RDKit
Open-source cheminformatics and machine learning.
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Classes | Functions
RDKit::SynthonSpaceSearch::details Namespace Reference

Classes

struct  MemoryMappedFileReader
 
struct  Stepper
 

Functions

RDKIT_SYNTHONSPACESEARCH_EXPORT bool checkTimeOut (const TimePoint *endTime)
 
RDKIT_SYNTHONSPACESEARCH_EXPORT std::vector< std::vector< unsigned int > > combMFromN (unsigned int m, unsigned int n)
 
RDKIT_SYNTHONSPACESEARCH_EXPORT std::vector< std::vector< unsigned int > > permMFromN (unsigned int m, unsigned int n)
 
RDKIT_SYNTHONSPACESEARCH_EXPORT std::vector< std::vector< std::shared_ptr< ROMol > > > splitMolecule (const ROMol &query, unsigned int maxNumFrags, const std::uint64_t maxNumFragSets, const TimePoint *endTime, const int numThreads, const FragSetUniquifyMode &uniquifyMode, bool &timedOut)
 
RDKIT_SYNTHONSPACESEARCH_EXPORT int countConnections (const ROMol &mol)
 
RDKIT_SYNTHONSPACESEARCH_EXPORT std::vector< boost::dynamic_bitset<> > getConnectorPatterns (const std::vector< std::shared_ptr< ROMol > > &fragSet)
 
RDKIT_SYNTHONSPACESEARCH_EXPORT boost::dynamic_bitset getConnectorPattern (const std::vector< std::shared_ptr< ROMol > > &fragSet)
 
RDKIT_SYNTHONSPACESEARCH_EXPORT std::vector< std::vector< std::vector< std::pair< Atom *, unsigned int > > > > getConnectorPermutations (const std::vector< std::unique_ptr< ROMol > > &molFrags, const boost::dynamic_bitset<> &fragConns, const boost::dynamic_bitset<> &reactionConns)
 
RDKIT_SYNTHONSPACESEARCH_EXPORT std::vector< std::vector< boost::dynamic_bitset<> > > getConnectorPermutations (const std::vector< boost::dynamic_bitset<> > &fragConnPatts, const boost::dynamic_bitset<> &reactionConns)
 
RDKIT_SYNTHONSPACESEARCH_EXPORT void expandBitSet (std::vector< boost::dynamic_bitset<> > &bitSets)
 
RDKIT_SYNTHONSPACESEARCH_EXPORT void bitSetsToVectors (const std::vector< boost::dynamic_bitset<> > &bitSets, std::vector< std::vector< size_t > > &outVecs)
 
RDKIT_SYNTHONSPACESEARCH_EXPORT std::unique_ptr< ROMol > buildConnRegion (const ROMol &mol)
 
RDKIT_SYNTHONSPACESEARCH_EXPORT bool removeQueryAtoms (RWMol &mol)
 
RDKIT_SYNTHONSPACESEARCH_EXPORT std::string buildProductName (const std::string &reactionId, const std::vector< std::string > &fragIds)
 
RDKIT_SYNTHONSPACESEARCH_EXPORT std::string buildProductName (const std::string &reactionId, const std::vector< const std::string * > &fragIds)
 
RDKIT_SYNTHONSPACESEARCH_EXPORT std::string buildProductName (const RDKit::SynthonSpaceSearch::SynthonSpaceHitSet *hitset, const std::vector< size_t > &fragNums)
 
RDKIT_SYNTHONSPACESEARCH_EXPORT std::size_t buildProductHash (const RDKit::SynthonSpaceSearch::SynthonSpaceHitSet *hitset, const std::vector< size_t > &fragNums)
 
RDKIT_SYNTHONSPACESEARCH_EXPORT std::unique_ptr< ROMol > buildProduct (const std::vector< const ROMol * > &synthons)
 
RDKIT_SYNTHONSPACESEARCH_EXPORT std::map< std::string, std::vector< ROMol * > > mapFragsBySmiles (std::vector< std::vector< std::shared_ptr< ROMol > > > &fragSets, bool &cancelled)
 
RDKIT_SYNTHONSPACESEARCH_EXPORT unsigned int countChiralAtoms (ROMol &mol, unsigned int *numExcDummies=nullptr)
 
RDKIT_SYNTHONSPACESEARCH_EXPORT bool hasUnspecifiedStereo (ROMol &mol)
 
RDKIT_SYNTHONSPACESEARCH_EXPORT void pruneShapes (ShapeSet &shapeSet, double simThreshold)
 
RDKIT_SYNTHONSPACESEARCH_EXPORT std::vector< std::unique_ptr< RWMol > > generateIsomerConformers (const ROMol &mol, unsigned int numConformers, bool enumerateStereo, const EnumerateStereoisomers::StereoEnumerationOptions &enumOpts, DGeomHelpers::EmbedParameters &dgParams, UserConfGenerator &userConfGenerator, unsigned int maxStereoCenters=std::numeric_limits< unsigned int >::max())
 
RDKIT_SYNTHONSPACESEARCH_EXPORT std::unique_ptr< RWMol > trimSampleMol (const ROMol &mol, size_t molNum)
 
RDKIT_SYNTHONSPACESEARCH_EXPORT void makeShapesFromMols (std::vector< std::unique_ptr< SampleMolRec > > &sampleMols, DGeomHelpers::EmbedParameters &dgParams, ShapeBuildParams &shapeBuildParams, std::unique_ptr< ProgressBar > &pbar)
 
RDKIT_SYNTHONSPACESEARCH_EXPORT void sortAndUniquifyToTry (std::vector< std::pair< const SynthonSpaceHitSet *, std::vector< size_t > > > &toTry)
 

Function Documentation

◆ bitSetsToVectors()

RDKIT_SYNTHONSPACESEARCH_EXPORT void RDKit::SynthonSpaceSearch::details::bitSetsToVectors ( const std::vector< boost::dynamic_bitset<> > & bitSets,
std::vector< std::vector< size_t > > & outVecs )

References RDKIT_SYNTHONSPACESEARCH_EXPORT.

◆ buildConnRegion()

RDKIT_SYNTHONSPACESEARCH_EXPORT std::unique_ptr< ROMol > RDKit::SynthonSpaceSearch::details::buildConnRegion ( const ROMol & mol)

References RDKIT_SYNTHONSPACESEARCH_EXPORT.

◆ buildProduct()

RDKIT_SYNTHONSPACESEARCH_EXPORT std::unique_ptr< ROMol > RDKit::SynthonSpaceSearch::details::buildProduct ( const std::vector< const ROMol * > & synthons)

References RDKIT_SYNTHONSPACESEARCH_EXPORT.

◆ buildProductHash()

RDKIT_SYNTHONSPACESEARCH_EXPORT std::size_t RDKit::SynthonSpaceSearch::details::buildProductHash ( const RDKit::SynthonSpaceSearch::SynthonSpaceHitSet * hitset,
const std::vector< size_t > & fragNums )

References RDKIT_SYNTHONSPACESEARCH_EXPORT.

◆ buildProductName() [1/3]

RDKIT_SYNTHONSPACESEARCH_EXPORT std::string RDKit::SynthonSpaceSearch::details::buildProductName ( const RDKit::SynthonSpaceSearch::SynthonSpaceHitSet * hitset,
const std::vector< size_t > & fragNums )

References RDKIT_SYNTHONSPACESEARCH_EXPORT.

◆ buildProductName() [2/3]

RDKIT_SYNTHONSPACESEARCH_EXPORT std::string RDKit::SynthonSpaceSearch::details::buildProductName ( const std::string & reactionId,
const std::vector< const std::string * > & fragIds )

References RDKIT_SYNTHONSPACESEARCH_EXPORT.

◆ buildProductName() [3/3]

RDKIT_SYNTHONSPACESEARCH_EXPORT std::string RDKit::SynthonSpaceSearch::details::buildProductName ( const std::string & reactionId,
const std::vector< std::string > & fragIds )

References RDKIT_SYNTHONSPACESEARCH_EXPORT.

◆ checkTimeOut()

RDKIT_SYNTHONSPACESEARCH_EXPORT bool RDKit::SynthonSpaceSearch::details::checkTimeOut ( const TimePoint * endTime)

References RDKIT_SYNTHONSPACESEARCH_EXPORT.

◆ combMFromN()

RDKIT_SYNTHONSPACESEARCH_EXPORT std::vector< std::vector< unsigned int > > RDKit::SynthonSpaceSearch::details::combMFromN ( unsigned int m,
unsigned int n )

References RDKIT_SYNTHONSPACESEARCH_EXPORT.

◆ countChiralAtoms()

RDKIT_SYNTHONSPACESEARCH_EXPORT unsigned int RDKit::SynthonSpaceSearch::details::countChiralAtoms ( ROMol & mol,
unsigned int * numExcDummies = nullptr )

References RDKIT_SYNTHONSPACESEARCH_EXPORT.

◆ countConnections()

RDKIT_SYNTHONSPACESEARCH_EXPORT int RDKit::SynthonSpaceSearch::details::countConnections ( const ROMol & mol)

References RDKIT_SYNTHONSPACESEARCH_EXPORT.

◆ expandBitSet()

RDKIT_SYNTHONSPACESEARCH_EXPORT void RDKit::SynthonSpaceSearch::details::expandBitSet ( std::vector< boost::dynamic_bitset<> > & bitSets)

References RDKIT_SYNTHONSPACESEARCH_EXPORT.

◆ generateIsomerConformers()

RDKIT_SYNTHONSPACESEARCH_EXPORT std::vector< std::unique_ptr< RWMol > > RDKit::SynthonSpaceSearch::details::generateIsomerConformers ( const ROMol & mol,
unsigned int numConformers,
bool enumerateStereo,
const EnumerateStereoisomers::StereoEnumerationOptions & enumOpts,
DGeomHelpers::EmbedParameters & dgParams,
UserConfGenerator & userConfGenerator,
unsigned int maxStereoCenters = std::numeric_limits< unsigned int >::max() )

◆ getConnectorPattern()

RDKIT_SYNTHONSPACESEARCH_EXPORT boost::dynamic_bitset RDKit::SynthonSpaceSearch::details::getConnectorPattern ( const std::vector< std::shared_ptr< ROMol > > & fragSet)

References RDKIT_SYNTHONSPACESEARCH_EXPORT.

◆ getConnectorPatterns()

RDKIT_SYNTHONSPACESEARCH_EXPORT std::vector< boost::dynamic_bitset<> > RDKit::SynthonSpaceSearch::details::getConnectorPatterns ( const std::vector< std::shared_ptr< ROMol > > & fragSet)

◆ getConnectorPermutations() [1/2]

RDKIT_SYNTHONSPACESEARCH_EXPORT std::vector< std::vector< boost::dynamic_bitset<> > > RDKit::SynthonSpaceSearch::details::getConnectorPermutations ( const std::vector< boost::dynamic_bitset<> > & fragConnPatts,
const boost::dynamic_bitset<> & reactionConns )

◆ getConnectorPermutations() [2/2]

RDKIT_SYNTHONSPACESEARCH_EXPORT std::vector< std::vector< std::vector< std::pair< Atom *, unsigned int > > > > RDKit::SynthonSpaceSearch::details::getConnectorPermutations ( const std::vector< std::unique_ptr< ROMol > > & molFrags,
const boost::dynamic_bitset<> & fragConns,
const boost::dynamic_bitset<> & reactionConns )

References RDKIT_SYNTHONSPACESEARCH_EXPORT.

◆ hasUnspecifiedStereo()

RDKIT_SYNTHONSPACESEARCH_EXPORT bool RDKit::SynthonSpaceSearch::details::hasUnspecifiedStereo ( ROMol & mol)

References RDKIT_SYNTHONSPACESEARCH_EXPORT.

◆ makeShapesFromMols()

RDKIT_SYNTHONSPACESEARCH_EXPORT void RDKit::SynthonSpaceSearch::details::makeShapesFromMols ( std::vector< std::unique_ptr< SampleMolRec > > & sampleMols,
DGeomHelpers::EmbedParameters & dgParams,
ShapeBuildParams & shapeBuildParams,
std::unique_ptr< ProgressBar > & pbar )

References RDKIT_SYNTHONSPACESEARCH_EXPORT.

◆ mapFragsBySmiles()

RDKIT_SYNTHONSPACESEARCH_EXPORT std::map< std::string, std::vector< ROMol * > > RDKit::SynthonSpaceSearch::details::mapFragsBySmiles ( std::vector< std::vector< std::shared_ptr< ROMol > > > & fragSets,
bool & cancelled )

◆ permMFromN()

RDKIT_SYNTHONSPACESEARCH_EXPORT std::vector< std::vector< unsigned int > > RDKit::SynthonSpaceSearch::details::permMFromN ( unsigned int m,
unsigned int n )

References RDKIT_SYNTHONSPACESEARCH_EXPORT.

◆ pruneShapes()

RDKIT_SYNTHONSPACESEARCH_EXPORT void RDKit::SynthonSpaceSearch::details::pruneShapes ( ShapeSet & shapeSet,
double simThreshold )

References RDKIT_SYNTHONSPACESEARCH_EXPORT.

◆ removeQueryAtoms()

RDKIT_SYNTHONSPACESEARCH_EXPORT bool RDKit::SynthonSpaceSearch::details::removeQueryAtoms ( RWMol & mol)

References RDKIT_SYNTHONSPACESEARCH_EXPORT.

◆ sortAndUniquifyToTry()

RDKIT_SYNTHONSPACESEARCH_EXPORT void RDKit::SynthonSpaceSearch::details::sortAndUniquifyToTry ( std::vector< std::pair< const SynthonSpaceHitSet *, std::vector< size_t > > > & toTry)

References RDKIT_SYNTHONSPACESEARCH_EXPORT.

◆ splitMolecule()

RDKIT_SYNTHONSPACESEARCH_EXPORT std::vector< std::vector< std::shared_ptr< ROMol > > > RDKit::SynthonSpaceSearch::details::splitMolecule ( const ROMol & query,
unsigned int maxNumFrags,
const std::uint64_t maxNumFragSets,
const TimePoint * endTime,
const int numThreads,
const FragSetUniquifyMode & uniquifyMode,
bool & timedOut )

◆ trimSampleMol()

RDKIT_SYNTHONSPACESEARCH_EXPORT std::unique_ptr< RWMol > RDKit::SynthonSpaceSearch::details::trimSampleMol ( const ROMol & mol,
size_t molNum )

References RDKIT_SYNTHONSPACESEARCH_EXPORT.