RDKit
Open-source cheminformatics and machine learning.
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Classes | Public Member Functions | Public Attributes | List of all members
RDKit::RGroupDecompData Struct Reference

#include <RGroupDecompData.h>

Classes

class  UsedLabels
 

Public Member Functions

 RGroupDecompData (const RWMol &inputCore, RGroupDecompositionParameters inputParams)
 
 RGroupDecompData (const std::vector< ROMOL_SPTR > &inputCores, RGroupDecompositionParameters inputParams)
 
void addCore (const ROMol &inputCore)
 
void prepareCores ()
 
void setRlabel (Atom *atom, int rlabel)
 
int getRlabel (Atom *atom) const
 
double scoreFromPrunedData (const std::vector< size_t > &permutation, bool reset=true)
 
void prune ()
 
std::vector< RGroupMatch > GetCurrentBestPermutation () const
 
void addCoreUserLabels (const RWMol &core, std::set< int > &userLabels)
 
void addAtoms (RWMol &mol, const std::vector< std::pair< Atom *, Atom * > > &atomsToAdd)
 
bool replaceHydrogenCoreDummy (const RGroupMatch &match, RWMol &core, const Atom &atom, const int currentLabel, const int rLabel)
 
void relabelCore (RWMol &core, std::map< int, int > &mappings, UsedLabels &used_labels, const std::set< int > &indexLabels, const std::map< int, std::vector< int > > &extraAtomRLabels, const RGroupMatch *const match=nullptr)
 
void relabelRGroup (RGroupData &rgroup, const std::map< int, int > &mappings)
 
void relabel ()
 
double score (const std::vector< size_t > &permutation, FingerprintVarianceScoreData *fingerprintVarianceScoreData=nullptr) const
 
RGroupDecompositionProcessResult process (bool pruneMatches, bool finalize=false)
 

Public Attributes

std::map< int, RCore > cores
 
std::map< std::string, int > newCores
 
int newCoreLabel = EMPTY_CORE_LABEL
 
size_t previousMatchSize = 0
 
bool prunePermutations = true
 
RGroupDecompositionParameters params
 
std::vector< std::vector< RGroupMatch > > matches
 
std::set< int > labels
 
std::vector< size_t > permutation
 
unsigned int pruneLength = 0U
 
FingerprintVarianceScoreData prunedFingerprintVarianceScoreData
 
std::map< int, std::vector< int > > userLabels
 
std::vector< int > processedRlabels
 
std::map< int, int > finalRlabelMapping
 
RGroupScorer rGroupScorer
 

Detailed Description

Definition at line 24 of file RGroupDecompData.h.

Constructor & Destructor Documentation

◆ RGroupDecompData() [1/2]

RDKit::RGroupDecompData::RGroupDecompData ( const RWMol &  inputCore,
RGroupDecompositionParameters  inputParams 
)

◆ RGroupDecompData() [2/2]

RDKit::RGroupDecompData::RGroupDecompData ( const std::vector< ROMOL_SPTR > &  inputCores,
RGroupDecompositionParameters  inputParams 
)

Member Function Documentation

◆ addAtoms()

void RDKit::RGroupDecompData::addAtoms ( RWMol &  mol,
const std::vector< std::pair< Atom *, Atom * > > &  atomsToAdd 
)

◆ addCore()

void RDKit::RGroupDecompData::addCore ( const ROMol &  inputCore)

◆ addCoreUserLabels()

void RDKit::RGroupDecompData::addCoreUserLabels ( const RWMol &  core,
std::set< int > &  userLabels 
)

◆ GetCurrentBestPermutation()

std::vector< RGroupMatch > RDKit::RGroupDecompData::GetCurrentBestPermutation ( ) const

◆ getRlabel()

int RDKit::RGroupDecompData::getRlabel ( Atom *  atom) const

◆ prepareCores()

void RDKit::RGroupDecompData::prepareCores ( )

◆ process()

RGroupDecompositionProcessResult RDKit::RGroupDecompData::process ( bool  pruneMatches,
bool  finalize = false 
)

◆ prune()

void RDKit::RGroupDecompData::prune ( )

◆ relabel()

void RDKit::RGroupDecompData::relabel ( )

◆ relabelCore()

void RDKit::RGroupDecompData::relabelCore ( RWMol &  core,
std::map< int, int > &  mappings,
UsedLabels &  used_labels,
const std::set< int > &  indexLabels,
const std::map< int, std::vector< int > > &  extraAtomRLabels,
const RGroupMatch *const  match = nullptr 
)

◆ relabelRGroup()

void RDKit::RGroupDecompData::relabelRGroup ( RGroupData &  rgroup,
const std::map< int, int > &  mappings 
)

◆ replaceHydrogenCoreDummy()

bool RDKit::RGroupDecompData::replaceHydrogenCoreDummy ( const RGroupMatch &  match,
RWMol &  core,
const Atom &  atom,
const int  currentLabel,
const int  rLabel 
)

◆ score()

double RDKit::RGroupDecompData::score ( const std::vector< size_t > &  permutation,
FingerprintVarianceScoreData *  fingerprintVarianceScoreData = nullptr 
) const

◆ scoreFromPrunedData()

double RDKit::RGroupDecompData::scoreFromPrunedData ( const std::vector< size_t > &  permutation,
bool  reset = true 
)

◆ setRlabel()

void RDKit::RGroupDecompData::setRlabel ( Atom *  atom,
int  rlabel 
)

Member Data Documentation

◆ cores

std::map<int, RCore> RDKit::RGroupDecompData::cores

Definition at line 26 of file RGroupDecompData.h.

◆ finalRlabelMapping

std::map<int, int> RDKit::RGroupDecompData::finalRlabelMapping

Definition at line 46 of file RGroupDecompData.h.

◆ labels

std::set<int> RDKit::RGroupDecompData::labels

Definition at line 38 of file RGroupDecompData.h.

◆ matches

std::vector<std::vector<RGroupMatch> > RDKit::RGroupDecompData::matches

Definition at line 37 of file RGroupDecompData.h.

◆ newCoreLabel

int RDKit::RGroupDecompData::newCoreLabel = EMPTY_CORE_LABEL

Definition at line 28 of file RGroupDecompData.h.

◆ newCores

std::map<std::string, int> RDKit::RGroupDecompData::newCores

Definition at line 27 of file RGroupDecompData.h.

◆ params

RGroupDecompositionParameters RDKit::RGroupDecompData::params

Definition at line 35 of file RGroupDecompData.h.

◆ permutation

std::vector<size_t> RDKit::RGroupDecompData::permutation

Definition at line 39 of file RGroupDecompData.h.

◆ previousMatchSize

size_t RDKit::RGroupDecompData::previousMatchSize = 0

Definition at line 31 of file RGroupDecompData.h.

◆ processedRlabels

std::vector<int> RDKit::RGroupDecompData::processedRlabels

Definition at line 44 of file RGroupDecompData.h.

◆ prunedFingerprintVarianceScoreData

FingerprintVarianceScoreData RDKit::RGroupDecompData::prunedFingerprintVarianceScoreData

Definition at line 41 of file RGroupDecompData.h.

◆ pruneLength

unsigned int RDKit::RGroupDecompData::pruneLength = 0U

Definition at line 40 of file RGroupDecompData.h.

◆ prunePermutations

bool RDKit::RGroupDecompData::prunePermutations = true

Definition at line 34 of file RGroupDecompData.h.

◆ rGroupScorer

RGroupScorer RDKit::RGroupDecompData::rGroupScorer
mutable

Definition at line 47 of file RGroupDecompData.h.

◆ userLabels

std::map<int, std::vector<int> > RDKit::RGroupDecompData::userLabels

Definition at line 42 of file RGroupDecompData.h.

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