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/**********************************************************************
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fingerprint.h - Base class for fingerprints and fast searching
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Copyright (C) 2005 by Chris Morley
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This file is part of the Open Babel project.
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For more information, see <http://openbabel.sourceforge.net/>
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This program is free software; you can redistribute it and/or modify
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it under the terms of the GNU General Public License as published by
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the Free Software Foundation version 2 of the License.
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This program is distributed in the hope that it will be useful,
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but WITHOUT ANY WARRANTY; without even the implied warranty of
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MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
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GNU General Public License for more details.
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***********************************************************************/
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#ifndef OB_FINGERPRINT_H
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#define OB_FINGERPRINT_H
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class OBBase; //Forward declaration; used only as pointer.
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/// \brief The base class for fingerprints
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class OBAPI OBFingerprint
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//see end of cpp file for detailed documentation
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void SetBit(std::vector<unsigned int>& vec, unsigned int n);
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/// Repeatedly ORs the top half with the bottom half until no smaller than nbits
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void Fold(std::vector<unsigned int>& vec, unsigned int nbits);
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/// Returns fingerprint in vector, which may be resized, folded to nbits (if nbits!=0)
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virtual bool GetFingerprint(OBBase* pOb, std::vector<unsigned int>& fp, int nbits=0)=0;
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/// Required short description of the fingerprint type.
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virtual std::string Description()=0;
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enum FptFlag{FPT_UNIQUEBITS=1};
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virtual unsigned int Flags() { return 0;};
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/// Obtain info on available fingerprints
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static bool GetNextFPrt(std::string& id, OBFingerprint*& pFPrt);
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/// Returns a pointer to a fingerprint (the default if ID is empty), or NULL if not available
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static OBFingerprint* FindFingerprint(std::string& ID);
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/// Returns the Tanimoto coefficient between two vectors (vector<unsigned int>& SeekPositions)
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static double Tanimoto(const std::vector<unsigned int>& vec1, const std::vector<unsigned int>& vec2);
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/// Inline version of Tanimoto() taking a pointer for the second vector
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static double Tanimoto(const std::vector<unsigned int>& vec1, const unsigned int* p2)
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///If used for two vectors, vec1 and vec2, call as Tanimoto(vec1, &vec2[0]);
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int andbits=0, orbits=0;
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for (i=0;i<vec1.size();++i)
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int andfp = vec1[i] & p2[i];
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int orfp = vec1[i] | p2[i];
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for(;andfp;andfp=andfp<<1)
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if(andfp<0) ++andbits;
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for(;orfp;orfp=orfp<<1)
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return((double)andbits/(double)orbits);
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static unsigned int Getbitsperint(){ return bitsperint; }
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///Function object to set bits
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unsigned int operator()(const unsigned int a, const unsigned int b)
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typedef std::map<std::string, OBFingerprint*> FPMapType;
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typedef FPMapType::iterator Fptpos;
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///This static function returns a reference to the FPtsMap
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///which, because it is a static local variable is constructed only once.
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///This fiddle is to avoid the "static initialization order fiasco"
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///See Marshall Cline's C++ FAQ Lite document, www.parashift.com/c++-faq-lite/".
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static FPMapType& FPtsMap()
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static FPMapType* fptm = NULL;
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fptm = new FPMapType;
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OBFingerprint(std::string ID, bool IsDefault=false)
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FPtsMap()[ID] = this; //registers the derived fingerprint class
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if(IsDefault || FPtsMap().empty())
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static OBFingerprint* _pDefault;
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static const unsigned int bitsperint;// = 8 * sizeof(unsigned int);
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//*************************************************************
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//Fast search routines
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///Header for fastsearch index file
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struct OBAPI FptIndexHeader
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unsigned int headerlength;///<offset to data: sizeof(FptIndexHeader)
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unsigned int nEntries; ///<number of fingerprints
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unsigned int words; ///<number 32bit words per fingerprint
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char fpid[16]; ///<ID of the fingerprint type
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char datafilename[256]; ///<the data that this is an index to
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/// Structure of fastsearch index files
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struct OBAPI FptIndex
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FptIndexHeader header;
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std::vector<unsigned int> fptdata;
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std::vector<unsigned int> seekdata;
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bool Read(std::istream* pIndexstream);
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///\brief Returns pointer to FP used or NULL and an error message
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OBFingerprint* CheckFP();
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/// \brief Class to search fingerprint index files
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class OBAPI FastSearch
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//see end of cpp file for detailed documentation
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std::string ReadIndex(std::istream* pIndexstream);
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virtual ~FastSearch(){};
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/// \brief Does substructure search and returns vector of the file positions of matches
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bool Find(OBBase* pOb, std::vector<unsigned int>& SeekPositions, unsigned int MaxCandidates);
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/// \brief Returns multimap containing objects whose Tanimoto coefficients with the target
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/// is greater than the value specified.
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bool FindSimilar(OBBase* pOb, std::multimap<double, unsigned int>& SeekposMap,
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/// \brief Returns multimap containing the nCandidates objects with largest Tanimoto
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/// coefficients with the target.
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bool FindSimilar(OBBase* pOb, std::multimap<double, unsigned int>& SeekposMap,
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/// \brief Returns a pointer to the fingerprint type used to constuct the index
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OBFingerprint* GetFingerprint() const{ return _pFP;};
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//**********************************************
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/// \brief Class to prepare fingerprint index files See FastSearch class for details
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class OBAPI FastSearchIndexer
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//see end of cpp file for detailed documentation
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///\brief Constructor with a new index
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FastSearchIndexer(std::string& datafilename, std::ostream* os, std::string& fpid,
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///\brief Constructor using existing index
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FastSearchIndexer(FptIndex* pindex, std::ostream* os);
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~FastSearchIndexer();
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///\brief Called for each object
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bool Add(OBBase* pOb, std::streampos seekpos);
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std::ostream* _indexstream;
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} //namespace OpenBabel
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//! \file fingerprint.h
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//! \brief Declaration of OBFingerprint base class and fastsearch classes
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src/fingerprint.h
