RDKit
Open-source cheminformatics and machine learning.
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Public Member Functions | Static Public Attributes | Protected Member Functions | Protected Attributes | Friends | List of all members
RDKit::EnumerationStrategyBase Class Referenceabstract

#include <EnumerationStrategyBase.h>

Inheritance diagram for RDKit::EnumerationStrategyBase:
RDKit::CartesianProductStrategy RDKit::EvenSamplePairsStrategy RDKit::RandomSampleAllBBsStrategy RDKit::RandomSampleStrategy

Public Member Functions

 EnumerationStrategyBase ()
 
virtual ~EnumerationStrategyBase ()
 
virtual const char * type () const
 
void initialize (const ChemicalReaction &reaction, const EnumerationTypes::BBS &building_blocks)
 
virtual void initializeStrategy (const ChemicalReaction &reaction, const EnumerationTypes::BBS &building_blocks)=0
 
virtual operator bool () const =0
 
virtual const EnumerationTypes::RGROUPS & next ()=0
 The current permutation {r1, r2, ...}.
 
virtual EnumerationStrategyBase * copy () const =0
 copy the enumeration strategy complete with current state
 
const EnumerationTypes::RGROUPS & getPosition () const
 The current position in the enumeration.
 
boost::uint64_t getNumPermutations () const
 
virtual boost::uint64_t getPermutationIdx () const =0
 Returns how many permutations have been processed by this strategy.
 
bool skip (boost::uint64_t skipCount)
 

Static Public Attributes

static const boost::uint64_t EnumerationOverflow
 

Protected Member Functions

void internalInitialize (const EnumerationTypes::RGROUPS &rgroups)
 

Protected Attributes

EnumerationTypes::RGROUPS m_permutation
 
EnumerationTypes::RGROUPS m_permutationSizes
 
boost::uint64_t m_numPermutations {}
 

Friends

class boost::serialization::access
 

Detailed Description

Base Class for enumeration strategies Usage: EnumerationStrategyBase must be initialized with both a reaction and the building block (molecule) vector to be sampled.

//!  EnumerationStrategyBase &eb = ...
//!   if(eb) { // can we get another entry
//!    const std::vector<int> &v = eb.next();
//!    v[0] // RGroup 0 position
//!    v[1] // RGroup 1 position...
//!   }
//!

Definition at line 123 of file EnumerationStrategyBase.h.

Constructor & Destructor Documentation

◆ EnumerationStrategyBase()

RDKit::EnumerationStrategyBase::EnumerationStrategyBase ( )
inline

Definition at line 134 of file EnumerationStrategyBase.h.

◆ ~EnumerationStrategyBase()

virtual RDKit::EnumerationStrategyBase::~EnumerationStrategyBase ( )
inlinevirtual

Definition at line 136 of file EnumerationStrategyBase.h.

Member Function Documentation

◆ copy()

virtual EnumerationStrategyBase * RDKit::EnumerationStrategyBase::copy ( ) const
pure virtual

copy the enumeration strategy complete with current state

Implemented in RDKit::CartesianProductStrategy, RDKit::EvenSamplePairsStrategy, RDKit::RandomSampleStrategy, and RDKit::RandomSampleAllBBsStrategy.

◆ getNumPermutations()

boost::uint64_t RDKit::EnumerationStrategyBase::getNumPermutations ( ) const
inline

a result of EnumerationOverflow indicates that the number of permutations is not computable with the current rdlonglong size.

Definition at line 185 of file EnumerationStrategyBase.h.

◆ getPermutationIdx()

virtual boost::uint64_t RDKit::EnumerationStrategyBase::getPermutationIdx ( ) const
pure virtual

Returns how many permutations have been processed by this strategy.

Implemented in RDKit::CartesianProductStrategy, RDKit::EvenSamplePairsStrategy, RDKit::RandomSampleStrategy, and RDKit::RandomSampleAllBBsStrategy.

◆ getPosition()

const EnumerationTypes::RGROUPS & RDKit::EnumerationStrategyBase::getPosition ( ) const
inline

The current position in the enumeration.

Definition at line 180 of file EnumerationStrategyBase.h.

◆ initialize()

void RDKit::EnumerationStrategyBase::initialize ( const ChemicalReaction &  reaction,
const EnumerationTypes::BBS &  building_blocks 
)
inline

Initialize the enumerator based on the reaction and the supplied building blocks This is the standard API point. This calls the derived class's initializeStrategy method which must be implemented

Definition at line 145 of file EnumerationStrategyBase.h.

References RDKit::computeNumProducts(), and RDKit::getSizesFromBBs().

◆ initializeStrategy()

virtual void RDKit::EnumerationStrategyBase::initializeStrategy ( const ChemicalReaction &  reaction,
const EnumerationTypes::BBS &  building_blocks 
)
pure virtual

Implemented in RDKit::CartesianProductStrategy, RDKit::EvenSamplePairsStrategy, RDKit::RandomSampleStrategy, and RDKit::RandomSampleAllBBsStrategy.

◆ internalInitialize()

void RDKit::EnumerationStrategyBase::internalInitialize ( const EnumerationTypes::RGROUPS &  rgroups)
inlineprotected

Initialize the internal data structures i.e. RGROUPS = {10,40,50};

Definition at line 202 of file EnumerationStrategyBase.h.

References RDKit::computeNumProducts().

◆ next()

virtual const EnumerationTypes::RGROUPS & RDKit::EnumerationStrategyBase::next ( )
pure virtual

The current permutation {r1, r2, ...}.

Implemented in RDKit::CartesianProductStrategy, RDKit::EvenSamplePairsStrategy, RDKit::RandomSampleStrategy, and RDKit::RandomSampleAllBBsStrategy.

◆ operator bool()

virtual RDKit::EnumerationStrategyBase::operator bool ( ) const
pure virtual

returns true if there are more permutations left random enumerators may always return true...

Implemented in RDKit::CartesianProductStrategy, RDKit::EvenSamplePairsStrategy, RDKit::RandomSampleStrategy, and RDKit::RandomSampleAllBBsStrategy.

◆ skip()

bool RDKit::EnumerationStrategyBase::skip ( boost::uint64_t  skipCount)
inline

Skip the specified number of permutations (useful for resetting state to a known position)

Definition at line 192 of file EnumerationStrategyBase.h.

◆ type()

virtual const char * RDKit::EnumerationStrategyBase::type ( ) const
inlinevirtual

Reimplemented in RDKit::CartesianProductStrategy, RDKit::EvenSamplePairsStrategy, RDKit::RandomSampleStrategy, and RDKit::RandomSampleAllBBsStrategy.

Definition at line 138 of file EnumerationStrategyBase.h.

Friends And Related Symbol Documentation

◆ boost::serialization::access

friend class boost::serialization::access
friend

Definition at line 210 of file EnumerationStrategyBase.h.

Member Data Documentation

◆ EnumerationOverflow

const boost::uint64_t RDKit::EnumerationStrategyBase::EnumerationOverflow
static
Initial value:
=
static_cast<boost::uint64_t>(-1)

Definition at line 132 of file EnumerationStrategyBase.h.

◆ m_numPermutations

boost::uint64_t RDKit::EnumerationStrategyBase::m_numPermutations {}
protected

Definition at line 129 of file EnumerationStrategyBase.h.

◆ m_permutation

EnumerationTypes::RGROUPS RDKit::EnumerationStrategyBase::m_permutation
protected

Definition at line 125 of file EnumerationStrategyBase.h.

◆ m_permutationSizes

EnumerationTypes::RGROUPS RDKit::EnumerationStrategyBase::m_permutationSizes
protected

Definition at line 127 of file EnumerationStrategyBase.h.

The documentation for this class was generated from the following file: