src/openbabel/fingerprint.hpp

/**********************************************************************
fingerprint.h - Base class for fingerprints and fast searching 
 
Copyright (C) 2005 by Chris Morley
 
This file is part of the Open Babel project.
For more information, see <http://openbabel.sourceforge.net/>
 
This program is free software; you can redistribute it and/or modify
it under the terms of the GNU General Public License as published by
the Free Software Foundation version 2 of the License.
 
This program is distributed in the hope that it will be useful,
but WITHOUT ANY WARRANTY; without even the implied warranty of
MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
GNU General Public License for more details.
***********************************************************************/

#ifndef OB_FINGERPRINT_H
#define OB_FINGERPRINT_H

#include <list>
#include <map>
#include <set>
#include <vector>
#include <string>

namespace OpenBabel
{
        class OBBase; //Forward declaration; used only as pointer.

/// \brief The base class for fingerprints
class OBAPI OBFingerprint
{
//see end of cpp file for detailed documentation
public:
        /// Sets the nth bit
        void SetBit(std::vector<unsigned int>& vec, unsigned int n);    

        /// Repeatedly ORs the top half with the bottom half until no smaller than nbits 
        void Fold(std::vector<unsigned int>& vec, unsigned int nbits); 

        /// Returns fingerprint in vector, which may be resized, folded to nbits (if nbits!=0)
        virtual bool GetFingerprint(OBBase* pOb, std::vector<unsigned int>& fp, int nbits=0)=0;

        /// Required short description of the fingerprint type.
        virtual std::string Description()=0;

        /// Optional flags
        enum FptFlag{FPT_UNIQUEBITS=1};
        virtual unsigned int Flags() { return 0;}; 

        /// Obtain info on available fingerprints
        static bool GetNextFPrt(std::string& id, OBFingerprint*& pFPrt);

        /// Returns a pointer to a fingerprint (the default if ID is empty), or NULL if not available
        static OBFingerprint* FindFingerprint(std::string& ID);

        /// Returns the Tanimoto coefficient between two vectors (vector<unsigned int>& SeekPositions)
        static double Tanimoto(const std::vector<unsigned int>& vec1, const std::vector<unsigned int>& vec2);
        
        /// Inline version of Tanimoto() taking a pointer for the second vector
        static double Tanimoto(const std::vector<unsigned int>& vec1, const unsigned int* p2) 
        {
                ///If used for two vectors, vec1 and vec2, call as Tanimoto(vec1, &vec2[0]);
                int andbits=0, orbits=0;
                unsigned int i;
                for (i=0;i<vec1.size();++i)
                {
                        int andfp = vec1[i] & p2[i];
                        int orfp = vec1[i] | p2[i];
                        //Count bits
                        for(;andfp;andfp=andfp<<1)
                                if(andfp<0) ++andbits;
                        for(;orfp;orfp=orfp<<1)
                                if(orfp<0) ++orbits;
                }
                        return((double)andbits/(double)orbits);
        };
        
        static const unsigned int bitsperint;// = 8 * sizeof(unsigned int);

private:
        ///Function object to set bits
        struct bit_or
        {
                unsigned int operator()(const unsigned int a, const unsigned int b)
                {
                        return a | b;   
                }
        };
        
        typedef std::map<std::string, OBFingerprint*> FPMapType;
        typedef FPMapType::iterator Fptpos;

protected:
        ///This static function returns a reference to the FPtsMap
        ///which, because it is a static local variable is constructed only once.
        ///This fiddle is to avoid the "static initialization order fiasco"
        ///See Marshall Cline's C++ FAQ Lite document, www.parashift.com/c++-faq-lite/". 
        static FPMapType& FPtsMap()
        {
                static FPMapType* fptm = new FPMapType;
                return *fptm;
        };

        OBFingerprint(std::string ID, bool IsDefault=false)
        {
                FPtsMap()[ID] = this; //registers the derived fingerprint class
                if(IsDefault || FPtsMap().empty())
                        _pDefault=this;
        };
        
private:
        static OBFingerprint* _pDefault;
};


//*************************************************************
//Fast search routines
///Header for fastsearch index file
struct OBAPI FptIndexHeader
{
        unsigned int headerlength;///<offset to data: sizeof(FptIndexHeader)
        unsigned int nEntries;    ///<number of fingerprints
        unsigned int words;                             ///<number 32bit words per fingerprint
        char fpid[16];            ///<ID of the fingerprint type
        char datafilename[256];   ///<the data that this is an index to
};
/// Structure of fastsearch index files
struct OBAPI FptIndex
{
        FptIndexHeader header;
        std::vector<unsigned int> fptdata;
        std::vector<unsigned int> seekdata;
};

/// \brief Class to search fingerprint index files
class OBAPI FastSearch
{
//see end of cpp file for detailed documentation
public:
  std::string ReadIndex(std::istream* pIndexstream);
        virtual ~FastSearch(){};

        /// \brief Does substructure search and returns vector of the file positions of matches 
        bool    Find(OBBase* pOb, std::vector<unsigned int>& SeekPositions, unsigned int MaxCandidates);

        /// \brief Returns multimap containing objects whose Tanimoto coefficients with the target
        ///     is greater than the value specified.
        bool    FindSimilar(OBBase* pOb, std::multimap<double, unsigned int>& SeekposMap,
                double MinTani);

        /// \brief Returns multimap containing the nCandidates objects with largest Tanimoto
        ///  coefficients with the target.
        bool    FindSimilar(OBBase* pOb, std::multimap<double, unsigned int>& SeekposMap,
                int nCandidates=0);

        /// \brief Returns a pointer to the fingerprint type used to constuct the index
        OBFingerprint* GetFingerprint() const{ return _pFP;};

private:
        FptIndex   _index;
        OBFingerprint* _pFP;
};

//**********************************************
/// \brief Class to prepare fingerprint index files See FastSearch class for details
class OBAPI FastSearchIndexer
{
//see end of cpp file for detailed documentation
public:
        FastSearchIndexer(std::string& datafilename, std::ostream* os, std::string& fpid,
                        int FptBits=0);
        ~FastSearchIndexer();

        ///\brief Called for each object
        bool Add(OBBase* pOb, std::streampos seekpos);

private:
        std::ostream* _indexstream;
        FptIndex*               _pindex;
        OBFingerprint* _pFP;
        int _nbits;
};

} //namespace OpenBabel
#endif

//! \file fingerprint.h
//! \brief Declaration of OBFingerprint base class and fastsearch classes
Revision:	746
Committed:	Wed Nov 16 21:22:51 2005 UTC (19 years, 5 months ago) by tim
File size:	6071 byte(s)
Log Message:	adding more readers/writers
#	User	Rev	Content
1	tim	741	/**********************************************************************
2			fingerprint.h - Base class for fingerprints and fast searching
3
4			Copyright (C) 2005 by Chris Morley
5
6			This file is part of the Open Babel project.
7			For more information, see <http://openbabel.sourceforge.net/>
8
9			This program is free software; you can redistribute it and/or modify
10			it under the terms of the GNU General Public License as published by
11			the Free Software Foundation version 2 of the License.
12
13			This program is distributed in the hope that it will be useful,
14			but WITHOUT ANY WARRANTY; without even the implied warranty of
15			MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
16			GNU General Public License for more details.
17			***********************************************************************/
18
19			#ifndef OB_FINGERPRINT_H
20			#define OB_FINGERPRINT_H
21
22			#include <list>
23			#include <map>
24			#include <set>
25			#include <vector>
26			#include <string>
27
28			namespace OpenBabel
29			{
30			class OBBase; //Forward declaration; used only as pointer.
31
32			/// \brief The base class for fingerprints
33			class OBAPI OBFingerprint
34			{
35			//see end of cpp file for detailed documentation
36			public:
37			/// Sets the nth bit
38			void SetBit(std::vector<unsigned int>& vec, unsigned int n);
39
40			/// Repeatedly ORs the top half with the bottom half until no smaller than nbits
41			void Fold(std::vector<unsigned int>& vec, unsigned int nbits);
42
43			/// Returns fingerprint in vector, which may be resized, folded to nbits (if nbits!=0)
44			virtual bool GetFingerprint(OBBase* pOb, std::vector<unsigned int>& fp, int nbits=0)=0;
45
46			/// Required short description of the fingerprint type.
47			virtual std::string Description()=0;
48
49			/// Optional flags
50			enum FptFlag{FPT_UNIQUEBITS=1};
51			virtual unsigned int Flags() { return 0;};
52
53			/// Obtain info on available fingerprints
54			static bool GetNextFPrt(std::string& id, OBFingerprint*& pFPrt);
55
56			/// Returns a pointer to a fingerprint (the default if ID is empty), or NULL if not available
57			static OBFingerprint* FindFingerprint(std::string& ID);
58
59			/// Returns the Tanimoto coefficient between two vectors (vector<unsigned int>& SeekPositions)
60			static double Tanimoto(const std::vector<unsigned int>& vec1, const std::vector<unsigned int>& vec2);
61
62			/// Inline version of Tanimoto() taking a pointer for the second vector
63	tim	746	static double Tanimoto(const std::vector<unsigned int>& vec1, const unsigned int* p2)
64	tim	741	{
65			///If used for two vectors, vec1 and vec2, call as Tanimoto(vec1, &vec2[0]);
66			int andbits=0, orbits=0;
67			unsigned int i;
68			for (i=0;i<vec1.size();++i)
69			{
70			int andfp = vec1[i] & p2[i];
71			int orfp = vec1[i] \| p2[i];
72			//Count bits
73			for(;andfp;andfp=andfp<<1)
74			if(andfp<0) ++andbits;
75			for(;orfp;orfp=orfp<<1)
76			if(orfp<0) ++orbits;
77			}
78			return((double)andbits/(double)orbits);
79			};
80
81			static const unsigned int bitsperint;// = 8 * sizeof(unsigned int);
82
83			private:
84			///Function object to set bits
85			struct bit_or
86			{
87			unsigned int operator()(const unsigned int a, const unsigned int b)
88			{
89			return a \| b;
90			}
91			};
92
93			typedef std::map<std::string, OBFingerprint*> FPMapType;
94			typedef FPMapType::iterator Fptpos;
95
96			protected:
97			///This static function returns a reference to the FPtsMap
98			///which, because it is a static local variable is constructed only once.
99			///This fiddle is to avoid the "static initialization order fiasco"
100			///See Marshall Cline's C++ FAQ Lite document, www.parashift.com/c++-faq-lite/".
101			static FPMapType& FPtsMap()
102			{
103			static FPMapType* fptm = new FPMapType;
104			return *fptm;
105			};
106
107			OBFingerprint(std::string ID, bool IsDefault=false)
108			{
109			FPtsMap()[ID] = this; //registers the derived fingerprint class
110			if(IsDefault \|\| FPtsMap().empty())
111			_pDefault=this;
112			};
113
114			private:
115			static OBFingerprint* _pDefault;
116			};
117
118
119
120
121			//*************************************************************
122			//Fast search routines
123			///Header for fastsearch index file
124			struct OBAPI FptIndexHeader
125			{
126			unsigned int headerlength;///<offset to data: sizeof(FptIndexHeader)
127			unsigned int nEntries; ///<number of fingerprints
128			unsigned int words; ///<number 32bit words per fingerprint
129			char fpid[16]; ///<ID of the fingerprint type
130			char datafilename[256]; ///<the data that this is an index to
131			};
132			/// Structure of fastsearch index files
133			struct OBAPI FptIndex
134			{
135			FptIndexHeader header;
136			std::vector<unsigned int> fptdata;
137			std::vector<unsigned int> seekdata;
138			};
139
140			/// \brief Class to search fingerprint index files
141			class OBAPI FastSearch
142			{
143			//see end of cpp file for detailed documentation
144			public:
145			std::string ReadIndex(std::istream* pIndexstream);
146			virtual ~FastSearch(){};
147
148			/// \brief Does substructure search and returns vector of the file positions of matches
149			bool Find(OBBase* pOb, std::vector<unsigned int>& SeekPositions, unsigned int MaxCandidates);
150
151			/// \brief Returns multimap containing objects whose Tanimoto coefficients with the target
152			/// is greater than the value specified.
153			bool FindSimilar(OBBase* pOb, std::multimap<double, unsigned int>& SeekposMap,
154			double MinTani);
155
156			/// \brief Returns multimap containing the nCandidates objects with largest Tanimoto
157			/// coefficients with the target.
158			bool FindSimilar(OBBase* pOb, std::multimap<double, unsigned int>& SeekposMap,
159			int nCandidates=0);
160
161			/// \brief Returns a pointer to the fingerprint type used to constuct the index
162			OBFingerprint* GetFingerprint() const{ return _pFP;};
163
164			private:
165			FptIndex _index;
166			OBFingerprint* _pFP;
167			};
168
169			//**********************************************
170			/// \brief Class to prepare fingerprint index files See FastSearch class for details
171			class OBAPI FastSearchIndexer
172			{
173			//see end of cpp file for detailed documentation
174			public:
175			FastSearchIndexer(std::string& datafilename, std::ostream* os, std::string& fpid,
176			int FptBits=0);
177			~FastSearchIndexer();
178
179			///\brief Called for each object
180			bool Add(OBBase* pOb, std::streampos seekpos);
181
182			private:
183			std::ostream* _indexstream;
184			FptIndex* _pindex;
185			OBFingerprint* _pFP;
186			int _nbits;
187			};
188
189			} //namespace OpenBabel
190			#endif
191
192			//! \file fingerprint.h
193			//! \brief Declaration of OBFingerprint base class and fastsearch classes