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
|
// $Id$
//
// Copyright (C) 2003-2008 greg Landrum and Rational Discovery LLC
//
// @@ 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 <RDBoost/Wrap.h>
#include <DataStructs/BitVects.h>
#include <RDBoost/PySequenceHolder.h>
#include "wrap_helpers.h"
namespace python = boost::python;
// allows BitVects to be pickled
struct sbv_pickle_suite : python::pickle_suite {
static python::tuple getinitargs(const SparseBitVect &self) {
std::string res = self.toString();
python::object retval = python::object(
python::handle<>(PyBytes_FromStringAndSize(res.c_str(), res.length())));
return python::make_tuple(retval);
};
};
std::string sbvClassDoc =
"A class to store sparse bit vectors.\n\
\n\
This class is most useful for situations where the size of the vector\n\
is large and relatively few bits are set\n\
\n\
For smaller or denser vectors, the _ExplicitBitVect_ class is much faster.\n\
\n\
As you would expect, _SparseBitVects_ support a set of binary operations\n\
so you can do things like:\n\
bv3 = bv1 & bv2 (bitwise and)\n\
bv3 = bv1 | bv2 (bitwise or)\n\
bv3 = bv1 ^ bv2 (bitwise xor)\n\
bv3 = ~bv1 (bitwise negation) NOTE: this operation is likely\n\
to be VERY slow and inefficient.\n\
\n\
Bits can be set and read using either the Set/UnsetBit() and GetBit() methods\n\
or by indexing (i.e. bv[i] = 1 or if bv[i]).\n\
\n";
struct SBV_wrapper {
static void wrap() {
python::class_<SparseBitVect>("SparseBitVect", sbvClassDoc.c_str(),
python::init<unsigned int>())
.def(python::init<std::string>())
.def("SetBit", (bool (SBV::*)(unsigned int)) & SBV::setBit,
"Turns on a particular bit. Returns the original state of the "
"bit.\n")
.def("SetBitsFromList",
(void (*)(SBV *, python::object))SetBitsFromList,
"Turns on a set of bits. The argument should be a tuple or list "
"of bit ids.\n")
.def("UnSetBit", (bool (SBV::*)(unsigned int)) & SBV::unsetBit,
"Turns off a particular bit. Returns the original state of the "
"bit.\n")
.def("UnSetBitsFromList",
(void (*)(SBV *, python::object))UnSetBitsFromList,
"Turns off a set of bits. The argument should be a tuple or list "
"of bit ids.\n")
.def("GetBit", (bool (SBV::*)(unsigned int) const) & SBV::getBit,
"Returns the value of a bit.\n")
.def("GetNumBits", &SBV::getNumBits,
"Returns the number of bits in the vector (the vector's size).\n")
.def("__len__", &SBV::getNumBits)
.def("GetNumOnBits", &SBV::getNumOnBits,
"Returns the number of on bits.\n")
.def("GetNumOffBits", &SBV::getNumOffBits,
"Returns the number of off bits.\n")
.def("__getitem__", (int (*)(const SBV &, int))get_VectItem)
.def("__setitem__", (int (*)(SBV &, int, int))set_VectItem)
.def("GetOnBits", (IntVect (*)(const SBV &))GetOnBits,
"Returns a tuple containing IDs of the on bits.\n")
.def("ToBinary", (python::object (*)(const SBV &))BVToBinary,
"Returns an internal binary representation of the vector.\n")
.def("FromBase64", (void (*)(SBV &, const std::string &))InitFromBase64,
"Initializes the vector from a base64 encoded binary string.\n")
.def("ToBase64", (std::string (*)(SBV &))ToBase64,
"Converts the vector to a base64 string (the base64 encoded "
"version of the results of ToString()).\n")
.def(python::self & python::self)
.def(python::self | python::self)
.def(python::self ^ python::self)
.def(~python::self)
.def(python::self == python::self)
.def(python::self != python::self)
.def_pickle(sbv_pickle_suite());
}
};
void wrap_SBV() { SBV_wrapper::wrap(); }
|
