1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
|
//
// Copyright (c) 2003-208 greg Landrum and Rational Discovery LLC
// Copyright (c) 2014, Novartis Institutes for BioMedical Research Inc.
//
// @@ All Rights Reserved @@
// This file is part of the RDKit.
// The contents are covered by the terms of the BSD license
// which is included in the file license.txt, found at the root
// of the RDKit source tree.
//
#include <RDGeneral/export.h>
#ifndef __RD_EXPLICITBITVECTS_H__
#define __RD_EXPLICITBITVECTS_H__
#include <RDGeneral/BoostStartInclude.h>
#include <boost/dynamic_bitset.hpp>
#include <RDGeneral/BoostEndInclude.h>
#include "BitVect.h"
//! a class for bit vectors that are densely occupied
/*!
ExplicitBitVect objects store all of their bits using
a boost::dynamic_bitset
These are very fast, but can require large amounts of memory for large,
sparsely occupied vectors.
*/
class RDKIT_DATASTRUCTS_EXPORT ExplicitBitVect : public BitVect {
public:
ExplicitBitVect() {}
//! initialize with a particular size;
explicit ExplicitBitVect(unsigned int size)
: dp_bits(nullptr), d_size(0), d_numOnBits(0) {
_initForSize(size);
}
//! initialize with a particular size and all bits set
ExplicitBitVect(unsigned int size, bool bitsSet);
ExplicitBitVect(const ExplicitBitVect &other);
ExplicitBitVect(ExplicitBitVect &&other) noexcept;
//! construct from a string pickle
ExplicitBitVect(const std::string &pkl);
//! construct from a text pickle
ExplicitBitVect(const char *, const unsigned int);
//! construct directly from a dynamic_bitset pointer
/// takes ownership of the pointer
ExplicitBitVect(boost::dynamic_bitset<> *bits)
: dp_bits(bits),
d_size(static_cast<unsigned int>(bits->size())),
d_numOnBits(static_cast<unsigned int>(bits->count())) {}
~ExplicitBitVect() override;
ExplicitBitVect &operator=(const ExplicitBitVect &other);
ExplicitBitVect &operator=(ExplicitBitVect &&other) noexcept;
bool operator[](const unsigned int which) const override;
bool setBit(const unsigned int which) override;
bool unsetBit(const unsigned int which) override;
bool getBit(const unsigned int which) const override;
ExplicitBitVect operator^(const ExplicitBitVect &other) const;
ExplicitBitVect operator&(const ExplicitBitVect &other) const;
ExplicitBitVect operator|(const ExplicitBitVect &other) const;
ExplicitBitVect operator~() const;
/* concatenate two ExplicitBitVects */
ExplicitBitVect operator+(const ExplicitBitVect &other) const;
ExplicitBitVect &operator^=(const ExplicitBitVect &other);
ExplicitBitVect &operator&=(const ExplicitBitVect &other);
ExplicitBitVect &operator|=(const ExplicitBitVect &other);
/* concatenate two ExplicitBitVects */
ExplicitBitVect &operator+=(const ExplicitBitVect &other);
unsigned int getNumBits() const override;
unsigned int getNumOnBits() const override;
unsigned int getNumOffBits() const override;
void getOnBits(IntVect &v) const override;
void clearBits() override { dp_bits->reset(); }
std::string toString() const override;
std::unique_ptr<boost::dynamic_bitset<>> dp_bits{
nullptr}; //!< our raw storage
bool operator==(const ExplicitBitVect &o) const {
return *dp_bits == *o.dp_bits;
}
bool operator!=(const ExplicitBitVect &o) const {
return *dp_bits != *o.dp_bits;
}
private:
unsigned int d_size{0};
unsigned int d_numOnBits{0};
void _initForSize(const unsigned int size) override;
};
#endif
|
