src/openbabel/bitvec.hpp

/**********************************************************************
bitvec.h - Vector of bits.
 
Copyright (C) 1998-2001 by OpenEye Scientific Software, Inc.
Some portions Copyright (C) 2001-2005 by Geoffrey R. Hutchison
 
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_BITVEC_H
#define OB_BITVEC_H

#include "config.h"

#ifdef WIN32
#pragma warning (disable : 4786)
#endif

#if HAVE_IOSTREAM
#include <iostream>
#elif HAVE_IOSTREAM_H
#include <iostream.h>
#endif

#include <algorithm>
#include <vector>
#include <string>

#ifndef SETWORD
#define SETWORD 32
#endif

#ifndef STARTWORDS
#define STARTWORDS 10
#endif //STARTBITS

namespace OpenBabel
{

// class introduction in bitvec.cpp
class OBAPI OBBitVec
{
    int _size;
    std::vector<int> _set;
public:
    OBBitVec()
    {
        _set.resize(STARTWORDS);
        _size=_set.size();
        Clear();
    }
    OBBitVec(int bits)
    {
        _set.resize(bits/SETWORD);
        _size=_set.size();
        Clear();
    }
    /// Copy constructor (result has same number of bits)
    OBBitVec(const OBBitVec&);
    void SetBitOn(int);
    void SetBitOff(int);
    void SetRangeOn(int, int);
    void SetRangeOff(int, int);
    void Fold(int);

    //! \return the index of the first bit that is set to true
    int FirstBit(int)
    {
        return (BitIsSet(0) ? 0  : NextBit(0));
    }
    int NextBit(int);
    //! \return the index of the last bit (for iterating)
    int EndBit()    {        return(-1);    }
    /// \return number of 32 bit words. NOT number of bits.
    int GetSize() const    { return(_size);    }
    /// \return the number of bits
    int CountBits();

    /// \deprecated Use IsEmpty() instead.
    bool Empty()   { return(IsEmpty()); }
    bool IsEmpty();
    ///Number of bits increased if necessary but never decreased
    bool Resize(int maxbits);

    bool BitIsSet(int bit)
    {
        return((bit/SETWORD >= GetSize()) ?
               false : _set[bit/SETWORD]>>(bit%SETWORD)&1);
    }
    bool BitIsOn(int bit)
    {
        return((bit/SETWORD >= GetSize()) ?
               false : _set[bit/SETWORD]>>(bit%SETWORD)&1);
    }

    void FromVecInt(std::vector<int>&);
    void FromString(std::string&,int);
    void ToVecInt(std::vector<int>&);
    void Clear(void);
    //! Inverts every bit in the vector
    void Negate()
    {
        for (int i= 0; i != _size; i++)
        {
            _set[i] = ~_set[i];
        }
    }

    ///Assignment operator but number of bits is not reduced 
    OBBitVec &operator= (const OBBitVec &);
    OBBitVec &operator&= (OBBitVec &);
    OBBitVec &operator|= (OBBitVec &);
    OBBitVec &operator|= (const int i)
    {
        SetBitOn(i);
        return(*this);
    }
    OBBitVec &operator^= (OBBitVec &);
    OBBitVec &operator-= (OBBitVec &);
    OBBitVec &operator+= (OBBitVec &bv);
    bool operator[] (int bit)
    {
        return((bit/SETWORD >= GetSize()) ?
               false : _set[bit/SETWORD]>>(bit%SETWORD)&1);
    }

    friend OBBitVec operator| (OBBitVec &, OBBitVec &);
    friend OBBitVec operator& (OBBitVec &,OBBitVec &);
    friend OBBitVec operator^ (OBBitVec &,OBBitVec &);
    friend OBBitVec operator- (OBBitVec &,OBBitVec &);
    friend bool operator== (const OBBitVec &,const OBBitVec &);

    friend std::istream& operator>> ( std::istream&, OBBitVec& );
    friend std::ostream& operator<< ( std::ostream&, const OBBitVec& ) ;
        
    ///Access to data in word size pieces CM
    void GetWords(std::vector<unsigned int>& vec)
      {
        std::vector<int>::iterator itr;
        for(itr=_set.begin();itr!=_set.end();itr++)
          vec.push_back(*itr);
      }
};

OBAPI extern void ThrowError(char *);
///This function can change the size of second parameter. There is an alternative with different parameters.
OBAPI double Tanimoto(OBBitVec&,OBBitVec&);

}

#endif // OB_BITVEC_H

//! \file bitvec.h
//! \brief Fast and efficient bitstring class
Revision:	751
Committed:	Thu Nov 17 20:38:45 2005 UTC (19 years, 11 months ago) by gezelter
File size:	4477 byte(s)
Log Message:	Unifying config.h stuff and making sure the OpenBabel codes can find our default (and environment variable) Force Field directories.
#	User	Rev	Content
1	tim	741	/**********************************************************************
2			bitvec.h - Vector of bits.
3
4			Copyright (C) 1998-2001 by OpenEye Scientific Software, Inc.
5			Some portions Copyright (C) 2001-2005 by Geoffrey R. Hutchison
6
7			This file is part of the Open Babel project.
8			For more information, see <http://openbabel.sourceforge.net/>
9
10			This program is free software; you can redistribute it and/or modify
11			it under the terms of the GNU General Public License as published by
12			the Free Software Foundation version 2 of the License.
13
14			This program is distributed in the hope that it will be useful,
15			but WITHOUT ANY WARRANTY; without even the implied warranty of
16			MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
17			GNU General Public License for more details.
18			***********************************************************************/
19
20			#ifndef OB_BITVEC_H
21			#define OB_BITVEC_H
22
23	gezelter	751	#include "config.h"
24	tim	741
25			#ifdef WIN32
26			#pragma warning (disable : 4786)
27			#endif
28
29			#if HAVE_IOSTREAM
30			#include <iostream>
31			#elif HAVE_IOSTREAM_H
32			#include <iostream.h>
33			#endif
34
35			#include <algorithm>
36			#include <vector>
37			#include <string>
38
39			#ifndef SETWORD
40			#define SETWORD 32
41			#endif
42
43			#ifndef STARTWORDS
44			#define STARTWORDS 10
45			#endif //STARTBITS
46
47			namespace OpenBabel
48			{
49
50			// class introduction in bitvec.cpp
51			class OBAPI OBBitVec
52			{
53			int _size;
54			std::vector<int> _set;
55			public:
56			OBBitVec()
57			{
58			_set.resize(STARTWORDS);
59			_size=_set.size();
60			Clear();
61			}
62			OBBitVec(int bits)
63			{
64			_set.resize(bits/SETWORD);
65			_size=_set.size();
66			Clear();
67			}
68			/// Copy constructor (result has same number of bits)
69			OBBitVec(const OBBitVec&);
70			void SetBitOn(int);
71			void SetBitOff(int);
72			void SetRangeOn(int, int);
73			void SetRangeOff(int, int);
74			void Fold(int);
75
76			//! \return the index of the first bit that is set to true
77			int FirstBit(int)
78			{
79			return (BitIsSet(0) ? 0 : NextBit(0));
80			}
81			int NextBit(int);
82			//! \return the index of the last bit (for iterating)
83			int EndBit() { return(-1); }
84			/// \return number of 32 bit words. NOT number of bits.
85			int GetSize() const { return(_size); }
86			/// \return the number of bits
87			int CountBits();
88
89			/// \deprecated Use IsEmpty() instead.
90			bool Empty() { return(IsEmpty()); }
91			bool IsEmpty();
92			///Number of bits increased if necessary but never decreased
93			bool Resize(int maxbits);
94
95			bool BitIsSet(int bit)
96			{
97			return((bit/SETWORD >= GetSize()) ?
98			false : _set[bit/SETWORD]>>(bit%SETWORD)&1);
99			}
100			bool BitIsOn(int bit)
101			{
102			return((bit/SETWORD >= GetSize()) ?
103			false : _set[bit/SETWORD]>>(bit%SETWORD)&1);
104			}
105
106			void FromVecInt(std::vector<int>&);
107			void FromString(std::string&,int);
108			void ToVecInt(std::vector<int>&);
109			void Clear(void);
110			//! Inverts every bit in the vector
111			void Negate()
112			{
113			for (int i= 0; i != _size; i++)
114			{
115			_set[i] = ~_set[i];
116			}
117			}
118
119			///Assignment operator but number of bits is not reduced
120			OBBitVec &operator= (const OBBitVec &);
121			OBBitVec &operator&= (OBBitVec &);
122			OBBitVec &operator\|= (OBBitVec &);
123			OBBitVec &operator\|= (const int i)
124			{
125			SetBitOn(i);
126			return(*this);
127			}
128			OBBitVec &operator^= (OBBitVec &);
129			OBBitVec &operator-= (OBBitVec &);
130			OBBitVec &operator+= (OBBitVec &bv);
131			bool operator[] (int bit)
132			{
133			return((bit/SETWORD >= GetSize()) ?
134			false : _set[bit/SETWORD]>>(bit%SETWORD)&1);
135			}
136
137			friend OBBitVec operator\| (OBBitVec &, OBBitVec &);
138			friend OBBitVec operator& (OBBitVec &,OBBitVec &);
139			friend OBBitVec operator^ (OBBitVec &,OBBitVec &);
140			friend OBBitVec operator- (OBBitVec &,OBBitVec &);
141			friend bool operator== (const OBBitVec &,const OBBitVec &);
142
143			friend std::istream& operator>> ( std::istream&, OBBitVec& );
144			friend std::ostream& operator<< ( std::ostream&, const OBBitVec& ) ;
145
146			///Access to data in word size pieces CM
147			void GetWords(std::vector<unsigned int>& vec)
148			{
149			std::vector<int>::iterator itr;
150			for(itr=_set.begin();itr!=_set.end();itr++)
151			vec.push_back(*itr);
152			}
153			};
154
155			OBAPI extern void ThrowError(char *);
156			///This function can change the size of second parameter. There is an alternative with different parameters.
157			OBAPI double Tanimoto(OBBitVec&,OBBitVec&);
158
159			}
160
161			#endif // OB_BITVEC_H
162
163			//! \file bitvec.h
164			//! \brief Fast and efficient bitstring class