("OffBitProjSimilarity",
+		(DoubleVect (*)(const SBV&,const SBV&))OffBitProjSimilarity);
+    python::def("OffBitProjSimilarity",
+		(DoubleVect (*)(const EBV&,const EBV&))OffBitProjSimilarity);
+
+    python::def("NumBitsInCommon",
+		(const int (*)(const SBV&,const SBV&))NumBitsInCommon);
+    python::def("NumBitsInCommon",
+		(const int (*)(const EBV&,const EBV&))NumBitsInCommon,
+		"Returns the total number of bits in common between the two bit vectors\n"
+		);
+    python::def("OnBitsInCommon",
+		(IntVect (*)(const SBV&,const SBV&))OnBitsInCommon);
+    python::def("OnBitsInCommon",
+		(IntVect (*)(const EBV&,const EBV&))OnBitsInCommon,
+		"Returns the number of on bits in common between the two bit vectors\n"
+		);
+    python::def("OffBitsInCommon",
+		(IntVect (*)(const SBV&,const SBV&))OffBitsInCommon);
+    python::def("OffBitsInCommon",
+		(IntVect (*)(const EBV&,const EBV&))OffBitsInCommon,
+		"Returns the number of off bits in common between the two bit vectors\n"
+		);
+
+    python::def("FoldFingerprint",
+		ff1,
+		sbv_fold_overloads(python::args("bv","foldFactor")
+				   )[python::return_value_policy<python::manage_new_object>()]);
+    python::def("FoldFingerprint",
+    		ff2,
+		ebv_fold_overloads(python::args("bv","foldFactor"),
+				   "Returns a folded version of the bit vector\n"
+				   )[python::return_value_policy<python::manage_new_object>()]);
+
+    python::def("AllProbeBitsMatch",(bool (*)(const SBV &,const std::string &))AllProbeBitsMatch);
+    python::def("AllProbeBitsMatch",(bool (*)(const EBV &,const std::string &))AllProbeBitsMatch);
+
+    python::def("BitVectToText",
+		(std::string (*)(const SBV&))BitVectToText);
+    python::def("BitVectToText",
+		(std::string (*)(const EBV&))BitVectToText,
+		"Returns a string of zeros and ones representing the bit vector."
+		);
+
+
+  }
+};
+
+void wrap_BitOps() {
+  BitOps_wrapper::wrap();
+}
+  

Code/DataStructs/Wrap/wrap_ExplicitBV.cpp

@@ -0,0 +1,101 @@
+// $Id: wrap_ExplicitBV.cpp 5061 2006-03-08 00:36:29Z glandrum $
+//
+//  Copyright (C) 2003-2006 greg Landrum and Rational Discovery LLC
+//
+//  @@ All Rights Reserved @@
+//
+#include <DataStructs/BitVects.h>
+#include <RDBoost/Wrap.h>
+#include <RDBoost/PySequenceHolder.h>
+#include "wrap_helpers.h"
+
+namespace python = boost::python;
+
+// allows BitVects to be pickled
+struct ebv_pickle_suite : python::pickle_suite
+{
+  static python::tuple
+  getinitargs(const ExplicitBitVect& self)
+  {
+    return python::make_tuple(self.ToString());
+  };
+};
+
+void SetBitsFromList(ExplicitBitVect *bv, python::object onBitList) {
+  PySequenceHolder<int> bitL(onBitList);
+  for (unsigned int i=0; i<bitL.size(); i++) {
+    bv->SetBit(bitL[i]);
+  }
+}
+
+std::string ebvClassDoc="A class to store explicit bit vectors.\n\
+\n\
+This class is most useful for situations where the size of the vector\n\
+is relatively small (tens of thousands or smaller).\n\
+\n\
+For larger vectors, use the _SparseBitVect_ class instead.\n\
+\n\
+As you would expect, _ExplicitBitVects_ support a set of binary operations\n\
+so you can do things like:\n\
+  bv3 = bv1 & bv2  (bitwise and)\n\
+  bv3 = bv1 | bv2  (bitwise or)\n\
+  bv3 = bv1 ^ bv2  (bitwise xor)\n\
+  bv3 = ~bv1       (bitwise negation)\n\
+\n\
+Bits can be set and read using either the Set/UnsetBit() and GetBit() methods\n\
+or by indexing (i.e. bv[i] = 1 or if bv[i]).\n\
+\n";
+
+struct EBV_wrapper {
+  static void wrap(){
+  python::class_<ExplicitBitVect>("ExplicitBitVect",ebvClassDoc.c_str(),
+				  python::init<unsigned int>())
+    .def(python::init<std::string>())
+    .def("SetBit",(bool (EBV::*)(unsigned int))&EBV::SetBit,
+	 "Turns on a particular bit on.  Returns the original state of the bit.\n")
+    .def("SetBitsFromList",SetBitsFromList,
+	 "Turns on a set of bits.  The argument should be a tuple or list of bit ids.\n")
+    .def("UnSetBit",(bool (EBV::*)(unsigned int))&EBV::UnSetBit,
+	 "Turns on a particular bit off.  Returns the original state of the bit.\n")
+    .def("GetBit",(bool (EBV::*)(unsigned int) const)&EBV::GetBit,
+	 "Returns the value of a bit.\n")
+    .def("GetNumBits",&EBV::GetNumBits,
+	 "Returns the number of bits in the vector (the vector's size).\n")
+    .def("__len__",&EBV::GetNumBits)
+    .def("GetNumOnBits",&EBV::GetNumOnBits,
+	 "Returns the number of on bits.\n")
+    .def("GetNumOffBits",&EBV::GetNumOffBits,
+	 "Returns the number of off bits.\n")
+    .def("__getitem__",
+	 (const int (*)(const EBV&,unsigned int))get_VectItem)
+    .def("__setitem__",
+	 (const int (*)(EBV&,unsigned int,int))set_VectItem)
+    .def("GetOnBits",
+	 (IntVect (*)(const EBV&))GetOnBits,
+	 "Returns a tuple containing IDs of the on bits.\n")
+    .def("ToBinary",&EBV::ToString,
+	 "Returns a binary string representation of the vector.\n")
+    .def("FromBase64",
+	 (void (*)(EBV &,const std::string &))InitFromBase64,
+	 "Initializes the vector from a base64 string (the Daylight encoding).\n")
+    .def("ToBase64",
+	 (std::string (*)(EBV &))ToBase64,
+	 "Converts the vector to a base64 string (the Daylight encoding).\n")
+    .def(python::self & python::self)
+    .def(python::self | python::self)
+    .def(python::self ^ python::self)
+    .def(~python::self)
+
+    .def_pickle(ebv_pickle_suite())
+  ;
+
+
+  }
+};
+
+void wrap_EBV() {
+  EBV_wrapper::wrap();
+
+
+}
+  

Code/DataStructs/Wrap/wrap_SparseBV.cpp

@@ -0,0 +1,100 @@
+// $Id: wrap_SparseBV.cpp 5061 2006-03-08 00:36:29Z glandrum $
+//
+//  Copyright (C) 2003-2006 greg Landrum and Rational Discovery LLC
+//
+//  @@ All Rights Reserved @@
+//
+#include <DataStructs/BitVects.h>
+#include <RDBoost/Wrap.h>
+#include <RDBoost/PySequenceHolder.h>
+
+#include "wrap_helpers.h"
+
+namespace python = boost::python;
+
+// allows BitVects to be pickled
+struct sbv_pickle_suite : python::pickle_suite
+{
+  static python::tuple
+  getinitargs(const SparseBitVect& self)
+  {
+    return python::make_tuple(self.ToString());
+  };
+};
+
+void SetBitsFromList(SparseBitVect *bv, python::object onBitList) {
+  PySequenceHolder<int> bitL(onBitList);
+  for (unsigned int i = 0; i < bitL.size(); i++) {
+    bv->SetBit(bitL[i]);
+  }
+}
+
+std::string sbvClassDoc="A class to store sparse bit vectors.\n\
+\n\
+This class is most useful for situations where the size of the vector\n\
+is large and relatively few bits are set\n\
+\n\
+For smaller or denser vectors, the _ExplicitBitVect_ class is much faster.\n\
+\n\
+As you would expect, _SparseBitVects_ support a set of binary operations\n\
+so you can do things like:\n\
+  bv3 = bv1 & bv2  (bitwise and)\n\
+  bv3 = bv1 | bv2  (bitwise or)\n\
+  bv3 = bv1 ^ bv2  (bitwise xor)\n\
+  bv3 = ~bv1       (bitwise negation) NOTE: this operation is likely\n\
+                    to be VERY slow and inefficient.\n\
+\n\
+Bits can be set and read using either the Set/UnsetBit() and GetBit() methods\n\
+or by indexing (i.e. bv[i] = 1 or if bv[i]).\n\
+\n";
+struct SBV_wrapper {
+  static void wrap(){
+    python::class_<SparseBitVect>("SparseBitVect",
+				  sbvClassDoc.c_str(),
+				  python::init<unsigned int>())
+      .def(python::init<std::string>())
+      .def("SetBit",(bool (SBV::*)(unsigned int))&SBV::SetBit,
+	 "Turns on a particular bit on.  Returns the original state of the bit.\n")
+      .def("SetBitsFromList",SetBitsFromList,
+	 "Turns on a set of bits.  The argument should be a tuple or list of bit ids.\n")
+      .def("UnSetBit",(bool (SBV::*)(unsigned int))&SBV::UnSetBit,
+	 "Turns on a particular bit off.  Returns the original state of the bit.\n")
+      .def("GetBit",(bool (SBV::*)(unsigned int) const)&SBV::GetBit,
+	 "Returns the value of a bit.\n")
+      .def("GetNumBits",&SBV::GetNumBits,
+	 "Returns the number of bits in the vector (the vector's size).\n")
+      .def("__len__",&SBV::GetNumBits)
+      .def("GetNumOnBits",&SBV::GetNumOnBits,
+	 "Returns the number of on bits.\n")
+      .def("GetNumOffBits",&SBV::GetNumOffBits,
+	 "Returns the number of off bits.\n")
+      .def("__getitem__",
+	   (const int (*)(const SBV&,unsigned int))get_VectItem)
+      .def("__setitem__",
+	   (const int (*)(SBV&,unsigned int,int))set_VectItem)
+      .def("GetOnBits",
+	   (IntVect (*)(const SBV&))GetOnBits,
+	   "Returns a tuple containing IDs of the on bits.\n")
+      .def("ToBinary",&SBV::ToString,
+	   "Returns a binary string representation of the vector.\n")
+      .def("FromBase64",
+	   (void (*)(SBV &,const std::string &))InitFromBase64,
+	   "Initializes the vector from a base64 string (the Daylight encoding).\n")
+      .def("ToBase64",
+	   (std::string (*)(SBV &))ToBase64,
+	   "Converts the vector to a base64 string (the Daylight encoding).\n")
+
+      .def(python::self & python::self)
+      .def(python::self | python::self)
+      .def(python::self ^ python::self)
+      .def(~python::self)
+
+      .def_pickle(sbv_pickle_suite())
+      ;
+  }
+};
+
+void wrap_SBV() {
+  SBV_wrapper::wrap();
+}
+  

Code/DataStructs/Wrap/wrap_Utils.cpp

@@ -0,0 +1,42 @@
+// $Id: wrap_Utils.cpp 5054 2006-03-06 22:39:29Z glandrum $
+//
+//  Copyright (C) 2003-2006 greg Landrum and Rational Discovery LLC
+//
+//  @@ All Rights Reserved @@
+//
+#include <DataStructs/BitVects.h>
+#include <DataStructs/BitVectUtils.h>
+#include <RDBoost/Wrap.h>
+namespace python = boost::python;
+
+ExplicitBitVect *createFromBitString(const std::string &bits){
+    ExplicitBitVect *res=new ExplicitBitVect(bits.length());
+    FromBitString(*res,bits);
+    return res;
+}
+
+struct Utils_wrapper {
+  static void wrap(){
+    python::def("ConvertToExplicit", convertToExplicit, 
+                python::return_value_policy<python::manage_new_object>());  
+    python::def("CreateFromBitString",createFromBitString,
+                python::return_value_policy<python::manage_new_object>());  
+
+    python::def("InitFromDaylightString",
+		(void (*)(SparseBitVect &,std::string))FromDaylightString);
+    python::def("InitFromDaylightString",
+		(void (*)(ExplicitBitVect &,std::string))FromDaylightString,
+		"Fill a BitVect using an ASCII (Daylight) encoding of fingerprint.\n\
+\n\
+   **Arguments**\n\
+     - bv: either a _SparseBitVect_ or an _ExplicitBitVect_\n\
+     - txt: a string with the Daylight encoding (this is the text that\n\
+            the Daylight tools put in the FP field of a TDT)\n\
+\n");
+  }
+};
+
+void wrap_Utils() {
+  Utils_wrapper::wrap();
+}
+  

Code/DataStructs/Wrap/wrap_helpers.h

@@ -0,0 +1,58 @@
+//
+//  Copyright (C) 2003-2006 greg Landrum and Rational Discovery LLC
+//
+//  @@ All Rights Reserved @@
+//
+#ifndef __RD_WRAPHELPERS_H__
+#define __RD_WRAPHELPERS_H__
+
+#include <DataStructs/BitVects.h>
+#include <DataStructs/BitOps.h>
+#include <RDBoost/Wrap.h>
+#include <DataStructs/base64.h>
+
+
+namespace python = boost::python;
+
+  template <typename T>
+  void InitFromBase64(T& self,const std::string &inD)
+  {
+    self.InitFromText(inD.c_str(),inD.length(),true);
+  };
+
+  template <typename T>
+  std::string ToBase64(T& self)
+  {
+    std::string tmp;
+    tmp = self.ToString();
+    return Base64Encode(tmp.c_str(),tmp.length());
+  };
+
+  // used to support __getitem__
+  template <typename T>
+  const int get_VectItem(const T& self,unsigned int which)
+  {
+    return self.GetBit(which);
+  }
+
+  // used to support __setitem__
+  template <typename T>
+  const int set_VectItem(T& self, const unsigned int which, const int val)
+  {
+    if(val){
+      return self.SetBit(which);
+    } else {
+      return self.UnSetBit(which);
+    }
+  }
+
+  // used to support GetOnBits()
+  template <typename T>
+  IntVect GetOnBits(const T& self)
+  {
+    IntVect res;
+    self.GetOnBits(res);
+    return res;
+  }
+
+#endif

Code/DataStructs/base64.cpp

@@ -0,0 +1,136 @@
+// $Id: base64.cpp 4946 2006-02-17 01:44:04Z glandrum $
+//
+// Copyright (c) 2002-2006 greg landrum and rational discovery llc
+//
+//  @@ All Rights Reserved @@
+//
+#include <malloc.h>
+#include <string.h>
+#include <iostream>
+#include "base64.h"
+// Encoding table from RFC 2045
+//
+//     Value Encoding  Value Encoding  Value Encoding  Value Encoding
+//         0 A            17 R            34 i            51 z
+//         1 B            18 S            35 j            52 0
+//         2 C            19 T            36 k            53 1
+//         3 D            20 U            37 l            54 2
+//         4 E            21 V            38 m            55 3
+//         5 F            22 W            39 n            56 4
+//         6 G            23 X            40 o            57 5
+//         7 H            24 Y            41 p            58 6
+//         8 I            25 Z            42 q            59 7
+//         9 J            26 a            43 r            60 8
+//        10 K            27 b            44 s            61 9
+//        11 L            28 c            45 t            62 +
+//        12 M            29 d            46 u            63 /
+//        13 N            30 e            47 v
+//        14 O            31 f            48 w         (pad) =
+//        15 P            32 g            49 x
+//        16 Q            33 h            50 y
+
+const int MaxLineLength=72;
+
+char *Base64Encode(const char *inText,const unsigned int inLen){
+  return Base64Encode((const unsigned char *)inText,inLen);
+}
+  
+
+char *Base64Encode(const unsigned char *inText,const unsigned int inLen){
+  // Notes:
+  //   - whoever calls us is responsible for free'ing the result we return
+  //   - we cheat and don't worry about breaking lines
+  static unsigned char transTable[64]={'A','B','C','D','E','F','G','H',
+				       'I','J','K','L','M','N','O','P',
+				       'Q','R','S','T','U','V','W','X',
+				       'Y','Z','a','b','c','d','e','f',
+				       'g','h','i','j','k','l','m','n',
+				       'o','p','q','r','s','t','u','v',
+				       'w','x','y','z','0','1','2','3',
+				       '4','5','6','7','8','9','+','/'};
+  
+  char *res;
+  int resSize;
+  resSize = (4*inLen)/3;
+  while(resSize % 4) resSize++;
+  res = (char *)malloc(resSize+1);
+  unsigned int i = 0;
+  int pos = 0;
+  while(i < inLen){
+    res[pos++]= transTable[inText[i]>>2];
+    if( i+1 < inLen){
+      res[pos++]= transTable[((inText[i]&3)<<4)|(inText[i+1]>>4)];
+      if(i+2 < inLen){
+	res[pos++] = transTable[((inText[i+1]&0xF)<<2)|(inText[i+2]>>6)];
+	res[pos++] = transTable[inText[i+2]&0x3F];
+      } else {
+	// single padding
+	res[pos++] = transTable[((inText[i+1]&0xF)<<2)];
+	res[pos++] = '=';
+      }
+    } else {
+      // double padding
+      res[pos++] = transTable[((inText[i]&3)<<4)];
+      res[pos++] = '=';
+      res[pos++] = '=';
+    }
+    i += 3;
+  }
+  res[resSize] = 0;
+  return res;
+}
+
+char *Base64Decode(const char *inText,unsigned int *size){
+  // Notes:
+  //   - whoever calls us is responsible for free'ing the result we return
+
+  unsigned char transTable[256];
+  int inLen = strlen(inText);
+
+  int i;
+  // FIX: we don't really need to build this table here
+  for(i= 0;i<255;i++){
+    transTable[i]= 0x80;
+  }
+  for(i='A';i<='Z';i++) transTable[i] = (unsigned char)i-'A';
+  for(i='a';i<='z';i++) transTable[i] = (unsigned char)i-'a'+26;
+  for(i='0';i<='9';i++) transTable[i] = (unsigned char)i-'0'+52;
+  transTable['+']=62;
+  transTable['/']=63;
+
+  int outLen = 3*inLen/4;
+  char *res = (char *)calloc(outLen,sizeof(char));
+  int pos = 0;
+  i = 0;
+  // decode 4 bytes at a time
+  unsigned char block[4];
+  int nInBlock=0;
+  while(i < inLen){
+    unsigned char c = inText[i];
+    
+    // above we set 0x80 as the junk marker in the translation table
+    if ( !(transTable[c]&0x80) ){
+      block[nInBlock++] = transTable[c];
+      if( nInBlock == 4 ) {
+	// finished a block
+	res[pos++] = (block[0]<<2)|(block[1]>>4);
+	res[pos++] = (block[1]<<4)|(block[2]>>2);
+	res[pos++] = (block[2]<<6)|block[3];
+	nInBlock = 0;
+      }
+    }
+    i++;
+  }
+
+  // okay, now there can be 2 or 3 chars remaining to be processed
+  //  (before the padding)
+  if(nInBlock>1){
+    res[pos++] = (block[0]<<2)|(block[1]>>4);
+    if(nInBlock > 2){
+      res[pos++] = (block[1]<<4)|(block[2]>>2);
+      res[pos] = (block[2]<<6);
+    }
+  }
+  *size = pos;
+  return res;
+}

Code/DataStructs/base64.h

@@ -0,0 +1,35 @@
+//
+// Copyright (C) 2002-2006 Greg Landrum and Rational Discovery LLC
+//
+//  @@ All Rights Reserved @@
+//
+#ifndef __RD_BASE64_H__
+#define __RD_BASE64_H__
+/*! \file base64.h
+
+  \brief Functionality for base64 encoding/decoding
+
+*/
+
+//! return the base64 encoding of an array of unsigned chars
+/*!
+   <b>Note:</b> The caller is responsible for calling \c free on the
+     char array returned by this function.
+ */
+char *Base64Encode(const unsigned char *,const unsigned int);
+
+//! return the base64 encoding of an array of chars
+/*!
+   <b>Note:</b> The caller is responsible for calling \c free on the
+     char array returned by this function.
+ */
+char *Base64Encode(const char *,const unsigned int);
+
+//! return the decoded version of a base64 encoded char array
+/*!
+   <b>Note:</b> The caller is responsible for calling \c free on the
+     char array returned by this function.
+ */
+char *Base64Decode(const char *,unsigned int *);
+
+#endif

Code/DataStructs/libDataStructs.dsp

@@ -0,0 +1,116 @@
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+# Microsoft Developer Studio Generated Build File, Format Version 6.00
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+
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+
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+!MESSAGE NMAKE /f "libDatastructs.mak" CFG="libDatastructs - Win32 Debug"
+!MESSAGE 
+!MESSAGE Possible choices for configuration are:
+!MESSAGE 
+!MESSAGE "libDatastructs - Win32 Release" (based on "Win32 (x86) Static Library")
+!MESSAGE "libDatastructs - Win32 Debug" (based on "Win32 (x86) Static Library")
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+# Begin Project
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+# ADD BASE RSC /l 0x409 /d "_DEBUG"
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+# ADD BASE LIB32 /nologo
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+
+# Begin Target
+
+# Name "libDatastructs - Win32 Release"
+# Name "libDatastructs - Win32 Debug"
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+# Begin Source File
+
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+# End Source File
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+
+SOURCE=.\BitVects\BitOps.cpp
+# End Source File
+# Begin Source File
+
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+# End Source File
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+
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+# End Source File
+# Begin Source File
+
+SOURCE=.\BitVects\SparseBitVect.cpp
+# End Source File
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+
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Code/DataStructs/libDatastructs.vcproj

@@ -0,0 +1,265 @@
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+	ProjectType="Visual C++"
+	Version="7.10"
+	Name="libDatastructs"
+	SccProjectName=""
+	SccLocalPath="">
+	<Platforms>
+		<Platform
+			Name="Win32"/>
+	</Platforms>
+	<Configurations>
+		<Configuration
+			Name="Debug|Win32"
+			OutputDirectory=".\libDatastructs___Win32_Debug0"
+			IntermediateDirectory=".\libDatastructs___Win32_Debug0"
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+			UseOfMFC="0"
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+				RuntimeTypeInfo="TRUE"
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+				PrecompiledHeaderFile=".\libDatastructs___Win32_Debug0/libDatastructs.pch"
+				AssemblerListingLocation=".\libDatastructs___Win32_Debug0/"
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+				ProgramDataBaseFileName=".\libDatastructs___Win32_Debug0/"
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+				Name="VCCustomBuildTool"/>
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+			Name="Release|Win32"
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+				PrecompiledHeaderFile=".\libDatastructs___Win32_Release/libDatastructs.pch"
+				AssemblerListingLocation=".\libDatastructs___Win32_Release/"
+				ObjectFile=".\libDatastructs___Win32_Release/"
+				ProgramDataBaseFileName=".\libDatastructs___Win32_Release/"
+				WarningLevel="3"
+				SuppressStartupBanner="TRUE"
+				CompileAs="0"/>
+			<Tool
+				Name="VCCustomBuildTool"/>
+			<Tool
+				Name="VCLibrarianTool"
+				OutputFile=".\libDatastructs___Win32_Release\libDatastructs.lib"
+				SuppressStartupBanner="TRUE"/>
+			<Tool
+				Name="VCMIDLTool"/>
+			<Tool
+				Name="VCPostBuildEventTool"/>
+			<Tool
+				Name="VCPreBuildEventTool"/>
+			<Tool
+				Name="VCPreLinkEventTool"/>
+			<Tool
+				Name="VCResourceCompilerTool"
+				PreprocessorDefinitions="NDEBUG"
+				Culture="1033"/>
+			<Tool
+				Name="VCWebServiceProxyGeneratorTool"/>
+			<Tool
+				Name="VCXMLDataGeneratorTool"/>
+			<Tool
+				Name="VCManagedWrapperGeneratorTool"/>
+			<Tool
+				Name="VCAuxiliaryManagedWrapperGeneratorTool"/>
+		</Configuration>
+	</Configurations>
+	<References>
+	</References>
+	<Files>
+		<Filter
+			Name="Source Files"
+			Filter="cpp;c;cxx;rc;def;r;odl;idl;hpj;bat">
+			<File
+				RelativePath="base64.cpp">
+				<FileConfiguration
+					Name="Debug|Win32">
+					<Tool
+						Name="VCCLCompilerTool"
+						Optimization="0"
+						AdditionalIncludeDirectories=""
+						PreprocessorDefinitions=""
+						BasicRuntimeChecks="3"/>
+				</FileConfiguration>
+				<FileConfiguration
+					Name="Release|Win32">
+					<Tool
+						Name="VCCLCompilerTool"
+						Optimization="2"
+						AdditionalIncludeDirectories=""
+						PreprocessorDefinitions=""/>
+				</FileConfiguration>
+			</File>
+			<File
+				RelativePath="BitOps.cpp">
+				<FileConfiguration
+					Name="Debug|Win32">
+					<Tool
+						Name="VCCLCompilerTool"
+						Optimization="0"
+						AdditionalIncludeDirectories=""
+						PreprocessorDefinitions=""
+						BasicRuntimeChecks="3"/>
+				</FileConfiguration>
+				<FileConfiguration
+					Name="Release|Win32">
+					<Tool
+						Name="VCCLCompilerTool"
+						Optimization="2"
+						AdditionalIncludeDirectories=""
+						PreprocessorDefinitions=""/>
+				</FileConfiguration>
+			</File>
+			<File
+				RelativePath="BitVect.cpp">
+				<FileConfiguration
+					Name="Debug|Win32">
+					<Tool
+						Name="VCCLCompilerTool"
+						Optimization="0"
+						AdditionalIncludeDirectories=""
+						PreprocessorDefinitions=""
+						BasicRuntimeChecks="3"/>
+				</FileConfiguration>
+				<FileConfiguration
+					Name="Release|Win32">
+					<Tool
+						Name="VCCLCompilerTool"
+						Optimization="2"
+						AdditionalIncludeDirectories=""
+						PreprocessorDefinitions=""/>
+				</FileConfiguration>
+			</File>
+			<File
+				RelativePath=".\DiscreteDistMat.cpp">
+			</File>
+			<File
+				RelativePath=".\DiscreteValueVect.cpp">
+			</File>
+			<File
+				RelativePath="ExplicitBitVect.cpp">
+				<FileConfiguration
+					Name="Debug|Win32">
+					<Tool
+						Name="VCCLCompilerTool"
+						Optimization="0"
+						AdditionalIncludeDirectories=""
+						PreprocessorDefinitions=""
+						BasicRuntimeChecks="3"/>
+				</FileConfiguration>
+				<FileConfiguration
+					Name="Release|Win32">
+					<Tool
+						Name="VCCLCompilerTool"
+						Optimization="2"
+						AdditionalIncludeDirectories=""
+						PreprocessorDefinitions=""/>
+				</FileConfiguration>
+			</File>
+			<File
+				RelativePath="SparseBitVect.cpp">
+				<FileConfiguration
+					Name="Debug|Win32">
+					<Tool
+						Name="VCCLCompilerTool"
+						Optimization="0"
+						AdditionalIncludeDirectories=""
+						PreprocessorDefinitions=""
+						BasicRuntimeChecks="3"/>
+				</FileConfiguration>
+				<FileConfiguration
+					Name="Release|Win32">
+					<Tool
+						Name="VCCLCompilerTool"
+						Optimization="2"
+						AdditionalIncludeDirectories=""
+						PreprocessorDefinitions=""/>
+				</FileConfiguration>
+			</File>
+			<File
+				RelativePath="Utils.cpp">
+				<FileConfiguration
+					Name="Debug|Win32">
+					<Tool
+						Name="VCCLCompilerTool"
+						Optimization="0"
+						AdditionalIncludeDirectories=""
+						PreprocessorDefinitions=""
+						BasicRuntimeChecks="3"/>
+				</FileConfiguration>
+				<FileConfiguration
+					Name="Release|Win32">
+					<Tool
+						Name="VCCLCompilerTool"
+						Optimization="2"
+						AdditionalIncludeDirectories=""
+						PreprocessorDefinitions=""/>
+				</FileConfiguration>
+			</File>
+		</Filter>
+		<Filter
+			Name="Header Files"
+			Filter="h;hpp;hxx;hm;inl">
+			<File
+				RelativePath=".\DiscreteDistMat.h">
+			</File>
+			<File
+				RelativePath=".\DiscreteValueVect.h">
+			</File>
+		</Filter>
+	</Files>
+	<Globals>
+	</Globals>
+</VisualStudioProject>

Code/DataStructs/testDatastructs.cpp

@@ -0,0 +1,371 @@
+// $Id: testDatastructs.cpp 4946 2006-02-17 01:44:04Z glandrum $
+//
+//  Copyright (C) 2001-2006 Rational Discovery LLC
+//
+//  @@ All Rights Reserved @@
+//
+#include <iostream>
+#include <sstream>
+#include <fstream>
+#include <ios>
+#include "BitVects.h"
+#include "BitOps.h"
+#include "BitVectUtils.h"
+#include <cmath>
+#include "DiscreteValueVect.h"
+#include <RDGeneral/Invariant.h>
+#include <RDGeneral/RDLog.h>
+#include <RDBoost/Exceptions.h>
+
+
+using namespace std;
+template< typename T >
+inline void TXTMSG(const char *__a__,T __b__){  BOOST_LOG(rdInfoLog) << (__a__) << " " << (__b__) << std::endl; }
+
+template<typename T> void Test(T arg){
+  T t1(20);
+  TXTMSG("Set 10:",t1.SetBit(10));
+  TXTMSG("Set 11:",t1.SetBit(11));
+  TXTMSG("Set 14:",t1.SetBit(14));
+  TXTMSG("Set 10:",t1.SetBit(10));
+  TXTMSG("Get 14:",t1.GetBit(14));
+  TXTMSG("Num:",t1.GetNumBits());
+  TXTMSG("NumOn:",t1.GetNumOnBits());
+  TXTMSG("NumOff:",t1.GetNumOffBits());
+
+  IntVect onBits;
+  t1.GetOnBits(onBits);
+  std::copy(onBits.begin(),onBits.end(),std::ostream_iterator<int>(std::cout,", "));
+  std::cout << std::endl;
+
+  T t2(t1);
+  //onBits = t2.GetOnBits();
+  TXTMSG("t2[19]:",t2[19]);
+  TXTMSG("t2[14]:",t2[14]);
+
+  t2 = t1;
+  //onBits = t2.GetOnBits();
+  TXTMSG("t2[19]:",t2[19]);
+  t2.UnSetBit(14);
+  TXTMSG("t2[14]:",t2[14]);
+  t2.SetBit(15);
+  t2.SetBit(17);
+
+
+  cout << "t1: ";
+  t1.GetOnBits(onBits);
+  std::copy(onBits.begin(),onBits.end(),std::ostream_iterator<int>(std::cout,", "));
+  std::cout << std::endl;
+
+  cout << "t2: ";
+  t2.GetOnBits(onBits);
+  std::copy(onBits.begin(),onBits.end(),std::ostream_iterator<int>(std::cout,", "));
+  std::cout << std::endl;
+
+  cout << "t1|t2: ";
+  T t3=t1|t2;
+  t3.GetOnBits(onBits);
+  std::copy(onBits.begin(),onBits.end(),std::ostream_iterator<int>(std::cout,", "));
+  std::cout << std::endl;
+
+  cout << "t1&t2: ";
+  t3=t1 & t2;
+  t3.GetOnBits(onBits);
+  std::copy(onBits.begin(),onBits.end(),std::ostream_iterator<int>(std::cout,", "));
+  std::cout << std::endl;
+  
+  cout << "t1^t2: ";
+  t3=t1 ^ t2;
+  t3.GetOnBits(onBits);
+  std::copy(onBits.begin(),onBits.end(),std::ostream_iterator<int>(std::cout,", "));
+  std::cout << std::endl;
+
+  cout << "~t1: ";
+  t3= ~t1;
+  t3.GetOnBits(onBits);
+  std::copy(onBits.begin(),onBits.end(),std::ostream_iterator<int>(std::cout,", "));
+  std::cout << std::endl;
+
+  try{
+    t3.GetBit(4000);
+  } catch (IndexErrorException) {
+    cout << " except " << endl;
+  } catch (...) {
+    cout << " ERROR EXCEPT " << endl;
+  }
+
+  T t4(t1.ToString());
+  cout << "tan(t1,t4): " << TanimotoSimilarity(t1,t4) << endl;
+  
+  T *t5 = FoldFingerprint(t1);
+  TEST_ASSERT(t5->GetNumBits() == t1.GetNumBits()/2);
+  TEST_ASSERT(t5->GetBit(0));
+  TEST_ASSERT(t5->GetBit(1));
+  TEST_ASSERT(t5->GetBit(4));
+  TEST_ASSERT(!t5->GetBit(2));
+  TEST_ASSERT(!t5->GetBit(3));
+  delete t5;
+}
+
+
+template<typename T> void TaniTest(T &arg){
+  std::string fps[4] = {
+    ".b+HHa.EgU6+ibEIr89.CpX0g8FZiXH+R0+Ps.mr6tg.2",
+    ".b7HEa..ccc+gWEIr89.8lV8gOF3aXFFR.+Ps.mZ6lg.2",
+    ".H+nHq2EcY09y5EIr9e.8p50h0NgiWGNx4+Hm+Gbslw.2",
+    ".1.HHa..cUI6i5E2rO8.Op10d0NoiWGVx.+Hm.Gb6lo.2",
+  };
+  double dists[] = {
+    1.0,0.788991,0.677165,0.686957,
+    1.0,0.578125,0.591304,
+    1.0,0.732759,
+    1.0
+  };
+  int idx=0;
+  for(int i=0;i<4;i++){
+    T v1(256);
+    FromDaylightString(v1,fps[i]);
+    for(int j=i;j<4;j++){
+      T v2(256);
+      FromDaylightString(v2,fps[j]);
+      double tani=TanimotoSimilarity(v1,v2);
+      TEST_ASSERT(abs(tani-dists[idx])<1e-4);
+      idx++;
+    }
+  }
+}
+
+
+template<typename T> void ProbeTest(T &arg){
+  int sz=1000;
+  T t1(sz),t2(sz);
+  for(int i=0;i<sz;i+=2){
+    t1.SetBit(i);
+    if(i<3*sz/4) t2.SetBit(i);
+  }
+  std::string pkl=t1.ToString();
+  TEST_ASSERT(AllProbeBitsMatch(t1,pkl));
+  TEST_ASSERT(AllProbeBitsMatch(t2,pkl));
+  TEST_ASSERT(AllProbeBitsMatch(t1.ToString(),pkl));
+  TEST_ASSERT(AllProbeBitsMatch(t2.ToString(),pkl));
+  TEST_ASSERT(AllProbeBitsMatch(t1.ToString().c_str(),pkl.c_str()));
+  TEST_ASSERT(AllProbeBitsMatch(t2.ToString().c_str(),pkl.c_str()));
+  pkl = t2.ToString();
+  TEST_ASSERT(!AllProbeBitsMatch(t1,pkl));
+  TEST_ASSERT(AllProbeBitsMatch(t2,pkl));
+  TEST_ASSERT(!AllProbeBitsMatch(t1.ToString(),pkl));
+  TEST_ASSERT(AllProbeBitsMatch(t2.ToString(),pkl));
+  TEST_ASSERT(!AllProbeBitsMatch(t1.ToString().c_str(),pkl.c_str()));
+  TEST_ASSERT(AllProbeBitsMatch(t2.ToString().c_str(),pkl.c_str()));
+}
+
+
+void test1DiscreteVect() {
+  DiscreteValueVect vect1(DiscreteValueVect::ONEBITVALUE, 30);
+  unsigned int i;
+  for (i = 0; i < 15; ++i) {
+    vect1.setVal(2*i, 1);
+  }
+
+  CHECK_INVARIANT(vect1.getLength() == 30, "");
+  CHECK_INVARIANT(vect1.getTotalVal() == 15, "");
+  for (i = 0; i < vect1.getLength(); ++i) {
+    CHECK_INVARIANT(vect1.getVal(i) ==  (i+1)%2, "");
+  }
+  try {
+    vect1.setVal(28,2);
+  } catch (ValueErrorException &dexp) {
+    std::cout << "Expected failure: " << dexp.message() << "\n";
+  }
+
+  // all these tests should fail if unsigned int changes from being 
+  // 32 bits
+  DiscreteValueVect vect2(DiscreteValueVect::TWOBITVALUE, 30);
+  for (i = 0; i < vect2.getLength(); ++i) {
+    vect2.setVal(i, i%4);
+  }
+
+  for (i = 0; i < vect2.getLength(); ++i) {
+    CHECK_INVARIANT(vect2.getVal(i) ==  i%4, "");
+  }
+  CHECK_INVARIANT(vect2.getTotalVal() == 43, "");
+  try {
+    vect2.setVal(28,10);
+  } catch (ValueErrorException &dexp) {
+    std::cout << "Expected failure: " << dexp.message() << "\n";
+  }
+
+  DiscreteValueVect vect4(DiscreteValueVect::FOURBITVALUE, 30);
+  for (i = 0; i < vect4.getLength(); ++i) {
+    vect4.setVal(i, i%16);
+  }
+
+  for (i = 0; i < vect4.getLength(); ++i) {
+    CHECK_INVARIANT(vect4.getVal(i) ==  i%16, "");
+  }
+  CHECK_INVARIANT(vect4.getTotalVal() == 211, "");
+  try {
+    vect4.setVal(28,16);
+  } catch (ValueErrorException &dexp) {
+    std::cout << "Expected failure: " << dexp.message() << "\n";
+  }
+
+  DiscreteValueVect vect8(DiscreteValueVect::EIGHTBITVALUE, 32);
+  for (i = 0; i < vect8.getLength(); ++i) {
+    vect8.setVal(i, i%256);
+  }
+
+  for (i = 0; i < vect8.getLength(); ++i) {
+    CHECK_INVARIANT(vect8.getVal(i) ==  i%256, "");
+  }
+  CHECK_INVARIANT(vect8.getTotalVal() == 496, "");
+  try {
+    vect8.setVal(28,257);
+  } catch (ValueErrorException &dexp) {
+    std::cout << "Expected failure: " << dexp.message() << "\n";
+  }
+
+  DiscreteValueVect vect16(DiscreteValueVect::SIXTEENBITVALUE, 300);
+  for (i = 0; i < vect16.getLength(); ++i) {
+    vect16.setVal(i, i%300);
+  }
+
+  for (i = 0; i < vect16.getLength(); ++i) {
+    CHECK_INVARIANT(vect16.getVal(i) ==  i%300, "");
+  }
+ 
+  CHECK_INVARIANT(vect16.getTotalVal() == 44850, "");
+  vect16.setVal(28,65535);
+  try {
+    vect16.setVal(28,65536);
+  } catch (ValueErrorException &dexp) {
+    std::cout << "Expected failure: " << dexp.message() << "\n";
+  }
+  
+}
+
+void test2DiscreteVectDists() {
+  DiscreteValueVect v1(DiscreteValueVect::ONEBITVALUE, 30);
+  DiscreteValueVect v2(DiscreteValueVect::ONEBITVALUE, 30);
+  unsigned int i;
+  for (i = 0; i < 15; ++i) {
+    v1.setVal(2*i, 1);
+    v2.setVal(2*i, 1);
+  }
+  CHECK_INVARIANT(computeL1Norm(v1, v2) == 0, " ");
+  for (i = 0; i < 30; ++i) {
+    v2.setVal(i, i%2);
+  }
+  
+  CHECK_INVARIANT(computeL1Norm(v1, v2) == 30, " ");
+  
+  for (i = 0; i < 30; ++i) {
+    if (i%3 == 0) {
+      v2.setVal(i, 1);
+    } else {
+      v2.setVal(i,0);
+    }
+  }
+  
+  CHECK_INVARIANT(computeL1Norm(v1, v2) == 15, " ");
+
+  DiscreteValueVect v21(DiscreteValueVect::TWOBITVALUE, 30);
+  DiscreteValueVect v22(DiscreteValueVect::TWOBITVALUE, 30);
+  for (i = 0; i < 30; ++i) {
+    v21.setVal(i, i%4);
+    v22.setVal(i, i%4);
+  }
+  CHECK_INVARIANT(computeL1Norm(v21, v22) == 0, " ");
+  for (i = 0; i < 30; ++i) {
+    v22.setVal(i, (i+1)%4);
+  }
+  CHECK_INVARIANT(computeL1Norm(v21, v22) == 44, " ");
+
+  DiscreteValueVect v41(DiscreteValueVect::FOURBITVALUE, 16);
+  DiscreteValueVect v42(DiscreteValueVect::FOURBITVALUE, 16);
+  for (i = 0; i < 16; ++i) {
+    v41.setVal(i, i%16);
+    v42.setVal(i, i%16);
+  }
+  CHECK_INVARIANT(computeL1Norm(v41, v42) == 0, " ");
+
+  for (i = 0; i < 16; ++i) {
+    v42.setVal(i, i%5);
+  }
+  CHECK_INVARIANT(computeL1Norm(v41, v42) ==90, " ");
+
+  DiscreteValueVect v43(v42);
+  CHECK_INVARIANT(computeL1Norm(v42, v43) == 0, " ");
+
+  DiscreteValueVect v81(DiscreteValueVect::EIGHTBITVALUE, 5);
+  DiscreteValueVect v82(DiscreteValueVect::EIGHTBITVALUE, 5);
+  v81.setVal(0, 34); v82.setVal(0, 34);
+  v81.setVal(1, 167); v82.setVal(1, 167);
+  v81.setVal(2, 3); v82.setVal(2, 3);
+  v81.setVal(3, 56); v82.setVal(3, 56);
+  v81.setVal(4, 128); v82.setVal(4, 128);
+  CHECK_INVARIANT(computeL1Norm(v81, v82) == 0, " ");
+
+  v82.setVal(0, 14); v82.setVal(1, 67);
+  v82.setVal(2, 103); v82.setVal(3, 6);
+  v82.setVal(4, 228); 
+  CHECK_INVARIANT(computeL1Norm(v81, v82) == 370, "");
+
+  DiscreteValueVect v161(DiscreteValueVect::SIXTEENBITVALUE, 3);
+  DiscreteValueVect v162(DiscreteValueVect::SIXTEENBITVALUE, 3);
+  v161.setVal(0, 2345); v162.setVal(0, 2345);
+  v161.setVal(1, 64578); v162.setVal(1, 64578);
+  v161.setVal(2, 34); v162.setVal(2, 34);
+  CHECK_INVARIANT(computeL1Norm(v161, v162) == 0, " ");
+
+  v162.setVal(0, 1345);
+  v162.setVal(1, 54578);
+  v162.setVal(2, 10034);
+  CHECK_INVARIANT(computeL1Norm(v161, v162) == 21000, " ");
+
+}
+
+int main(){
+  try{
+    throw IndexErrorException(3);
+  } catch (IndexErrorException) {
+    cerr << "pass" << endl;
+  }
+
+  stringstream ss(ios_base::binary|ios_base::out|ios_base::in);
+  int v1=4,v2=5,v3,v4;
+
+  ss.write((const char *)&v1,sizeof(v1));
+  ss.write((const char *)&v2,sizeof(v2));
+#if 0
+  ss.close();
+  fstream ss2("blah.bin",ios_base::binary|ios_base::in);
+  ss2.read((char *)&v3,sizeof(v3));
+  ss2.read((char *)&v4,sizeof(v4));
+#endif
+  ss.seekp(0,ios_base::beg);
+  ss.read((char *)&v3,sizeof(v3));
+  ss.read((char *)&v4,sizeof(v4));
+  
+  TXTMSG("v3",v3);
+  TXTMSG("v4",v4);
+  
+  cerr << " SPARSE -----------------------------------------" << endl;
+  SparseBitVect sparseFoo(10);
+  Test(sparseFoo);
+  TaniTest(sparseFoo);
+  ProbeTest(sparseFoo);
+  cerr << " Explicit -----------------------------------------" << endl;
+  ExplicitBitVect explicitFoo(10);
+  Test(explicitFoo);
+  TaniTest(explicitFoo);
+  cerr << " Done" << endl;
+  
+  std::cout << " Test DiscreteValue Vectors 1 ------------------------------------" << endl;
+  test1DiscreteVect();
+  std::cout << " Test DiscreteValue Vectors 2 ------------------------------------" << endl;
+  test2DiscreteVectDists();
+
+  return 0;
+  
+}

Code/DataStructs/test_list.py

@@ -0,0 +1,9 @@
+
+tests=[
+  ("testExecs/test.exe","",{}),
+  ]
+
+
+
+longTests=[]
+

Code/Demos/PgSQL/funcs/Makefile

@@ -0,0 +1,30 @@
+#-------------------------------------------------------------------------
+#
+# Makefile--
+#    Makefile for tutorial
+#
+# IDENTIFICATION
+#    $Header: /cvsroot/pgsql-server/src/tutorial/Makefile,v 1.16 2002/09/05 18:28:46 petere Exp $
+#
+#-------------------------------------------------------------------------
+
+include $(RDBASE)/Code/rdvars.make
+
+CXXFLAGS = $(BASECXXFLAGS) $(RDKITINCFLAGS) -fpic -I/usr/src/redhat/SOURCES/postgresql-8.0.1/src/include
+DLSUFFIX=.so
+
+#DLOBJS= $(RDBASE)/bin/funcs$(DLSUFFIX)
+DLOBJS= funcs$(DLSUFFIX)
+
+QUERIES= test1.sql
+
+all: $(DLOBJS) $(QUERIES)
+
+#$(RDBASE)/bin/funcs$(DLSUFFIX): funcs.o
+#	g++ -shared -o $(RDBASE)/bin/funcs$(DLSUFFIX) funcs.o
+#	g++ -shared -o $(RDBASE)/bin/funcs$(DLSUFFIX) funcs.o $(RDSMILES) $(RDSUBSTRUCT) $(RDKIT) $(RDGENERAL)
+funcs$(DLSUFFIX): funcs.o
+	g++ -shared -o funcs$(DLSUFFIX) funcs.o  $(RDSMILES) $(RDSUBSTRUCT) $(RDKIT) $(RDGENERAL) $(RDGEOMETRY) $(RDFINGERPRINTS) $(RDSUBGRAPHS) $(VFLIB) $(LAPACKLIB) 
+
+clean:
+	rm -f $(DLOBJS)

Code/Demos/PgSQL/funcs/funcs.cpp

@@ -0,0 +1,100 @@
+//  $Id$
+//
+//  Copyright (C) 2005 Rational Discovery LLC
+//   All Rights Reserved
+//
+
+extern "C" {
+#include "postgres.h"
+#include "fmgr.h"				/* for argument/result macros */
+#include "libpq/pqformat.h"		/* needed for send/recv functions */
+#include <stdlib.h>
+}
+#ifdef gettext
+#undef gettext
+#endif
+#include <iostream>
+
+
+#include <DataStructs/BitVects.h>
+#include <GraphMol/RDKitBase.h>
+#include <GraphMol/SmilesParse/SmilesParse.h>
+#include <GraphMol/Substruct/SubstructMatch.h>
+#include <GraphMol/Fingerprints/Fingerprints.h>
+
+
+/* These prototypes just prevent possible warnings from gcc. */
+
+extern "C" {
+  PG_FUNCTION_INFO_V1(substruct);
+  Datum substruct(PG_FUNCTION_ARGS);
+  PG_FUNCTION_INFO_V1(substructfp);
+  Datum substructfp(PG_FUNCTION_ARGS);
+  PG_FUNCTION_INFO_V1(fpsize);
+  Datum fpsize(PG_FUNCTION_ARGS);
+}
+
+
+Datum substruct(PG_FUNCTION_ARGS)
+{
+  text *smi = PG_GETARG_TEXT_P(0);
+  text *sma = PG_GETARG_TEXT_P(1);
+
+  RDKit::RWMol *probe=0;
+
+  std::string smiS(VARDATA(smi),VARSIZE(smi)-VARHDRSZ);
+  std::string smaS(VARDATA(sma),VARSIZE(sma)-VARHDRSZ);
+  bool res = false;
+  //elog(INFO,"smi(%d,%d,%d): %s\n",smi->vl_len,VARSIZE(smi),VARHDRSZ,smiS.c_str());
+  RDKit::RWMol *mol=RDKit::SmilesToMol(smiS);
+  if(mol) {
+    probe=RDKit::SmartsToMol(smaS);
+    if(probe){
+      RDKit::MatchVectType matchVect;
+      res = RDKit::SubstructMatch(mol,probe,matchVect);
+    }
+    delete mol;
+  }
+  //elog(INFO,"%d %s",res,smiS.c_str());
+  PG_RETURN_INT32(res);
+}
+
+Datum substructfp(PG_FUNCTION_ARGS)
+{
+  text *smi = PG_GETARG_TEXT_P(0);
+  int fpSize=2048;
+  std::string smiS(VARDATA(smi),VARSIZE(smi)-VARHDRSZ);
+
+  ExplicitBitVect *bv=0;
+  RDKit::RWMol *mol=RDKit::SmilesToMol(smiS);
+  if(mol) {
+    try{
+      bv = DaylightFingerprintMol(mol,1,7,fpSize);
+    } catch (...) {
+      bv = new ExplicitBitVect(fpSize);
+    }
+    delete mol;
+  } else {
+    bv = new ExplicitBitVect(fpSize);
+  }
+  std::string pkl=bv->ToString();
+  delete bv;
+
+  StringInfoData buf;
+  pq_begintypsend(&buf);
+  pq_sendtext(&buf,pkl.c_str(),pkl.size());
+  PG_RETURN_BYTEA_P(pq_endtypsend(&buf));
+}
+
+Datum fpsize(PG_FUNCTION_ARGS)
+{
+  int res=0;
+  if(!PG_ARGISNULL(0)) {
+    bytea *buf=PG_GETARG_BYTEA_P(0);
+    std::string pkl(VARDATA(buf),VARSIZE(buf)-VARHDRSZ);
+    ExplicitBitVect bv(pkl);
+    res = bv.GetNumBits();
+  }
+  PG_RETURN_INT32(res);
+
+}

Code/Demos/PgSQL/funcs/test1.sql

@@ -0,0 +1,42 @@
+---------------------------------------------------------------------------
+--
+-- funcs.sql-
+--	  Tutorial on using functions in POSTGRES.
+--
+--
+-- Copyright (c) 1994-5, Regents of the University of California
+--
+-- $Id: funcs.source,v 1.5 2001/10/26 20:45:33 tgl Exp $
+--
+---------------------------------------------------------------------------
+
+-----------------------------
+-- Creating C Functions
+--	in addition to SQL functions, you can also create C functions. 
+--	See funcs.c for the definition of the C functions.
+-----------------------------
+
+CREATE FUNCTION substruct(text,text) RETURNS int
+    AS '/home2/glandrum/RD/trunk/Code/Demos/PgSQL/funcs/funcs' LANGUAGE 'c';
+CREATE FUNCTION substructfp(text) RETURNS bytea
+    AS '/home2/glandrum/RD/trunk/Code/Demos/PgSQL/funcs/funcs' LANGUAGE 'c';
+CREATE FUNCTION fpsize(bytea) RETURNS int
+    AS '/home2/glandrum/RD/trunk/Code/Demos/PgSQL/funcs/funcs' LANGUAGE 'c';
+
+SELECT substruct('c1ccccc1C','cC');
+drop table temp;
+create table temp (id text,smiles varchar(256));
+insert into temp values ('mol-1','CCC');
+insert into temp values ('mol-2','Cc1ncccc1');
+select * from temp where substruct(smiles,'Cc1ncccc1')=1;
+
+-- select * from d1 where substruct(smiles,'Cc1ncccc1')=1;
+
+select substructfp('c1ccccc1');
+select substructfp('');
+select fpsize(substructfp(''));
+
+
+DROP FUNCTION substruct(text,text);
+DROP FUNCTION substructfp(text);
+

Code/Demos/RDKit/Minimize/MinimizeCLI.cpp

@@ -0,0 +1,106 @@
+// $Id: MinimizeCLI.cpp 4421 2005-02-09 16:55:05Z glandrum $
+//
+//  Copyright (C) 2004 Rational Discovery LLC
+//   All Rights Reserved
+//
+#include <iostream>
+#include <RDGeneral/Invariant.h>
+#include <RDGeneral/utils.h>
+
+#include <GraphMol/RDKitBase.h>
+#include <GraphMol/FileParsers/FileParsers.h>
+#include <GraphMol/FileParsers/MolSupplier.h>
+
+#include <GraphMol/ForceFieldHelpers/UFF/AtomTyper.h>
+#include <GraphMol/ForceFieldHelpers/UFF/Builder.h>
+#include <ForceField/ForceField.h>
+
+using namespace RDKit;
+
+
+void runMol(ROMol *mol,int checkEvery=10,bool verbose=true){
+  ForceFields::ForceField *field;
+  try{
+    field=UFF::constructForceField(mol,2.5);
+  } catch (...) {
+    field=0;
+  }
+  if(field){
+    field->initialize();
+    int needMore=1;
+    int nPasses=0;
+    while(needMore){
+#if 1
+      needMore = field->minimize(checkEvery);
+      if(verbose) std::cerr << "\t" << ++nPasses << std::endl;
+#else
+      needMore = field->minimize(1);
+      std::cout << MolToMolBlock(mol) << "$$$$" << std::endl;
+#endif
+    }
+    std::cout << MolToMolBlock(mol) << "$$$$" << std::endl;
+    delete field;
+  } else {
+    std::cerr << "failed";
+  }
+  
+}
+
+void runMolFile(std::string fileName,int checkEvery=10){
+  RWMol *mol=MolFileToMol(fileName,false);
+  TEST_ASSERT(mol);
+  MolOps::sanitizeMol(*mol);
+
+  ROMol *mol2=MolOps::addHs(mol,false,true);
+
+  runMol(mol2,checkEvery);
+
+  delete mol;
+  delete mol2;
+}
+
+void runSDFile(std::string fileName,int checkEvery=10){
+  SDMolSupplier suppl(fileName,false);
+  
+  RWMol *mol;
+
+  mol = (RWMol *)suppl.next();
+  while(mol){
+    std::string name;
+    mol->getProp("_Name",name);
+    std::cerr << "Mol: " << name << std::endl;
+    try{
+      MolOps::sanitizeMol(*mol);
+    } catch (...) {
+      std::cerr << " sanitization failed" << std::endl;
+      delete mol;
+      mol = 0;
+    }
+    if(mol){
+      ROMol *mol2=MolOps::addHs(mol,false,true);
+      delete mol;
+      runMol(mol2,checkEvery,false);
+      delete mol2;
+    }
+    mol = (RWMol *)suppl.next();
+
+  }
+
+}
+
+//-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*
+//
+//-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*
+int main(int argc,char *argv[]){
+  PRECONDITION(argc>1,"bad arguments");
+  std::string fileName=argv[1];
+  int checkEvery=10;
+  std::cerr << ">" << fileName<< " " << fileName.find(".sdf") << std::endl;
+  if(fileName.find(".sdf")==std::string::npos){
+    runMolFile(fileName,checkEvery);
+  } else {
+    runSDFile(fileName,checkEvery);
+  }
+
+  std::cerr << "done" << std::endl;
+}

Code/Demos/RDKit/Minimize/MinimizeCLI.vcproj

@@ -0,0 +1,152 @@
+<?xml version="1.0" encoding="Windows-1252"?>
+<VisualStudioProject
+	ProjectType="Visual C++"
+	Version="7.10"
+	Name="demo - MinimizeCLI"
+	ProjectGUID="{A33253EE-6147-4E21-997E-C68509F218EA}"
+	SccProjectName=""
+	SccLocalPath="">
+	<Platforms>
+		<Platform
+			Name="Win32"/>
+	</Platforms>
+	<Configurations>
+		<Configuration
+			Name="Debug|Win32"
+			OutputDirectory=".\DemoMinimizeCLI___Win32_Debug"
+			IntermediateDirectory=".\DemoMinimizeCLI___Win32_Debug"
+			ConfigurationType="1"
+			UseOfMFC="0"
+			ATLMinimizesCRunTimeLibraryUsage="FALSE"
+			CharacterSet="2">
+			<Tool
+				Name="VCCLCompilerTool"
+				Optimization="0"
+				AdditionalIncludeDirectories="$(RDBASE)/External/boost/include/$(BOOSTBASE),$(RDBASE)/Code"
+				PreprocessorDefinitions="WIN32;_DEBUG;_CONSOLE"
+				BasicRuntimeChecks="3"
+				RuntimeLibrary="3"
+				PrecompiledHeaderFile=".\DemoMinimizeCLI___Win32_Debug/DemoMinimizeCLI.pch"
+				AssemblerListingLocation=".\DemoMinimizeCLI___Win32_Debug/"
+				ObjectFile=".\DemoMinimizeCLI___Win32_Debug/"
+				ProgramDataBaseFileName=".\DemoMinimizeCLI___Win32_Debug/"
+				WarningLevel="3"
+				SuppressStartupBanner="TRUE"
+				DebugInformationFormat="4"/>
+			<Tool
+				Name="VCCustomBuildTool"/>
+			<Tool
+				Name="VCLinkerTool"
+				OutputFile="MinimizeCLI.exe"
+				LinkIncremental="1"
+				SuppressStartupBanner="TRUE"
+				GenerateDebugInformation="TRUE"
+				ProgramDatabaseFile=".\DemoMinimizeCLI___Win32_Debug/test.pdb"
+				SubSystem="1"
+				TargetMachine="1"/>
+			<Tool
+				Name="VCMIDLTool"
+				TypeLibraryName=".\DemoMinimizeCLI___Win32_Debug/DemoMinimizeCLI.tlb"
+				HeaderFileName=""/>
+			<Tool
+				Name="VCPostBuildEventTool"/>
+			<Tool
+				Name="VCPreBuildEventTool"/>
+			<Tool
+				Name="VCPreLinkEventTool"/>
+			<Tool
+				Name="VCResourceCompilerTool"
+				PreprocessorDefinitions="_DEBUG"
+				Culture="1033"/>
+			<Tool
+				Name="VCWebServiceProxyGeneratorTool"/>
+			<Tool
+				Name="VCXMLDataGeneratorTool"/>
+			<Tool
+				Name="VCWebDeploymentTool"/>
+			<Tool
+				Name="VCManagedWrapperGeneratorTool"/>
+			<Tool
+				Name="VCAuxiliaryManagedWrapperGeneratorTool"/>
+		</Configuration>
+		<Configuration
+			Name="Release|Win32"
+			OutputDirectory=".\testExecs\"
+			IntermediateDirectory=".\Release"
+			ConfigurationType="1"
+			UseOfMFC="0"
+			ATLMinimizesCRunTimeLibraryUsage="FALSE"
+			CharacterSet="2">
+			<Tool
+				Name="VCCLCompilerTool"
+				Optimization="2"
+				InlineFunctionExpansion="1"
+				AdditionalIncludeDirectories="$(RDBASE)/External/boost/include/$(BOOSTBASE),$(RDBASE)/Code"
+				PreprocessorDefinitions="WIN32;NDEBUG;_CONSOLE"
+				StringPooling="TRUE"
+				RuntimeLibrary="2"
+				EnableFunctionLevelLinking="TRUE"
+				PrecompiledHeaderFile=".\Release/DemoMinimizeCLI.pch"
+				AssemblerListingLocation=".\Release/"
+				ObjectFile=".\Release/"
+				ProgramDataBaseFileName=".\Release/"
+				WarningLevel="3"
+				SuppressStartupBanner="TRUE"/>
+			<Tool
+				Name="VCCustomBuildTool"/>
+			<Tool
+				Name="VCLinkerTool"
+				OutputFile="MinimizeCLI.exe"
+				LinkIncremental="1"
+				SuppressStartupBanner="TRUE"
+				ProgramDatabaseFile=".\Release/test.pdb"
+				SubSystem="1"
+				TargetMachine="1"/>
+			<Tool
+				Name="VCMIDLTool"
+				TypeLibraryName=".\Release/DemoMinimizeCLI.tlb"
+				HeaderFileName=""/>
+			<Tool
+				Name="VCPostBuildEventTool"/>
+			<Tool
+				Name="VCPreBuildEventTool"/>
+			<Tool
+				Name="VCPreLinkEventTool"/>
+			<Tool
+				Name="VCResourceCompilerTool"
+				PreprocessorDefinitions="NDEBUG"
+				Culture="1033"/>
+			<Tool
+				Name="VCWebServiceProxyGeneratorTool"/>
+			<Tool
+				Name="VCXMLDataGeneratorTool"/>
+			<Tool
+				Name="VCWebDeploymentTool"/>
+			<Tool
+				Name="VCManagedWrapperGeneratorTool"/>
+			<Tool
+				Name="VCAuxiliaryManagedWrapperGeneratorTool"/>
+		</Configuration>
+	</Configurations>
+	<References>
+	</References>
+	<Files>
+		<Filter
+			Name="Source Files"
+			Filter="cpp;c;cxx;rc;def;r;odl;idl;hpj;bat">
+			<File
+				RelativePath=".\MinimizeCLI.cpp">
+			</File>
+		</Filter>
+		<Filter
+			Name="Header Files"
+			Filter="h;hpp;hxx;hm;inl">
+		</Filter>
+		<Filter
+			Name="Resource Files"
+			Filter="ico;cur;bmp;dlg;rc2;rct;bin;rgs;gif;jpg;jpeg;jpe">
+		</Filter>
+	</Files>
+	<Globals>
+	</Globals>
+</VisualStudioProject>

Code/Demos/RDKit/TemplEnum/Makefile

@@ -0,0 +1,18 @@
+include $(RDBASE)/Code/rdvars.make
+CXXFLAGS=$(BASECXXFLAGS)
+
+LDFLAGS= $(RDFILEPARSE) $(RDSMILES) $(RDSUBSTRUCT) $(VFLIB) $(RDKIT) $(RDBITVECS) \
+         $(RDMOLTRANSFORMS) $(RDGENERAL) $(RDGEOMETRY)
+
+OBJS=main.o TemplEnumTools.o
+
+main.exe: $(OBJS)
+	g++ -o main.exe $(CXXFLAGS) $(OBJS) $(LDFLAGS)
+
+SIMPLEOBJS=simple.o TemplEnumTools.o
+simple.exe: $(SIMPLEOBJS)
+	g++ -o simple.exe $(CXXFLAGS) $(SIMPLEOBJS) $(LDFLAGS)
+
+clean:
+	rm -f main.exe $(OBJS)
+

Code/Demos/RDKit/TemplEnum/TemplEnum.h

@@ -0,0 +1,39 @@
+//  $Id: TemplEnum.h 4421 2005-02-09 16:55:05Z glandrum $
+//
+//  Copyright (C) 2003 Rational Discovery LLC
+//   All Rights Reserved
+//
+#ifndef _TEMPLENUM_H_
+#define _TEMPLENUM_H_
+#include <exception>
+#include <vector>
+#include <GraphMol/RDKitBase.h>
+
+namespace TemplateEnum {
+  using namespace RDKit;
+
+  class EnumException : public std::exception {
+  public :
+    EnumException(const char *msg) : _msg(msg) {};
+    EnumException(const std::string msg) : _msg(msg) {};
+    const char *message () const { return _msg.c_str(); };
+    ~EnumException () throw () {};
+  private :
+    std::string _msg;
+  };
+
+  void orientSidechain(RWMol *mol,RWMol *sidechain,
+		       int molAttachIdx,int sidechainAttachIdx);
+
+  typedef std::vector< RWMOL_SPTR_VECT > VECT_RWMOL_SPTR_VECT;
+  void markAttachmentPoints(RWMOL_SPTR *mol,char frontMarker='X');
+  void markAttachmentPoints(RWMol *mol,char frontMarker='X');
+  void prepareSidechains(RWMOL_SPTR_VECT *sidechains,char frontMarker='Y');
+  RWMOL_SPTR_VECT enumerateLibrary(RWMol *mol,VECT_RWMOL_SPTR_VECT &sidechains,
+				   bool orientSidechains=true);
+  RWMOL_SPTR_VECT enumFromFiles(const char *templateName,
+				std::vector<const char *> &sidechainName);
+
+} // end of TemplateEnum namespace
+#endif
+

Code/Demos/RDKit/TemplEnum/TemplEnumTools.cpp

@@ -0,0 +1,419 @@
+//  $Id: TemplEnumTools.cpp 4421 2005-02-09 16:55:05Z glandrum $
+//
+//  Copyright (C) 2003,2004 Rational Discovery LLC
+//   All Rights Reserved
+//
+#include "TemplEnum.h"
+#include <Geometry/Transform3D.h>
+#include <GraphMol/MolTransforms/MolTransforms.h>
+#include <GraphMol/FileParsers/FileParsers.h>
+#define FEQ(_a_,_b_) (fabs((_a_)-(_b_))<1e-4)
+
+namespace TemplateEnum {
+  using namespace RDKit;
+
+  // ------------------------------------------------------------------
+  //
+  // transforms a sidechain so that it is oriented better for attachment
+  // to a molecule
+  //
+  //  Arguments:
+  //   mol: core molecule 
+  //   sidechain: sidechain to attach.
+  //   molConnectorIdx: the index of the attachment point atom in the
+  //     molecule.
+  //   sidechainConnectorIdx: the index of the attachment point atom
+  //     in the sidechain.
+  // 
+  // ------------------------------------------------------------------
+  void orientSidechain(RWMol *mol,RWMol *sidechain,
+		       int molAttachIdx,int sidechainAttachIdx){
+    PRECONDITION(mol,"bad molecule");
+    PRECONDITION(sidechain,"bad molecule");
+
+    // ---------
+    // start by getting our 4 atoms
+    // ---------
+    Atom *molConnAtom,*molAttachAtom;
+    Atom *chainConnAtom,*chainAttachAtom;
+    molAttachAtom = mol->getAtomWithIdx(molAttachIdx);
+    chainAttachAtom = sidechain->getAtomWithIdx(sidechainAttachIdx);
+    PRECONDITION(molAttachAtom->getDegree()==1,"attachment points must be degree 1");
+    PRECONDITION(chainAttachAtom->getDegree()==1,"attachment points must be degree 1");
+    RWMol::ADJ_ITER nbrIdx,endNbrs;
+    boost::tie(nbrIdx,endNbrs) = mol->getAtomNeighbors(molAttachAtom);
+    molConnAtom=mol->getAtomWithIdx(*nbrIdx);
+    boost::tie(nbrIdx,endNbrs) = sidechain->getAtomNeighbors(chainAttachAtom);
+    chainConnAtom=sidechain->getAtomWithIdx(*nbrIdx);
+
+    //-----------------------------------------
+    //  Notation:
+    //    Pmc: molecule connection point (the atom that will be
+    //     removed from the molecule).
+    //    Pma: molecule attachment point (the atom to which we'll form
+    //     the bond).
+    //    Psc: sidechain connection point
+    //    Psa: sidechain attachment point
+    //    Vm: Pmc-Pma (molecular attachment vector)
+    //    Vs: Psc-Psa (sidechain attachment vector)
+    //
+    //-----------------------------------------
+    RDGeom::Transform3D sidechainTform,templateTform,tmpTform;
+
+    RDGeom::Point3D Vm,Um,Pmc,Pma;
+    RDGeom::Point3D Vs,Us,Psc,Psa;
+    Pmc = molConnAtom->getPos();
+    Pma = molAttachAtom->getPos();
+    std::cerr << "p=array(["<<Pma.x<<","<<Pma.y<<","<<Pma.z<<"])" << std::endl;
+    Psc = chainConnAtom->getPos();
+    Psa = chainAttachAtom->getPos();
+
+    templateTform.setToIdentity();
+    Vm = Pmc - Pma;
+    // note the opposite direction here:
+    Vs = Psa - Psc;
+    Um = Vm;
+    Um.normalize();
+    std::cerr << "Um=array(["<<Um.x<<","<<Um.y<<","<<Um.z<<"])" << std::endl;
+    Us = Vs;
+    Us.normalize();
+    std::cerr << "Us=array(["<<Us.x<<","<<Us.y<<","<<Us.z<<"])" << std::endl;
+    // translate Psc -> Pma
+    //RDGeom::Point3D headTrans = Pma-Psc;
+    
+    templateTform.setToIdentity();
+
+    tmpTform.setToIdentity();
+    tmpTform.SetTranslation(Pma);
+    templateTform = templateTform*tmpTform;
+
+    double sinT,cosT;
+    cosT = Us.dotProduct(Um);
+    if(cosT>1.0) cosT = 1.0;
+    if(fabs(cosT)<1.0){
+      tmpTform.setToIdentity();
+      sinT = sqrt(1.0-cosT*cosT);
+      RDGeom::Point3D rotnAxis=Us.crossProduct(Um);
+      rotnAxis.normalize();
+      std::cerr << "ax=array(["<<rotnAxis.x<<","<<rotnAxis.y<<","<<rotnAxis.z<<"])" << std::endl;
+      tmpTform.SetRotation(cosT,sinT,rotnAxis);
+      templateTform = templateTform*tmpTform;
+    } else if(cosT==1.0){
+      RDGeom::Point3D normal(1,0,0);
+      if(fabs(Us.dotProduct(normal))==1.0){
+	normal = RDGeom::Point3D(0,1,0);
+      }
+      RDGeom::Point3D rotnAxis=Us.crossProduct(normal);
+      templateTform.SetRotation(-1,0,rotnAxis);
+    }
+    
+    tmpTform.setToIdentity();
+    tmpTform.SetTranslation(Psc*-1.0);
+    templateTform = templateTform*tmpTform;
+
+    // ---------
+    // transform the atomic positions in the sidechain:
+    // ---------
+    MolTransforms::transformMolsAtoms(sidechain,templateTform);
+
+
+    // that's it!
+  }
+  // ------------------------------------------------------------------
+  //
+  // attaches a sidechain fragment to a molecule.
+  //
+  //  Arguments:
+  //   mol: molecule to be modified
+  //   sidechain: sidechain to attach.  The sidechain is copied in.
+  //   molConnectorIdx: the index of the attachment point atom in the
+  //     molecule.
+  //   sidechainConnectorIdx: the index of the attachment point atom
+  //     in the sidechain.
+  //   bondType: type of the bond to form between the atoms
+  //
+  //  The connector atoms are *NOT* part of the final molecule, they
+  //  merely serve to establish where things connect.
+  // 
+  // ------------------------------------------------------------------
+  void molAddSidechain(RWMol *mol,RWMol *sidechain,
+		       int molConnectorIdx,int sidechainConnectorIdx,
+		       Bond::BondType bondType){
+    PRECONDITION(mol,"bad molecule provided");
+    PRECONDITION(sidechain,"bad sidechain provided");
+    int origNumAtoms=mol->getNumAtoms();
+    mol->insertMol(sidechain);
+
+    // get pointers to the two connectors (these are the atoms
+    // we'll end up removing)
+    Atom *molConnAtom,*sidechainConnAtom;
+    molConnAtom = mol->getAtomWithIdx(molConnectorIdx);
+    sidechainConnAtom = mol->getAtomWithIdx(sidechainConnectorIdx+origNumAtoms);
+
+    // now use those pointers to get the atoms which will remain
+    // (we're going to connect these) and remove the original
+    // connection points from the molecule
+    Atom *tmpAtom;
+    RWMol::ADJ_ITER nbrIdx,endNbrs;
+    boost::tie(nbrIdx,endNbrs) = mol->getAtomNeighbors(molConnAtom);
+
+    // we are assuming that the first neighbor is the correct one.
+    // Really we should be able to assume that there is only a single
+    // attachment point.
+    tmpAtom = molConnAtom;
+    molConnAtom = mol->getAtomWithIdx(*nbrIdx);
+    mol->removeAtom(tmpAtom);
+    // repeat that process for the sidechain:
+    boost::tie(nbrIdx,endNbrs) = mol->getAtomNeighbors(sidechainConnAtom);
+    tmpAtom = sidechainConnAtom;
+    sidechainConnAtom = mol->getAtomWithIdx(*nbrIdx);
+    mol->removeAtom(tmpAtom);
+
+    // finally connect the remaining atoms:
+    mol->addBond(molConnAtom,sidechainConnAtom,bondType);
+  }
+
+
+  // used as a starting point for connection bookmarks
+  const int CONNECT_BOOKMARK_START=0x23424223;
+
+  // ------------------------------------------------------------------
+  //
+  // Loop through all the atoms and bookmark the attachment points
+  //
+  //  attachment points are assumed to have one of these properties:
+  //   - "molFileAlias" (set by the mol file parser)
+  //   - "dummyLabel"   (set by the SMILES parser)
+  //  frontMarker is the "recognition character" to be used to pick
+  //  valid labels.  e.g. if the frontMarker is 'X', a label beginning
+  //  with 'Y' will not be marked.
+  //
+  //  In addition to bookmarking the attachment points, we also set
+  //  the "maxAttachIdx" property, which holds an integer with the
+  //  maximum attachment bookmark index. This is used in the
+  //  enumeration to prevent us from having to scan through all the
+  //  molecule's bookmarks
+  //
+  //
+  // ------------------------------------------------------------------
+  void markAttachmentPoints(RWMOL_SPTR mol,char frontMarker){
+    markAttachmentPoints(mol.get(),frontMarker);
+  }
+  void markAttachmentPoints(RWMol *mol,char frontMarker){
+    PRECONDITION(mol,"bad molecule");
+
+    RWMol::AtomIterator atomIt;
+    int maxAttachIdx=0;
+
+    // scan through the atoms and mark those that have aliases
+    //  (these might be attachment points)
+    for(atomIt=mol->beginAtoms();atomIt!=mol->endAtoms();atomIt++){
+      // start by finding possible attachment point properties:
+      std::string attachLabel="";
+      if((*atomIt)->hasProp("molFileAlias")){
+	(*atomIt)->getProp("molFileAlias",attachLabel);
+      } else if((*atomIt)->hasProp("dummyLabel")){
+	(*atomIt)->getProp("dummyLabel",attachLabel);
+      }
+
+      // if we got one and it starts with the appropriate front
+      // marker, proceed:
+      if(attachLabel!="" && attachLabel[0]==frontMarker ){
+	// to avoid trouble later, we guarantee that the attachment
+	// point has degree 1 (one bond to it).
+	if((*atomIt)->getDegree()>1)
+	  throw EnumException("More than one bond to an attachment point.");
+
+	int offset = CONNECT_BOOKMARK_START;
+	if(attachLabel.length()>1){
+	  if(attachLabel[1]>='a' && attachLabel[1]<='z'){
+	    offset += (int)attachLabel[1] - (int)'a';
+	  }
+	}
+	mol->setAtomBookmark(*atomIt,offset);
+	if(offset>maxAttachIdx) maxAttachIdx=offset;
+      }
+    }
+    if(maxAttachIdx){
+      mol->setProp("maxAttachIdx",maxAttachIdx);
+    }
+  }
+
+  // ------------------------------------------------------------------
+  //
+  // loops through the sidechain molecules and calls
+  // _markAttachmentPoints()_ on each.
+  //
+  // ------------------------------------------------------------------
+  void prepareSidechains(RWMOL_SPTR_VECT *sidechains,char frontMarker){
+    PRECONDITION(sidechains,"bad sidechain list");
+    RWMOL_SPTR_VECT::iterator mpvI;
+    for(mpvI=sidechains->begin();mpvI!=sidechains->end();mpvI++){
+      markAttachmentPoints(*mpvI,frontMarker);
+    }
+  }
+
+  // ------------------------------------------------------------------
+  //
+  // Enumerates the library around a template and returns the result.
+  //
+  //
+  // ------------------------------------------------------------------
+  RWMOL_SPTR_VECT enumerateLibrary(RWMol *templateMol,
+				   VECT_RWMOL_SPTR_VECT &sidechains,
+				   bool orientSidechains){
+    PRECONDITION(templateMol,"bad molecule");
+    RWMOL_SPTR_VECT res,tmp;
+    res.push_back(RWMOL_SPTR(new RWMol(*templateMol)));
+
+    // if there's no attachment point on the molecule or no
+    // sidechains, return now: 
+    if(!templateMol->hasProp("maxAttachIdx") || sidechains.size()==0 )
+      return res;
+
+    int maxIdx;
+    templateMol->getProp("maxAttachIdx",maxIdx);
+
+    tmp.clear();
+    // loop over the sidechains and attach them
+    for(unsigned int i=0;i<sidechains.size();i++){
+      int tgtMark=CONNECT_BOOKMARK_START+i;
+      // here's another boundary condition
+      if(tgtMark>maxIdx) break;
+
+      /// loop over all atoms with the appropriate mark
+      //  This means that if a mol has two attachment points with the
+      //  same name (e.g. two Xa's) they'll always have the same
+      //  sidechain attached to them.  This is a feature.
+      RWMOL_SPTR_VECT::iterator sidechainIt;
+      for(sidechainIt=sidechains[i].begin();
+	  sidechainIt!=sidechains[i].end();
+	  sidechainIt++){
+	// we've got our sidechain, find the atom it attaches from
+	if( (*sidechainIt)->hasAtomBookmark(CONNECT_BOOKMARK_START) ){
+	  //
+	  // NOTE: If there's more than one marked atom in the sidechain,
+	  ///      we'll only use the first for the moment.
+	  //
+	  int sidechainAtomIdx = (*sidechainIt)->getAtomWithBookmark(CONNECT_BOOKMARK_START)->getIdx();
+	
+	  // now add the sidechain to each molecule
+	  RWMOL_SPTR_VECT::iterator templMolIt;
+	  // loop over all the mols we've generated to this point
+	  for(templMolIt=res.begin();templMolIt!=res.end();templMolIt++){
+	    RWMol *templ =  new RWMol(**templMolIt);
+	    std::string name,tmpStr;
+	    if(templ->hasProp("_Name")){
+	      templ->getProp("_Name",tmpStr);
+	      name = name + " " + tmpStr;
+	    }
+	    while(templ->hasAtomBookmark(tgtMark)){
+	      // this is the atom we'll be replacing in the template
+	      Atom *at = templ->getAtomWithBookmark(tgtMark);
+
+	      // copy and transform the sidechain:
+	      RWMol *sidechain;
+	      if(orientSidechains){
+		sidechain = new RWMol(*(sidechainIt->get()));
+		orientSidechain(templ,sidechain,
+				at->getIdx(),sidechainAtomIdx);
+	      } else {
+		sidechain = sidechainIt->get();
+	      }
+	      // FIX: need to use the actual bond order here:
+	      molAddSidechain(templ,sidechain,
+			      at->getIdx(),sidechainAtomIdx,
+			      Bond::SINGLE);
+	      if(sidechain->hasProp("_Name")){
+		sidechain->getProp("_Name",tmpStr);
+		name = name + " " + tmpStr;
+	      }
+	      templ->clearAtomBookmark(tgtMark,at);
+	      if(orientSidechains){
+		delete sidechain;
+	      }
+	    }
+	    //std::cout << templ << "> " << MolToSmiles(*templ) << std::endl;
+	    if(name != "") templ->setProp("_Name",name);
+	    tmp.push_back(RWMOL_SPTR(templ));
+	  }
+	}
+      }
+
+      //
+      // if we just made any molecules, free up the memory used by the
+      // existing result set and move the molecules we just generated
+      // over
+      if(tmp.size()){
+#if 0      
+	RWMOL_SPTR_VECT::iterator tmpMolIt;
+	for(tmpMolIt=res.begin();tmpMolIt!=res.end();tmpMolIt++){
+	  delete *tmpMolIt;
+	}
+#endif
+	res = tmp;
+	tmp.clear();
+      }
+    }
+    return res;
+  }
+
+  // ------------------------------------------------------------------
+  //
+  //  Reads a template and library of sidechains from input files.
+  //   the template file should be a mol file and the sidechain files
+  //   SD files
+  //
+  // ------------------------------------------------------------------
+  RWMOL_SPTR_VECT enumFromFiles(const char *templateName,
+			    std::vector<const char *> &sidechainNames){
+    PRECONDITION(templateName,"bad template file name passed in");
+
+    // build and mark the template molecule
+    RWMol *templ = MolFileToMol(templateName,false);
+    if(!templ) throw EnumException("could not construct template molecule"); 
+    markAttachmentPoints(templ,'X');
+
+    // now build and mark each set of sidechains:
+    RWMOL_SPTR_VECT sidechains;
+    VECT_RWMOL_SPTR_VECT allSidechains;
+    for(std::vector<const char*>::const_iterator i=sidechainNames.begin();
+	i!=sidechainNames.end();i++){
+      sidechains = SDFileToMols(*i,false);
+      if(!sidechains.size()){
+	std::string err="no sidechains read from file: ";
+	err += *i;
+	throw EnumException(err.c_str());
+      }
+      prepareSidechains(&sidechains,'X');
+      allSidechains.push_back(sidechains);
+    }
+
+    // enumerate the library:
+    RWMOL_SPTR_VECT library=enumerateLibrary(templ,allSidechains);
+
+
+    //--------------------------
+    //
+    // Clean up the molecules and sidechains we constructed along the
+    // way. 
+    //
+    //--------------------------
+    delete templ;
+#if 0
+    VECT_RWMOL_SPTR_VECT::iterator vmpvI;
+    for(vmpvI=allSidechains.begin();vmpvI!=allSidechains.end();vmpvI++){
+      RWMOL_SPTR_VECT::iterator mpvI;
+      for(mpvI=vmpvI->begin();mpvI!=vmpvI->end();mpvI++){
+	delete *mpvI;
+      }
+      vmpvI->clear();
+    }
+#endif
+    allSidechains.clear();
+
+    return library;
+  }  
+
+} // end of TemplateEnum namespace
+

Code/Demos/RDKit/TemplEnum/Ts.1.sdf

@@ -0,0 +1,20 @@
+Structure1
+csChFnd70/05230312262D
+
+  5  4  0  0  0  0  0  0  0  0999 V2000
+    0.0000    0.0000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
+    0.0000    1.0000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
+    0.0000   -1.0000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
+    1.0000    0.0000    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
+   -1.5000    0.0000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
+  1  2  1  0  0  0  0
+  1  3  1  0  0  0  0
+  1  4  1  0  0  0  0
+  1  5  1  0  0  0  0
+A    5
+X
+M  END
+>  <ID> (3)
+Lig1
+
+$$$$

Code/Demos/RDKit/TemplEnum/Ts.4.sdf

@@ -0,0 +1,20 @@
+Structure4
+csChFnd70/05230312262D
+
+  5  4  0  0  0  0  0  0  0  0999 V2000
+    0.0000    0.0000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
+    1.0000    0.0000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
+   -1.0000    0.0000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
+    0.0000   -1.0000    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
+    0.0000    1.5000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
+  1  2  1  0  0  0  0
+  1  3  1  0  0  0  0
+  1  4  1  0  0  0  0
+  1  5  1  0  0  0  0
+A    5
+X
+M  END
+>  <ID> (6)
+Lig4
+
+$$$$

Code/Demos/RDKit/TemplEnum/Ts.sdf

@@ -0,0 +1,80 @@
+Structure1
+csChFnd70/05230312262D
+
+  5  4  0  0  0  0  0  0  0  0999 V2000
+    0.0000    0.0000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
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+    1.0000    0.0000    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
+   -1.5000    0.0000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
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+  1  3  1  0  0  0  0
+  1  4  1  0  0  0  0
+  1  5  1  0  0  0  0
+A    5
+X
+M  END
+>  <ID> (3)
+Lig1
+
+$$$$
+Structure2
+csChFnd70/05230312262D
+
+  5  4  0  0  0  0  0  0  0  0999 V2000
+    0.0000    0.0000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
+    0.0000   -1.0000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
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+   -1.0000    0.0000    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
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+  1  3  1  0  0  0  0
+  1  4  1  0  0  0  0
+  1  5  1  0  0  0  0
+A    5
+X
+M  END
+>  <ID> (4)
+Lig2
+
+$$$$
+Structure3
+csChFnd70/05230312262D
+
+  5  4  0  0  0  0  0  0  0  0999 V2000
+    0.0000    0.0000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
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+    0.0000    1.0000    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
+    0.0000   -1.5000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
+  1  2  1  0  0  0  0
+  1  3  1  0  0  0  0
+  1  4  1  0  0  0  0
+  1  5  1  0  0  0  0
+A    5
+X
+M  END
+>  <ID> (5)
+Lig3
+
+$$$$
+Structure4
+csChFnd70/05230312262D
+
+  5  4  0  0  0  0  0  0  0  0999 V2000
+    0.0000    0.0000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
+    1.0000    0.0000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
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+  1  4  1  0  0  0  0
+  1  5  1  0  0  0  0
+A    5
+X
+M  END
+>  <ID> (6)
+Lig4
+
+$$$$

Code/Demos/RDKit/TemplEnum/box.1.mol

@@ -0,0 +1,17 @@
+box.mol
+  ChemDraw05280309452D
+
+  5  5  0  0  0  0  0  0  0  0999 V2000
+   -0.5000    0.5000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
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+  1  2  1  0      
+  2  3  1  0      
+  3  4  1  0      
+  4  1  1  0      
+  2  5  1  0      
+A    5
+Xa
+M  END

Code/Demos/RDKit/TemplEnum/box.1a.mol

@@ -0,0 +1,17 @@
+box.mol
+  ChemDraw05280309452D
+
+  5  5  0  0  0  0  0  0  0  0999 V2000
+   -0.5000    0.5000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
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+  1  2  1  0      
+  2  3  1  0      
+  3  4  1  0      
+  4  1  1  0      
+  2  5  1  0      
+A    5
+Xa
+M  END

Code/Demos/RDKit/TemplEnum/box.mol

@@ -0,0 +1,29 @@
+box.mol
+  ChemDraw05280309452D
+
+  8  8  0  0  0  0  0  0  0  0999 V2000
+   -0.5000    0.5000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
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+A    5
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+A    6
+Xa
+A    7
+Xa
+A    8
+Xa
+M  END

Code/Demos/RDKit/TemplEnum/esters.2.sdf

@@ -0,0 +1,42 @@
+Structure1
+csChFnd70/05230312262D
+
+  5  4  0  0  0  0  0  0  0  0999 V2000
+    1.2124    0.0000    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
+    2.4249    0.7000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
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+  2  4  2  0  0  0  0
+  1  5  1  0  0  0  0
+A    5
+X
+M  END
+>  <ID> (3)
+Lig1
+
+$$$$
+Structure1
+csChFnd70/05230312262D
+
+  6  5  0  0  0  0  0  0  0  0999 V2000
+    1.2124    0.0000    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
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+X
+M  END
+>  <ID> (4)
+Lig2
+
+$$$$

Code/Demos/RDKit/TemplEnum/esters.sdf

@@ -0,0 +1,142 @@
+Structure1
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+
+  5  4  0  0  0  0  0  0  0  0999 V2000
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+  2  4  2  0  0  0  0
+  1  5  1  0  0  0  0
+A    5
+X
+M  END
+>  <ID> (3)
+Lig1
+
+$$$$
+Structure1
+csChFnd70/05230312262D
+
+  6  5  0  0  0  0  0  0  0  0999 V2000
+    1.2124    0.0000    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
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+X
+M  END
+>  <ID> (4)
+Lig2
+
+$$$$
+Structure1
+csChFnd70/05230312262D
+
+  7  6  0  0  0  0  0  0  0  0999 V2000
+    1.2124    1.3977    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
+    2.4249    2.0977    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
+    3.6373    1.3977    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
+    2.4249    3.4977    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
+    0.0000    2.0977    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
+    4.8477    2.0965    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
+    3.6373    0.0000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
+  1  2  1  0  0  0  0
+  2  3  1  0  0  0  0
+  2  4  2  0  0  0  0
+  1  5  1  0  0  0  0
+  3  6  1  0  0  0  0
+  3  7  1  0  0  0  0
+A    5
+X
+M  END
+>  <ID> (5)
+Lig3
+
+$$$$
+Structure1
+csChFnd70/05230312262D
+
+  7  6  0  0  0  0  0  0  0  0999 V2000
+    1.2124    0.0000    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
+    2.4249    0.7000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
+    3.6373    0.0000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
+    2.4249    2.1000    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
+    0.0000    0.7000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
+    4.8477    0.6988    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
+    6.0581    0.0000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
+  1  2  1  0  0  0  0
+  2  3  1  0  0  0  0
+  2  4  2  0  0  0  0
+  1  5  1  0  0  0  0
+  3  6  1  0  0  0  0
+  6  7  1  0  0  0  0
+A    5
+X
+M  END
+>  <ID> (6)
+Lig4
+
+$$$$
+Structure1
+csChFnd70/05230312262D
+
+  8  7  0  0  0  0  0  0  0  0999 V2000
+    1.2124    1.3977    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
+    2.4249    2.0977    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
+    3.6373    1.3977    0.0000 C   0  0  3  0  0  0  0  0  0  0  0  0
+    2.4249    3.4977    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
+    0.0000    2.0977    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
+    4.8477    2.0965    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
+    6.0581    1.3977    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
+    3.6373    0.0000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
+  1  2  1  0  0  0  0
+  2  3  1  0  0  0  0
+  2  4  2  0  0  0  0
+  1  5  1  0  0  0  0
+  3  6  1  0  0  0  0
+  6  7  1  0  0  0  0
+  3  8  1  0  0  0  0
+A    5
+X
+M  END
+>  <ID> (7)
+Lig5
+
+$$$$
+Structure1
+csChFnd70/05230312262D
+
+  8  7  0  0  0  0  0  0  0  0999 V2000
+    1.2124    0.0000    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
+    2.4249    0.7000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
+    3.6373    0.0000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
+    2.4249    2.1000    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
+    0.0000    0.7000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
+    4.8477    0.6988    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
+    6.0581    0.0000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
+    4.8477    2.0965    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
+  1  2  1  0  0  0  0
+  2  3  1  0  0  0  0
+  2  4  2  0  0  0  0
+  1  5  1  0  0  0  0
+  3  6  1  0  0  0  0
+  6  7  1  0  0  0  0
+  6  8  1  0  0  0  0
+A    5
+X
+M  END
+>  <ID> (8)
+Lig6
+
+$$$$

Code/Demos/RDKit/TemplEnum/main.cpp

@@ -0,0 +1,443 @@
+//  $Id: main.cpp 4421 2005-02-09 16:55:05Z glandrum $
+//
+//  Copyright (C) 2003-2004 Rational Discovery LLC
+//   All Rights Reserved
+//
+#include "TemplEnum.h"
+#include <GraphMol/SmilesParse/SmilesParse.h>
+#include <GraphMol/SmilesParse/SmilesWrite.h>
+#include <GraphMol/FileParsers/FileParsers.h>
+
+using namespace RDKit;
+using namespace TemplateEnum;
+
+#include <math.h>
+
+bool feq(double v1,double v2,double tol=1e-4){
+  return fabs(v1-v2)<=tol;
+}
+bool feq(RDGeom::Point3D p1,RDGeom::Point3D p2,double tol=1e-4){
+  return feq(p1.x,p2.x,tol)&&feq(p1.y,p2.y,tol)&&feq(p1.z,p2.z,tol);
+}
+
+void test1(){
+  // single attachment point, small list
+  std::cout << " ----------> Test1 " << std::endl;
+  RWMOL_SPTR_VECT library;
+  std::vector<const char *>fileNames;
+  fileNames.push_back("esters.2.sdf");
+  fileNames.push_back("esters.2.sdf");
+  library = enumFromFiles("template.1.mol",fileNames);
+
+  CHECK_INVARIANT(library.size()==2,"");
+  CHECK_INVARIANT(library[0]->getNumAtoms()==10,"");
+  CHECK_INVARIANT(library[1]->getNumAtoms()==11,"");
+
+  library.clear();
+  std::cout << " <---------- Done " << std::endl;
+}
+
+
+void test2(){
+  // single attachment point, larger list
+  std::cout << " ----------> Test2 " << std::endl;
+  RWMOL_SPTR_VECT library;
+  std::vector<const char *>fileNames;
+  fileNames.push_back("esters.sdf");
+  fileNames.push_back("esters.sdf");
+  library = enumFromFiles("template.1.mol",fileNames);
+
+  CHECK_INVARIANT(library.size()==6,"");
+  CHECK_INVARIANT(library[0]->getNumAtoms()==10,"");
+  CHECK_INVARIANT(library[1]->getNumAtoms()==11,"");
+  CHECK_INVARIANT(library[2]->getNumAtoms()==12,"");
+  CHECK_INVARIANT(library[3]->getNumAtoms()==12,"");
+  CHECK_INVARIANT(library[4]->getNumAtoms()==13,"");
+  CHECK_INVARIANT(library[5]->getNumAtoms()==13,"");
+
+  library.clear();
+  std::cout << " <---------- Done " << std::endl;
+}
+
+void test3(){
+  // two attachment points, small list
+  std::cout << " ----------> Test3 " << std::endl;
+  RWMOL_SPTR_VECT library;
+  std::vector<const char *>fileNames;
+  fileNames.push_back("esters.2.sdf");
+  fileNames.push_back("esters.2.sdf");
+  library = enumFromFiles("template.mol",fileNames);
+
+  CHECK_INVARIANT(library.size()==4,"");
+  CHECK_INVARIANT(library[0]->getNumAtoms()==14,"");
+  CHECK_INVARIANT(library[1]->getNumAtoms()==15,"");
+  CHECK_INVARIANT(library[2]->getNumAtoms()==15,"");
+  CHECK_INVARIANT(library[3]->getNumAtoms()==16,"");
+
+  library.clear();
+  std::cout << " <---------- Done " << std::endl;
+}
+
+void test4(){
+  // test templates that have repeated attachment points
+  std::cout << " ----------> Test4 " << std::endl;
+  RWMOL_SPTR_VECT library;
+  std::vector<const char *>fileNames;
+  fileNames.push_back("esters.2.sdf");
+  fileNames.push_back("esters.2.sdf");
+  library = enumFromFiles("template.2.mol",fileNames);
+
+  CHECK_INVARIANT(library.size()==2,"");
+  library[0]->debugMol(std::cout);
+  std::cout << "smi0: " << MolToSmiles(*library[0],0) << std::endl;
+  std::cout << "smi1: " << MolToSmiles(*library[1],0) << std::endl;
+  CHECK_INVARIANT(library[0]->getNumAtoms()==14,"");
+  CHECK_INVARIANT(library[1]->getNumAtoms()==16,"");
+
+
+  library.clear();
+  std::cout << " <---------- Done " << std::endl;
+}
+
+void test5(){
+  // test working from SMILES
+  std::cout << " ----------> Test5 " << std::endl;
+  RWMol *m1 = SmilesToMol("[Xa]CC([Xb])CC",0,0);
+  CHECK_INVARIANT(m1,"");
+  markAttachmentPoints(m1,'X');
+  
+  RWMOL_SPTR_VECT sidechains;
+  sidechains.push_back(RWMOL_SPTR(SmilesToMol("[X]OC(=O)",0,0)));
+  sidechains.push_back(RWMOL_SPTR(SmilesToMol("[X]OC(=O)C",0,0)));
+  sidechains.push_back(RWMOL_SPTR(SmilesToMol("[X]OC(=O)CCC",0,0)));
+  prepareSidechains(&sidechains,'X');
+
+  VECT_RWMOL_SPTR_VECT allSideChains;
+  allSideChains.push_back(sidechains);
+  allSideChains.push_back(sidechains);
+
+  RWMOL_SPTR_VECT library;
+  library = enumerateLibrary(m1,allSideChains,false);
+
+  CHECK_INVARIANT(library.size()==9,"");
+  CHECK_INVARIANT(library[0]->getNumAtoms()==10,"");
+  CHECK_INVARIANT(library[1]->getNumAtoms()==11,"");
+  CHECK_INVARIANT(library[2]->getNumAtoms()==13,"");
+  CHECK_INVARIANT(library[3]->getNumAtoms()==11,"");
+  CHECK_INVARIANT(library[4]->getNumAtoms()==12,"");
+  CHECK_INVARIANT(library[5]->getNumAtoms()==14,"");
+  CHECK_INVARIANT(library[6]->getNumAtoms()==13,"");
+  CHECK_INVARIANT(library[7]->getNumAtoms()==14,"");
+  CHECK_INVARIANT(library[8]->getNumAtoms()==16,"");
+
+  library.clear();
+  std::cout << " <---------- Done " << std::endl;
+}
+
+void test6(){
+  // test working from SMILES with no matches
+  std::cout << " ----------> Test6 " << std::endl;
+  RWMol *m1 = SmilesToMol("[Xa]CC([Xb])CC",0,0);
+  CHECK_INVARIANT(m1,"");
+  markAttachmentPoints(m1,'X');
+  
+  RWMOL_SPTR_VECT sidechains;
+  sidechains.push_back(RWMOL_SPTR(SmilesToMol("OC(=O)",0,0)));
+  sidechains.push_back(RWMOL_SPTR(SmilesToMol("OC(=O)C",0,0)));
+  sidechains.push_back(RWMOL_SPTR(SmilesToMol("OC(=O)CCC",0,0)));
+  prepareSidechains(&sidechains,'X');
+
+  VECT_RWMOL_SPTR_VECT allSideChains;
+  allSideChains.push_back(sidechains);
+  allSideChains.push_back(sidechains);
+
+  RWMOL_SPTR_VECT library;
+  library = enumerateLibrary(m1,allSideChains,false);
+
+  CHECK_INVARIANT(library.size()==1,"");
+  CHECK_INVARIANT(library[0]->getNumAtoms()==6,"");
+
+  library.clear();
+  std::cout << " <---------- Done " << std::endl;
+}
+
+void test7(){
+  // test transforms
+  std::cout << " ----------> Test7 " << std::endl;
+  RWMOL_SPTR_VECT library;
+  RWMOL_SPTR mol;
+  Atom *at1,*at2;
+  int i;
+  std::vector<const char *>fileNames;
+  fileNames.push_back("Ts.1.sdf");
+  library = enumFromFiles("box.1.mol",fileNames);
+  CHECK_INVARIANT(library.size()==1,"");
+  CHECK_INVARIANT(library[0]->getNumAtoms()==8,"");
+  mol = library[0];
+  at1=mol->getAtomWithIdx(0);
+  at2=mol->getAtomWithIdx(4);
+  CHECK_INVARIANT(feq(at1->getPos().x,at2->getPos().x),"");
+  CHECK_INVARIANT(at1->getPos().y-at2->getPos().y==-1.0,"");
+  library.clear();
+
+  // try another orientation of the sidechain molecule:
+  fileNames.clear();
+  fileNames.push_back("Ts.4.sdf");
+  library = enumFromFiles("box.1.mol",fileNames);
+  CHECK_INVARIANT(library.size()==1,"");
+  CHECK_INVARIANT(library[0]->getNumAtoms()==8,"");
+  mol = library[0];
+  std::cout << MolToMolBlock(mol.get());
+  std::cout << std::endl;
+
+  at1=mol->getAtomWithIdx(0);
+  at2=mol->getAtomWithIdx(7);
+  TEST_ASSERT(feq(mol->getAtomWithIdx(7)->getPos(),RDGeom::Point3D(-.5,2.5,0.0)));
+  library.clear();
+
+  
+  // now use an SD file that has the same molecule in different
+  // orientations as sidechains:
+  fileNames.clear();
+  fileNames.push_back("Ts.sdf");
+  library = enumFromFiles("box.1.mol",fileNames);
+  CHECK_INVARIANT(library.size()==4,"");
+
+  CHECK_INVARIANT(library[0]->getNumAtoms()==8,"");
+  CHECK_INVARIANT(library[1]->getNumAtoms()==8,"");
+  CHECK_INVARIANT(library[2]->getNumAtoms()==8,"");
+  CHECK_INVARIANT(library[3]->getNumAtoms()==8,"");
+
+  for(i=0;i<library.size();i++){
+    std::cout << "------ Mol: " << i << "------" << std::endl;
+    mol = library[i];
+    std::cout << MolToMolBlock(mol.get());
+    std::cout << std::endl;
+  }
+  for(i=0;i<library[0]->getNumAtoms();i++){
+    at1 = library[0]->getAtomWithIdx(i);
+    at2 = library[1]->getAtomWithIdx(i);
+    CHECK_INVARIANT(feq(at1->getPos().x,at2->getPos().x),"");
+    CHECK_INVARIANT(feq(at1->getPos().y,at2->getPos().y),"");
+    CHECK_INVARIANT(feq(at1->getPos().z,at2->getPos().z),"");
+
+    at2 = library[2]->getAtomWithIdx(i);
+    CHECK_INVARIANT(feq(at1->getPos().x,at2->getPos().x),"");
+    CHECK_INVARIANT(feq(at1->getPos().y,at2->getPos().y),"");
+    CHECK_INVARIANT(feq(at1->getPos().z,at2->getPos().z),"");
+
+    at2 = library[3]->getAtomWithIdx(i);
+    CHECK_INVARIANT(feq(at1->getPos(),at2->getPos()),"");
+  }
+  library.clear();
+
+  // move the attachment point on the template.  This should
+  // make no difference.
+  library = enumFromFiles("box.1a.mol",fileNames);
+  CHECK_INVARIANT(library.size()==4,"");
+
+  CHECK_INVARIANT(library[0]->getNumAtoms()==8,"");
+  CHECK_INVARIANT(library[1]->getNumAtoms()==8,"");
+  CHECK_INVARIANT(library[2]->getNumAtoms()==8,"");
+  CHECK_INVARIANT(library[3]->getNumAtoms()==8,"");
+
+  for(i=0;i<library[0]->getNumAtoms();i++){
+    at1 = library[0]->getAtomWithIdx(i);
+
+    at2 = library[1]->getAtomWithIdx(i);
+    CHECK_INVARIANT(feq(at1->getPos().x,at2->getPos().x),"");
+    CHECK_INVARIANT(feq(at1->getPos().y,at2->getPos().y),"");
+    CHECK_INVARIANT(feq(at1->getPos().z,at2->getPos().z),"");
+
+    at2 = library[2]->getAtomWithIdx(i);
+    CHECK_INVARIANT(feq(at1->getPos().x,at2->getPos().x),"");
+    CHECK_INVARIANT(feq(at1->getPos().y,at2->getPos().y),"");
+    CHECK_INVARIANT(feq(at1->getPos().z,at2->getPos().z),"");
+
+    at2 = library[3]->getAtomWithIdx(i);
+    //std::cout << i << "\t" << at1->getPos() << std::endl;
+    //std::cout << "\t" << at2->getPos() << std::endl;
+    CHECK_INVARIANT(feq(at1->getPos().x,at2->getPos().x),"");
+    CHECK_INVARIANT(feq(at1->getPos().y,at2->getPos().y),"");
+    CHECK_INVARIANT(feq(at1->getPos().z,at2->getPos().z),"");
+  }
+  library.clear();
+
+  // move the attachment point on the template.  This should
+  // make no difference.
+  library = enumFromFiles("box.mol",fileNames);
+  CHECK_INVARIANT(library.size()==4,"");
+
+  CHECK_INVARIANT(library[0]->getNumAtoms()==20,"");
+  CHECK_INVARIANT(library[1]->getNumAtoms()==20,"");
+  CHECK_INVARIANT(library[2]->getNumAtoms()==20,"");
+  CHECK_INVARIANT(library[3]->getNumAtoms()==20,"");
+
+  for(i=0;i<library[0]->getNumAtoms();i++){
+    at1 = library[0]->getAtomWithIdx(i);
+
+    at2 = library[1]->getAtomWithIdx(i);
+    CHECK_INVARIANT(feq(at1->getPos().x,at2->getPos().x),"");
+    CHECK_INVARIANT(feq(at1->getPos().y,at2->getPos().y),"");
+    CHECK_INVARIANT(feq(at1->getPos().z,at2->getPos().z),"");
+
+    at2 = library[2]->getAtomWithIdx(i);
+    CHECK_INVARIANT(feq(at1->getPos().x,at2->getPos().x),"");
+    CHECK_INVARIANT(feq(at1->getPos().y,at2->getPos().y),"");
+    CHECK_INVARIANT(feq(at1->getPos().z,at2->getPos().z),"");
+
+    at2 = library[3]->getAtomWithIdx(i);
+    CHECK_INVARIANT(feq(at1->getPos().x,at2->getPos().x),"");
+    CHECK_INVARIANT(feq(at1->getPos().y,at2->getPos().y),"");
+    CHECK_INVARIANT(feq(at1->getPos().z,at2->getPos().z),"");
+  }
+  library.clear();
+
+
+  
+  std::cout << " <---------- Done " << std::endl;
+}
+
+
+void testCoords(){
+  std::cout << " ----------> Test Coords " << std::endl;
+  RWMol *m1 = SmilesToMol("[Xa]C",0,0);
+  CHECK_INVARIANT(m1,"");
+  m1->getAtomWithIdx(1)->setPos(0,0,0);
+  m1->getAtomWithIdx(0)->setPos(0.0,1.5,0.0);
+
+  RWMol *m2 = SmilesToMol("[X]C(C)(C)C",0,0);
+  TEST_ASSERT(m2);
+  m2->getAtomWithIdx(0)->setPos(3.0,1,1);
+  m2->getAtomWithIdx(1)->setPos(1.5,1,1);
+  m2->getAtomWithIdx(2)->setPos(0.0,1,1);
+  m2->getAtomWithIdx(3)->setPos(1.5,2.5,1);
+  m2->getAtomWithIdx(4)->setPos(1.5,1,2.5);
+
+  orientSidechain(m1,m2,0,0);
+  std::cout << "Atoms:" << std::endl;
+  for(int i=0;i<m2->getNumAtoms();i++){
+    std::cout << i << " " << m2->getAtomWithIdx(i)->getPos() << std::endl;
+  }
+
+  TEST_ASSERT(feq(m1->getAtomWithIdx(0)->getPos(),
+		  m2->getAtomWithIdx(1)->getPos()));
+
+  TEST_ASSERT(feq(m2->getAtomWithIdx(0)->getPos(),
+		  RDGeom::Point3D(0,0,0)));
+  TEST_ASSERT(feq(m2->getAtomWithIdx(1)->getPos(),
+		  RDGeom::Point3D(0,1.5,0)));
+  TEST_ASSERT(feq(m2->getAtomWithIdx(2)->getPos(),
+		  RDGeom::Point3D(0,3.0,0)));
+  TEST_ASSERT(feq(m2->getAtomWithIdx(3)->getPos(),
+		  RDGeom::Point3D(1.5,1.5,0)));
+  TEST_ASSERT(feq(m2->getAtomWithIdx(4)->getPos(),
+		  RDGeom::Point3D(0,1.5,1.5)));
+  
+  // ---------------------------------------------------
+  std::cout << "-*-*-*-*-*-*-*-*-*-*-*-*-" << std::endl;
+  m1->getAtomWithIdx(1)->setPos(0,0,0);
+  m1->getAtomWithIdx(0)->setPos(0.0,-1.5,0.0);
+  m2->getAtomWithIdx(0)->setPos(3.0,1,1);
+  m2->getAtomWithIdx(1)->setPos(1.5,1,1);
+  m2->getAtomWithIdx(2)->setPos(0.0,1,1);
+  m2->getAtomWithIdx(3)->setPos(1.5,2.5,1);
+  m2->getAtomWithIdx(4)->setPos(1.5,1,2.5);
+
+  orientSidechain(m1,m2,0,0);
+  std::cout << "Atoms:" << std::endl;
+  for(int i=0;i<m2->getNumAtoms();i++){
+    std::cout << i << " " << m2->getAtomWithIdx(i)->getPos() << std::endl;
+  }
+  TEST_ASSERT(feq(m1->getAtomWithIdx(0)->getPos(),
+		  m2->getAtomWithIdx(1)->getPos()));
+
+  TEST_ASSERT(feq(m2->getAtomWithIdx(0)->getPos(),
+		  RDGeom::Point3D(0,0,0)));
+  TEST_ASSERT(feq(m2->getAtomWithIdx(1)->getPos(),
+		  RDGeom::Point3D(0,-1.5,0)));
+  TEST_ASSERT(feq(m2->getAtomWithIdx(2)->getPos(),
+		  RDGeom::Point3D(0,-3.0,0)));
+  TEST_ASSERT(feq(m2->getAtomWithIdx(3)->getPos(),
+		  RDGeom::Point3D(-1.5,-1.5,0)));
+  TEST_ASSERT(feq(m2->getAtomWithIdx(4)->getPos(),
+		  RDGeom::Point3D(0,-1.5,1.5)));
+
+  // ---------------------------------------------------
+  std::cout << "-*-*-*-*-*-*-*-*-*-*-*-*-" << std::endl;
+  m1->getAtomWithIdx(1)->setPos(1,0,0);
+  m1->getAtomWithIdx(0)->setPos(1.0,-1.5,0);
+  m2->getAtomWithIdx(0)->setPos(3.0,1,1);
+  m2->getAtomWithIdx(1)->setPos(1.5,1,1);
+  m2->getAtomWithIdx(2)->setPos(0.0,1,1);
+  m2->getAtomWithIdx(3)->setPos(1.5,2.5,1);
+  m2->getAtomWithIdx(4)->setPos(1.5,1,2.5);
+
+  orientSidechain(m1,m2,0,0);
+  std::cout << "Atoms:" << std::endl;
+  for(int i=0;i<m2->getNumAtoms();i++){
+    std::cout << i << " " << m2->getAtomWithIdx(i)->getPos() << std::endl;
+  }
+  TEST_ASSERT(feq(m1->getAtomWithIdx(0)->getPos(),
+		  m2->getAtomWithIdx(1)->getPos()));
+
+  TEST_ASSERT(feq(m2->getAtomWithIdx(0)->getPos(),
+		  RDGeom::Point3D(1,0,0)));
+  TEST_ASSERT(feq(m2->getAtomWithIdx(1)->getPos(),
+		  RDGeom::Point3D(1,-1.5,0)));
+  TEST_ASSERT(feq(m2->getAtomWithIdx(2)->getPos(),
+		  RDGeom::Point3D(1,-3.0,0)));
+  TEST_ASSERT(feq(m2->getAtomWithIdx(3)->getPos(),
+		  RDGeom::Point3D(-0.5,-1.5,0)));
+  TEST_ASSERT(feq(m2->getAtomWithIdx(4)->getPos(),
+		  RDGeom::Point3D(1,-1.5,1.5)));
+
+  // ---------------------------------------------------
+  std::cout << "-*-*-*-*-*-*-*-*-*-*-*-*-" << std::endl;
+  m1->getAtomWithIdx(1)->setPos(3.0,0,0);
+  m1->getAtomWithIdx(0)->setPos(1.5,0.0,0.0);
+  m2->getAtomWithIdx(0)->setPos(3.0,1,1);
+  m2->getAtomWithIdx(1)->setPos(1.5,1,1);
+  m2->getAtomWithIdx(2)->setPos(0.0,1,1);
+  m2->getAtomWithIdx(3)->setPos(1.5,2.5,1);
+  m2->getAtomWithIdx(4)->setPos(1.5,1,2.5);
+
+  orientSidechain(m1,m2,0,0);
+  std::cout << "Atoms:" << std::endl;
+  for(int i=0;i<m2->getNumAtoms();i++){
+    std::cout << i << " " << m2->getAtomWithIdx(i)->getPos() << std::endl;
+  }
+  TEST_ASSERT(feq(m1->getAtomWithIdx(0)->getPos(),
+		  m2->getAtomWithIdx(1)->getPos()));
+
+  TEST_ASSERT(feq(m2->getAtomWithIdx(0)->getPos(),
+		  RDGeom::Point3D(3,0,0)));
+  TEST_ASSERT(feq(m2->getAtomWithIdx(1)->getPos(),
+		  RDGeom::Point3D(1.5,0,0)));
+  TEST_ASSERT(feq(m2->getAtomWithIdx(2)->getPos(),
+		  RDGeom::Point3D(0,0,0)));
+  TEST_ASSERT(feq(m2->getAtomWithIdx(3)->getPos(),
+		  RDGeom::Point3D(1.5,1.5,0)));
+  TEST_ASSERT(feq(m2->getAtomWithIdx(4)->getPos(),
+		  RDGeom::Point3D(1.5,0,1.5)));
+
+
+  delete m1;
+  delete m2;
+  
+  std::cout << " <---------- Done " << std::endl;
+}
+
+
+int main(){
+#if 1
+  test1();
+  test2();
+  test3();
+  //test4();
+  test5();
+  test6();
+#endif
+  test7();
+  testCoords();
+}

Code/Demos/RDKit/TemplEnum/simple.cpp

@@ -0,0 +1,42 @@
+//  $Id: simple.cpp 4421 2005-02-09 16:55:05Z glandrum $
+//
+//  Copyright (C) 2004 Rational Discovery LLC
+//   All Rights Reserved
+//
+#include "TemplEnum.h"
+#include <GraphMol/FileParsers/FileParsers.h>
+
+using namespace RDKit;
+using namespace TemplateEnum;
+
+#include <math.h>
+
+bool feq(double v1,double v2,double tol=1e-4){
+  return fabs(v1-v2)<=tol;
+}
+bool feq(RDGeom::Point3D p1,RDGeom::Point3D p2,double tol=1e-4){
+  return feq(p1.x,p2.x,tol)&&feq(p1.y,p2.y,tol)&&feq(p1.z,p2.z,tol);
+}
+
+
+int main(int argc,const char *argv[]){
+  if(argc<3){
+    std::cerr << " Usage: simple.exe <template.mol> [attach1.sdf, attach2.sdf, ...]" << std::endl;
+    exit(-1);
+  }
+  std::vector<const char *>fileNames;
+  for(int i=2;i<argc;i++){
+    fileNames.push_back( argv[i] );
+  }
+  RWMOL_SPTR_VECT library=enumFromFiles(argv[1],fileNames);
+
+  std::cerr << "Created: " << library.size() << " compounds." << std::endl;
+  for(int i=0;i<library.size();i++){
+    RWMOL_SPTR mol = library[i];
+    std::cout << MolToMolBlock(mol.get(),false);
+    std::cout << "$$$$" << std::endl;
+  }
+  
+  exit(0);
+
+}

Code/Demos/RDKit/TemplEnum/simpleEnum.vcproj

@@ -0,0 +1,160 @@
+<?xml version="1.0" encoding="Windows-1252"?>
+<VisualStudioProject
+	ProjectType="Visual C++"
+	Version="7.10"
+	Name="demo - simpleEnum"
+	ProjectGUID="{F0680DF9-9AC4-4B9A-A95A-BAC39A15FC4F}"
+	SccProjectName=""
+	SccLocalPath="">
+	<Platforms>
+		<Platform
+			Name="Win32"/>
+	</Platforms>
+	<Configurations>
+		<Configuration
+			Name="Release|Win32"
+			OutputDirectory=".\testExecs\"
+			IntermediateDirectory=".\Release"
+			ConfigurationType="1"
+			UseOfMFC="0"
+			ATLMinimizesCRunTimeLibraryUsage="FALSE"
+			CharacterSet="2">
+			<Tool
+				Name="VCCLCompilerTool"
+				Optimization="2"
+				InlineFunctionExpansion="1"
+				AdditionalIncludeDirectories="$(RDBASE)/External/boost/include/$(BOOSTBASE),.,$(RDBASE)/code,$(RDBASE)/code/graphmol"
+				PreprocessorDefinitions="WIN32;NDEBUG;_CONSOLE"
+				StringPooling="TRUE"
+				RuntimeLibrary="2"
+				EnableFunctionLevelLinking="TRUE"
+				PrecompiledHeaderFile=".\Release/simpleEnum.pch"
+				AssemblerListingLocation=".\Release/"
+				ObjectFile=".\Release/"
+				ProgramDataBaseFileName=".\Release/"
+				WarningLevel="3"
+				SuppressStartupBanner="TRUE"
+				CompileAs="0"/>
+			<Tool
+				Name="VCCustomBuildTool"/>
+			<Tool
+				Name="VCLinkerTool"
+				OutputFile="./testExecs/simpleEnum.exe"
+				LinkIncremental="1"
+				SuppressStartupBanner="TRUE"
+				ProgramDatabaseFile=".\Release/simpleEnum.pdb"
+				SubSystem="1"
+				TargetMachine="1"/>
+			<Tool
+				Name="VCMIDLTool"
+				TypeLibraryName=".\Release/simpleEnum.tlb"
+				HeaderFileName=""/>
+			<Tool
+				Name="VCPostBuildEventTool"/>
+			<Tool
+				Name="VCPreBuildEventTool"/>
+			<Tool
+				Name="VCPreLinkEventTool"/>
+			<Tool
+				Name="VCResourceCompilerTool"
+				PreprocessorDefinitions="NDEBUG"
+				Culture="1033"/>
+			<Tool
+				Name="VCWebServiceProxyGeneratorTool"/>
+			<Tool
+				Name="VCXMLDataGeneratorTool"/>
+			<Tool
+				Name="VCWebDeploymentTool"/>
+			<Tool
+				Name="VCManagedWrapperGeneratorTool"/>
+			<Tool
+				Name="VCAuxiliaryManagedWrapperGeneratorTool"/>
+		</Configuration>
+		<Configuration
+			Name="Debug|Win32"
+			OutputDirectory=".\simpleEnum___Win32_Debug"
+			IntermediateDirectory=".\simpleEnum___Win32_Debug"
+			ConfigurationType="1"
+			UseOfMFC="0"
+			ATLMinimizesCRunTimeLibraryUsage="FALSE"
+			CharacterSet="2">
+			<Tool
+				Name="VCCLCompilerTool"
+				Optimization="0"
+				AdditionalIncludeDirectories="$(RDBASE)/External/boost/include/$(BOOSTBASE),.,$(RDBASE)/code,$(RDBASE)/code/graphmol"
+				PreprocessorDefinitions="WIN32;_DEBUG;_CONSOLE"
+				BasicRuntimeChecks="3"
+				RuntimeLibrary="3"
+				PrecompiledHeaderFile=".\simpleEnum___Win32_Debug/simpleEnum.pch"
+				AssemblerListingLocation=".\simpleEnum___Win32_Debug/"
+				ObjectFile=".\simpleEnum___Win32_Debug/"
+				ProgramDataBaseFileName=".\simpleEnum___Win32_Debug/"
+				WarningLevel="3"
+				SuppressStartupBanner="TRUE"
+				DebugInformationFormat="4"
+				CompileAs="0"/>
+			<Tool
+				Name="VCCustomBuildTool"/>
+			<Tool
+				Name="VCLinkerTool"
+				OutputFile="./testExecs/simpleEnum.exe"
+				LinkIncremental="1"
+				SuppressStartupBanner="TRUE"
+				GenerateDebugInformation="TRUE"
+				ProgramDatabaseFile=".\simpleEnum___Win32_Debug/simpleEnum.pdb"
+				SubSystem="1"
+				TargetMachine="1"/>
+			<Tool
+				Name="VCMIDLTool"
+				TypeLibraryName=".\simpleEnum___Win32_Debug/simpleEnum.tlb"
+				HeaderFileName=""/>
+			<Tool
+				Name="VCPostBuildEventTool"/>
+			<Tool
+				Name="VCPreBuildEventTool"/>
+			<Tool
+				Name="VCPreLinkEventTool"/>
+			<Tool
+				Name="VCResourceCompilerTool"
+				PreprocessorDefinitions="_DEBUG"
+				Culture="1033"/>
+			<Tool
+				Name="VCWebServiceProxyGeneratorTool"/>
+			<Tool
+				Name="VCXMLDataGeneratorTool"/>
+			<Tool
+				Name="VCWebDeploymentTool"/>
+			<Tool
+				Name="VCManagedWrapperGeneratorTool"/>
+			<Tool
+				Name="VCAuxiliaryManagedWrapperGeneratorTool"/>
+		</Configuration>
+	</Configurations>
+	<References>
+	</References>
+	<Files>
+		<Filter
+			Name="Source Files"
+			Filter="cpp;c;cxx;rc;def;r;odl;idl;hpj;bat">
+			<File
+				RelativePath=".\simple.cpp">
+			</File>
+			<File
+				RelativePath=".\TemplEnumTools.cpp">
+			</File>
+		</Filter>
+		<Filter
+			Name="Header Files"
+			Filter="h;hpp;hxx;hm;inl">
+			<File
+				RelativePath=".\TemplEnum.h">
+			</File>
+		</Filter>
+		<Filter
+			Name="Resource Files"
+			Filter="ico;cur;bmp;dlg;rc2;rct;bin;rgs;gif;jpg;jpeg;jpe">
+		</Filter>
+	</Files>
+	<Globals>
+	</Globals>
+</VisualStudioProject>

Code/Demos/RDKit/TemplEnum/template.1.mol

@@ -0,0 +1,21 @@
+template.mol
+  ChemDraw05230310522D
+
+  7  7  0  0  0  0  0  0  0  0999 V2000
+   -0.7145    0.4125    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
+   -0.7145   -0.4125    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
+    0.0000   -0.8250    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
+    0.7145   -0.4125    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
+    0.7145    0.4125    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
+    0.0000    0.8250    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
+   -1.4289    0.8250    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
+  1  2  2  0      
+  2  3  1  0      
+  3  4  2  0      
+  4  5  1  0      
+  5  6  2  0      
+  6  1  1  0      
+  1  7  1  0      
+A    7
+Xa
+M  END

Code/Demos/RDKit/TemplEnum/template.2.mol

@@ -0,0 +1,25 @@
+template.mol
+  ChemDraw05230310522D
+
+  8  8  0  0  0  0  0  0  0  0999 V2000
+   -0.7145    0.4125    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
+   -0.7145   -0.4125    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
+    0.0000   -0.8250    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
+    0.7145   -0.4125    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
+    0.7145    0.4125    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
+    0.0000    0.8250    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
+   -1.4289    0.8250    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
+    1.4289    0.8250    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
+  1  2  2  0      
+  2  3  1  0      
+  3  4  2  0      
+  4  5  1  0      
+  5  6  2  0      
+  6  1  1  0      
+  1  7  1  0      
+  5  8  1  0      
+A    7
+Xa
+A    8
+Xa
+M  END

Code/Demos/RDKit/TemplEnum/template.mol

@@ -0,0 +1,25 @@
+template.mol
+  ChemDraw05230310522D
+
+  8  8  0  0  0  0  0  0  0  0999 V2000
+   -0.7145    0.4125    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
+   -0.7145   -0.4125    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
+    0.0000   -0.8250    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
+    0.7145   -0.4125    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
+    0.7145    0.4125    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
+    0.0000    0.8250    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
+   -1.4289    0.8250    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
+    1.4289    0.8250    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
+  1  2  2  0      
+  2  3  1  0      
+  3  4  2  0      
+  4  5  1  0      
+  5  6  2  0      
+  6  1  1  0      
+  1  7  1  0      
+  5  8  1  0      
+A    7
+Xa
+A    8
+Xb
+M  END

Code/Demos/RDKit/TemplEnum/testTemplateEnum.vcproj

@@ -0,0 +1,164 @@
+<?xml version="1.0" encoding="Windows-1252"?>
+<VisualStudioProject
+	ProjectType="Visual C++"
+	Version="7.10"
+	Name="testTemplateEnum"
+	ProjectGUID="{C89F425E-5244-4D8D-AEDA-C90537B3D0A9}"
+	SccProjectName=""
+	SccLocalPath="">
+	<Platforms>
+		<Platform
+			Name="Win32"/>
+	</Platforms>
+	<Configurations>
+		<Configuration
+			Name="Release|Win32"
+			OutputDirectory=".\testExecs\"
+			IntermediateDirectory=".\Release"
+			ConfigurationType="1"
+			UseOfMFC="0"
+			ATLMinimizesCRunTimeLibraryUsage="FALSE"
+			CharacterSet="2">
+			<Tool
+				Name="VCCLCompilerTool"
+				Optimization="2"
+				InlineFunctionExpansion="1"
+				AdditionalIncludeDirectories="$(RDBASE)/External/boost/include/$(BOOSTBASE),.,$(RDBASE)/code,$(RDBASE)/code/graphmol"
+				PreprocessorDefinitions="WIN32;NDEBUG;_CONSOLE"
+				StringPooling="TRUE"
+				RuntimeLibrary="2"
+				EnableFunctionLevelLinking="TRUE"
+				PrecompiledHeaderFile=".\Release/testTemplateEnum.pch"
+				AssemblerListingLocation=".\Release/"
+				ObjectFile=".\Release/"
+				ProgramDataBaseFileName=".\Release/"
+				WarningLevel="3"
+				SuppressStartupBanner="TRUE"
+				CompileAs="0"/>
+			<Tool
+				Name="VCCustomBuildTool"/>
+			<Tool
+				Name="VCLinkerTool"
+				AdditionalDependencies="boost_log-vc71-mt-$(BOOSTVERSION).lib "
+				OutputFile="./testExecs/testTemplateEnum.exe"
+				LinkIncremental="1"
+				SuppressStartupBanner="TRUE"
+				AdditionalLibraryDirectories="$(RDBASE)\External\boost\lib"
+				ProgramDatabaseFile=".\Release/testTemplateEnum.pdb"
+				SubSystem="1"
+				TargetMachine="1"/>
+			<Tool
+				Name="VCMIDLTool"
+				TypeLibraryName=".\Release/testTemplateEnum.tlb"
+				HeaderFileName=""/>
+			<Tool
+				Name="VCPostBuildEventTool"/>
+			<Tool
+				Name="VCPreBuildEventTool"/>
+			<Tool
+				Name="VCPreLinkEventTool"/>
+			<Tool
+				Name="VCResourceCompilerTool"
+				PreprocessorDefinitions="NDEBUG"
+				Culture="1033"/>
+			<Tool
+				Name="VCWebServiceProxyGeneratorTool"/>
+			<Tool
+				Name="VCXMLDataGeneratorTool"/>
+			<Tool
+				Name="VCWebDeploymentTool"/>
+			<Tool
+				Name="VCManagedWrapperGeneratorTool"/>
+			<Tool
+				Name="VCAuxiliaryManagedWrapperGeneratorTool"/>
+		</Configuration>
+		<Configuration
+			Name="Debug|Win32"
+			OutputDirectory=".\testTemplateEnum___Win32_Debug"
+			IntermediateDirectory=".\testTemplateEnum___Win32_Debug"
+			ConfigurationType="1"
+			UseOfMFC="0"
+			ATLMinimizesCRunTimeLibraryUsage="FALSE"
+			CharacterSet="2">
+			<Tool
+				Name="VCCLCompilerTool"
+				Optimization="0"
+				AdditionalIncludeDirectories="$(RDBASE)/External/boost/include/$(BOOSTBASE),.,$(RDBASE)/code,$(RDBASE)/code/graphmol"
+				PreprocessorDefinitions="WIN32;_DEBUG;_CONSOLE"
+				BasicRuntimeChecks="3"
+				RuntimeLibrary="3"
+				PrecompiledHeaderFile=".\testTemplateEnum___Win32_Debug/testTemplateEnum.pch"
+				AssemblerListingLocation=".\testTemplateEnum___Win32_Debug/"
+				ObjectFile=".\testTemplateEnum___Win32_Debug/"
+				ProgramDataBaseFileName=".\testTemplateEnum___Win32_Debug/"
+				WarningLevel="3"
+				SuppressStartupBanner="TRUE"
+				DebugInformationFormat="4"
+				CompileAs="0"/>
+			<Tool
+				Name="VCCustomBuildTool"/>
+			<Tool
+				Name="VCLinkerTool"
+				AdditionalDependencies="boost_log-vc71-mt-gd-$(BOOSTVERSION).lib "
+				OutputFile="./testExecs/testTemplateEnum.exe"
+				LinkIncremental="1"
+				SuppressStartupBanner="TRUE"
+				AdditionalLibraryDirectories="$(RDBASE)\External\boost\lib"
+				GenerateDebugInformation="TRUE"
+				ProgramDatabaseFile=".\testTemplateEnum___Win32_Debug/testTemplateEnum.pdb"
+				SubSystem="1"
+				TargetMachine="1"/>
+			<Tool
+				Name="VCMIDLTool"
+				TypeLibraryName=".\testTemplateEnum___Win32_Debug/testTemplateEnum.tlb"
+				HeaderFileName=""/>
+			<Tool
+				Name="VCPostBuildEventTool"/>
+			<Tool
+				Name="VCPreBuildEventTool"/>
+			<Tool
+				Name="VCPreLinkEventTool"/>
+			<Tool
+				Name="VCResourceCompilerTool"
+				PreprocessorDefinitions="_DEBUG"
+				Culture="1033"/>
+			<Tool
+				Name="VCWebServiceProxyGeneratorTool"/>
+			<Tool
+				Name="VCXMLDataGeneratorTool"/>
+			<Tool
+				Name="VCWebDeploymentTool"/>
+			<Tool
+				Name="VCManagedWrapperGeneratorTool"/>
+			<Tool
+				Name="VCAuxiliaryManagedWrapperGeneratorTool"/>
+		</Configuration>
+	</Configurations>
+	<References>
+	</References>
+	<Files>
+		<Filter
+			Name="Source Files"
+			Filter="cpp;c;cxx;rc;def;r;odl;idl;hpj;bat">
+			<File
+				RelativePath=".\main.cpp">
+			</File>
+			<File
+				RelativePath=".\TemplEnumTools.cpp">
+			</File>
+		</Filter>
+		<Filter
+			Name="Header Files"
+			Filter="h;hpp;hxx;hm;inl">
+			<File
+				RelativePath=".\TemplEnum.h">
+			</File>
+		</Filter>
+		<Filter
+			Name="Resource Files"
+			Filter="ico;cur;bmp;dlg;rc2;rct;bin;rgs;gif;jpg;jpeg;jpe">
+		</Filter>
+	</Files>
+	<Globals>
+	</Globals>
+</VisualStudioProject>