RDKit
Open-source cheminformatics and machine learning.
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Public Member Functions | List of all members
RDKit::SynthonSpaceSearch::SynthonSet Class Reference

#include <SynthonSet.h>

Public Member Functions

 SynthonSet ()=default
 
 SynthonSet (const std::string &id)
 
 SynthonSet (const SynthonSet &rhs)=delete
 
 SynthonSet (SynthonSet &&rhs)=delete
 
const std::string & getId () const
 
const std::vector< std::vector< std::pair< std::string, Synthon * > > > & getSynthons () const
 
const std::pair< std::string, Synthon * > getSubstructureOrderedSynthon (size_t setNum, size_t synthonNum) const
 
const std::pair< std::string, Synthon * > getFingerprintOrderedSynthon (size_t setNum, size_t synthonNum) const
 
const std::pair< std::string, Synthon * > getRascalOrderedSynthon (size_t setNum, size_t synthonNum) const
 
size_t getSubstructureOrderedSynthonNum (size_t setNum, size_t synthonNum) const
 
size_t getFingerprintOrderedSynthonNum (size_t setNum, size_t synthonNum) const
 
size_t getRascalOrderedSynthonNum (size_t setNum, size_t synthonNum) const
 
const boost::dynamic_bitset & getConnectors () const
 
const std::vector< boost::dynamic_bitset<> > & getSynthonConnectorPatterns () const
 
const std::vector< std::shared_ptr< ROMol > > & getConnectorRegions () const
 
const std::vector< std::string > & getConnectorRegionSmiles () const
 
const std::vector< std::unique_ptr< ExplicitBitVect > > & getConnRegFPs () const
 
const std::unique_ptr< ExplicitBitVect > & getAddFP () const
 
const std::unique_ptr< ExplicitBitVect > & getSubtractFP () const
 
const std::vector< int > & getNumConnectors () const
 
std::uint64_t getNumProducts () const
 
bool hasFingerprints () const
 
bool hasAddAndSubtractFPs () const
 
unsigned int getNumRingFormers () const
 
void writeToDBStream (std::ostream &os) const
 
void readFromDBStream (std::istream &is, const SynthonSpace &space, std::uint32_t version)
 
void enumerateToStream (std::ostream &os) const
 
void addSynthon (int synthonSetNum, Synthon *newSynthon, const std::string &synthonId)
 
void removeEmptySynthonSets ()
 
void makeSynthonSearchMols ()
 
void buildConnectorRegions ()
 
void assignConnectorsUsed ()
 
void buildSynthonFingerprints (const FingerprintGenerator< std::uint64_t > &fpGen)
 
void buildAddAndSubtractFPs (const FingerprintGenerator< std::uint64_t > &fpGen, unsigned int numBits)
 
std::vector< std::vector< ROMol * > > getSynthons (const std::vector< boost::dynamic_bitset<> > &reqSynths) const
 
std::string buildProductName (const std::vector< size_t > &synthNums) const
 
std::unique_ptr< ROMol > buildProduct (const std::vector< size_t > &synthNums) const
 
void initializeSearchOrders ()
 
std::vector< std::vector< size_t > > orderSynthonsForSearch (const std::function< bool(const Synthon *synthon1, const Synthon *synthon2)> &cmp)
 
std::unique_ptr< SampleMolRec > makeSampleMolecule (Synthon *synthon) const
 
std::unique_ptr< ROMol > buildMolecule (const std::vector< size_t > &synthonNums) const
 
void assessRingFormers ()
 

Detailed Description

Definition at line 51 of file SynthonSet.h.

Constructor & Destructor Documentation

◆ SynthonSet() [1/4]

RDKit::SynthonSpaceSearch::SynthonSet::SynthonSet ( )
default

Referenced by SynthonSet(), and SynthonSet().

◆ SynthonSet() [2/4]

RDKit::SynthonSpaceSearch::SynthonSet::SynthonSet ( const std::string & id)
inlineexplicit

Definition at line 54 of file SynthonSet.h.

◆ SynthonSet() [3/4]

RDKit::SynthonSpaceSearch::SynthonSet::SynthonSet ( const SynthonSet & rhs)
delete

References SynthonSet().

◆ SynthonSet() [4/4]

RDKit::SynthonSpaceSearch::SynthonSet::SynthonSet ( SynthonSet && rhs)
delete

References SynthonSet().

Member Function Documentation

◆ addSynthon()

void RDKit::SynthonSpaceSearch::SynthonSet::addSynthon ( int synthonSetNum,
Synthon * newSynthon,
const std::string & synthonId )

◆ assessRingFormers()

void RDKit::SynthonSpaceSearch::SynthonSet::assessRingFormers ( )

◆ assignConnectorsUsed()

void RDKit::SynthonSpaceSearch::SynthonSet::assignConnectorsUsed ( )

◆ buildAddAndSubtractFPs()

void RDKit::SynthonSpaceSearch::SynthonSet::buildAddAndSubtractFPs ( const FingerprintGenerator< std::uint64_t > & fpGen,
unsigned int numBits )

◆ buildConnectorRegions()

void RDKit::SynthonSpaceSearch::SynthonSet::buildConnectorRegions ( )

◆ buildMolecule()

std::unique_ptr< ROMol > RDKit::SynthonSpaceSearch::SynthonSet::buildMolecule ( const std::vector< size_t > & synthonNums) const

◆ buildProduct()

std::unique_ptr< ROMol > RDKit::SynthonSpaceSearch::SynthonSet::buildProduct ( const std::vector< size_t > & synthNums) const

◆ buildProductName()

std::string RDKit::SynthonSpaceSearch::SynthonSet::buildProductName ( const std::vector< size_t > & synthNums) const

◆ buildSynthonFingerprints()

void RDKit::SynthonSpaceSearch::SynthonSet::buildSynthonFingerprints ( const FingerprintGenerator< std::uint64_t > & fpGen)

◆ enumerateToStream()

void RDKit::SynthonSpaceSearch::SynthonSet::enumerateToStream ( std::ostream & os) const

◆ getAddFP()

const std::unique_ptr< ExplicitBitVect > & RDKit::SynthonSpaceSearch::SynthonSet::getAddFP ( ) const

◆ getConnectorRegions()

const std::vector< std::shared_ptr< ROMol > > & RDKit::SynthonSpaceSearch::SynthonSet::getConnectorRegions ( ) const

◆ getConnectorRegionSmiles()

const std::vector< std::string > & RDKit::SynthonSpaceSearch::SynthonSet::getConnectorRegionSmiles ( ) const

◆ getConnectors()

const boost::dynamic_bitset & RDKit::SynthonSpaceSearch::SynthonSet::getConnectors ( ) const
inline

Definition at line 80 of file SynthonSet.h.

◆ getConnRegFPs()

const std::vector< std::unique_ptr< ExplicitBitVect > > & RDKit::SynthonSpaceSearch::SynthonSet::getConnRegFPs ( ) const

◆ getFingerprintOrderedSynthon()

const std::pair< std::string, Synthon * > RDKit::SynthonSpaceSearch::SynthonSet::getFingerprintOrderedSynthon ( size_t setNum,
size_t synthonNum ) const

◆ getFingerprintOrderedSynthonNum()

size_t RDKit::SynthonSpaceSearch::SynthonSet::getFingerprintOrderedSynthonNum ( size_t setNum,
size_t synthonNum ) const

◆ getId()

const std::string & RDKit::SynthonSpaceSearch::SynthonSet::getId ( ) const
inline

Definition at line 58 of file SynthonSet.h.

◆ getNumConnectors()

const std::vector< int > & RDKit::SynthonSpaceSearch::SynthonSet::getNumConnectors ( ) const

◆ getNumProducts()

std::uint64_t RDKit::SynthonSpaceSearch::SynthonSet::getNumProducts ( ) const

◆ getNumRingFormers()

unsigned int RDKit::SynthonSpaceSearch::SynthonSet::getNumRingFormers ( ) const
inline

Definition at line 94 of file SynthonSet.h.

◆ getRascalOrderedSynthon()

const std::pair< std::string, Synthon * > RDKit::SynthonSpaceSearch::SynthonSet::getRascalOrderedSynthon ( size_t setNum,
size_t synthonNum ) const

◆ getRascalOrderedSynthonNum()

size_t RDKit::SynthonSpaceSearch::SynthonSet::getRascalOrderedSynthonNum ( size_t setNum,
size_t synthonNum ) const

◆ getSubstructureOrderedSynthon()

const std::pair< std::string, Synthon * > RDKit::SynthonSpaceSearch::SynthonSet::getSubstructureOrderedSynthon ( size_t setNum,
size_t synthonNum ) const

◆ getSubstructureOrderedSynthonNum()

size_t RDKit::SynthonSpaceSearch::SynthonSet::getSubstructureOrderedSynthonNum ( size_t setNum,
size_t synthonNum ) const

◆ getSubtractFP()

const std::unique_ptr< ExplicitBitVect > & RDKit::SynthonSpaceSearch::SynthonSet::getSubtractFP ( ) const

◆ getSynthonConnectorPatterns()

const std::vector< boost::dynamic_bitset<> > & RDKit::SynthonSpaceSearch::SynthonSet::getSynthonConnectorPatterns ( ) const
inline

Definition at line 81 of file SynthonSet.h.

◆ getSynthons() [1/2]

const std::vector< std::vector< std::pair< std::string, Synthon * > > > & RDKit::SynthonSpaceSearch::SynthonSet::getSynthons ( ) const
inline

Definition at line 60 of file SynthonSet.h.

◆ getSynthons() [2/2]

std::vector< std::vector< ROMol * > > RDKit::SynthonSpaceSearch::SynthonSet::getSynthons ( const std::vector< boost::dynamic_bitset<> > & reqSynths) const

◆ hasAddAndSubtractFPs()

bool RDKit::SynthonSpaceSearch::SynthonSet::hasAddAndSubtractFPs ( ) const

◆ hasFingerprints()

bool RDKit::SynthonSpaceSearch::SynthonSet::hasFingerprints ( ) const

◆ initializeSearchOrders()

void RDKit::SynthonSpaceSearch::SynthonSet::initializeSearchOrders ( )

◆ makeSampleMolecule()

std::unique_ptr< SampleMolRec > RDKit::SynthonSpaceSearch::SynthonSet::makeSampleMolecule ( Synthon * synthon) const

◆ makeSynthonSearchMols()

void RDKit::SynthonSpaceSearch::SynthonSet::makeSynthonSearchMols ( )

◆ orderSynthonsForSearch()

std::vector< std::vector< size_t > > RDKit::SynthonSpaceSearch::SynthonSet::orderSynthonsForSearch ( const std::function< bool(const Synthon *synthon1, const Synthon *synthon2)> & cmp)

◆ readFromDBStream()

void RDKit::SynthonSpaceSearch::SynthonSet::readFromDBStream ( std::istream & is,
const SynthonSpace & space,
std::uint32_t version )

◆ removeEmptySynthonSets()

void RDKit::SynthonSpaceSearch::SynthonSet::removeEmptySynthonSets ( )

◆ writeToDBStream()

void RDKit::SynthonSpaceSearch::SynthonSet::writeToDBStream ( std::ostream & os) const
The documentation for this class was generated from the following file: