RDCatalog::HierarchCatalog< entryType, paramType, orderType > Class Template Reference
A Catalog with a hierarchical structure. More...
#include <Catalog.h>
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 Member Functions | |
| HierarchCatalog () | |
| HierarchCatalog (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 () | |
| void | toStream (std::ostream &ss) const |
| serializes this object to a stream | |
| std::string | Serialize () const |
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 |
| 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) |
| 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 |
| 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 | |
Classes | |
| struct | vertex_entry_t |
| used by the BGL to set up the node properties in our graph More... | |
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
0will 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
0will be the first entry with order 1.
Definition at line 125 of file Catalog.h.
Member Typedef Documentation
| typedef boost::property<vertex_entry_t, entryType *> RDCatalog::HierarchCatalog< entryType, paramType, orderType >::EntryProperty |
| typedef boost::adjacency_list<boost::vecS, boost::vecS, boost::bidirectionalS, EntryProperty> RDCatalog::HierarchCatalog< entryType, paramType, orderType >::CatalogGraph |
| typedef boost::graph_traits<CatalogGraph> RDCatalog::HierarchCatalog< entryType, paramType, orderType >::CAT_GRAPH_TRAITS |
| typedef CAT_GRAPH_TRAITS::vertex_iterator RDCatalog::HierarchCatalog< entryType, paramType, orderType >::VER_ITER |
| typedef std::pair<VER_ITER, VER_ITER> RDCatalog::HierarchCatalog< entryType, paramType, orderType >::ENT_ITER_PAIR |
| typedef CAT_GRAPH_TRAITS::adjacency_iterator RDCatalog::HierarchCatalog< entryType, paramType, orderType >::DOWN_ENT_ITER |
| typedef std::pair<DOWN_ENT_ITER, DOWN_ENT_ITER> RDCatalog::HierarchCatalog< entryType, paramType, orderType >::DOWN_ENT_ITER_PAIR |
Constructor & Destructor Documentation
| RDCatalog::HierarchCatalog< entryType, paramType, orderType >::HierarchCatalog | ( | ) | [inline] |
| RDCatalog::HierarchCatalog< entryType, paramType, orderType >::HierarchCatalog | ( | paramType * | params | ) | [inline] |
| RDCatalog::HierarchCatalog< entryType, paramType, orderType >::HierarchCatalog | ( | const std::string & | pickle | ) | [inline] |
Construct from a pickle (a serialized form of the HierarchCatalog).
| RDCatalog::HierarchCatalog< entryType, paramType, orderType >::~HierarchCatalog | ( | ) | [inline] |
Member Function Documentation
| void RDCatalog::HierarchCatalog< entryType, paramType, orderType >::toStream | ( | std::ostream & | ss | ) | const [inline] |
serializes this object to a stream
Definition at line 171 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().
| std::string RDCatalog::HierarchCatalog< entryType, paramType, orderType >::Serialize | ( | ) | const [inline, virtual] |
serializes this object and returns the resulting pickle
Implements RDCatalog::Catalog< entryType, paramType >.
Definition at line 217 of file Catalog.h.
References RDCatalog::HierarchCatalog< entryType, paramType, orderType >::toStream().
| 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 225 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().
| unsigned int RDCatalog::HierarchCatalog< entryType, paramType, orderType >::getNumEntries | ( | ) | const [inline, virtual] |
returns the number of entries
Implements RDCatalog::Catalog< entryType, paramType >.
Definition at line 272 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().
| 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 278 of file Catalog.h.
References RDCatalog::HierarchCatalog< entryType, paramType, orderType >::initFromStream().
| unsigned int RDCatalog::HierarchCatalog< entryType, paramType, orderType >::addEntry | ( | entryType * | entry, | |
| bool | updateFPLength = true | |||
| ) | [inline, virtual] |
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 295 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().
| 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 326 of file Catalog.h.
References RDCatalog::HierarchCatalog< entryType, paramType, orderType >::getNumEntries(), and RANGE_CHECK.
Referenced by RDCatalog::HierarchCatalog< entryType, paramType, orderType >::initFromStream().
| const entryType* RDCatalog::HierarchCatalog< entryType, paramType, orderType >::getEntryWithIdx | ( | unsigned int | idx | ) | const [inline, virtual] |
returns a pointer to our entry with a particular index
Implements RDCatalog::Catalog< entryType, paramType >.
Definition at line 346 of file Catalog.h.
References RDCatalog::HierarchCatalog< entryType, paramType, orderType >::getNumEntries(), and RANGE_CHECK.
Referenced by RDCatalog::HierarchCatalog< entryType, paramType, orderType >::toStream().
| 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 356 of file Catalog.h.
References RDCatalog::Catalog< entryType, paramType >::getFPLength(), RDCatalog::HierarchCatalog< entryType, paramType, orderType >::getNumEntries(), and RANGE_CHECK.
| 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 373 of file Catalog.h.
References RDCatalog::Catalog< entryType, paramType >::getFPLength(), RDCatalog::HierarchCatalog< entryType, paramType, orderType >::getNumEntries(), and RANGE_CHECK.
| 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 390 of file Catalog.h.
Referenced by RDCatalog::HierarchCatalog< entryType, paramType, orderType >::toStream().
| const RDKit::INT_VECT& RDCatalog::HierarchCatalog< entryType, paramType, orderType >::getEntriesOfOrder | ( | orderType | ord | ) | [inline] |
| 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 413 of file Catalog.h.
References CHECK_INVARIANT.
The documentation for this class was generated from the following file:
