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  boost::uint64_t m_numPermutationsProcessed;
67  boost::minstd_rand m_rng;
68  std::vector<boost::random::uniform_int_distribution<> > m_distributions;
69 
70  public:
73  m_numPermutationsProcessed(),
74  m_rng(),
75  m_distributions() {
76  for (size_t i = 0; i < m_permutation.size(); ++i) {
77  m_distributions.push_back(
78  boost::random::uniform_int_distribution<>(0, m_permutation[i] - 1));
79  }
80  }
81 
83 
85  m_distributions.clear();
86  for (size_t i = 0; i < m_permutationSizes.size(); ++i) {
87  m_distributions.push_back(boost::random::uniform_int_distribution<>(
88  0, m_permutationSizes[i] - 1));
89  }
90 
91  m_numPermutationsProcessed = 0;
92  }
93 
94  virtual const char *type() const { return "RandomSampleStrategy"; }
95 
96  //! The current permutation {r1, r2, ...}
97  virtual const EnumerationTypes::RGROUPS &next() {
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  virtual boost::uint64_t getPermutationIdx() const {
108  return m_numPermutationsProcessed; }
109 
110  virtual operator bool() const { return true; }
111 
113  return new RandomSampleStrategy(*this);
114  }
115 
116  private:
117 #ifdef RDK_USE_BOOST_SERIALIZATION
118  friend class boost::serialization::access;
119 
120  template <class Archive>
121  void save(Archive &ar, const unsigned int /*version*/) const {
122  // invoke serialization of the base class
123  ar << boost::serialization::base_object<const EnumerationStrategyBase>(
124  *this);
125  ar << m_numPermutationsProcessed;
126 
127  std::stringstream random;
128  random << m_rng;
129  std::string s = random.str();
130  ar << s;
131  }
132 
133  template <class Archive>
134  void load(Archive &ar, const unsigned int /*version*/) {
135  // invoke serialization of the base class
136  ar >> boost::serialization::base_object<EnumerationStrategyBase>(*this);
137  ar >> m_numPermutationsProcessed;
138  std::string s;
139  ar >> s;
140  std::stringstream random(s);
141  random >> m_rng;
142 
143  // reset the uniform distributions
144  m_distributions.clear();
145  for (size_t i = 0; i < m_permutationSizes.size(); ++i) {
146  m_distributions.push_back(boost::random::uniform_int_distribution<>(
147  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 }
158 
159 #ifdef RDK_USE_BOOST_SERIALIZATION
160 BOOST_CLASS_VERSION(RDKit::RandomSampleStrategy, 1)
161 #endif
162 
163 #endif
virtual void initializeStrategy(const ChemicalReaction &, const EnumerationTypes::BBS &)
Definition: RandomSample.h:84
void initialize(const ChemicalReaction &reaction, const EnumerationTypes::BBS &building_blocks)
This is a class for storing and applying general chemical reactions.
Definition: Reaction.h:118
virtual boost::uint64_t getPermutationIdx() const
Returns how many permutations have been processed by this strategy.
Definition: RandomSample.h:107
This is a class for fully randomly sampling reagents.
Definition: RandomSample.h:65
virtual const char * type() const
Definition: RandomSample.h:94
std::vector< MOL_SPTR_VECT > BBS
Std stuff.
Definition: Atom.h:30
virtual const EnumerationTypes::RGROUPS & next()
The current permutation {r1, r2, ...}.
Definition: RandomSample.h:97
std::vector< boost::uint64_t > RGROUPS
#define RDKIT_CHEMREACTIONS_EXPORT
Definition: export.h:60
EnumerationStrategyBase * copy() const
copy the enumeration strategy complete with current state
Definition: RandomSample.h:112