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.

◆ 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.

◆ ~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.

Referenced by RDCatalog::HierarchCatalog< FragCatalogEntry, FragCatParams, int >::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.

Referenced by RDCatalog::HierarchCatalog< FragCatalogEntry, FragCatParams, int >::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< FragCatalogEntry, FragCatParams, int >::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.

◆ 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.

◆ 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.

Referenced by RDCatalog::HierarchCatalog< FragCatalogEntry, FragCatParams, int >::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.

◆ 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< FragCatalogEntry, FragCatParams, int >::addEdge(), RDCatalog::HierarchCatalog< FragCatalogEntry, FragCatParams, int >::getEntryWithBitId(), RDCatalog::HierarchCatalog< FragCatalogEntry, FragCatParams, int >::getEntryWithIdx(), RDCatalog::HierarchCatalog< FragCatalogEntry, FragCatParams, int >::getIdOfEntryWithBitId(), and RDCatalog::HierarchCatalog< FragCatalogEntry, FragCatParams, int >::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.

Referenced by RDCatalog::HierarchCatalog< FragCatalogEntry, FragCatParams, int >::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.

Referenced by RDCatalog::HierarchCatalog< FragCatalogEntry, FragCatParams, int >::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.

◆ 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.

Referenced by RDCatalog::HierarchCatalog< FragCatalogEntry, FragCatParams, int >::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()