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
|
//
// Copyright (c) 2016, Novartis Institutes for BioMedical Research Inc.
// All rights reserved.
//
// Redistribution and use in source and binary forms, with or without
// modification, are permitted provided that the following conditions are
// met:
//
// * Redistributions of source code must retain the above copyright
// notice, this list of conditions and the following disclaimer.
// * Redistributions in binary form must reproduce the above
// copyright notice, this list of conditions and the following
// disclaimer in the documentation and/or other materials provided
// with the distribution.
// * Neither the name of Novartis Institutes for BioMedical Research Inc.
// nor the names of its contributors may be used to endorse or promote
// products derived from this software without specific prior written
// permission.
//
// THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS
// "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT
// LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR
// A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT
// OWNER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL,
// SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT
// LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE,
// DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY
// THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT
// (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE
// OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
//
#include <RDGeneral/export.h>
#ifndef RGROUP_EVEN_SAMPLE_H
#define RGROUP_EVEN_SAMPLE_H
#include "EnumerationStrategyBase.h"
#ifdef RDK_USE_BOOST_SERIALIZATION
#include <boost/serialization/set.hpp>
#endif
#include <boost/cstdint.hpp>
namespace RDKit {
//! EvenSamplePairsStrategy
/*! Randomly sample Pairs evenly from a collection of building blocks
This is a good strategy for choosing a relatively small selection
of building blocks from a larger set. As the amount of work needed
to retrieve the next evenly sample building block grows with the
number of samples, this method performs progressively worse as the
number of samples gets larger.
See EnumeartionStrategyBase for more details.
*/
class RDKIT_CHEMREACTIONS_EXPORT EvenSamplePairsStrategy : public EnumerationStrategyBase {
boost::uint64_t m_numPermutationsProcessed;
std::vector<boost::int64_t> used_count;
std::vector<std::vector<boost::uint64_t> > var_used;
std::vector<std::vector<boost::uint64_t> > pair_used;
std::vector<std::vector<boost::uint64_t> > pair_counts;
std::set<boost::uint64_t> selected;
boost::uint64_t seed; // last seed for permutation (starts at 0)
boost::uint64_t M, a, b; // random number stuff
boost::uint64_t nslack, min_nslack;
boost::uint64_t rejected_period, rejected_unique;
boost::uint64_t rejected_slack_condition, rejected_bb_sampling_condition;
public:
EvenSamplePairsStrategy()
: EnumerationStrategyBase(),
m_numPermutationsProcessed(),
used_count(),
var_used(),
pair_used(),
pair_counts(),
selected(),
seed(),
M(),
a(),
b(),
nslack(),
min_nslack(),
rejected_period(),
rejected_unique(),
rejected_slack_condition(),
rejected_bb_sampling_condition() {}
EvenSamplePairsStrategy(const EvenSamplePairsStrategy &rhs)
: EnumerationStrategyBase(rhs),
m_numPermutationsProcessed(rhs.m_numPermutationsProcessed),
used_count(rhs.used_count),
var_used(rhs.var_used),
pair_used(rhs.pair_used),
pair_counts(rhs.pair_counts),
selected(rhs.selected),
seed(rhs.seed),
M(rhs.M),
a(rhs.a),
b(rhs.b),
nslack(rhs.nslack),
min_nslack(rhs.min_nslack),
rejected_period(rhs.rejected_period),
rejected_unique(rhs.rejected_unique),
rejected_slack_condition(rhs.rejected_slack_condition),
rejected_bb_sampling_condition(rhs.rejected_bb_sampling_condition) {}
virtual const char *type() const { return "EvenSamplePairsStrategy"; }
//! This is a class for enumerating RGroups using Cartesian Products of
//! reagents.
/*!
basic usage:
\verbatim
std::vector<MOL_SPTR_VECT> bbs;
bbs.push_back( bbs_for_reactants_1 );
bbs.push_back( bbs_for_reactants_2 );
EvenSamplePairsStrategy rgroups;
rgroups.initialize(rxn, bbs);
for(boost::uint64_t i=0; i<num_samples && rgroups; ++i) {
MOL_SPTR_VECT rvect = getReactantsFromRGroups(bbs, rgroups.next());
std::vector<MOL_SPTR_VECT> lprops = rxn.RunReactants(rvect);
...
}
\endverbatim
*/
using EnumerationStrategyBase::initialize;
virtual void initializeStrategy(const ChemicalReaction &,
const EnumerationTypes::BBS &);
//! The current permutation {r1, r2, ...}
virtual const EnumerationTypes::RGROUPS &next();
virtual boost::uint64_t getPermutationIdx() const {
return m_numPermutationsProcessed;
}
virtual operator bool() const { return true; }
EnumerationStrategyBase *copy() const {
return new EvenSamplePairsStrategy(*this);
}
std::string stats() const;
private:
friend class boost::serialization::access;
// decode a packed integer into an RGroup selection
const EnumerationTypes::RGROUPS &decode(boost::uint64_t seed) {
for (boost::int64_t j = m_permutationSizes.size() - 1; j >= 0; j--) {
m_permutation[j] = seed % m_permutationSizes[j];
seed /= m_permutationSizes[j];
}
return m_permutation;
}
bool try_add(boost::uint64_t seed);
public:
#ifdef RDK_USE_BOOST_SERIALIZATION
template <class Archive>
void serialize(Archive &ar, const unsigned int /*version*/) {
// invoke serialization of the base class
ar &boost::serialization::base_object<EnumerationStrategyBase>(*this);
ar &m_numPermutationsProcessed;
ar &used_count;
ar &var_used;
ar &pair_used;
ar &pair_counts;
ar &selected;
ar &seed;
ar &M;
ar &a;
ar &b;
ar &nslack;
ar &min_nslack;
ar &rejected_period;
ar &rejected_unique;
ar &rejected_slack_condition;
ar &rejected_bb_sampling_condition;
}
#endif
};
}
BOOST_CLASS_VERSION(RDKit::EvenSamplePairsStrategy, 1)
#endif
|
