RDKit
Open-source cheminformatics and machine learning.
RandomSample.h
Go to the documentation of this file.
1 //
2 // Copyright (c) 2015, Novartis Institutes for BioMedical Research Inc.
3 // All rights reserved.
4 //
5 // Redistribution and use in source and binary forms, with or without
6 // modification, are permitted provided that the following conditions are
7 // met:
8 //
9 // * Redistributions of source code must retain the above copyright
10 // notice, this list of conditions and the following disclaimer.
11 // * Redistributions in binary form must reproduce the above
12 // copyright notice, this list of conditions and the following
13 // disclaimer in the documentation and/or other materials provided
14 // with the distribution.
15 // * Neither the name of Novartis Institutes for BioMedical Research Inc.
16 // nor the names of its contributors may be used to endorse or promote
17 // products derived from this software without specific prior written
18 // permission.
19 //
20 // THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS
21 // "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT
22 // LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR
23 // A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT
24 // OWNER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL,
25 // SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT
26 // LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE,
27 // DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY
28 // THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT
29 // (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE
30 // OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
31 //
32 
33 #include <RDGeneral/export.h>
34 #ifndef RGROUP_RANDOM_SAMPLE_H
35 #define RGROUP_RANDOM_SAMPLE_H
36 
38 #include <boost/random.hpp>
39 #include <boost/random/uniform_int_distribution.hpp>
40 #include <sstream>
41 
42 namespace RDKit {
43 
44 //! This is a class for fully randomly sampling reagents.
45 // Note that this enumerator never halts.
46 /*!
47  basic usage:
48 
49  \verbatim
50  std::vector<MOL_SPTR_VECT> bbs;
51  bbs.push_back( bbs_for_reactants_1 );
52  bbs.push_back( bbs_for_reactants_2 );
53 
54  RandomSampleStrategy rgroups;
55  rgroups.initialize(rxn, bbs);
56  for(size_t i=0; i<num_samples && rgroups; ++i) {
57  MOL_SPTR_VECT rvect = getReactantsFromRGroups(bbs, rgroups.next());
58  std::vector<MOL_SPTR_VECT> lprops = rxn.RunReactants(rvect);
59  ...
60  }
61  \endverbatim
62 
63  See EnumerationStrategyBase for more details and usage.
64 */
66  : public EnumerationStrategyBase {
67  boost::uint64_t m_numPermutationsProcessed;
68  boost::minstd_rand m_rng;
69  std::vector<boost::random::uniform_int_distribution<>> m_distributions;
70 
71  public:
74  m_numPermutationsProcessed(),
75  m_rng(),
76  m_distributions() {
77  for (size_t i = 0; i < m_permutation.size(); ++i) {
78  m_distributions.push_back(
79  boost::random::uniform_int_distribution<>(0, m_permutation[i] - 1));
80  }
81  }
82 
84 
85  virtual void initializeStrategy(const ChemicalReaction &,
86  const EnumerationTypes::BBS &) {
87  m_distributions.clear();
88  for (size_t i = 0; i < m_permutationSizes.size(); ++i) {
89  m_distributions.push_back(boost::random::uniform_int_distribution<>(
90  0, m_permutationSizes[i] - 1));
91  }
92 
93  m_numPermutationsProcessed = 0;
94  }
95 
96  virtual const char *type() const { return "RandomSampleStrategy"; }
97 
98  //! The current permutation {r1, r2, ...}
99  virtual const EnumerationTypes::RGROUPS &next() {
100  for (size_t i = 0; i < m_permutation.size(); ++i) {
101  m_permutation[i] = m_distributions[i](m_rng);
102  }
103 
104  ++m_numPermutationsProcessed;
105 
106  return m_permutation;
107  }
108 
109  virtual boost::uint64_t getPermutationIdx() const {
110  return m_numPermutationsProcessed;
111  }
112 
113  virtual operator bool() const { return true; }
114 
116  return new RandomSampleStrategy(*this);
117  }
118 
119  private:
120 #ifdef RDK_USE_BOOST_SERIALIZATION
121  friend class boost::serialization::access;
122 
123  template <class Archive>
124  void save(Archive &ar, const unsigned int /*version*/) const {
125  // invoke serialization of the base class
126  ar << boost::serialization::base_object<const EnumerationStrategyBase>(
127  *this);
128  ar << m_numPermutationsProcessed;
129 
130  std::stringstream random;
131  random << m_rng;
132  std::string s = random.str();
133  ar << s;
134  }
135 
136  template <class Archive>
137  void load(Archive &ar, const unsigned int /*version*/) {
138  // invoke serialization of the base class
139  ar >> boost::serialization::base_object<EnumerationStrategyBase>(*this);
140  ar >> m_numPermutationsProcessed;
141  std::string s;
142  ar >> s;
143  std::stringstream random(s);
144  random >> m_rng;
145 
146  // reset the uniform distributions
147  m_distributions.clear();
148  for (size_t i = 0; i < m_permutationSizes.size(); ++i) {
149  m_distributions.push_back(boost::random::uniform_int_distribution<>(
150  0, m_permutationSizes[i] - 1));
151  }
152  }
153 
154  template <class Archive>
155  void serialize(Archive &ar, const unsigned int file_version) {
156  boost::serialization::split_member(ar, *this, file_version);
157  }
158 #endif
159 };
160 } // namespace RDKit
161 
162 #ifdef RDK_USE_BOOST_SERIALIZATION
163 BOOST_CLASS_VERSION(RDKit::RandomSampleStrategy, 1)
164 #endif
165 
166 #endif
EnumerationStrategyBase.h
RDKit::RandomSampleStrategy::initializeStrategy
virtual void initializeStrategy(const ChemicalReaction &, const EnumerationTypes::BBS &)
Definition: RandomSample.h:85
RDKit::EnumerationTypes::BBS
std::vector< MOL_SPTR_VECT > BBS
Definition: EnumerateTypes.h:42
RDKit::RandomSampleStrategy::getPermutationIdx
virtual boost::uint64_t getPermutationIdx() const
Returns how many permutations have been processed by this strategy.
Definition: RandomSample.h:109
RDKit::ChemicalReaction
This is a class for storing and applying general chemical reactions.
Definition: Reaction.h:119
RDKit::RandomSampleStrategy::next
virtual const EnumerationTypes::RGROUPS & next()
The current permutation {r1, r2, ...}.
Definition: RandomSample.h:99
RDKit::EnumerationStrategyBase
Definition: EnumerationStrategyBase.h:120
RDKit::EnumerationTypes::RGROUPS
std::vector< boost::uint64_t > RGROUPS
Definition: EnumerateTypes.h:56
RDKit::RandomSampleStrategy::type
virtual const char * type() const
Definition: RandomSample.h:96
RDKit
Std stuff.
Definition: Atom.h:30
RDKIT_CHEMREACTIONS_EXPORT
#define RDKIT_CHEMREACTIONS_EXPORT
Definition: export.h:60
RDKit::EnumerationStrategyBase::initialize
void initialize(const ChemicalReaction &reaction, const EnumerationTypes::BBS &building_blocks)
Definition: EnumerationStrategyBase.h:141
RDKit::RandomSampleStrategy
This is a class for fully randomly sampling reagents.
Definition: RandomSample.h:65
RDKit::RandomSampleStrategy::copy
EnumerationStrategyBase * copy() const
copy the enumeration strategy complete with current state
Definition: RandomSample.h:115
RDKit::RandomSampleStrategy::RandomSampleStrategy
RandomSampleStrategy()
Definition: RandomSample.h:72
export.h