Pharm::ScreeningDBCreator implementation that builds optimized pharmacophore screening databases in the built-in PSD format. More...

#include <PSDScreeningDBCreator.hpp>

Inheritance diagram for CDPL::Pharm::PSDScreeningDBCreator:

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

Public Types inherited from CDPL::Pharm::ScreeningDBCreator
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
	PSDScreeningDBCreator ()
	Constructs a `PSDScreeningDBCreator` instance without an associated database. More...

	PSDScreeningDBCreator (const std::string &name, Mode mode=CREATE, bool allow_dup_entries=true)
	Constructs a `PSDScreeningDBCreator` instance that will write data to the database-file specified by name in the given insert mode. More...

	PSDScreeningDBCreator (const PSDScreeningDBCreator &)=delete

	~PSDScreeningDBCreator ()
	Destructor. More...

PSDScreeningDBCreator &	operator= (const PSDScreeningDBCreator &)=delete

void	open (const std::string &name, Mode mode=CREATE, bool allow_dup_entries=true)
	Opens the database-file specified by name in the given insert mode. More...

void	close ()
	Closes the currently associated database-file (if any). More...

Mode	getMode () const
	Returns the currently configured insert mode. More...

bool	allowDuplicateEntries () const
	Tells whether duplicate database entries are currently allowed. More...

bool	process (const Chem::MolecularGraph &molgraph)
	Processes molgraph and inserts the resulting molecule (with derived conformer pharmacophores) into the database. More...

bool	merge (const ScreeningDBAccessor &db_acc, const ProgressCallbackFunction &func)
	Merges all molecule/pharmacophore records of db_acc into the currently open database. More...

const std::string &	getDatabaseName () const
	Returns the name of the currently associated database-file. More...

std::size_t	getNumProcessed () const
	Returns the total number of input molecules processed since the database was opened. More...

std::size_t	getNumRejected () const
	Returns the number of processed molecules that were rejected (e.g. as duplicates). More...

std::size_t	getNumDeleted () const
	Returns the number of pre-existing database entries that were deleted (under Mode::UPDATE/CREATE). More...

std::size_t	getNumInserted () const
	Returns the number of new database entries that were inserted. More...

Public Member Functions inherited from CDPL::Pharm::ScreeningDBCreator
virtual	~ScreeningDBCreator ()
	Virtual destructor. More...

Additional Inherited Members
Protected Member Functions inherited from CDPL::Pharm::ScreeningDBCreator
ScreeningDBCreator &	operator= (const ScreeningDBCreator &)

Detailed Description

Pharm::ScreeningDBCreator implementation that builds optimized pharmacophore screening databases in the built-in PSD format.

Member Typedef Documentation

◆ SharedPointer

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

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

Constructor & Destructor Documentation

◆ PSDScreeningDBCreator() [1/3]

CDPL::Pharm::PSDScreeningDBCreator::PSDScreeningDBCreator ( )

Constructs a PSDScreeningDBCreator instance without an associated database.

◆ PSDScreeningDBCreator() [2/3]

CDPL::Pharm::PSDScreeningDBCreator::PSDScreeningDBCreator	(	const std::string &	name,
		Mode	mode = `CREATE`,
		bool	allow_dup_entries = `true`
	)

Constructs a PSDScreeningDBCreator instance that will write data to the database-file specified by name in the given insert mode.

Parameters

name	The name of the database-file.
mode	Specifies whether to (re)create the database or to update/append to existing records.
allow_dup_entries	Specifies whether input molecules that are duplicates of already stored molecules should be discarded.

◆ PSDScreeningDBCreator() [3/3]

CDPL::Pharm::PSDScreeningDBCreator::PSDScreeningDBCreator ( const PSDScreeningDBCreator & )

delete

◆ ~PSDScreeningDBCreator()

CDPL::Pharm::PSDScreeningDBCreator::~PSDScreeningDBCreator ( )

Destructor.

Member Function Documentation

◆ operator=()

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

delete

◆ open()

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

virtual

Opens the database-file specified by name in the given insert mode.

Parameters

name	The name of the database-file.
mode	Specifies whether to (re)create the database or to update/append to existing records.
allow_dup_entries	Specifies whether input molecules that are duplicates of already stored molecules should be discarded.

Implements CDPL::Pharm::ScreeningDBCreator.

◆ close()

void CDPL::Pharm::PSDScreeningDBCreator::close ( )

virtual

Closes the currently associated database-file (if any).

Implements CDPL::Pharm::ScreeningDBCreator.

◆ getMode()

Mode CDPL::Pharm::PSDScreeningDBCreator::getMode ( ) const

virtual

Returns the currently configured insert mode.

Returns: The Pharm::ScreeningDBCreator::Mode value.

Implements CDPL::Pharm::ScreeningDBCreator.

◆ allowDuplicateEntries()

bool CDPL::Pharm::PSDScreeningDBCreator::allowDuplicateEntries ( ) const

virtual

Tells whether duplicate database entries are currently allowed.

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

Implements CDPL::Pharm::ScreeningDBCreator.

◆ process()

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

virtual

Processes molgraph and inserts the resulting molecule (with derived conformer pharmacophores) into the database.

Parameters

molgraph The molecular graph to process.

Returns: true if the molecule was inserted, and false if it was rejected (e.g. as a duplicate).

Implements CDPL::Pharm::ScreeningDBCreator.

◆ merge()

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

virtual

Merges all molecule/pharmacophore records of db_acc into the currently open database.

Parameters

db_acc	The source database accessor.
func	A progress-reporting callback invoked during the merge.

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

Implements CDPL::Pharm::ScreeningDBCreator.

◆ getDatabaseName()

const std::string& CDPL::Pharm::PSDScreeningDBCreator::getDatabaseName ( ) const

virtual

Returns the name of the currently associated database-file.

Returns: A const reference to the database-file name (or an empty string if no database is open).

Implements CDPL::Pharm::ScreeningDBCreator.

◆ getNumProcessed()

std::size_t CDPL::Pharm::PSDScreeningDBCreator::getNumProcessed ( ) const

virtual

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

Returns: The processed-molecule count.

Implements CDPL::Pharm::ScreeningDBCreator.

◆ getNumRejected()

std::size_t CDPL::Pharm::PSDScreeningDBCreator::getNumRejected ( ) const

virtual

Returns the number of processed molecules that were rejected (e.g. as duplicates).

Returns: The rejected-molecule count.

Implements CDPL::Pharm::ScreeningDBCreator.

◆ getNumDeleted()

std::size_t CDPL::Pharm::PSDScreeningDBCreator::getNumDeleted ( ) const

virtual

Returns the number of pre-existing database entries that were deleted (under Mode::UPDATE/CREATE).

Returns: The deleted-entry count.

Implements CDPL::Pharm::ScreeningDBCreator.

◆ getNumInserted()

std::size_t CDPL::Pharm::PSDScreeningDBCreator::getNumInserted ( ) const

virtual

Returns the number of new database entries that were inserted.

Returns: The inserted-entry count.

Implements CDPL::Pharm::ScreeningDBCreator.

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

PSDScreeningDBCreator.hpp

Public Types

Public Member Functions

Additional Inherited Members

Detailed Description

Member Typedef Documentation

◆ SharedPointer

Constructor & Destructor Documentation

◆ PSDScreeningDBCreator() [1/3]

◆ PSDScreeningDBCreator() [2/3]

◆ PSDScreeningDBCreator() [3/3]

◆ ~PSDScreeningDBCreator()

Member Function Documentation

◆ operator=()

◆ open()

◆ close()

◆ getMode()

◆ allowDuplicateEntries()

◆ process()

◆ merge()

◆ getDatabaseName()

◆ getNumProcessed()

◆ getNumRejected()

◆ getNumDeleted()

◆ getNumInserted()