Pharm::ScreeningDBAccessor implementation that reads pharmacophore screening databases stored in the built-in optimized PSD format. More...

#include <PSDScreeningDBAccessor.hpp>

Inheritance diagram for CDPL::Pharm::PSDScreeningDBAccessor:

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

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

Public Member Functions
	PSDScreeningDBAccessor ()
	Constructs a `PSDScreeningDBAccessor` instance without an associated database. More...

	PSDScreeningDBAccessor (const std::string &name)
	Constructs a `PSDScreeningDBAccessor` instance that will read data from the database-file specified by name. More...

	PSDScreeningDBAccessor (const PSDScreeningDBAccessor &)=delete

	~PSDScreeningDBAccessor ()
	Destructor. More...

PSDScreeningDBAccessor &	operator= (const PSDScreeningDBAccessor &)=delete

void	open (const std::string &name)
	Opens the database-file specified by name. More...

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

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

std::size_t	getNumMolecules () const
	Returns the total number of molecules stored in the database. More...

std::size_t	getNumPharmacophores () const
	Returns the total number of pharmacophores stored in the database. More...

std::size_t	getNumPharmacophores (std::size_t mol_idx) const
	Returns the number of pharmacophores (conformers) stored for the molecule at index mol_idx. More...

void	getMolecule (std::size_t mol_idx, Chem::Molecule &mol, bool overwrite=true) const
	Retrieves the molecule at index mol_idx and stores it in mol. More...

void	getPharmacophore (std::size_t pharm_idx, Pharmacophore &pharm, bool overwrite=true) const
	Retrieves the pharmacophore at index pharm_idx and stores it in pharm. More...

void	getPharmacophore (std::size_t mol_idx, std::size_t mol_conf_idx, Pharmacophore &pharm, bool overwrite=true) const
	Retrieves the pharmacophore for the given (molecule, conformer) pair and stores it in pharm. More...

std::size_t	getMoleculeIndex (std::size_t pharm_idx) const
	Returns the molecule index of the pharmacophore at index pharm_idx. More...

std::size_t	getConformationIndex (std::size_t pharm_idx) const
	Returns the conformer index (within its owning molecule) of the pharmacophore at index pharm_idx. More...

const FeatureTypeHistogram &	getFeatureCounts (std::size_t pharm_idx) const
	Returns the per-feature-type counts of the pharmacophore at index pharm_idx. More...

const FeatureTypeHistogram &	getFeatureCounts (std::size_t mol_idx, std::size_t mol_conf_idx) const
	Returns the per-feature-type counts of the pharmacophore for the given (molecule, conformer) pair. More...

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

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

Detailed Description

Pharm::ScreeningDBAccessor implementation that reads pharmacophore screening databases stored in the built-in optimized PSD format.

Member Typedef Documentation

◆ SharedPointer

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

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

Constructor & Destructor Documentation

◆ PSDScreeningDBAccessor() [1/3]

CDPL::Pharm::PSDScreeningDBAccessor::PSDScreeningDBAccessor ( )

Constructs a PSDScreeningDBAccessor instance without an associated database.

◆ PSDScreeningDBAccessor() [2/3]

CDPL::Pharm::PSDScreeningDBAccessor::PSDScreeningDBAccessor ( const std::string & name )

Constructs a PSDScreeningDBAccessor instance that will read data from the database-file specified by name.

Parameters

name	The name of the database-file.

◆ PSDScreeningDBAccessor() [3/3]

CDPL::Pharm::PSDScreeningDBAccessor::PSDScreeningDBAccessor ( const PSDScreeningDBAccessor & )

delete

◆ ~PSDScreeningDBAccessor()

CDPL::Pharm::PSDScreeningDBAccessor::~PSDScreeningDBAccessor ( )

Destructor.

Member Function Documentation

◆ operator=()

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

delete

◆ open()

void CDPL::Pharm::PSDScreeningDBAccessor::open ( const std::string & name )

virtual

Opens the database-file specified by name.

Parameters

name	The name of the database-file.

Implements CDPL::Pharm::ScreeningDBAccessor.

◆ close()

void CDPL::Pharm::PSDScreeningDBAccessor::close ( )

virtual

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

Implements CDPL::Pharm::ScreeningDBAccessor.

◆ getDatabaseName()

const std::string& CDPL::Pharm::PSDScreeningDBAccessor::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::ScreeningDBAccessor.

◆ getNumMolecules()

std::size_t CDPL::Pharm::PSDScreeningDBAccessor::getNumMolecules ( ) const

virtual

Returns the total number of molecules stored in the database.

Returns: The molecule count.

Implements CDPL::Pharm::ScreeningDBAccessor.

◆ getNumPharmacophores() [1/2]

std::size_t CDPL::Pharm::PSDScreeningDBAccessor::getNumPharmacophores ( ) const

virtual

Returns the total number of pharmacophores stored in the database.

Returns: The pharmacophore count (the sum of getNumPharmacophores(mol_idx) over all molecules).

Implements CDPL::Pharm::ScreeningDBAccessor.

◆ getNumPharmacophores() [2/2]

std::size_t CDPL::Pharm::PSDScreeningDBAccessor::getNumPharmacophores ( std::size_t mol_idx ) const

virtual

Returns the number of pharmacophores (conformers) stored for the molecule at index mol_idx.

Parameters

mol_idx The zero-based molecule index.

Returns: The per-molecule pharmacophore count.

Implements CDPL::Pharm::ScreeningDBAccessor.

◆ getMolecule()

void CDPL::Pharm::PSDScreeningDBAccessor::getMolecule	(	std::size_t	mol_idx,
		Chem::Molecule &	mol,
		bool	overwrite = `true`
	)		const

virtual

Retrieves the molecule at index mol_idx and stores it in mol.

Parameters

mol_idx	The zero-based molecule index.
mol	The output molecule.
overwrite	If `true`, the output molecule is cleared before the database molecule is copied into it.

Implements CDPL::Pharm::ScreeningDBAccessor.

◆ getPharmacophore() [1/2]

void CDPL::Pharm::PSDScreeningDBAccessor::getPharmacophore	(	std::size_t	pharm_idx,
		Pharmacophore &	pharm,
		bool	overwrite = `true`
	)		const

virtual

Retrieves the pharmacophore at index pharm_idx and stores it in pharm.

Parameters

pharm_idx	The zero-based pharmacophore index.
pharm	The output pharmacophore.
overwrite	If `true`, the output pharmacophore is cleared before the database pharmacophore is copied into it.

Implements CDPL::Pharm::ScreeningDBAccessor.

◆ getPharmacophore() [2/2]

void CDPL::Pharm::PSDScreeningDBAccessor::getPharmacophore	(	std::size_t	mol_idx,
		std::size_t	mol_conf_idx,
		Pharmacophore &	pharm,
		bool	overwrite = `true`
	)		const

virtual

Retrieves the pharmacophore for the given (molecule, conformer) pair and stores it in pharm.

Parameters

mol_idx	The zero-based molecule index.
mol_conf_idx	The zero-based conformer index within the molecule.
pharm	The output pharmacophore.
overwrite	If `true`, the output pharmacophore is cleared before the database pharmacophore is copied into it.

Implements CDPL::Pharm::ScreeningDBAccessor.

◆ getMoleculeIndex()

std::size_t CDPL::Pharm::PSDScreeningDBAccessor::getMoleculeIndex ( std::size_t pharm_idx ) const

virtual

Returns the molecule index of the pharmacophore at index pharm_idx.

Parameters

pharm_idx The zero-based pharmacophore index.

Returns: The owning molecule index.

Implements CDPL::Pharm::ScreeningDBAccessor.

◆ getConformationIndex()

std::size_t CDPL::Pharm::PSDScreeningDBAccessor::getConformationIndex ( std::size_t pharm_idx ) const

virtual

Returns the conformer index (within its owning molecule) of the pharmacophore at index pharm_idx.

Parameters

pharm_idx The zero-based pharmacophore index.

Returns: The conformer index.

Implements CDPL::Pharm::ScreeningDBAccessor.

◆ getFeatureCounts() [1/2]

const FeatureTypeHistogram& CDPL::Pharm::PSDScreeningDBAccessor::getFeatureCounts ( std::size_t pharm_idx ) const

virtual

Returns the per-feature-type counts of the pharmacophore at index pharm_idx.

Parameters

pharm_idx The zero-based pharmacophore index.

Returns: A const reference to the feature-type histogram.

Implements CDPL::Pharm::ScreeningDBAccessor.

◆ getFeatureCounts() [2/2]

const FeatureTypeHistogram& CDPL::Pharm::PSDScreeningDBAccessor::getFeatureCounts	(	std::size_t	mol_idx,
		std::size_t	mol_conf_idx
	)		const

virtual

Returns the per-feature-type counts of the pharmacophore for the given (molecule, conformer) pair.

Parameters

mol_idx	The zero-based molecule index.
mol_conf_idx	The zero-based conformer index within the molecule.

Returns: A const reference to the feature-type histogram.

Implements CDPL::Pharm::ScreeningDBAccessor.

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

PSDScreeningDBAccessor.hpp

Public Types

Public Member Functions

Additional Inherited Members

Detailed Description

Member Typedef Documentation

◆ SharedPointer

Constructor & Destructor Documentation

◆ PSDScreeningDBAccessor() [1/3]

◆ PSDScreeningDBAccessor() [2/3]

◆ PSDScreeningDBAccessor() [3/3]

◆ ~PSDScreeningDBAccessor()

Member Function Documentation

◆ operator=()

◆ open()

◆ close()

◆ getDatabaseName()

◆ getNumMolecules()

◆ getNumPharmacophores() [1/2]

◆ getNumPharmacophores() [2/2]

◆ getMolecule()

◆ getPharmacophore() [1/2]

◆ getPharmacophore() [2/2]

◆ getMoleculeIndex()

◆ getConformationIndex()

◆ getFeatureCounts() [1/2]

◆ getFeatureCounts() [2/2]