Substructure Search a library of molecules. More...

#include <SubstructLibrary.h>

Public Member Functions
	SubstructLibrary ()

	SubstructLibrary (boost::shared_ptr< MolHolderBase > molecules)

	SubstructLibrary (boost::shared_ptr< MolHolderBase > molecules, boost::shared_ptr< FPHolderBase > fingerprints)

	SubstructLibrary (boost::shared_ptr< MolHolderBase > molecules, boost::shared_ptr< KeyHolderBase > keys)

	SubstructLibrary (boost::shared_ptr< MolHolderBase > molecules, boost::shared_ptr< FPHolderBase > fingerprints, boost::shared_ptr< KeyHolderBase > keys)

	SubstructLibrary (const std::string &pickle)

boost::shared_ptr< MolHolderBase > &	getMolHolder ()
	Get the underlying molecule holder implementation.

const boost::shared_ptr< MolHolderBase > &	getMolHolder () const

boost::shared_ptr< FPHolderBase > &	getFpHolder ()
	Get the underlying molecule holder implementation.

const boost::shared_ptr< FPHolderBase > &	getFpHolder () const
	Get the underlying molecule holder implementation.

boost::shared_ptr< KeyHolderBase > &	getKeyHolder ()
	Get the underlying molecule holder implementation.

const boost::shared_ptr< KeyHolderBase > &	getKeyHolder () const
	Get the underlying molecule holder implementation.

const MolHolderBase &	getMolecules () const

FPHolderBase &	getFingerprints ()
	Get the underlying fingerprint implementation.

const FPHolderBase &	getFingerprints () const

KeyHolderBase &	getKeys ()
	Get the underlying key holder implementation.

const KeyHolderBase &	getKeys () const
	Get the underlying key holder implementation.

unsigned int	addMol (const ROMol &mol)
	Add a molecule to the library.

template<class Query >
std::vector< unsigned int >	getMatches (const Query &query, bool recursionPossible=true, bool useChirality=true, bool useQueryQueryMatches=false, int numThreads=-1, int maxResults=-1) const
	Get the matching indices for the query.

template<class Query >
std::vector< unsigned int >	getMatches (const Query &query, const SubstructMatchParameters &params, int numThreads=-1, int maxResults=-1) const
	overload

template<class Query >
std::vector< unsigned int >	getMatches (const Query &query, unsigned int startIdx, unsigned int endIdx, bool recursionPossible=true, bool useChirality=true, bool useQueryQueryMatches=false, int numThreads=-1, int maxResults=-1) const
	Get the matching indices for the query between the given indices.

std::vector< unsigned int >	getMatches (const ROMol &query, unsigned int startIdx, unsigned int endIdx, const SubstructMatchParameters &params, int numThreads=-1, int maxResults=-1) const
	overload

std::vector< unsigned int >	getMatches (const MolBundle &query, unsigned int startIdx, unsigned int endIdx, const SubstructMatchParameters &params, int numThreads=-1, int maxResults=-1) const
	overload

std::vector< unsigned int >	getMatches (const TautomerQuery &query, unsigned int startIdx, unsigned int endIdx, const SubstructMatchParameters &params, int numThreads=-1, int maxResults=-1) const
	overload

std::vector< unsigned int >	getMatches (const ExtendedQueryMol &query, unsigned int startIdx, unsigned int endIdx, const SubstructMatchParameters &params, int numThreads=-1, int maxResults=-1) const
	overload

template<class Query >
unsigned int	countMatches (const Query &query, bool recursionPossible=true, bool useChirality=true, bool useQueryQueryMatches=false, int numThreads=-1) const
	Return the number of matches for the query.

template<class Query >
unsigned int	countMatches (const Query &query, const SubstructMatchParameters &params, int numThreads=-1) const
	overload

template<class Query >
unsigned int	countMatches (const Query &query, unsigned int startIdx, unsigned int endIdx, bool recursionPossible=true, bool useChirality=true, bool useQueryQueryMatches=false, int numThreads=-1) const
	Return the number of matches for the query.

unsigned int	countMatches (const ROMol &query, unsigned int startIdx, unsigned int endIdx, const SubstructMatchParameters &params, int numThreads=-1) const
	overload

unsigned int	countMatches (const TautomerQuery &query, unsigned int startIdx, unsigned int endIdx, const SubstructMatchParameters &params, int numThreads=-1) const
	overload

unsigned int	countMatches (const MolBundle &query, unsigned int startIdx, unsigned int endIdx, const SubstructMatchParameters &params, int numThreads=-1) const
	overload

unsigned int	countMatches (const ExtendedQueryMol &query, unsigned int startIdx, unsigned int endIdx, const SubstructMatchParameters &params, int numThreads=-1) const
	overload

template<class Query >
bool	hasMatch (const Query &query, bool recursionPossible=true, bool useChirality=true, bool useQueryQueryMatches=false, int numThreads=-1) const
	Returns true if any match exists for the query.

template<class Query >
bool	hasMatch (const Query &query, const SubstructMatchParameters &params, int numThreads=-1) const
	overload

template<class Query >
bool	hasMatch (const Query &query, unsigned int startIdx, unsigned int endIdx, bool recursionPossible=true, bool useChirality=true, bool useQueryQueryMatches=false, int numThreads=-1) const

bool	hasMatch (const ROMol &query, unsigned int startIdx, unsigned int endIdx, const SubstructMatchParameters &params, int numThreads=-1) const
	overload

bool	hasMatch (const TautomerQuery &query, unsigned int startIdx, unsigned int endIdx, const SubstructMatchParameters &params, int numThreads=-1) const
	overload

bool	hasMatch (const MolBundle &query, unsigned int startIdx, unsigned int endIdx, const SubstructMatchParameters &params, int numThreads=-1) const
	overload

bool	hasMatch (const ExtendedQueryMol &query, unsigned int startIdx, unsigned int endIdx, const SubstructMatchParameters &params, int numThreads=-1) const
	overload

boost::shared_ptr< ROMol >	getMol (unsigned int idx) const
	Returns the molecule at the given index.

boost::shared_ptr< ROMol >	operator[] (unsigned int idx)
	Returns the molecule at the given index.

unsigned int	size () const
	return the number of molecules in the library

void	setSearchOrder (const std::vector< unsigned int > &order)
	does error checking

const std::vector< unsigned int > &	getSearchOrder () const

std::vector< unsigned int > &	getSearchOrder ()

void	resetHolders ()
	access required for serialization

void	toStream (std::ostream &ss) const
	serializes (pickles) to a stream

std::string	Serialize () const
	returns a string with a serialized (pickled) representation

void	initFromStream (std::istream &ss)
	initializes from a stream pickle

void	initFromString (const std::string &text)
	initializes from a string pickle

Detailed Description

Substructure Search a library of molecules.

This class allows for multithreaded substructure searches of large datasets.

The implementations can use fingerprints to speed up searches and have molecules cached as binary forms to reduce memory usage.

basic usage:

SubstructLibrary lib;
lib.addMol(mol);
std::vector<unsigned int> results = lib.getMatches(query);
for(std::vector<unsigned int>::const_iterator matchIndex=results.begin();
        matchIndex != results.end();
        ++matchIndex) {
  boost::shared_ptr<ROMol> match = lib.getMol(*matchIndex);
}

Using different mol holders and pattern fingerprints.

boost::shared_ptr<CachedTrustedSmilesMolHolder> molHolder = \
   boost::make_shared<CachedTrustedSmilesMolHolder>();
boost::shared_ptr<PatternHolder> patternHolder = \
   boost::make_shared<PatternHolder>();
 
SubstructLibrary lib(molHolder, patternHolder);
lib.addMol(mol);

Cached molecule holders create molecules on demand. There are currently three styles of cached molecules.

CachedMolHolder: stores molecules in the rdkit binary format. CachedSmilesMolHolder: stores molecules in smiles format. CachedTrustedSmilesMolHolder: stores molecules in smiles format.

The CachedTrustedSmilesMolHolder is made to add molecules from a trusted source. This makes the basic assumption that RDKit was used to sanitize and canonicalize the smiles string. In practice this is considerably faster than using arbitrary smiles strings since certain assumptions can be made. Molecules generated from trusted smiles do not have ring information (although this is created in the molecule being searched if necessary).

When loading from external data, as opposed to using the "addMol" API, care must be taken to ensure that the pattern fingerprints and smiles are synchronized.

Each pattern holder has an API point for making its fingerprint. This is useful to ensure that the pattern stored in the database will be compatible with the patterns made when analyzing queries.

boost::shared_ptr<CachedTrustedSmilesMolHolder> molHolder = \
    boost::make_shared<CachedTrustedSmilesMolHolder>();
boost::shared_ptr<PatternHolder> patternHolder =    \
    boost::make_shared<PatternHolder>();
 
// the PatternHolder instance is able to make fingerprints.
//  These, of course, can be read from a file.  For demonstration
//   purposes we construct them here.
const std::string trustedSmiles = "c1ccccc1";
ROMol *m = SmilesToMol(trustedSmiles);
const ExplicitBitVect *bitVector = patternHolder->makeFingerprint(*m);
 
// The trusted smiles and bitVector can be read from any source.
//  This is the fastest way to load a substruct library.
molHolder->addSmiles( trustedSmiles );
patternHolder->addFingerprint( *bitVector );
SubstructLibrary lib(molHolder, patternHolder);
delete m;
delete bitVector;

Finally, using the KeyFromPropHolder will store user ids or keys. By default, it uses RDKit's default _Name prop, but can be changed to any property.

boost::shared_ptr<CachedTrustedSmilesMolHolder> molHolder = \
    boost::make_shared<CachedTrustedSmilesMolHolder>();
boost::shared_ptr<KeyFromPropHolder> keyHolder = \
    boost::make_shared<KeyFromPropHolder>();
SubstructLibrary lib(molHolder, keyHolder);
...
 
You can get the keys in multiple through the use of the keyholder
auto key = lib.getKeys().getKey(idx);
auto keys = lib.getKeys().getKeys(lib.GetMatch(query));

Definition at line 519 of file SubstructLibrary.h.

Constructor & Destructor Documentation

◆ SubstructLibrary() [1/6]

RDKit::SubstructLibrary::SubstructLibrary ( )

inline

Definition at line 530 of file SubstructLibrary.h.

◆ SubstructLibrary() [2/6]

RDKit::SubstructLibrary::SubstructLibrary ( boost::shared_ptr< MolHolderBase > molecules )

inline

Definition at line 536 of file SubstructLibrary.h.

◆ SubstructLibrary() [3/6]

RDKit::SubstructLibrary::SubstructLibrary	(	boost::shared_ptr< MolHolderBase >	molecules,
		boost::shared_ptr< FPHolderBase >	fingerprints )

inline

Definition at line 543 of file SubstructLibrary.h.

◆ SubstructLibrary() [4/6]

RDKit::SubstructLibrary::SubstructLibrary	(	boost::shared_ptr< MolHolderBase >	molecules,
		boost::shared_ptr< KeyHolderBase >	keys )

inline

Definition at line 556 of file SubstructLibrary.h.

◆ SubstructLibrary() [5/6]

RDKit::SubstructLibrary::SubstructLibrary	(	boost::shared_ptr< MolHolderBase >	molecules,
		boost::shared_ptr< FPHolderBase >	fingerprints,
		boost::shared_ptr< KeyHolderBase >	keys )

inline

Definition at line 569 of file SubstructLibrary.h.

◆ SubstructLibrary() [6/6]

RDKit::SubstructLibrary::SubstructLibrary ( const std::string & pickle )

inline

Definition at line 583 of file SubstructLibrary.h.

Member Function Documentation

◆ addMol()

unsigned int RDKit::SubstructLibrary::addMol ( const ROMol & mol )

Add a molecule to the library.

Parameters

mol	Molecule to add

returns index for the molecule in the library

◆ countMatches() [1/7]

unsigned int RDKit::SubstructLibrary::countMatches	(	const ExtendedQueryMol &	query,
		unsigned int	startIdx,
		unsigned int	endIdx,
		const SubstructMatchParameters &	params,
		int	numThreads = -1 ) const

overload

◆ countMatches() [2/7]

unsigned int RDKit::SubstructLibrary::countMatches	(	const MolBundle &	query,
		unsigned int	startIdx,
		unsigned int	endIdx,
		const SubstructMatchParameters &	params,
		int	numThreads = -1 ) const

overload

◆ countMatches() [3/7]

template<class Query >

unsigned int RDKit::SubstructLibrary::countMatches	(	const Query &	query,
		bool	recursionPossible = true,
		bool	useChirality = true,
		bool	useQueryQueryMatches = false,
		int	numThreads = -1 ) const

inline

Return the number of matches for the query.

Parameters

query	Molecule or Tautomer Query to match against molecules
recursionPossible	flags whether or not recursive matches are allowed [default true]
useChirality	use atomic CIP codes as part of the comparison [default true]
useQueryQueryMatches	if set, the contents of atom and bond queries will be used as part of the matching [default false]
numThreads	If -1 use all available processors [default -1]

Definition at line 770 of file SubstructLibrary.h.

References RDKit::SubstructMatchParameters::recursionPossible, RDKit::SubstructMatchParameters::useChirality, and RDKit::SubstructMatchParameters::useQueryQueryMatches.

◆ countMatches() [4/7]

template<class Query >

unsigned int RDKit::SubstructLibrary::countMatches	(	const Query &	query,
		const SubstructMatchParameters &	params,
		int	numThreads = -1 ) const

inline

overload

Definition at line 782 of file SubstructLibrary.h.

◆ countMatches() [5/7]

template<class Query >

unsigned int RDKit::SubstructLibrary::countMatches	(	const Query &	query,
		unsigned int	startIdx,
		unsigned int	endIdx,
		bool	recursionPossible = true,
		bool	useChirality = true,
		bool	useQueryQueryMatches = false,
		int	numThreads = -1 ) const

inline

Return the number of matches for the query.

Return the number of matches for the query between the given indices

Parameters

query	Query to match against molecules
startIdx	Start index of the search
endIdx	Ending idx (non-inclusive) of the search.
recursionPossible	flags whether or not recursive matches are allowed [default true]
useChirality	use atomic CIP codes as part of the comparison [default true]
useQueryQueryMatches	if set, the contents of atom and bond queries will be used as part of the matching [default false]
numThreads	If -1 use all available processors [default -1]

Definition at line 805 of file SubstructLibrary.h.

References RDKit::SubstructMatchParameters::recursionPossible, RDKit::SubstructMatchParameters::useChirality, and RDKit::SubstructMatchParameters::useQueryQueryMatches.

◆ countMatches() [6/7]

unsigned int RDKit::SubstructLibrary::countMatches	(	const ROMol &	query,
		unsigned int	startIdx,
		unsigned int	endIdx,
		const SubstructMatchParameters &	params,
		int	numThreads = -1 ) const

overload

◆ countMatches() [7/7]

unsigned int RDKit::SubstructLibrary::countMatches	(	const TautomerQuery &	query,
		unsigned int	startIdx,
		unsigned int	endIdx,
		const SubstructMatchParameters &	params,
		int	numThreads = -1 ) const

overload

◆ getFingerprints() [1/2]

FPHolderBase & RDKit::SubstructLibrary::getFingerprints ( )

inline

Get the underlying fingerprint implementation.

Throws a value error if no fingerprints have been set

Definition at line 625 of file SubstructLibrary.h.

◆ getFingerprints() [2/2]

const FPHolderBase & RDKit::SubstructLibrary::getFingerprints ( ) const

inline

Definition at line 632 of file SubstructLibrary.h.

◆ getFpHolder() [1/2]

boost::shared_ptr< FPHolderBase > & RDKit::SubstructLibrary::getFpHolder ( )

inline

Get the underlying molecule holder implementation.

Definition at line 603 of file SubstructLibrary.h.

◆ getFpHolder() [2/2]

const boost::shared_ptr< FPHolderBase > & RDKit::SubstructLibrary::getFpHolder ( ) const

inline

Get the underlying molecule holder implementation.

Definition at line 606 of file SubstructLibrary.h.

◆ getKeyHolder() [1/2]

boost::shared_ptr< KeyHolderBase > & RDKit::SubstructLibrary::getKeyHolder ( )

inline

Get the underlying molecule holder implementation.

Definition at line 611 of file SubstructLibrary.h.

◆ getKeyHolder() [2/2]

const boost::shared_ptr< KeyHolderBase > & RDKit::SubstructLibrary::getKeyHolder ( ) const

inline

Get the underlying molecule holder implementation.

Definition at line 614 of file SubstructLibrary.h.

◆ getKeys() [1/2]

KeyHolderBase & RDKit::SubstructLibrary::getKeys ( )

inline

Get the underlying key holder implementation.

Throws a value error if no keyholder have been set

Definition at line 641 of file SubstructLibrary.h.

◆ getKeys() [2/2]

const KeyHolderBase & RDKit::SubstructLibrary::getKeys ( ) const

inline

Get the underlying key holder implementation.

Throws a value error if no keyholder have been set

Definition at line 650 of file SubstructLibrary.h.

◆ getMatches() [1/7]

std::vector< unsigned int > RDKit::SubstructLibrary::getMatches	(	const ExtendedQueryMol &	query,
		unsigned int	startIdx,
		unsigned int	endIdx,
		const SubstructMatchParameters &	params,
		int	numThreads = -1,
		int	maxResults = -1 ) const

overload

◆ getMatches() [2/7]

std::vector< unsigned int > RDKit::SubstructLibrary::getMatches	(	const MolBundle &	query,
		unsigned int	startIdx,
		unsigned int	endIdx,
		const SubstructMatchParameters &	params,
		int	numThreads = -1,
		int	maxResults = -1 ) const

overload

◆ getMatches() [3/7]

template<class Query >

std::vector< unsigned int > RDKit::SubstructLibrary::getMatches	(	const Query &	query,
		bool	recursionPossible = true,
		bool	useChirality = true,
		bool	useQueryQueryMatches = false,
		int	numThreads = -1,
		int	maxResults = -1 ) const

inline

Get the matching indices for the query.

Parameters

query	Query or Tautomer Query to match against molecules
recursionPossible	flags whether or not recursive matches are allowed [default true]
useChirality	use atomic CIP codes as part of the comparison [default true]
useQueryQueryMatches	if set, the contents of atom and bond queries will be used as part of the matching [default false]
numThreads	If -1 use all available processors [default -1]
maxResults	Maximum results to return, -1 means return all [default -1]

Definition at line 680 of file SubstructLibrary.h.

References RDKit::SubstructMatchParameters::recursionPossible, RDKit::SubstructMatchParameters::useChirality, and RDKit::SubstructMatchParameters::useQueryQueryMatches.

◆ getMatches() [4/7]

template<class Query >

std::vector< unsigned int > RDKit::SubstructLibrary::getMatches	(	const Query &	query,
		const SubstructMatchParameters &	params,
		int	numThreads = -1,
		int	maxResults = -1 ) const

inline

overload

Definition at line 694 of file SubstructLibrary.h.

◆ getMatches() [5/7]

template<class Query >

std::vector< unsigned int > RDKit::SubstructLibrary::getMatches	(	const Query &	query,
		unsigned int	startIdx,
		unsigned int	endIdx,
		bool	recursionPossible = true,
		bool	useChirality = true,
		bool	useQueryQueryMatches = false,
		int	numThreads = -1,
		int	maxResults = -1 ) const

inline

Get the matching indices for the query between the given indices.

Parameters

query	Query to match against molecules
startIdx	Start index of the search
endIdx	Ending idx (non-inclusive) of the search.
recursionPossible	flags whether or not recursive matches are allowed [default true]
useChirality	use atomic CIP codes as part of the comparison [default true]
useQueryQueryMatches	if set, the contents of atom and bond queries will be used as part of the matching [default false]
numThreads	If -1 use all available processors [default -1]
maxResults	Maximum results to return, -1 means return all [default -1]

Definition at line 717 of file SubstructLibrary.h.

References RDKit::SubstructMatchParameters::recursionPossible, RDKit::SubstructMatchParameters::useChirality, and RDKit::SubstructMatchParameters::useQueryQueryMatches.

◆ getMatches() [6/7]

std::vector< unsigned int > RDKit::SubstructLibrary::getMatches	(	const ROMol &	query,
		unsigned int	startIdx,
		unsigned int	endIdx,
		const SubstructMatchParameters &	params,
		int	numThreads = -1,
		int	maxResults = -1 ) const

overload

◆ getMatches() [7/7]

std::vector< unsigned int > RDKit::SubstructLibrary::getMatches	(	const TautomerQuery &	query,
		unsigned int	startIdx,
		unsigned int	endIdx,
		const SubstructMatchParameters &	params,
		int	numThreads = -1,
		int	maxResults = -1 ) const

overload

◆ getMol()

boost::shared_ptr< ROMol > RDKit::SubstructLibrary::getMol ( unsigned int idx ) const

inline

Returns the molecule at the given index.

Parameters

idx	Index of the molecule in the library (n.b. could contain null)

Definition at line 910 of file SubstructLibrary.h.

References RDKit::MolHolderBase::getMol(), and PRECONDITION.

◆ getMolecules()

const MolHolderBase & RDKit::SubstructLibrary::getMolecules ( ) const

inline

Definition at line 618 of file SubstructLibrary.h.

References PRECONDITION.

◆ getMolHolder() [1/2]

boost::shared_ptr< MolHolderBase > & RDKit::SubstructLibrary::getMolHolder ( )

inline

Get the underlying molecule holder implementation.

Definition at line 596 of file SubstructLibrary.h.

◆ getMolHolder() [2/2]

const boost::shared_ptr< MolHolderBase > & RDKit::SubstructLibrary::getMolHolder ( ) const

inline

Definition at line 598 of file SubstructLibrary.h.

◆ getSearchOrder() [1/2]

std::vector< unsigned int > & RDKit::SubstructLibrary::getSearchOrder ( )

inline

Definition at line 947 of file SubstructLibrary.h.

◆ getSearchOrder() [2/2]

const std::vector< unsigned int > & RDKit::SubstructLibrary::getSearchOrder ( ) const

inline

Definition at line 943 of file SubstructLibrary.h.

◆ hasMatch() [1/7]

bool RDKit::SubstructLibrary::hasMatch	(	const ExtendedQueryMol &	query,
		unsigned int	startIdx,
		unsigned int	endIdx,
		const SubstructMatchParameters &	params,
		int	numThreads = -1 ) const

overload

◆ hasMatch() [2/7]

bool RDKit::SubstructLibrary::hasMatch	(	const MolBundle &	query,
		unsigned int	startIdx,
		unsigned int	endIdx,
		const SubstructMatchParameters &	params,
		int	numThreads = -1 ) const

overload

◆ hasMatch() [3/7]

template<class Query >

bool RDKit::SubstructLibrary::hasMatch	(	const Query &	query,
		bool	recursionPossible = true,
		bool	useChirality = true,
		bool	useQueryQueryMatches = false,
		int	numThreads = -1 ) const

inline

Returns true if any match exists for the query.

Parameters

query	Molecule or Tautomer Query to match against molecules
recursionPossible	flags whether or not recursive matches are allowed [default true]
useChirality	use atomic CIP codes as part of the comparison [default true]
useQueryQueryMatches	if set, the contents of atom and bond queries will be used as part of the matching [default false]
numThreads	If -1 use all available processors [default -1]

Definition at line 851 of file SubstructLibrary.h.

References RDKit::SubstructMatchParameters::recursionPossible, RDKit::SubstructMatchParameters::useChirality, and RDKit::SubstructMatchParameters::useQueryQueryMatches.

◆ hasMatch() [4/7]

template<class Query >

bool RDKit::SubstructLibrary::hasMatch	(	const Query &	query,
		const SubstructMatchParameters &	params,
		int	numThreads = -1 ) const

inline

overload

Definition at line 862 of file SubstructLibrary.h.

◆ hasMatch() [5/7]

template<class Query >

bool RDKit::SubstructLibrary::hasMatch	(	const Query &	query,
		unsigned int	startIdx,
		unsigned int	endIdx,
		bool	recursionPossible = true,
		bool	useChirality = true,
		bool	useQueryQueryMatches = false,
		int	numThreads = -1 ) const

inline

Returns true if any match exists for the query between the specified indices

Parameters

query	Query to match against molecules
startIdx	Start index of the search
endIdx	Ending idx (inclusive) of the search.
recursionPossible	flags whether or not recursive matches are allowed [default true]
useChirality	use atomic CIP codes as part of the comparison [default true]
useQueryQueryMatches	if set, the contents of atom and bond queries will be used as part of the matching [default false]
numThreads	If -1 use all available processors [default -1]

Definition at line 880 of file SubstructLibrary.h.

References RDKit::SubstructMatchParameters::recursionPossible, RDKit::SubstructMatchParameters::useChirality, and RDKit::SubstructMatchParameters::useQueryQueryMatches.

◆ hasMatch() [6/7]

bool RDKit::SubstructLibrary::hasMatch	(	const ROMol &	query,
		unsigned int	startIdx,
		unsigned int	endIdx,
		const SubstructMatchParameters &	params,
		int	numThreads = -1 ) const

overload

◆ hasMatch() [7/7]

bool RDKit::SubstructLibrary::hasMatch	(	const TautomerQuery &	query,
		unsigned int	startIdx,
		unsigned int	endIdx,
		const SubstructMatchParameters &	params,
		int	numThreads = -1 ) const

overload

◆ initFromStream()

void RDKit::SubstructLibrary::initFromStream ( std::istream & ss )

initializes from a stream pickle

◆ initFromString()

void RDKit::SubstructLibrary::initFromString ( const std::string & text )

initializes from a string pickle

◆ operator[]()

boost::shared_ptr< ROMol > RDKit::SubstructLibrary::operator[] ( unsigned int idx )

inline

Returns the molecule at the given index.

Parameters

idx	Index of the molecule in the library (n.b. could contain null)

Definition at line 921 of file SubstructLibrary.h.

References RDKit::MolHolderBase::getMol(), and PRECONDITION.

◆ resetHolders()

void RDKit::SubstructLibrary::resetHolders ( )

inline

access required for serialization

Definition at line 949 of file SubstructLibrary.h.

◆ Serialize()

std::string RDKit::SubstructLibrary::Serialize ( ) const

returns a string with a serialized (pickled) representation

◆ setSearchOrder()

void RDKit::SubstructLibrary::setSearchOrder ( const std::vector< unsigned int > & order )

inline

does error checking

Definition at line 934 of file SubstructLibrary.h.

References RDKit::MolHolderBase::size().

◆ size()

unsigned int RDKit::SubstructLibrary::size ( ) const

inline

return the number of molecules in the library

Definition at line 928 of file SubstructLibrary.h.

References PRECONDITION.

◆ toStream()

void RDKit::SubstructLibrary::toStream ( std::ostream & ss ) const

serializes (pickles) to a stream

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

SubstructLibrary.h

Public Member Functions

Detailed Description

Constructor & Destructor Documentation

◆ SubstructLibrary() [1/6]

◆ SubstructLibrary() [2/6]

◆ SubstructLibrary() [3/6]

◆ SubstructLibrary() [4/6]

◆ SubstructLibrary() [5/6]

◆ SubstructLibrary() [6/6]

Member Function Documentation

◆ addMol()

◆ countMatches() [1/7]

◆ countMatches() [2/7]

◆ countMatches() [3/7]

◆ countMatches() [4/7]

◆ countMatches() [5/7]

◆ countMatches() [6/7]

◆ countMatches() [7/7]

◆ getFingerprints() [1/2]

◆ getFingerprints() [2/2]

◆ getFpHolder() [1/2]

◆ getFpHolder() [2/2]

◆ getKeyHolder() [1/2]

◆ getKeyHolder() [2/2]

◆ getKeys() [1/2]

◆ getKeys() [2/2]

◆ getMatches() [1/7]

◆ getMatches() [2/7]

◆ getMatches() [3/7]

◆ getMatches() [4/7]

◆ getMatches() [5/7]

◆ getMatches() [6/7]

◆ getMatches() [7/7]

◆ getMol()

◆ getMolecules()

◆ getMolHolder() [1/2]

◆ getMolHolder() [2/2]

◆ getSearchOrder() [1/2]

◆ getSearchOrder() [2/2]

◆ hasMatch() [1/7]

◆ hasMatch() [2/7]

◆ hasMatch() [3/7]

◆ hasMatch() [4/7]

◆ hasMatch() [5/7]

◆ hasMatch() [6/7]

◆ hasMatch() [7/7]

◆ initFromStream()

◆ initFromString()

◆ operator[]()

◆ resetHolders()

◆ Serialize()

◆ setSearchOrder()

◆ size()

◆ toStream()