RDKit: CartesianProduct.h Source File

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CartesianProduct.h
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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
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20// THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS
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32
33#include <RDGeneral/export.h>
34#ifndef CARTESIANPRODUCT_H
35#define CARTESIANPRODUCT_H
36
37#include "EnumerationStrategyBase.h"
38
39namespace RDKit {
40//! This is a class for enumerating reagents using Cartesian Products of
41/// reagents.
42/*!
43 CartesianProductStrategy produces a standard walk through all possible
44 reagent combinations:
45
46 (0,0,0), (1,0,0), (2,0,0) ...
47
48 basic usage:
49
50 \verbatim
51 std::vector<MOL_SPTR_VECT> bbs;
52 bbs.push_back( bbs_for_reactants_1 );
53 bbs.push_back( bbs_for_reactants_2 );
54
55 RGRUOPS num_bbs;
56 num_bbs.push_back(bbs[0].size());
57 num_bbs.push_back(bbs[1].size());
58
59 CartesianProductStrategy rgroups(num_bbs);
60 for(size_t i=0; i<num_samples && rgroups; ++i) {
61 MOL_SPTR_VECT rvect = getReactantsFromRGroups(bbs, rgroups.next());
62 std::vector<MOL_SPTR_VECT> lprops = rxn.RunReactants(rvect);
63 ...
64 }
65 \endverbatim
66
67See EnumerationStrategyBase for more details and usage.
68*/
69
70 class RDKIT_CHEMREACTIONS_EXPORT CartesianProductStrategy
71 : public EnumerationStrategyBase {
72 size_t m_numPermutationsProcessed{};
73
74 public:
75 CartesianProductStrategy() : EnumerationStrategyBase() {}
76
77 using EnumerationStrategyBase::initialize;
78
79 void initializeStrategy(const ChemicalReaction &,
80 const EnumerationTypes::BBS &) override {
81 m_numPermutationsProcessed = 0;
82 }
83
84 const char *type() const override { return "CartesianProductStrategy"; }
85
86 //! The current permutation {r1, r2, ...}
87 const EnumerationTypes::RGROUPS &next() override {
88 if (m_numPermutationsProcessed) {
89 increment();
90 } else {
91 ++m_numPermutationsProcessed;
92 }
93
94 return m_permutation;
95 }
96
97 boost::uint64_t getPermutationIdx() const override {
98 return m_numPermutationsProcessed;
99 }
100
101 operator bool() const override { return hasNext(); }
102
103 EnumerationStrategyBase *copy() const override {
104 return new CartesianProductStrategy(*this);
105 }
106
107 private:
108 void increment() {
109 next(0);
110 ++m_numPermutationsProcessed;
111 }
112
113 bool hasNext() const {
114 // Fix me -> use multiprecision int here???
115 return m_numPermutations == EnumerationStrategyBase::EnumerationOverflow ||
116 m_numPermutationsProcessed < rdcast<size_t>(m_numPermutations);
117 }
118
119 void next(size_t rowToIncrement) {
120 if (!hasNext()) {
121 return;
122 }
123 m_permutation[rowToIncrement] += 1;
124 size_t max_index_of_row = m_permutationSizes[rowToIncrement] - 1;
125 if (m_permutation[rowToIncrement] > max_index_of_row) {
126 m_permutation[rowToIncrement] = 0;
127 next(rowToIncrement + 1);
128 }
129 }
130
131 private:
132#ifdef RDK_USE_BOOST_SERIALIZATION
133 friend class boost::serialization::access;
134 template <class Archive>
135 void serialize(Archive &ar, const unsigned int /*version*/) {
136 ar &boost::serialization::base_object<EnumerationStrategyBase>(*this);
137 ar & m_numPermutationsProcessed;
138 }
139#endif
140};
141} // namespace RDKit
142
143#ifdef RDK_USE_BOOST_SERIALIZATION
144BOOST_CLASS_VERSION(RDKit::CartesianProductStrategy, 1)
145#endif
146
147#endif
EnumerationStrategyBase.h
RDKit::CartesianProductStrategy
Definition CartesianProduct.h:71
RDKit::CartesianProductStrategy::getPermutationIdx
boost::uint64_t getPermutationIdx() const override
Returns how many permutations have been processed by this strategy.
Definition CartesianProduct.h:97
RDKit::CartesianProductStrategy::copy
EnumerationStrategyBase * copy() const override
copy the enumeration strategy complete with current state
Definition CartesianProduct.h:103
RDKit::CartesianProductStrategy::type
const char * type() const override
Definition CartesianProduct.h:84
RDKit::CartesianProductStrategy::next
const EnumerationTypes::RGROUPS & next() override
The current permutation {r1, r2, ...}.
Definition CartesianProduct.h:87
RDKit::CartesianProductStrategy::initializeStrategy
void initializeStrategy(const ChemicalReaction &, const EnumerationTypes::BBS &) override
Definition CartesianProduct.h:79
RDKit::CartesianProductStrategy::CartesianProductStrategy
CartesianProductStrategy()
Definition CartesianProduct.h:75
RDKit::ChemicalReaction
This is a class for storing and applying general chemical reactions.
Definition Reaction.h:121
RDKit::EnumerationStrategyBase::initialize
void initialize(const ChemicalReaction &reaction, const EnumerationTypes::BBS &building_blocks)
Definition EnumerationStrategyBase.h:145
RDKit::EnumerationStrategyBase::m_permutation
EnumerationTypes::RGROUPS m_permutation
Definition EnumerationStrategyBase.h:125
RDKit::EnumerationStrategyBase::EnumerationStrategyBase
EnumerationStrategyBase()
Definition EnumerationStrategyBase.h:134
export.h
RDKIT_CHEMREACTIONS_EXPORT
#define RDKIT_CHEMREACTIONS_EXPORT
Definition export.h:57
RDKit::EnumerationTypes::RGROUPS
std::vector< boost::uint64_t > RGROUPS
Definition EnumerateTypes.h:56
RDKit::EnumerationTypes::BBS
std::vector< MOL_SPTR_VECT > BBS
Definition EnumerateTypes.h:42
RDKit::MolStandardize::Operations::serialize
RDKIT_MOLSTANDARDIZE_EXPORT void serialize(RWMOL_SPTR_PAIR output, PipelineResult &result, const PipelineOptions &options)
RDKit
Std stuff.
Definition Abbreviations.h:19