00001 /********************************************************************** 00002 bitvec.h - Vector of bits. 00003 00004 Copyright (C) 1998-2001 by OpenEye Scientific Software, Inc. 00005 Some portions Copyright (C) 2001-2006 by Geoffrey R. Hutchison 00006 00007 This file is part of the Open Babel project. 00008 For more information, see <http://openbabel.sourceforge.net/> 00009 00010 This program is free software; you can redistribute it and/or modify 00011 it under the terms of the GNU General Public License as published by 00012 the Free Software Foundation version 2 of the License. 00013 00014 This program is distributed in the hope that it will be useful, 00015 but WITHOUT ANY WARRANTY; without even the implied warranty of 00016 MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the 00017 GNU General Public License for more details. 00018 ***********************************************************************/ 00019 00020 #ifndef OB_BITVEC_H 00021 #define OB_BITVEC_H 00022 00023 #include <openbabel/babelconfig.h> 00024 00025 #include <vector> 00026 #include <string> 00027 00028 #ifndef USE_64BIT_INTEGER 00029 // For 32-bit architecture 00030 #define SETWORD 32 00031 // SETWORD = 2 ^ WORDROLL 00032 #define WORDROLL 5 00033 // WORDMASK = SETWORD - 1 00034 #define WORDMASK 31 00035 #else 00036 // For 64-bit architecture 00037 #define SETWORD 64 00038 // SETWORD = 2 ^ WORDROLL 00039 #define WORDROLL 6 00040 // WORDMASK = SETWORD - 1 00041 #define WORDMASK 63 00042 #endif // 64 bit 00043 00044 #define WORDSIZE_OF_BITSIZE( bit_size ) ( ( bit_size >> WORDROLL ) + (( bit_size & WORDMASK ) ? 1 : 0) ) 00045 00046 #ifndef STARTWORDS 00047 #define STARTWORDS 10 00048 #endif // STARTWORDS 00049 00050 namespace OpenBabel 00051 { 00053 00061 class OBERROR OBBitVec 00062 { 00063 public: 00064 typedef std::vector<unsigned> word_vector; 00065 00066 private: 00068 size_t _size; //was unsigned 00070 word_vector _set; 00071 00072 public: 00074 00077 OBBitVec() 00078 :_set(STARTWORDS, 0) 00079 { _size = _set.size(); } 00081 00086 OBBitVec(unsigned size_in_bits) 00087 :_set(WORDSIZE_OF_BITSIZE(size_in_bits), 0) 00088 { _size = _set.size(); } 00090 00094 OBBitVec(const OBBitVec & bv) 00095 :_size(0) 00096 { (*this) = bv; } 00098 void SetBitOn(unsigned bit_offset); 00100 void SetBitOff(unsigned bit_offset); 00102 void SetRangeOn(unsigned lo_bit_offset, unsigned hi_bit_offset); 00104 void SetRangeOff(unsigned lo_bit_offset, unsigned hi_bit_offset); 00106 void Fold(unsigned new_bit_size); 00108 00112 int FirstBit(unsigned bit_offset = 0) const 00113 { 00114 return (BitIsSet(bit_offset) ? 0 : NextBit(bit_offset)); 00115 } 00117 int NextBit(int last_bit_offset) const; 00119 int EndBit() const { return -1; } 00121 unsigned GetSize() const { return(_size); } 00123 unsigned CountBits() const; 00124 00126 bool Empty() const { return(IsEmpty()); } 00128 bool IsEmpty() const; 00130 00134 bool Resize(unsigned size_in_bits) 00135 { 00136 return ResizeWords( WORDSIZE_OF_BITSIZE(size_in_bits) ); 00137 } 00139 00143 bool ResizeWords(unsigned size_in_words) 00144 { 00145 if (size_in_words <= _size) 00146 return false; 00147 _set.resize(size_in_words, 0); // increase the vector with zeroed bits 00148 _size = _set.size(); 00149 return true; 00150 } 00152 00156 bool BitIsSet(unsigned bit_offset) const 00157 { 00158 bool rtn = false; 00159 unsigned word_offset = bit_offset >> WORDROLL; 00160 if (word_offset < GetSize()) 00161 { 00162 bit_offset &= WORDMASK; 00163 rtn = (( _set[word_offset] >> bit_offset ) & 1); 00164 } 00165 return rtn; 00166 } 00168 bool BitIsOn(int bit_offset) const 00169 { return BitIsSet((unsigned)bit_offset); } 00170 00172 void FromVecInt(const std::vector<int> & bit_offsets); 00174 void FromString(const std::string & line, int bits); 00176 void ToVecInt(std::vector<int> & bit_offsets) const; 00178 void Clear(); 00180 00184 void Negate() 00185 { 00186 for (word_vector::iterator wx = _set.begin(), wy = _set.end(); wx != wy; ++wx) 00187 * wx = ~(* wx); 00188 } 00190 00194 void GetWords(word_vector & vec) 00195 { 00196 vec.insert(vec.end(), _set.begin(),_set.end()); 00197 } 00198 00200 OBBitVec & operator= (const OBBitVec & bv); 00202 OBBitVec & operator&= (const OBBitVec & bv); 00204 OBBitVec & operator|= (const OBBitVec & bv); 00206 00208 OBBitVec & operator|= (int bit_offset) 00209 { 00210 SetBitOn(bit_offset); 00211 return(*this); 00212 } 00214 OBBitVec & operator^= (const OBBitVec & bv); 00216 OBBitVec & operator-= (const OBBitVec & bv); 00218 OBBitVec & operator+= (const OBBitVec & bv); 00220 00224 bool operator[] (int bit_offset) const 00225 { return BitIsSet(bit_offset); } 00226 00228 friend OBERROR OBBitVec operator| (const OBBitVec & bv1, const OBBitVec & bv2); 00230 friend OBERROR OBBitVec operator& (const OBBitVec & bv1,const OBBitVec & bv2); 00232 friend OBERROR OBBitVec operator^ (const OBBitVec & bv1,const OBBitVec & bv2); 00234 friend OBERROR OBBitVec operator- (const OBBitVec & bv1,const OBBitVec & bv2); 00236 friend OBERROR bool operator== (const OBBitVec & bv1,const OBBitVec & bv2); 00238 friend OBERROR bool operator< (const OBBitVec & bv1, const OBBitVec & bv2); 00239 00241 friend OBERROR std::istream& operator>> ( std::istream & is, OBBitVec & bv ); 00243 friend OBERROR std::ostream& operator<< ( std::ostream & os, const OBBitVec & bv ) ; 00244 }; 00245 00247 OBERROR double Tanimoto(const OBBitVec & bv1, const OBBitVec & bv2); 00248 00249 } // end namespace OpenBabel 00250 00251 #endif // OB_BITVEC_H 00252
This file is part of the documentation for Open Babel, version 2.2.0.
1.5.6.