OESubSearchDatabase

Attention

PRELIMINARY-IMAGE This is a preliminary API until 2020.Oct and may be improved based on user feedback. It is currently available in C++ and Python.

class OESubSearchDatabase

The OESubSearchDatabase class is designed to perform fast multi-threaded substructure search. Each OESubSearchDatabase is associated with one screen type (OESubSearchScreenTypeBase) that is set when the database is initialized from a pre-generated binary substructure search file.

../../_images/FastSSSearch.png

Schematic representation of using substructure search database

The OESubSearchDatabase class provides the following search methods:

Method Returns Type
NumMatches number of matched molecules full search
GetMatchIndices indices of matched molecules limited search
GetMatchTitles titles of matched molecules limited search
Search OESubSearchResult (indices of molecules, progress of search) full/limited search (cancelable)

See also

Constructors

OESubSearchDatabase(const std::string &dbfile,
                    const unsigned memtype=OESubSearchDatabaseType::Default,
                    const unsigned numprocesssors=0u)
OESubSearchDatabase(const unsigned memtype=OESubSearchDatabaseType::Default,
                    const unsigned numprocesssors=0u)

Constructs an OESubSearchDatabase object.

dbfile
The name of the file that contains the substructure search data (molecules with pre-generated screens). The file has to be generated with the OECreateSubSearchDatabaseFile function. If no file name is defined, the database has to be initialized by calling the OESubSearchDatabase.Open method.
memtype
Defines the type of the substructure database. This value has to be from the OESubSearchDatabaseType namespace.
numprocesssors
The maximum number of threads that can be used to search the database. When set to 0, the number of processors used will be the number returned by the OEGetNumProcessors function. If numprocesssors == 1, all searches are executed using the main thread only.

GetDatabaseType

unsigned GetDatabaseType() const

Returns the type of the substructure search database. The return value is taken from the OESubSearchDatabaseType namespace.

GetMatchIndices

OESystem::OEIterBase<size_t>* GetMatchIndices(const OESubSearchQuery &) const

Returns the indices of molecules matched to the given query (OESubSearchQuery). The search terminates if the limit set for the query is reached (GetMaxMatches). The matched molecules can be retried from the database by using the OESubSearchDatabase.GetMolecule method.

GetMatchTitles

OESystem::OEIterBase<std::string>* GetMatchTitles(const OESubSearchQuery &) const

Returns the titles of the molecules matched to the given query (OESubSearchQuery). The search terminates if the limit set for the query is reached (GetMaxMatches).

GetMolecule

bool GetMolecule(OEMolBase &mol, const size_t index) const

Retrieves the molecule stored in the database with the specified index.

GetScreenType

const OESubSearchScreenTypeBase *GetScreenType() const

Returns the screen type of the OESubSearchDatabase object. An OESubSearchDatabase object can only store screens with identical types.

GetTitle

std::string GetTitle(const size_t index) const

Retrieves the title of the molecule stored in the database with the specified index.

IsValid

bool IsValid() const

Returns whether the OESubSearchDatabase object is valid.

NumMatches

size_t NumMatches(const OEQMolBase &query) const

Returns the number of molecules matched to the given query (OESubSearchQuery) in the entire database.

NumMolecules

size_t NumMolecules() const

Returns the number of molecules stored in the OESubSearchDatabase object.

NumProcessors

unsigned NumProcessors() const

Returns the maximum number of threads that can be used to search the database. This is determined when the database is initialized.

Open

bool Open(oemolistream &ifs,
          OESystem::OETracerBase &tracer=OESystem::OENoTracer)
bool Open(const std::string & filename,
          OESystem::OETracerBase &tracer=OESystem::OENoTracer)

Initializes the substructure search database. These methods return true if the database was successfully initialized.

ifs
The molecule stream from which the substructure search database is initialized.
filename
The name of the file from which the substructure search database is initialized.
tracer
The tracer that can be used to report the progress of the database load.

See also

Search

unsigned Search(OESubSearchResult & result, const OESubSearchQuery &query) const

This search method is designed for interactive searches.

query
The OESubSearchQuery object that stores the query molecule with search parameters.
result
The OESubSearchResult object that stores the result of the search along with the progress of the search. The OESubSearchResult is updated regularly during the search as more and more matches identified. It also provides a mechanism to cancel a long running search via OESubSearchResult.Cancel.

The OESubSearchDatabase.Search method returns:

See also