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
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
115
116
117
118
119
120
121
122
123
124
125
126
127
128
129
130
131
132
133
134
135
136
137
138
139
140
141
142
143
144
145
146
147
148
149
150
151
152
153
154
155
156
157
158
159
160
161
162
163
164
165
166
167
168
169
170
171
172
173
174
175
176
177
178
179
180
181
182
183
184
185
186
187
188
189
190
191
192
193
194
195
196
197
198
199
200
201
202
203
204
205
206
207
208
209
210
211
212
213
214
215
216
217
218
219
220
221
222
223
224
225
226
227
228
229
230
231
232
233
234
235
236
237
238
239
240
241
242
243
244
245
246
247
248
249
250
251
252
253
254
255
256
257
258
259
260
261
262
263
264
265
266
267
268
269
270
271
272
273
274
275
276
277
278
279
280
281
282
283
284
285
286
287
288
289
290
291
292
293
294
295
296
297
298
299
300
301
|
//
// Copyright (c) 2016 Greg Landrum
//
// @@ 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 <boost/tuple/tuple_comparison.hpp>
#include <RDGeneral/Invariant.h>
#include <RDGeneral/Ranking.h>
#include <RDGeneral/RDThreads.h>
#ifdef RDK_THREADSAFE_SSS
#include <thread>
#include <future>
#endif
#include <boost/foreach.hpp>
#include "MultiFPBReader.h"
#include <algorithm>
namespace RDKit {
namespace detail {
boost::uint8_t *bitsetToBytes(const boost::dynamic_bitset<> &bitset);
}
namespace {
struct tplSorter
: public std::binary_function<MultiFPBReader::ResultTuple,
MultiFPBReader::ResultTuple, bool> {
bool operator()(const MultiFPBReader::ResultTuple &v1,
const MultiFPBReader::ResultTuple &v2) const {
if (v1.get<0>() == v2.get<0>()) {
if (v1.get<2>() == v2.get<2>()) {
return v1.get<1>() < v2.get<1>();
} else {
return v1.get<2>() < v2.get<2>();
}
} else {
return v1.get<0>() > v2.get<0>();
}
}
};
struct pairSorter
: public std::binary_function<std::pair<unsigned int, unsigned int>,
std::pair<unsigned int, unsigned int>, bool> {
bool operator()(const std::pair<unsigned int, unsigned int> &v1,
const std::pair<unsigned int, unsigned int> &v2) const {
if (v1.first == v2.first) {
return v1.second < v2.second;
} else {
return v1.first < v2.first;
}
}
};
struct sim_args {
const boost::uint8_t *bv;
double ca, cb;
double threshold;
const std::vector<FPBReader *> &readers;
std::vector<std::vector<MultiFPBReader::ResultTuple>> *res;
bool initOnSearch;
};
void tversky_helper(unsigned int threadId, unsigned int numThreads,
const sim_args *args) {
for (unsigned int i = threadId; i < args->readers.size(); i += numThreads) {
if (args->initOnSearch) args->readers[i]->init();
std::vector<std::pair<double, unsigned int>> r_res =
args->readers[i]->getTverskyNeighbors(args->bv, args->ca, args->cb,
args->threshold);
(*args->res)[i].clear();
(*args->res)[i].reserve(r_res.size());
for (std::vector<std::pair<double, unsigned int>>::const_iterator rit =
r_res.begin();
rit != r_res.end(); ++rit) {
(*args->res)[i].push_back(
MultiFPBReader::ResultTuple(rit->first, rit->second, i));
}
}
}
void tani_helper(unsigned int threadId, unsigned int numThreads,
const sim_args *args) {
for (unsigned int i = threadId; i < args->readers.size(); i += numThreads) {
if (args->initOnSearch) args->readers[i]->init();
std::vector<std::pair<double, unsigned int>> r_res =
args->readers[i]->getTanimotoNeighbors(args->bv, args->threshold);
(*args->res)[i].clear();
(*args->res)[i].reserve(r_res.size());
for (std::vector<std::pair<double, unsigned int>>::const_iterator rit =
r_res.begin();
rit != r_res.end(); ++rit) {
(*args->res)[i].push_back(
MultiFPBReader::ResultTuple(rit->first, rit->second, i));
}
}
}
template <typename T>
void generic_nbr_helper(std::vector<MultiFPBReader::ResultTuple> &res, T func,
const sim_args &args, unsigned int numThreads) {
res.clear();
res.resize(0);
numThreads = getNumThreadsToUse(numThreads);
#ifdef RDK_THREADSAFE_SSS
std::vector<std::future<void>> tg;
#endif
if (numThreads == 1) {
func(0, 1, &args);
}
#ifdef RDK_THREADSAFE_SSS
else {
for (unsigned int tid = 0; tid < numThreads && tid < args.readers.size();
++tid) {
tg.emplace_back(
std::async(std::launch::async, func, tid, numThreads, &args));
}
for (auto &fut : tg) {
fut.get();
}
}
#endif
for (unsigned int i = 0; i < args.readers.size(); ++i) {
res.reserve(res.size() + (*args.res).size());
res.insert(res.end(), (*args.res)[i].begin(), (*args.res)[i].end());
}
std::sort(res.begin(), res.end(), tplSorter());
}
void get_tani_nbrs(const std::vector<FPBReader *> &d_readers,
const boost::uint8_t *bv, double threshold,
std::vector<MultiFPBReader::ResultTuple> &res,
int numThreads, bool initOnSearch) {
std::vector<std::vector<MultiFPBReader::ResultTuple>> accum(d_readers.size());
sim_args args = {bv, 0., 0., threshold, d_readers, &accum, initOnSearch};
generic_nbr_helper(res, tani_helper, args, numThreads);
}
void get_tversky_nbrs(const std::vector<FPBReader *> &d_readers,
const boost::uint8_t *bv, double a, double b,
double threshold,
std::vector<MultiFPBReader::ResultTuple> &res,
int numThreads, bool initOnSearch) {
std::vector<std::vector<MultiFPBReader::ResultTuple>> accum(d_readers.size());
sim_args args = {bv, a, b, threshold, d_readers, &accum, initOnSearch};
generic_nbr_helper(res, tversky_helper, args, numThreads);
}
void contain_helper(unsigned int threadId, unsigned int numThreads,
const boost::uint8_t *bv,
const std::vector<FPBReader *> *readers,
std::vector<std::vector<unsigned int>> *accum,
bool initOnSearch) {
for (unsigned int i = threadId; i < readers->size(); i += numThreads) {
if (initOnSearch) (*readers)[i]->init();
(*accum)[i] = (*readers)[i]->getContainingNeighbors(bv);
}
}
void get_containing_nbrs(
const std::vector<FPBReader *> &d_readers, const boost::uint8_t *bv,
std::vector<std::pair<unsigned int, unsigned int>> &res,
unsigned int numThreads, bool initOnSearch) {
numThreads = getNumThreadsToUse(numThreads);
#ifdef RDK_THREADSAFE_SSS
std::vector<std::future<void>> tg;
#endif
std::vector<std::vector<unsigned int>> accum(d_readers.size());
if (numThreads == 1) {
contain_helper(0, 1, bv, &d_readers, &accum, initOnSearch);
}
#ifdef RDK_THREADSAFE_SSS
else {
for (unsigned int tid = 0; tid < numThreads && tid < d_readers.size();
++tid) {
tg.emplace_back(std::async(std::launch::async, contain_helper, tid,
numThreads, bv, &d_readers, &accum,
initOnSearch));
}
for (auto &fut : tg) {
fut.get();
}
}
#endif
res.clear();
for (unsigned int i = 0; i < d_readers.size(); ++i) {
std::vector<unsigned int> &r_res = accum[i];
BOOST_FOREACH (unsigned int ri, r_res) {
res.push_back(std::make_pair(ri, i));
}
}
std::sort(res.begin(), res.end(), pairSorter());
}
} // end of anonymous namespace
void MultiFPBReader::init() {
unsigned int nBits = 0;
BOOST_FOREACH (FPBReader *rdr, d_readers) {
rdr->init();
if (!nBits) {
nBits = rdr->nBits();
} else {
if (rdr->nBits() != nBits)
throw ValueErrorException("bit lengths of child readers don't match");
}
}
df_init = true;
};
MultiFPBReader::MultiFPBReader(std::vector<FPBReader *> &readers,
bool takeOwnership, bool initOnSearch) {
df_init = false;
df_takeOwnership = takeOwnership;
df_initOnSearch = initOnSearch;
BOOST_FOREACH (FPBReader *rdr, readers) {
PRECONDITION(rdr != nullptr, "bad reader");
}
d_readers = readers;
}
FPBReader *MultiFPBReader::getReader(unsigned int which) {
URANGE_CHECK(which, d_readers.size());
return d_readers[which];
}
unsigned int MultiFPBReader::nBits() const {
PRECONDITION(d_readers.size(), "no readers");
PRECONDITION(df_init, "not initialized");
return d_readers[0]->nBits();
}
std::vector<MultiFPBReader::ResultTuple> MultiFPBReader::getTanimotoNeighbors(
const boost::uint8_t *bv, double threshold, int numThreads) const {
PRECONDITION(df_init || df_initOnSearch, "not initialized");
std::vector<MultiFPBReader::ResultTuple> res;
get_tani_nbrs(d_readers, bv, threshold, res, numThreads, df_initOnSearch);
return res;
}
std::vector<MultiFPBReader::ResultTuple> MultiFPBReader::getTanimotoNeighbors(
const ExplicitBitVect &ebv, double threshold, int numThreads) const {
PRECONDITION(df_init || df_initOnSearch, "not initialized");
std::vector<MultiFPBReader::ResultTuple> res;
boost::uint8_t *bv = detail::bitsetToBytes(*(ebv.dp_bits));
get_tani_nbrs(d_readers, bv, threshold, res, numThreads, df_initOnSearch);
delete[] bv;
return res;
}
std::vector<MultiFPBReader::ResultTuple> MultiFPBReader::getTverskyNeighbors(
const boost::uint8_t *bv, double ca, double cb, double threshold,
int numThreads) const {
PRECONDITION(df_init || df_initOnSearch, "not initialized");
std::vector<MultiFPBReader::ResultTuple> res;
get_tversky_nbrs(d_readers, bv, ca, cb, threshold, res, numThreads,
df_initOnSearch);
return res;
}
std::vector<MultiFPBReader::ResultTuple> MultiFPBReader::getTverskyNeighbors(
const ExplicitBitVect &ebv, double ca, double cb, double threshold,
int numThreads) const {
PRECONDITION(df_init || df_initOnSearch, "not initialized");
std::vector<MultiFPBReader::ResultTuple> res;
boost::uint8_t *bv = detail::bitsetToBytes(*(ebv.dp_bits));
get_tversky_nbrs(d_readers, bv, ca, cb, threshold, res, numThreads,
df_initOnSearch);
delete[] bv;
return res;
}
std::vector<std::pair<unsigned int, unsigned int>>
MultiFPBReader::getContainingNeighbors(const boost::uint8_t *bv,
int numThreads) const {
PRECONDITION(df_init || df_initOnSearch, "not initialized");
std::vector<std::pair<unsigned int, unsigned int>> res;
get_containing_nbrs(d_readers, bv, res, numThreads, df_initOnSearch);
return res;
}
std::vector<std::pair<unsigned int, unsigned int>>
MultiFPBReader::getContainingNeighbors(const ExplicitBitVect &ebv,
int numThreads) const {
PRECONDITION(df_init || df_initOnSearch, "not initialized");
std::vector<std::pair<unsigned int, unsigned int>> res;
boost::uint8_t *bv = detail::bitsetToBytes(*(ebv.dp_bits));
get_containing_nbrs(d_readers, bv, res, numThreads, df_initOnSearch);
delete[] bv;
return res;
}
} // end of RDKit namespace
|
