Open Babel: fingerprint.h Source File

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# fingerprint.h

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    00001 /**********************************************************************
    00002 fingerprint.h - Base class for fingerprints and fast searching
    00003
    00004 Copyright (C) 2005 by Chris Morley
    00005
    00006 This file is part of the Open Babel project.
    00007 For more information, see <http://openbabel.org/>
    00008
    00009 This program is free software; you can redistribute it and/or modify
    00010 it under the terms of the GNU General Public License as published by
    00011 the Free Software Foundation version 2 of the License.
    00012
    00013 This program is distributed in the hope that it will be useful,
    00014 but WITHOUT ANY WARRANTY; without even the implied warranty of
    00015 MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
    00016 GNU General Public License for more details.
    00017 ***********************************************************************/
    00018
    00019 #ifndef OB_FINGERPRINT_H
    00020 #define OB_FINGERPRINT_H
    00021
    00022 #include <list>
    00023 #include <map>
    00024 #include <set>
    00025 #include <vector>
    00026 #include <string>
    00027
    00028 #include <openbabel/plugin.h>
    00029
    00030 #ifndef OBFPRT
    00031 #define OBFPRT
    00032 #endif
    00033
    00034 namespace OpenBabel
    00035 {
    00036   class OBBase; //Forward declaration; used only as pointer.
    00037
    00039 class OBFPRT OBFingerprint : public OBPlugin
    00040 {
    00041 //see end of cpp file for detailed documentation
    00042
    00043 MAKE_PLUGIN(OBFingerprint)
    00044
    00045 const char* TypeID()
    00046         {
    00047                 return "fingerprints";
    00048         }
    00049
    00050         //Rest of OBFingerprints declarations
    00051 public:
    00052
    00053   virtual ~OBFingerprint(){}
    00054
    00056   void SetBit(std::vector<unsigned int>& vec, const unsigned int n);
    00057
    00059   bool GetBit(const std::vector<unsigned int>& vec, const unsigned int n);
    00060
    00062   void Fold(std::vector<unsigned int>& vec, unsigned int nbits);
    00063
    00065   virtual bool GetFingerprint(OBBase* pOb, std::vector<unsigned int>& fp, int nbits=0)=0;
    00066
    00068   enum FptFlag{FPT_UNIQUEBITS=1, FPT_NOINFO=2};
    00069   virtual unsigned int Flags() { return 0;};
    00071   virtual void SetFlags(unsigned int){}
    00072
    00075   virtual std::string DescribeBits(const std::vector<unsigned int> /* fp */,
    00076                                    bool /* bSet */ =true)
    00077   {
    00078     std::string txt("");
    00079     return txt;
    00080   }
    00081
    00083   static double Tanimoto(const std::vector<unsigned int>& vec1, const std::vector<unsigned int>& vec2);
    00084
    00086   static double Tanimoto(const std::vector<unsigned int>& vec1, const unsigned int* p2)
    00087   {
    00089     int andbits=0, orbits=0;
    00090     unsigned int i;
    00091     for (i=0;i<vec1.size();++i)
    00092     {
    00093       int andfp = vec1[i] & p2[i];
    00094       int orfp = vec1[i] | p2[i];
    00095       // Count bits
    00096       /* GCC 3.4 supports a "population count" builtin, which on many targets is
    00097          implemented with a single instruction.  There is a fallback definition
    00098          in libgcc in case a target does not have one, which should be just as
    00099          good as the static function below.  */
    00100 #if __GNUC__ > 3 || (__GNUC__ == 3 && __GNUC_MINOR__ >= 4)
    00101       andbits += __builtin_popcount(andfp);
    00102       orbits += __builtin_popcount(orfp);
    00103 #else
    00104       for(;andfp;andfp=andfp<<1)
    00105         if(andfp<0) ++andbits;
    00106       for(;orfp;orfp=orfp<<1)
    00107         if(orfp<0) ++orbits;
    00108 #endif
    00109     }
    00110       return((double)andbits/(double)orbits);
    00111   };
    00112
    00113   static unsigned int Getbitsperint(){ return bitsperint; }
    00114
    00115 private:
    00117   struct bit_or
    00118   {
    00119     unsigned int operator()(const unsigned int a, const unsigned int b)
    00120     {
    00121       return a | b;
    00122     }
    00123   };
    00124
    00125
    00126 public:
    00129 static OBFingerprint* FindFingerprint(const char* ID){ return FindType(ID);}
    00130
    00131 private:
    00132   static const unsigned int bitsperint;// = 8 * sizeof(unsigned int);
    00133 };
    00134
    00135 //Fast search routines
    00138 struct OBFPRT FptIndexHeader
    00139 {
    00140   unsigned int headerlength;
    00141   unsigned int nEntries;
    00142   unsigned int words;
    00143   char fpid[16];
    00144   char datafilename[256];
    00145 };
    00146
    00149 struct OBFPRT FptIndex
    00150 {
    00151   FptIndexHeader header;
    00152   std::vector<unsigned int> fptdata;
    00153   std::vector<unsigned int> seekdata;
    00154   bool Read(std::istream* pIndexstream);
    00155   bool ReadIndex(std::istream* pIndexstream);
    00156   bool ReadHeader(std::istream* pIndexstream);
    00157
    00159   OBFingerprint* CheckFP();
    00160 };
    00161
    00164 class OBFPRT FastSearch
    00165 {
    00166 //see end of cpp file for detailed documentation
    00167 public:
    00169   std::string ReadIndexFile(std::string IndexFilename);
    00170   std::string ReadIndex(std::istream* pIndexstream);
    00171
    00172   virtual ~FastSearch(){};
    00173
    00175   bool    Find(OBBase* pOb, std::vector<unsigned int>& SeekPositions, unsigned int MaxCandidates);
    00176
    00179   bool    FindMatch(OBBase* pOb, std::vector<unsigned int>& SeekPositions,
    00180                             unsigned int MaxCandidates);
    00181
    00184   bool    FindSimilar(OBBase* pOb, std::multimap<double, unsigned int>& SeekposMap,
    00185     double MinTani, double MaxTani = 1.1 );
    00186
    00189   bool    FindSimilar(OBBase* pOb, std::multimap<double, unsigned int>& SeekposMap,
    00190     int nCandidates=0);
    00191
    00193   OBFingerprint* GetFingerprint() const{ return _pFP;};
    00194
    00196   const FptIndexHeader& GetIndexHeader() const{ return _index.header;};
    00197
    00198 private:
    00199   FptIndex   _index;
    00200   OBFingerprint* _pFP;
    00201 };
    00202
    00205 class OBFPRT FastSearchIndexer
    00206 {
    00207 //see end of cpp file for detailed documentation
    00208 public:
    00210   FastSearchIndexer(std::string& datafilename, std::ostream* os, std::string& fpid,
    00211       int FptBits=0, int nmols=0);
    00212
    00214   FastSearchIndexer(FptIndex* pindex, std::ostream* os, int nmols=0);
    00215
    00216   ~FastSearchIndexer();
    00217
    00219   bool Add(OBBase* pOb, std::streampos seekpos);
    00220
    00221 private:
    00222   std::ostream* _indexstream;
    00223   FptIndex*             _pindex;
    00224   OBFingerprint* _pFP;
    00225   int _nbits;
    00226 };
    00227
    00228 } //namespace OpenBabel
    00229 #endif
    00230

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