RDKit
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Enumerate.h
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32 #include <RDGeneral/export.h>
33 #ifndef RDKIT_ENUMERATE_H
34 #define RDKIT_ENUMERATE_H
35 #include "EnumerateBase.h"
36 
37 /*! \file Enumerate.h
38 
39 \brief Contains the public API of the for the reaction enumeration engine
40 
41 \b Note that this should be considered beta and that the API may change in
42 future releases.
43 
44 */
45 
46 namespace RDKit {
47 
48 //! This is a class for providing enumeration options that control
49 /// how enumerations are performed.
50 /*!
51  Option
52  reagentMaxMatchCount [default INT_MAX]
53  This specifies how many times the reactant template can match a reagent.
54 
55  sanePartialProducts [default false]
56  If true, forces all products of the reagent plus the product templates\n\
57  pass chemical sanitization. Note that if the product template itself\n\
58  does not pass sanitization, then none of the products will.
59 */
61  int reagentMaxMatchCount{INT_MAX};
62  bool sanePartialProducts{false};
64 
66  : reagentMaxMatchCount(rhs.reagentMaxMatchCount),
67  sanePartialProducts(rhs.sanePartialProducts) {}
68 };
69 
70 //! Helper function, remove reagents that are incompatible
71 /// with the reaction.
72 /// rxn must be sanitized, initialized and preprocessed.
73 /// this happens automatically in EnumerateLibrary
76  const EnumerationParams &params = EnumerationParams());
77 
78 //! This is a class for running reactions on sets of reagents.
79 /*!
80  This class is a fully self contained reaction engine that can be
81  serialized and restarted. For example, a million products can
82  be generated, the engine can be saved for later and reloaded
83  to retrieve the next million products.
84 
85  basic usage will be something like:
86  \verbatim
87  ChemicalReaction rxn = ...
88  BBS bbs(num_rgroups);
89  ... somehow LoadRGroups(bbs[0]);
90  ... somehow LoadRGroups(bbs[1]..);
91  ...
92  EnumerateLibrary enumerator(en, bbs);
93  for(; (bool)en; ++i) {
94  // This is the same as rxn.run_Reactants( reagents );
95  std::vector<MOL_SPTR_VECT> products = en.next();
96  ...
97  }
98  \endverbatim
99 
100  In general, reactions will enumerate to more products than desired,
101  a standard use is:
102 
103  \verbatim
104  for(int i=0;i<num_samples && (bool)en; ++i) {
105  std::vector<MOL_SPTR_VECT> products = en.next();
106  ...
107  }
108  \endverbatim
109  */
110 
112  : public EnumerateLibraryBase {
113  EnumerationTypes::BBS m_bbs;
114 
115  public:
117  EnumerateLibrary(const std::string &s) : EnumerateLibraryBase(), m_bbs() {
118  initFromString(s);
119  }
120 
122  const EnumerationTypes::BBS &reagents,
123  const EnumerationParams &params = EnumerationParams());
125  const EnumerationTypes::BBS &reagents,
126  const EnumerationStrategyBase &enumerator,
127  const EnumerationParams &params = EnumerationParams());
129 
130  //! Return the reagents used in the library
131  const EnumerationTypes::BBS &getReagents() const { return m_bbs; }
132 
133  //! Get the next product set
134  std::vector<MOL_SPTR_VECT> next() override;
135 
136  void toStream(std::ostream &ss) const override;
137  void initFromStream(std::istream &ss) override;
138 
139  private:
140 #ifdef RDK_USE_BOOST_SERIALIZATION
141  friend class boost::serialization::access;
142  template <class Archive>
143  void save(Archive &ar, const unsigned int /*version*/) const {
144  ar &boost::serialization::base_object<EnumerateLibraryBase>(*this);
145  size_t sz = m_bbs.size();
146  ar &sz;
147 
148  std::string pickle;
149  for (size_t i = 0; i < m_bbs.size(); ++i) {
150  sz = m_bbs[i].size();
151  ar &sz;
152  for (size_t j = 0; j < m_bbs[i].size(); ++j) {
153  MolPickler::pickleMol(*m_bbs[i][j], pickle);
154  ar &pickle;
155  }
156  }
157  }
158  template <class Archive>
159  void load(Archive &ar, const unsigned int /*version*/) {
160  ar &boost::serialization::base_object<EnumerateLibraryBase>(*this);
161 
162  size_t sz;
163  ar &sz;
164 
165  m_bbs.resize(sz);
166 
167  for (size_t i = 0; i < m_bbs.size(); ++i) {
168  ar &sz;
169  m_bbs[i].resize(sz);
170  std::string pickle;
171  for (size_t j = 0; j < m_bbs[i].size(); ++j) {
172  ar &pickle;
173  RWMol *mol = new RWMol();
175  m_bbs[i][j].reset(mol);
176  }
177  }
178  }
179 
180  BOOST_SERIALIZATION_SPLIT_MEMBER();
181 #endif
182 };
183 
185 
186 } // namespace RDKit
187 #endif
This is a class for storing and applying general chemical reactions.
Definition: Reaction.h:121
This is a class for running reactions on sets of reagents.
Definition: Enumerate.h:112
EnumerateLibrary(const std::string &s)
Definition: Enumerate.h:117
std::vector< MOL_SPTR_VECT > next() override
Get the next product set.
EnumerateLibrary(const EnumerateLibrary &rhs)
void toStream(std::ostream &ss) const override
serializes (pickles) to a stream
void initFromStream(std::istream &ss) override
initializes from a stream pickle
EnumerateLibrary(const ChemicalReaction &rxn, const EnumerationTypes::BBS &reagents, const EnumerationParams &params=EnumerationParams())
const EnumerationTypes::BBS & getReagents() const
Return the reagents used in the library.
Definition: Enumerate.h:131
EnumerateLibrary(const ChemicalReaction &rxn, const EnumerationTypes::BBS &reagents, const EnumerationStrategyBase &enumerator, const EnumerationParams &params=EnumerationParams())
static void molFromPickle(const std::string &pickle, ROMol *mol, unsigned int propertyFlags)
constructs a molecule from a pickle stored in a string
static void pickleMol(const ROMol *mol, std::ostream &ss)
pickles a molecule and sends the results to stream ss
#define RDKIT_CHEMREACTIONS_EXPORT
Definition: export.h:49
RDKIT_CHEMREACTIONS_EXPORT void pickle(const boost::shared_ptr< EnumerationStrategyBase > &enumerator, std::ostream &ss)
pickles a EnumerationStrategy and adds the results to a stream ss
std::vector< MOL_SPTR_VECT > BBS
Std stuff.
Definition: Abbreviations.h:18
RDKIT_CHEMREACTIONS_EXPORT EnumerationTypes::BBS removeNonmatchingReagents(const ChemicalReaction &rxn, EnumerationTypes::BBS bbs, const EnumerationParams &params=EnumerationParams())
RDKIT_CHEMREACTIONS_EXPORT bool EnumerateLibraryCanSerialize()
EnumerationParams(const EnumerationParams &rhs)
Definition: Enumerate.h:65