Abstract base class for creators that build optimized pharmacophore screening databases. More...

#include <ScreeningDBCreator.hpp>

Inheritance diagram for CDPL::Pharm::ScreeningDBCreator:

Public Types
enum	Mode { CREATE , UPDATE , APPEND }
	Specifies how an existing database file is treated by open(). More...

typedef std::shared_ptr< ScreeningDBCreator >	SharedPointer
	A reference-counted smart pointer [SHPTR] for dynamically allocated `ScreeningDBCreator` instances. More...

typedef std::function< bool(double)>	ProgressCallbackFunction
	Type of the progress-reporting callback (argument: fraction in [0, 1], return: `true` to continue, `false` to abort). More...

Public Member Functions
virtual	~ScreeningDBCreator ()
	Virtual destructor. More...

virtual void	open (const std::string &name, Mode mode=CREATE, bool allow_dup_entries=true)=0
	Opens the database identified by name in the specified mode. More...

virtual void	close ()=0
	Closes the currently open database. More...

virtual Mode	getMode () const =0
	Returns the mode in which the currently open database was opened. More...

virtual bool	allowDuplicateEntries () const =0
	Tells whether duplicate molecule entries are allowed. More...

virtual bool	process (const Chem::MolecularGraph &molgraph)=0
	Processes molgraph and adds it (or its derived pharmacophores) to the database. More...

virtual bool	merge (const ScreeningDBAccessor &db_acc, const ProgressCallbackFunction &func)=0
	Merges the contents of db_acc into the currently open database. More...

virtual const std::string &	getDatabaseName () const =0
	Returns the name of the currently open database. More...

virtual std::size_t	getNumProcessed () const =0
	Returns the number of molecules processed since the database was opened. More...

virtual std::size_t	getNumRejected () const =0
	Returns the number of molecules that were rejected (e.g. as duplicates) since the database was opened. More...

virtual std::size_t	getNumDeleted () const =0
	Returns the number of entries that were deleted since the database was opened. More...

virtual std::size_t	getNumInserted () const =0
	Returns the number of entries that were inserted since the database was opened. More...

Protected Member Functions
ScreeningDBCreator &	operator= (const ScreeningDBCreator &)

Detailed Description

Abstract base class for creators that build optimized pharmacophore screening databases.

Member Typedef Documentation

◆ SharedPointer

typedef std::shared_ptr<ScreeningDBCreator> CDPL::Pharm::ScreeningDBCreator::SharedPointer

A reference-counted smart pointer [SHPTR] for dynamically allocated ScreeningDBCreator instances.

◆ ProgressCallbackFunction

typedef std::function<bool(double)> CDPL::Pharm::ScreeningDBCreator::ProgressCallbackFunction

Type of the progress-reporting callback (argument: fraction in [0, 1], return: true to continue, false to abort).

Member Enumeration Documentation

◆ Mode

enum CDPL::Pharm::ScreeningDBCreator::Mode

Specifies how an existing database file is treated by open().

Enumerator
CREATE	Create a new database (replacing any existing file).
UPDATE	Update an existing database in place.
APPEND	Append to an existing database.

Constructor & Destructor Documentation

◆ ~ScreeningDBCreator()

virtual CDPL::Pharm::ScreeningDBCreator::~ScreeningDBCreator ( )

inlinevirtual

Virtual destructor.

Member Function Documentation

◆ open()

virtual void CDPL::Pharm::ScreeningDBCreator::open	(	const std::string &	name,
		Mode	mode = `CREATE`,
		bool	allow_dup_entries = `true`
	)

pure virtual

Opens the database identified by name in the specified mode.

Parameters

name	The database name (path, URI, etc., interpreted by the concrete subclass).
mode	The open mode (see Mode).
allow_dup_entries	If `true`, duplicate molecule entries are allowed; if `false`, duplicates are rejected.

Implemented in CDPL::Pharm::PSDScreeningDBCreator.

◆ close()

virtual void CDPL::Pharm::ScreeningDBCreator::close ( )

pure virtual

Closes the currently open database.

Implemented in CDPL::Pharm::PSDScreeningDBCreator.

◆ getMode()

virtual Mode CDPL::Pharm::ScreeningDBCreator::getMode ( ) const

pure virtual

Returns the mode in which the currently open database was opened.

Returns: The open mode.

Implemented in CDPL::Pharm::PSDScreeningDBCreator.

◆ allowDuplicateEntries()

virtual bool CDPL::Pharm::ScreeningDBCreator::allowDuplicateEntries ( ) const

pure virtual

Tells whether duplicate molecule entries are allowed.

Returns: true if duplicates are allowed, and false otherwise.

Implemented in CDPL::Pharm::PSDScreeningDBCreator.

◆ process()

virtual bool CDPL::Pharm::ScreeningDBCreator::process ( const Chem::MolecularGraph & molgraph )

pure virtual

Processes molgraph and adds it (or its derived pharmacophores) to the database.

Parameters

molgraph The molecular graph to process.

Returns: true if at least one entry was inserted, and false otherwise (e.g. when duplicates are rejected).

Implemented in CDPL::Pharm::PSDScreeningDBCreator.

◆ merge()

virtual bool CDPL::Pharm::ScreeningDBCreator::merge	(	const ScreeningDBAccessor &	db_acc,
		const ProgressCallbackFunction &	func
	)

pure virtual

Merges the contents of db_acc into the currently open database.

Parameters

db_acc	The source database accessor.
func	An optional progress-reporting callback (called repeatedly with a fraction in [0, 1]).

Returns: true if the merge completed successfully, and false if it was aborted by the callback.

Implemented in CDPL::Pharm::PSDScreeningDBCreator.

◆ getDatabaseName()

virtual const std::string& CDPL::Pharm::ScreeningDBCreator::getDatabaseName ( ) const

pure virtual

Returns the name of the currently open database.

Returns: A const reference to the database name.

Implemented in CDPL::Pharm::PSDScreeningDBCreator.

◆ getNumProcessed()

virtual std::size_t CDPL::Pharm::ScreeningDBCreator::getNumProcessed ( ) const

pure virtual

Returns the number of molecules processed since the database was opened.

Returns: The processed-molecule count.

Implemented in CDPL::Pharm::PSDScreeningDBCreator.

◆ getNumRejected()

virtual std::size_t CDPL::Pharm::ScreeningDBCreator::getNumRejected ( ) const

pure virtual

Returns the number of molecules that were rejected (e.g. as duplicates) since the database was opened.

Returns: The rejected-molecule count.

Implemented in CDPL::Pharm::PSDScreeningDBCreator.

◆ getNumDeleted()

virtual std::size_t CDPL::Pharm::ScreeningDBCreator::getNumDeleted ( ) const

pure virtual

Returns the number of entries that were deleted since the database was opened.

Returns: The deleted-entry count.

Implemented in CDPL::Pharm::PSDScreeningDBCreator.

◆ getNumInserted()

virtual std::size_t CDPL::Pharm::ScreeningDBCreator::getNumInserted ( ) const

pure virtual

Returns the number of entries that were inserted since the database was opened.

Returns: The inserted-entry count.

Implemented in CDPL::Pharm::PSDScreeningDBCreator.

◆ operator=()

ScreeningDBCreator& CDPL::Pharm::ScreeningDBCreator::operator= ( const ScreeningDBCreator & )

inlineprotected

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

ScreeningDBCreator.hpp

Public Types

Public Member Functions

Protected Member Functions

Detailed Description

Member Typedef Documentation

◆ SharedPointer

◆ ProgressCallbackFunction

Member Enumeration Documentation

◆ Mode

Constructor & Destructor Documentation

◆ ~ScreeningDBCreator()

Member Function Documentation

◆ open()

◆ close()

◆ getMode()

◆ allowDuplicateEntries()

◆ process()

◆ merge()

◆ getDatabaseName()

◆ getNumProcessed()

◆ getNumRejected()

◆ getNumDeleted()

◆ getNumInserted()

◆ operator=()