RDKit: RandomSample.h Source File

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RandomSample.h
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1 //
2 // Copyright (c) 2015, Novartis Institutes for BioMedical Research Inc.
3 // All rights reserved.
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14 // with the distribution.
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32
33 #ifndef RGROUP_RANDOM_SAMPLE_H
34 #define RGROUP_RANDOM_SAMPLE_H
35
36 #include "EnumerationStrategyBase.h"
37 #include <boost/random.hpp>
38 #include <boost/random/uniform_int_distribution.hpp>
39 #include <sstream>
40
41 namespace RDKit {
42
43 //! This is a class for fully randomly sampling reagents.
44 // Note that this enumerator never halts.
45 /*!
46 basic usage:
47
48 \verbatim
49 std::vector<MOL_SPTR_VECT> bbs;
50 bbs.push_back( bbs_for_reactants_1 );
51 bbs.push_back( bbs_for_reactants_2 );
52
53 RandomSampleStrategy rgroups;
54 rgroups.initialize(rxn, bbs);
55 for(size_t i=0; i<num_samples && rgroups; ++i) {
56 MOL_SPTR_VECT rvect = getReactantsFromRGroups(bbs, rgroups.next());
57 std::vector<MOL_SPTR_VECT> lprops = rxn.RunReactants(rvect);
58 ...
59 }
60 \endverbatim
61
62 See EnumerationStrategyBase for more details and usage.
63 */
64 class RandomSampleStrategy : public EnumerationStrategyBase {
65 boost::uint64_t m_numPermutationsProcessed;
66 boost::minstd_rand m_rng;
67 std::vector<boost::random::uniform_int_distribution<> > m_distributions;
68
69 public:
70 RandomSampleStrategy()
71 : EnumerationStrategyBase(),
72 m_numPermutationsProcessed(),
73 m_rng(),
74 m_distributions() {
75 for (size_t i = 0; i < m_permutation.size(); ++i) {
76 m_distributions.push_back(
77 boost::random::uniform_int_distribution<>(0, m_permutation[i] - 1));
78 }
79 }
80
81 using EnumerationStrategyBase::initialize;
82
83 virtual void initializeStrategy(const ChemicalReaction &, const EnumerationTypes::BBS &) {
84 m_distributions.clear();
85 for (size_t i = 0; i < m_permutationSizes.size(); ++i) {
86 m_distributions.push_back(boost::random::uniform_int_distribution<>(
87 0, m_permutationSizes[i] - 1));
88 }
89
90 m_numPermutationsProcessed = 0;
91 }
92
93 virtual const char *type() const { return "RandomSampleStrategy"; }
94
95 //! The current permutation {r1, r2, ...}
96 virtual const EnumerationTypes::RGROUPS &next() {
97 for (size_t i = 0; i < m_permutation.size(); ++i) {
98 m_permutation[i] = m_distributions[i](m_rng);
99 }
100
101 ++m_numPermutationsProcessed;
102
103 return m_permutation;
104 }
105
106 virtual boost::uint64_t getPermutationIdx() const {
107 return m_numPermutationsProcessed; }
108
109 virtual operator bool() const { return true; }
110
111 EnumerationStrategyBase *copy() const {
112 return new RandomSampleStrategy(*this);
113 }
114
115 private:
116 #ifdef RDK_USE_BOOST_SERIALIZATION
117 friend class boost::serialization::access;
118
119 template <class Archive>
120 void save(Archive &ar, const unsigned int /*version*/) const {
121 // invoke serialization of the base class
122 ar << boost::serialization::base_object<const EnumerationStrategyBase>(
123 *this);
124 ar << m_numPermutationsProcessed;
125
126 std::stringstream random;
127 random << m_rng;
128 std::string s = random.str();
129 ar << s;
130 }
131
132 template <class Archive>
133 void load(Archive &ar, const unsigned int /*version*/) {
134 // invoke serialization of the base class
135 ar >> boost::serialization::base_object<EnumerationStrategyBase>(*this);
136 ar >> m_numPermutationsProcessed;
137 std::string s;
138 ar >> s;
139 std::stringstream random(s);
140 random >> m_rng;
141
142 // reset the uniform distributions
143 m_distributions.clear();
144 for (size_t i = 0; i < m_permutationSizes.size(); ++i) {
145 m_distributions.push_back(boost::random::uniform_int_distribution<>(
146 0, m_permutationSizes[i] - 1));
147 }
148 }
149
150 template <class Archive>
151 void serialize(Archive &ar, const unsigned int file_version) {
152 boost::serialization::split_member(ar, *this, file_version);
153 }
154 #endif
155 };
156 }
157
158 #ifdef RDK_USE_BOOST_SERIALIZATION
159 BOOST_CLASS_VERSION(RDKit::RandomSampleStrategy, 1)
160 #endif
161
162 #endif
RDKit::RandomSampleStrategy::initializeStrategy
virtual void initializeStrategy(const ChemicalReaction &, const EnumerationTypes::BBS &)
Definition: RandomSample.h:83
RDKit::RandomSampleStrategy::RandomSampleStrategy
RandomSampleStrategy()
Definition: RandomSample.h:70
EnumerationStrategyBase.h
RDKit::EnumerationStrategyBase::initialize
void initialize(const ChemicalReaction &reaction, const EnumerationTypes::BBS &building_blocks)
Definition: EnumerationStrategyBase.h:135
RDKit::ChemicalReaction
This is a class for storing and applying general chemical reactions.
Definition: Reaction.h:116
RDKit::RandomSampleStrategy::type
virtual const char * type() const
Definition: RandomSample.h:93
RDKit::EnumerationStrategyBase::m_permutation
EnumerationTypes::RGROUPS m_permutation
Definition: EnumerationStrategyBase.h:116
RDKit::RandomSampleStrategy
This is a class for fully randomly sampling reagents.
Definition: RandomSample.h:64
RDKit::EnumerationTypes::BBS
std::vector< MOL_SPTR_VECT > BBS
Definition: EnumerateTypes.h:41
RDKit
Std stuff.
Definition: Atom.h:29
RDKit::EnumerationStrategyBase
Definition: EnumerationStrategyBase.h:114
RDKit::RandomSampleStrategy::next
virtual const EnumerationTypes::RGROUPS & next()
The current permutation {r1, r2, ...}.
Definition: RandomSample.h:96
RDKit::RandomSampleStrategy::copy
EnumerationStrategyBase * copy() const
copy the enumeration strategy complete with current state
Definition: RandomSample.h:111
RDKit::EnumerationTypes::RGROUPS
std::vector< boost::uint64_t > RGROUPS
Definition: EnumerateTypes.h:55
RDKit::EnumerationStrategyBase::m_permutationSizes
EnumerationTypes::RGROUPS m_permutationSizes
Definition: EnumerationStrategyBase.h:118
RDKit::RandomSampleStrategy::getPermutationIdx
virtual boost::uint64_t getPermutationIdx() const
Returns how many permutations have been processed by this strategy.
Definition: RandomSample.h:106