RDKit
Open-source cheminformatics and machine learning.
RandomSample.h
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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 
75  m_rng(),
76  m_distributions() {
77  for (size_t i = 0; i < m_permutation.size(); ++i) {
78  m_distributions.emplace_back(0, m_permutation[i] - 1);
79  }
80  }
81 
83 
85  const EnumerationTypes::BBS &) override {
86  m_distributions.clear();
87  for (size_t i = 0; i < m_permutationSizes.size(); ++i) {
88  m_distributions.emplace_back(0, m_permutationSizes[i] - 1);
89  }
90 
91  m_numPermutationsProcessed = 0;
92  }
93 
94  const char *type() const override { return "RandomSampleStrategy"; }
95 
96  //! The current permutation {r1, r2, ...}
97  const EnumerationTypes::RGROUPS &next() override {
98  for (size_t i = 0; i < m_permutation.size(); ++i) {
99  m_permutation[i] = m_distributions[i](m_rng);
100  }
101 
102  ++m_numPermutationsProcessed;
103 
104  return m_permutation;
105  }
106 
107  boost::uint64_t getPermutationIdx() const override {
108  return m_numPermutationsProcessed;
109  }
110 
111  operator bool() const override { return true; }
112 
113  EnumerationStrategyBase *copy() const override {
114  return new RandomSampleStrategy(*this);
115  }
116 
117  private:
118 #ifdef RDK_USE_BOOST_SERIALIZATION
119  friend class boost::serialization::access;
120 
121  template <class Archive>
122  void save(Archive &ar, const unsigned int /*version*/) const {
123  // invoke serialization of the base class
124  ar << boost::serialization::base_object<const EnumerationStrategyBase>(
125  *this);
126  ar << m_numPermutationsProcessed;
127 
128  std::stringstream random;
129  random << m_rng;
130  std::string s = random.str();
131  ar << s;
132  }
133 
134  template <class Archive>
135  void load(Archive &ar, const unsigned int /*version*/) {
136  // invoke serialization of the base class
137  ar >> boost::serialization::base_object<EnumerationStrategyBase>(*this);
138  ar >> m_numPermutationsProcessed;
139  std::string s;
140  ar >> s;
141  std::stringstream random(s);
142  random >> m_rng;
143 
144  // reset the uniform distributions
145  m_distributions.clear();
146  for (size_t i = 0; i < m_permutationSizes.size(); ++i) {
147  m_distributions.emplace_back(0, m_permutationSizes[i] - 1);
148  }
149  }
150 
151  template <class Archive>
152  void serialize(Archive &ar, const unsigned int file_version) {
153  boost::serialization::split_member(ar, *this, file_version);
154  }
155 #endif
156 };
157 } // namespace RDKit
158 
159 #ifdef RDK_USE_BOOST_SERIALIZATION
160 BOOST_CLASS_VERSION(RDKit::RandomSampleStrategy, 1)
161 #endif
162 
163 #endif
This is a class for storing and applying general chemical reactions.
Definition: Reaction.h:121
void initialize(const ChemicalReaction &reaction, const EnumerationTypes::BBS &building_blocks)
boost::uint64_t getPermutationIdx() const override
Returns how many permutations have been processed by this strategy.
Definition: RandomSample.h:107
const char * type() const override
Definition: RandomSample.h:94
const EnumerationTypes::RGROUPS & next() override
The current permutation {r1, r2, ...}.
Definition: RandomSample.h:97
void initializeStrategy(const ChemicalReaction &, const EnumerationTypes::BBS &) override
Definition: RandomSample.h:84
EnumerationStrategyBase * copy() const override
copy the enumeration strategy complete with current state
Definition: RandomSample.h:113
#define RDKIT_CHEMREACTIONS_EXPORT
Definition: export.h:49
std::vector< boost::uint64_t > RGROUPS
std::vector< MOL_SPTR_VECT > BBS
Std stuff.
Definition: Abbreviations.h:19