RDKit: DiscreteValueVect.h Source File

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DiscreteValueVect.h
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1//
2// Copyright (C) 2004-2008 Greg Landrum and Rational Discovery LLC
3//
4// @@ All Rights Reserved @@
5// This file is part of the RDKit.
6// The contents are covered by the terms of the BSD license
7// which is included in the file license.txt, found at the root
8// of the RDKit source tree.
9//
10#include <RDGeneral/export.h>
11#ifndef __RD_DISCRETE_VALUE_VECT_20050124__
12#define __RD_DISCRETE_VALUE_VECT_20050124__
13
14#include <boost/smart_ptr.hpp>
15#include <string>
16#include <cstring>
17#include <cstdint>
18
19namespace RDKit {
20// we require 32bit unsigneds using the std::uint32_t type:
21 const unsigned int BITS_PER_INT = 32;
22
23//! a class for efficiently storing vectors of discrete values
24 class RDKIT_DATASTRUCTS_EXPORT DiscreteValueVect {
25 public:
26 typedef boost::shared_array<std::uint32_t> DATA_SPTR;
27
28 //! used to define the possible range of the values
29 typedef enum {
30 ONEBITVALUE = 0,
31 TWOBITVALUE,
32 FOURBITVALUE,
33 EIGHTBITVALUE,
34 SIXTEENBITVALUE,
35 } DiscreteValueType;
36
37 //! initialize with a particular type and size
38 DiscreteValueVect(DiscreteValueType valType, unsigned int length)
39 : d_type(valType), d_length(length) {
40 d_bitsPerVal = (1 << static_cast<unsigned int>(valType));
41 d_valsPerInt = BITS_PER_INT / d_bitsPerVal;
42 d_numInts = (length + d_valsPerInt - 1) / d_valsPerInt;
43 d_mask = ((1 << d_bitsPerVal) - 1);
44 auto *data = new std::uint32_t[d_numInts];
45 memset(static_cast<void *>(data), 0, d_numInts * sizeof(std::uint32_t));
46 d_data.reset(data);
47 }
48
49 //! Copy constructor
50 DiscreteValueVect(const DiscreteValueVect &other);
51
52 DiscreteValueVect &operator=(const DiscreteValueVect &other);
53
54 //! constructor from a pickle
55 DiscreteValueVect(const std::string &pkl) {
56 initFromText(pkl.c_str(), static_cast<unsigned int>(pkl.size()));
57 }
58 //! constructor from a pickle
59 DiscreteValueVect(const char *pkl, const unsigned int len) {
60 initFromText(pkl, len);
61 }
62
63 ~DiscreteValueVect() = default;
64
65 //! return the value at an index
66 unsigned int getVal(unsigned int i) const;
67
68 //! support indexing using []
69 int operator[](unsigned int idx) const { return getVal(idx); }
70
71 //! set the value at an index
72 /*!
73 NOTE: it is an error to have val > the max value this
74 DiscreteValueVect can accommodate
75 */
76 void setVal(unsigned int i, unsigned int val);
77
78 //! returns the sum of all the elements in the vect
79 unsigned int getTotalVal() const;
80
81 //! returns the length
82 unsigned int getLength() const;
83 //! returns the length
84 unsigned int size() const { return getLength(); }
85
86 //! return a pointer to our raw data storage
87 const std::uint32_t *getData() const;
88
89 //! return the number of bits used to store each value
90 unsigned int getNumBitsPerVal() const { return d_bitsPerVal; }
91
92 //! return the type of value being stored
93 DiscreteValueType getValueType() const { return d_type; }
94
95 //! returns the size of our storage
96 unsigned int getNumInts() const { return d_numInts; }
97
98 //! support dvv3 = dvv1&dvv2
99 /*!
100
101 operator& returns the minimum value for each element.
102 e.g.:
103 [0,1,2,0] & [0,1,1,1] -> [0,1,1,0]
104
105 */
106 DiscreteValueVect operator&(const DiscreteValueVect &other) const;
107 //! support dvv3 = dvv1|dvv2
108 /*!
109
110 operator& returns the maximum value for each element.
111 e.g.:
112 [0,1,2,0] | [0,1,1,1] -> [0,1,2,1]
113
114 */
115 DiscreteValueVect operator|(const DiscreteValueVect &other) const;
116 // DiscreteValueVect operator^ (const DiscreteValueVect &other) const;
117 // DiscreteValueVect operator~ () const;
118
119 DiscreteValueVect &operator+=(const DiscreteValueVect &other);
120 DiscreteValueVect &operator-=(const DiscreteValueVect &other);
121
122 //! returns a binary string representation (pickle)
123 std::string toString() const;
124
125 private:
126 DiscreteValueType d_type;
127 unsigned int d_bitsPerVal;
128 unsigned int d_valsPerInt;
129 unsigned int d_numInts;
130 unsigned int d_length;
131 unsigned int d_mask;
132 DATA_SPTR d_data;
133
134 void initFromText(const char *pkl, const unsigned int len);
135};
136
137 RDKIT_DATASTRUCTS_EXPORT unsigned int computeL1Norm(
138 const DiscreteValueVect &v1, const DiscreteValueVect &v2);
139
140 RDKIT_DATASTRUCTS_EXPORT DiscreteValueVect
141operator+(const DiscreteValueVect &p1, const DiscreteValueVect &p2);
142 RDKIT_DATASTRUCTS_EXPORT DiscreteValueVect
143operator-(const DiscreteValueVect &p1, const DiscreteValueVect &p2);
144} // namespace RDKit
145
146#endif
RDKit::DiscreteValueVect
a class for efficiently storing vectors of discrete values
Definition DiscreteValueVect.h:24
RDKit::DiscreteValueVect::size
unsigned int size() const
returns the length
Definition DiscreteValueVect.h:84
RDKit::DiscreteValueVect::DiscreteValueVect
DiscreteValueVect(const std::string &pkl)
constructor from a pickle
Definition DiscreteValueVect.h:55
RDKit::DiscreteValueVect::DiscreteValueVect
DiscreteValueVect(const DiscreteValueVect &other)
Copy constructor.
RDKit::DiscreteValueVect::toString
std::string toString() const
returns a binary string representation (pickle)
RDKit::DiscreteValueVect::getVal
unsigned int getVal(unsigned int i) const
return the value at an index
RDKit::DiscreteValueVect::getLength
unsigned int getLength() const
returns the length
RDKit::DiscreteValueVect::DiscreteValueType
DiscreteValueType
used to define the possible range of the values
Definition DiscreteValueVect.h:29
RDKit::DiscreteValueVect::TWOBITVALUE
@ TWOBITVALUE
Definition DiscreteValueVect.h:31
RDKit::DiscreteValueVect::ONEBITVALUE
@ ONEBITVALUE
Definition DiscreteValueVect.h:30
RDKit::DiscreteValueVect::SIXTEENBITVALUE
@ SIXTEENBITVALUE
Definition DiscreteValueVect.h:34
RDKit::DiscreteValueVect::FOURBITVALUE
@ FOURBITVALUE
Definition DiscreteValueVect.h:32
RDKit::DiscreteValueVect::EIGHTBITVALUE
@ EIGHTBITVALUE
Definition DiscreteValueVect.h:33
RDKit::DiscreteValueVect::~DiscreteValueVect
~DiscreteValueVect()=default
RDKit::DiscreteValueVect::getTotalVal
unsigned int getTotalVal() const
returns the sum of all the elements in the vect
RDKit::DiscreteValueVect::operator|
DiscreteValueVect operator|(const DiscreteValueVect &other) const
support dvv3 = dvv1|dvv2
RDKit::DiscreteValueVect::DiscreteValueVect
DiscreteValueVect(DiscreteValueType valType, unsigned int length)
initialize with a particular type and size
Definition DiscreteValueVect.h:38
RDKit::DiscreteValueVect::operator&
DiscreteValueVect operator&(const DiscreteValueVect &other) const
support dvv3 = dvv1&dvv2
RDKit::DiscreteValueVect::operator=
DiscreteValueVect & operator=(const DiscreteValueVect &other)
RDKit::DiscreteValueVect::DATA_SPTR
boost::shared_array< std::uint32_t > DATA_SPTR
Definition DiscreteValueVect.h:26
RDKit::DiscreteValueVect::getValueType
DiscreteValueType getValueType() const
return the type of value being stored
Definition DiscreteValueVect.h:93
RDKit::DiscreteValueVect::operator-=
DiscreteValueVect & operator-=(const DiscreteValueVect &other)
RDKit::DiscreteValueVect::getData
const std::uint32_t * getData() const
return a pointer to our raw data storage
RDKit::DiscreteValueVect::getNumInts
unsigned int getNumInts() const
returns the size of our storage
Definition DiscreteValueVect.h:96
RDKit::DiscreteValueVect::operator[]
int operator[](unsigned int idx) const
support indexing using []
Definition DiscreteValueVect.h:69
RDKit::DiscreteValueVect::getNumBitsPerVal
unsigned int getNumBitsPerVal() const
return the number of bits used to store each value
Definition DiscreteValueVect.h:90
RDKit::DiscreteValueVect::DiscreteValueVect
DiscreteValueVect(const char *pkl, const unsigned int len)
constructor from a pickle
Definition DiscreteValueVect.h:59
RDKit::DiscreteValueVect::setVal
void setVal(unsigned int i, unsigned int val)
set the value at an index
RDKit::DiscreteValueVect::operator+=
DiscreteValueVect & operator+=(const DiscreteValueVect &other)
export.h
RDKIT_DATASTRUCTS_EXPORT
#define RDKIT_DATASTRUCTS_EXPORT
Definition export.h:89
RDKit::v1
Definition ReactionParser.h:91
RDKit::v2
Definition ReactionParser.h:71
RDKit
Std stuff.
Definition Abbreviations.h:19
RDKit::computeL1Norm
RDKIT_DATASTRUCTS_EXPORT unsigned int computeL1Norm(const DiscreteValueVect &v1, const DiscreteValueVect &v2)
RDKit::operator-
RDKIT_DATASTRUCTS_EXPORT DiscreteValueVect operator-(const DiscreteValueVect &p1, const DiscreteValueVect &p2)
RDKit::operator+
RDKIT_DATASTRUCTS_EXPORT DiscreteValueVect operator+(const DiscreteValueVect &p1, const DiscreteValueVect &p2)
RDKit::BITS_PER_INT
const unsigned int BITS_PER_INT
Definition DiscreteValueVect.h:21