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RDKit
Open-source cheminformatics and machine learning.
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33 #ifndef ENUMERATION_STRATEGY_H
34 #define ENUMERATION_STRATEGY_H
37 #include "../Reaction.h"
41 #ifdef RDK_USE_BOOST_SERIALIZATION
42 #include <boost/serialization/assume_abstract.hpp>
43 #include <boost/serialization/vector.hpp>
45 #include <boost/serialization/singleton.hpp>
46 #include <boost/serialization/extended_type_info.hpp>
47 #include <boost/serialization/shared_ptr.hpp>
57 :
public std::exception {
61 const char *
what() const noexcept
override {
return _msg.c_str(); };
62 const char *
message() const noexcept {
return what(); };
76 const std::vector<std::vector<T>> &bbs) {
78 for (
size_t i = 0; i < bbs.size(); ++i) sizes.push_back(bbs[i].size());
87 const std::vector<MOL_SPTR_VECT> &bbs);
130 static const boost::uint64_t EnumerationOverflow =
131 static_cast<boost::uint64_t
>(-1);
133 : m_permutation(), m_permutationSizes(), m_numPermutations() {}
137 virtual const char *
type()
const {
return "EnumerationStrategyBase"; }
148 m_permutation.resize(m_permutationSizes.size());
151 std::fill(m_permutation.begin(), m_permutation.end(), 0);
153 initializeStrategy(reaction, building_blocks);
167 virtual operator bool()
const = 0;
188 bool skip(boost::uint64_t skipCount) {
189 for (boost::uint64_t i = 0; i < skipCount; ++i) next();
197 m_permutation.resize(rgroups.size());
198 m_permutationSizes = rgroups;
200 std::fill(m_permutation.begin(), m_permutation.end(), 0);
204 friend class boost::serialization::access;
205 template <
class Archive>
206 void serialize(Archive &ar,
const unsigned int ) {
208 ar &m_permutationSizes;
209 ar &m_numPermutations;
212 #ifdef RDK_USE_BOOST_SERIALIZATION
213 BOOST_SERIALIZATION_ASSUME_ABSTRACT(EnumerationStrategyBase)
217 #ifdef RDK_USE_BOOST_SERIALIZATION
class for flagging enumeration strategy errors
virtual void initializeStrategy(const ChemicalReaction &reaction, const EnumerationTypes::BBS &building_blocks)=0
boost::uint64_t m_numPermutations
virtual boost::uint64_t getPermutationIdx() const =0
Returns how many permutations have been processed by this strategy.
~EnumerationStrategyException() noexcept
const char * what() const noexcept override
virtual const EnumerationTypes::RGROUPS & next()=0
The current permutation {r1, r2, ...}.
const EnumerationTypes::RGROUPS & getPosition() const
The current position in the enumeration.
boost::uint64_t getNumPermutations() const
RDKIT_CHEMREACTIONS_EXPORT MOL_SPTR_VECT getReactantsFromRGroups(const std::vector< MOL_SPTR_VECT > &bbs, const EnumerationTypes::RGROUPS &rgroups)
void internalInitialize(const EnumerationTypes::RGROUPS &rgroups)
EnumerationStrategyException(const char *msg)
bool skip(boost::uint64_t skipCount)
EnumerationTypes::RGROUPS m_permutationSizes
pulls in the core RDKit functionality
std::vector< boost::shared_ptr< ROMol > > MOL_SPTR_VECT
std::vector< MOL_SPTR_VECT > BBS
EnumerationStrategyBase()
This is a class for storing and applying general chemical reactions.
EnumerationStrategyException(const std::string &msg)
virtual const char * type() const
RDKIT_CHEMREACTIONS_EXPORT EnumerationTypes::RGROUPS getSizesFromReactants(const std::vector< MOL_SPTR_VECT > &bbs)
virtual EnumerationStrategyBase * copy() const =0
copy the enumeration strategy complete with current state
std::vector< boost::uint64_t > RGROUPS
RDKIT_CHEMREACTIONS_EXPORT boost::uint64_t computeNumProducts(const EnumerationTypes::RGROUPS &sizes)
virtual ~EnumerationStrategyBase()
#define RDKIT_CHEMREACTIONS_EXPORT
EnumerationTypes::RGROUPS getSizesFromBBs(const std::vector< std::vector< T >> &bbs)
Return the number of elements per input vector.
EnumerationTypes::RGROUPS m_permutation
void initialize(const ChemicalReaction &reaction, const EnumerationTypes::BBS &building_blocks)
const char * message() const noexcept