A Catalog with a hierarchical structure. More...

#include <Catalog.h>

Inheritance diagram for RDCatalog::HierarchCatalog< entryType, paramType, orderType >:

Classes
struct	vertex_entry_t
	used by the BGL to set up the node properties in our graph More...

Public Types
typedef boost::property< vertex_entry_t, entryType * >	EntryProperty

typedef boost::adjacency_list< boost::vecS, boost::vecS, boost::bidirectionalS, EntryProperty >	CatalogGraph
	the type of the graph itself:

typedef boost::graph_traits< CatalogGraph >	CAT_GRAPH_TRAITS

typedef CAT_GRAPH_TRAITS::vertex_iterator	VER_ITER

typedef std::pair< VER_ITER, VER_ITER >	ENT_ITER_PAIR

typedef CAT_GRAPH_TRAITS::adjacency_iterator	DOWN_ENT_ITER

typedef std::pair< DOWN_ENT_ITER, DOWN_ENT_ITER >	DOWN_ENT_ITER_PAIR

Public Types inherited from RDCatalog::Catalog< entryType, paramType >
typedef entryType	entryType_t

typedef paramType	paramType_t

Public Member Functions
	HierarchCatalog ()

	HierarchCatalog (const paramType *params)
	Construct by making a copy of the input `params` object.

	HierarchCatalog (const std::string &pickle)
	Construct from a `pickle` (a serialized form of the HierarchCatalog)

	~HierarchCatalog () override

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

std::string	Serialize () const override
	serializes this object and returns the resulting `pickle`

void	initFromStream (std::istream &ss)
	fills the contents of this object from a stream containing a `pickle`

unsigned int	getNumEntries () const override
	returns the number of entries

void	initFromString (const std::string &text)
	fills the contents of this object from a string containing a `pickle`

unsigned int	addEntry (entryType *entry, bool updateFPLength=true) override
	add a new entry to the catalog

void	addEdge (unsigned int id1, unsigned int id2)
	adds an edge between two entries in the catalog

const entryType *	getEntryWithIdx (unsigned int idx) const override
	returns a pointer to our entry with a particular index

const entryType *	getEntryWithBitId (unsigned int idx) const
	returns a pointer to our entry with a particular bit ID

int	getIdOfEntryWithBitId (unsigned int idx) const
	returns the index of the entry with a particular bit ID

RDKit::INT_VECT	getDownEntryList (unsigned int idx) const
	returns a list of the indices of entries below the one passed in

const RDKit::INT_VECT &	getEntriesOfOrder (orderType ord)
	returns a list of the indices that have a particular order

const RDKit::INT_VECT &	getEntriesOfOrder (orderType ord) const
	returns a list of the indices that have a particular order

Public Member Functions inherited from RDCatalog::Catalog< entryType, paramType >
	Catalog ()

virtual	~Catalog ()

unsigned int	getFPLength () const
	returns the length of our fingerprint

void	setFPLength (unsigned int val)
	sets our fingerprint length

virtual void	setCatalogParams (const paramType *params)
	sets our parameters by copying the `params` argument

const paramType *	getCatalogParams () const
	returns a pointer to our parameters

Additional Inherited Members
Protected Attributes inherited from RDCatalog::Catalog< entryType, paramType >
unsigned int	d_fpLength {0}
	the length of our fingerprint

paramType *	dp_cParams
	our params object

Detailed Description

template<class entryType, class paramType, class orderType>
class RDCatalog::HierarchCatalog< entryType, paramType, orderType >

A Catalog with a hierarchical structure.

The entries of a HierarchCatalog are arranged in a directed graph

The difference between Indices and Bit Ids

A HierarchCatalog may contain more entries than the user is actually interested in. For example a HierarchCatalog constructed to contain orders 5 through 8 may well contain information about orders 1-5, in order to facilitate some search optimizations.

Bit Ids refer to the "interesting" bits. So, in the above example, Bit Id 0 will be the first entry with order 5.
Indices refer to the underlying structure of the catalog. So, in the above example, the entry with index 0 will be the first entry with order 1.

Definition at line 135 of file Catalog.h.

Member Typedef Documentation

◆ CAT_GRAPH_TRAITS

template<class entryType , class paramType , class orderType >

typedef boost::graph_traits<CatalogGraph> RDCatalog::HierarchCatalog< entryType, paramType, orderType >::CAT_GRAPH_TRAITS

Definition at line 155 of file Catalog.h.

◆ CatalogGraph

template<class entryType , class paramType , class orderType >

typedef boost::adjacency_list< boost::vecS, boost::vecS, boost::bidirectionalS, EntryProperty> RDCatalog::HierarchCatalog< entryType, paramType, orderType >::CatalogGraph

the type of the graph itself:

Definition at line 153 of file Catalog.h.

◆ DOWN_ENT_ITER

template<class entryType , class paramType , class orderType >

typedef CAT_GRAPH_TRAITS::adjacency_iterator RDCatalog::HierarchCatalog< entryType, paramType, orderType >::DOWN_ENT_ITER

Definition at line 158 of file Catalog.h.

◆ DOWN_ENT_ITER_PAIR

template<class entryType , class paramType , class orderType >

typedef std::pair<DOWN_ENT_ITER, DOWN_ENT_ITER> RDCatalog::HierarchCatalog< entryType, paramType, orderType >::DOWN_ENT_ITER_PAIR

Definition at line 159 of file Catalog.h.

◆ ENT_ITER_PAIR

template<class entryType , class paramType , class orderType >

typedef std::pair<VER_ITER, VER_ITER> RDCatalog::HierarchCatalog< entryType, paramType, orderType >::ENT_ITER_PAIR

Definition at line 157 of file Catalog.h.

◆ EntryProperty

template<class entryType , class paramType , class orderType >

typedef boost::property<vertex_entry_t, entryType *> RDCatalog::HierarchCatalog< entryType, paramType, orderType >::EntryProperty

Definition at line 144 of file Catalog.h.

◆ VER_ITER

template<class entryType , class paramType , class orderType >

typedef CAT_GRAPH_TRAITS::vertex_iterator RDCatalog::HierarchCatalog< entryType, paramType, orderType >::VER_ITER

Definition at line 156 of file Catalog.h.

Constructor & Destructor Documentation

◆ HierarchCatalog() [1/3]

template<class entryType , class paramType , class orderType >

RDCatalog::HierarchCatalog< entryType, paramType, orderType >::HierarchCatalog ( )

inline

Definition at line 162 of file Catalog.h.

◆ HierarchCatalog() [2/3]

template<class entryType , class paramType , class orderType >

RDCatalog::HierarchCatalog< entryType, paramType, orderType >::HierarchCatalog ( const paramType * params )

inline

Construct by making a copy of the input params object.

Definition at line 166 of file Catalog.h.

References RDCatalog::Catalog< entryType, paramType >::setCatalogParams().

◆ HierarchCatalog() [3/3]

template<class entryType , class paramType , class orderType >

RDCatalog::HierarchCatalog< entryType, paramType, orderType >::HierarchCatalog ( const std::string & pickle )

inline

Construct from a pickle (a serialized form of the HierarchCatalog)

Definition at line 172 of file Catalog.h.

References RDCatalog::HierarchCatalog< entryType, paramType, orderType >::initFromString().

◆ ~HierarchCatalog()

template<class entryType , class paramType , class orderType >

RDCatalog::HierarchCatalog< entryType, paramType, orderType >::~HierarchCatalog ( )

inlineoverride

Definition at line 175 of file Catalog.h.

Member Function Documentation

◆ addEdge()

template<class entryType , class paramType , class orderType >

void RDCatalog::HierarchCatalog< entryType, paramType, orderType >::addEdge	(	unsigned int	id1,
		unsigned int	id2 )

inline

adds an edge between two entries in the catalog

Since we are using a bidirectional graph - the order in which the ids are supplied here makes a difference

Parameters

id1	index of the edge's beginning
id2	index of the edge's end

Definition at line 338 of file Catalog.h.

References RDCatalog::HierarchCatalog< entryType, paramType, orderType >::getNumEntries(), and URANGE_CHECK.

Referenced by RDCatalog::HierarchCatalog< entryType, paramType, orderType >::initFromStream().

◆ addEntry()

template<class entryType , class paramType , class orderType >

unsigned int RDCatalog::HierarchCatalog< entryType, paramType, orderType >::addEntry	(	entryType *	entry,
		bool	updateFPLength = true )

inlineoverridevirtual

add a new entry to the catalog

Parameters

entry	the entry to be added
updateFPLength	(optional) if this is true, our internal fingerprint length will also be updated.

Implements RDCatalog::Catalog< entryType, paramType >.

Definition at line 306 of file Catalog.h.

References RDCatalog::Catalog< entryType, paramType >::getFPLength(), PRECONDITION, and RDCatalog::Catalog< entryType, paramType >::setFPLength().

Referenced by RDCatalog::HierarchCatalog< entryType, paramType, orderType >::initFromStream().

◆ getDownEntryList()

template<class entryType , class paramType , class orderType >

RDKit::INT_VECT RDCatalog::HierarchCatalog< entryType, paramType, orderType >::getDownEntryList ( unsigned int idx ) const

inline

returns a list of the indices of entries below the one passed in

Definition at line 401 of file Catalog.h.

Referenced by RDCatalog::HierarchCatalog< entryType, paramType, orderType >::toStream().

◆ getEntriesOfOrder() [1/2]

template<class entryType , class paramType , class orderType >

const RDKit::INT_VECT & RDCatalog::HierarchCatalog< entryType, paramType, orderType >::getEntriesOfOrder ( orderType ord )

inline

returns a list of the indices that have a particular order

Definition at line 415 of file Catalog.h.

◆ getEntriesOfOrder() [2/2]

template<class entryType , class paramType , class orderType >

const RDKit::INT_VECT & RDCatalog::HierarchCatalog< entryType, paramType, orderType >::getEntriesOfOrder ( orderType ord ) const

inline

returns a list of the indices that have a particular order

This is an overloaded member function, provided for convenience. It differs from the above function only in what argument(s) it accepts.

Definition at line 424 of file Catalog.h.

References CHECK_INVARIANT.

◆ getEntryWithBitId()

template<class entryType , class paramType , class orderType >

const entryType * RDCatalog::HierarchCatalog< entryType, paramType, orderType >::getEntryWithBitId ( unsigned int idx ) const

inline

returns a pointer to our entry with a particular bit ID

Definition at line 367 of file Catalog.h.

References RDCatalog::Catalog< entryType, paramType >::getFPLength(), RDCatalog::HierarchCatalog< entryType, paramType, orderType >::getNumEntries(), and URANGE_CHECK.

◆ getEntryWithIdx()

template<class entryType , class paramType , class orderType >

const entryType * RDCatalog::HierarchCatalog< entryType, paramType, orderType >::getEntryWithIdx ( unsigned int idx ) const

inlineoverridevirtual

returns a pointer to our entry with a particular index

Implements RDCatalog::Catalog< entryType, paramType >.

Definition at line 357 of file Catalog.h.

References RDCatalog::HierarchCatalog< entryType, paramType, orderType >::getNumEntries(), and URANGE_CHECK.

Referenced by RDCatalog::HierarchCatalog< entryType, paramType, orderType >::toStream().

◆ getIdOfEntryWithBitId()

template<class entryType , class paramType , class orderType >

int RDCatalog::HierarchCatalog< entryType, paramType, orderType >::getIdOfEntryWithBitId ( unsigned int idx ) const

inline

returns the index of the entry with a particular bit ID

Definition at line 384 of file Catalog.h.

References RDCatalog::Catalog< entryType, paramType >::getFPLength(), RDCatalog::HierarchCatalog< entryType, paramType, orderType >::getNumEntries(), and URANGE_CHECK.

◆ getNumEntries()

template<class entryType , class paramType , class orderType >

unsigned int RDCatalog::HierarchCatalog< entryType, paramType, orderType >::getNumEntries ( ) const

inlineoverridevirtual

returns the number of entries

Implements RDCatalog::Catalog< entryType, paramType >.

Definition at line 282 of file Catalog.h.

Referenced by RDCatalog::HierarchCatalog< entryType, paramType, orderType >::addEdge(), RDCatalog::HierarchCatalog< entryType, paramType, orderType >::getEntryWithBitId(), RDCatalog::HierarchCatalog< entryType, paramType, orderType >::getEntryWithIdx(), RDCatalog::HierarchCatalog< entryType, paramType, orderType >::getIdOfEntryWithBitId(), and RDCatalog::HierarchCatalog< entryType, paramType, orderType >::toStream().

◆ initFromStream()

template<class entryType , class paramType , class orderType >

void RDCatalog::HierarchCatalog< entryType, paramType, orderType >::initFromStream ( std::istream & ss )

inline

fills the contents of this object from a stream containing a pickle

Definition at line 234 of file Catalog.h.

References RDCatalog::HierarchCatalog< entryType, paramType, orderType >::addEdge(), RDCatalog::HierarchCatalog< entryType, paramType, orderType >::addEntry(), RDCatalog::Catalog< entryType, paramType >::setCatalogParams(), RDCatalog::Catalog< entryType, paramType >::setFPLength(), and RDKit::streamRead().

Referenced by RDCatalog::HierarchCatalog< entryType, paramType, orderType >::initFromString().

◆ initFromString()

template<class entryType , class paramType , class orderType >

void RDCatalog::HierarchCatalog< entryType, paramType, orderType >::initFromString ( const std::string & text )

inline

fills the contents of this object from a string containing a pickle

Definition at line 288 of file Catalog.h.

References RDCatalog::HierarchCatalog< entryType, paramType, orderType >::initFromStream().

Referenced by RDCatalog::HierarchCatalog< entryType, paramType, orderType >::HierarchCatalog().

◆ Serialize()

template<class entryType , class paramType , class orderType >

std::string RDCatalog::HierarchCatalog< entryType, paramType, orderType >::Serialize ( ) const

inlineoverridevirtual

serializes this object and returns the resulting pickle

Implements RDCatalog::Catalog< entryType, paramType >.

Definition at line 225 of file Catalog.h.

References RDCatalog::HierarchCatalog< entryType, paramType, orderType >::toStream().

◆ toStream()

template<class entryType , class paramType , class orderType >

void RDCatalog::HierarchCatalog< entryType, paramType, orderType >::toStream ( std::ostream & ss ) const

inline

serializes this object to a stream

Definition at line 179 of file Catalog.h.

References RDCatalog::endianId, RDCatalog::Catalog< entryType, paramType >::getCatalogParams(), RDCatalog::HierarchCatalog< entryType, paramType, orderType >::getDownEntryList(), RDCatalog::HierarchCatalog< entryType, paramType, orderType >::getEntryWithIdx(), RDCatalog::Catalog< entryType, paramType >::getFPLength(), RDCatalog::HierarchCatalog< entryType, paramType, orderType >::getNumEntries(), PRECONDITION, RDKit::streamWrite(), RDCatalog::versionMajor, RDCatalog::versionMinor, and RDCatalog::versionPatch.

Referenced by RDCatalog::HierarchCatalog< entryType, paramType, orderType >::Serialize().

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

Catalog.h

Classes

Public Types

Public Member Functions

Additional Inherited Members

Detailed Description

Member Typedef Documentation

◆ CAT_GRAPH_TRAITS

◆ CatalogGraph

◆ DOWN_ENT_ITER

◆ DOWN_ENT_ITER_PAIR

◆ ENT_ITER_PAIR

◆ EntryProperty

◆ VER_ITER

Constructor & Destructor Documentation

◆ HierarchCatalog() [1/3]

◆ HierarchCatalog() [2/3]

◆ HierarchCatalog() [3/3]

◆ ~HierarchCatalog()

Member Function Documentation

◆ addEdge()

◆ addEntry()

◆ getDownEntryList()

◆ getEntriesOfOrder() [1/2]

◆ getEntriesOfOrder() [2/2]

◆ getEntryWithBitId()

◆ getEntryWithIdx()

◆ getIdOfEntryWithBitId()

◆ getNumEntries()

◆ initFromStream()

◆ initFromString()

◆ Serialize()

◆ toStream()