Abstract base class for accessors that read the data stored in pharmacophore screening databases. More...

#include <ScreeningDBAccessor.hpp>

Inheritance diagram for CDPL::Pharm::ScreeningDBAccessor:

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

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

virtual void	open (const std::string &name)=0
	Opens the screening database identified by name. More...

virtual void	close ()=0
	Closes 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	getNumMolecules () const =0
	Returns the total number of molecules stored in the database. More...

virtual std::size_t	getNumPharmacophores () const =0
	Returns the total number of pharmacophores stored in the database (one per molecule conformer). More...

virtual std::size_t	getNumPharmacophores (std::size_t mol_idx) const =0
	Returns the number of pharmacophores stored for the molecule at index mol_idx. More...

virtual void	getMolecule (std::size_t mol_idx, Chem::Molecule &mol, bool overwrite=true) const =0
	Reads the molecule at index mol_idx into mol. More...

virtual void	getPharmacophore (std::size_t pharm_idx, Pharmacophore &pharm, bool overwrite=true) const =0
	Reads the pharmacophore at index pharm_idx into pharm. More...

virtual void	getPharmacophore (std::size_t mol_idx, std::size_t mol_conf_idx, Pharmacophore &pharm, bool overwrite=true) const =0
	Reads the pharmacophore corresponding to conformer mol_conf_idx of molecule mol_idx into pharm. More...

virtual std::size_t	getMoleculeIndex (std::size_t pharm_idx) const =0
	Returns the molecule index of the pharmacophore at index pharm_idx. More...

virtual std::size_t	getConformationIndex (std::size_t pharm_idx) const =0
	Returns the conformer index within the parent molecule of the pharmacophore at index pharm_idx. More...

virtual const FeatureTypeHistogram &	getFeatureCounts (std::size_t pharm_idx) const =0
	Returns the cached per Pharm::FeatureType frequency histogram of the pharmacophore at index pharm_idx. More...

virtual const FeatureTypeHistogram &	getFeatureCounts (std::size_t mol_idx, std::size_t mol_conf_idx) const =0
	Returns the cached per Pharm::FeatureType frequency histogram of conformer mol_conf_idx of molecule mol_idx. More...

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

Detailed Description

Abstract base class for accessors that read the data stored in pharmacophore screening databases.

Member Typedef Documentation

◆ SharedPointer

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

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

Constructor & Destructor Documentation

◆ ~ScreeningDBAccessor()

virtual CDPL::Pharm::ScreeningDBAccessor::~ScreeningDBAccessor ( )

inlinevirtual

Virtual destructor.

Member Function Documentation

◆ open()

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

pure virtual

Opens the screening database identified by name.

Parameters

name	The database name (path, URI, etc., interpreted by the concrete subclass).

Implemented in CDPL::Pharm::PSDScreeningDBAccessor.

◆ close()

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

pure virtual

Closes the currently open database.

Implemented in CDPL::Pharm::PSDScreeningDBAccessor.

◆ getDatabaseName()

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

pure virtual

Returns the name of the currently open database.

Returns: A const reference to the database name.

Implemented in CDPL::Pharm::PSDScreeningDBAccessor.

◆ getNumMolecules()

virtual std::size_t CDPL::Pharm::ScreeningDBAccessor::getNumMolecules ( ) const

pure virtual

Returns the total number of molecules stored in the database.

Returns: The molecule count.

Implemented in CDPL::Pharm::PSDScreeningDBAccessor.

◆ getNumPharmacophores() [1/2]

virtual std::size_t CDPL::Pharm::ScreeningDBAccessor::getNumPharmacophores ( ) const

pure virtual

Returns the total number of pharmacophores stored in the database (one per molecule conformer).

Returns: The pharmacophore count.

Implemented in CDPL::Pharm::PSDScreeningDBAccessor.

◆ getNumPharmacophores() [2/2]

virtual std::size_t CDPL::Pharm::ScreeningDBAccessor::getNumPharmacophores ( std::size_t mol_idx ) const

pure virtual

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

Parameters

mol_idx The zero-based molecule index.

Returns: The pharmacophore count for the molecule.

Implemented in CDPL::Pharm::PSDScreeningDBAccessor.

◆ getMolecule()

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

pure virtual

Reads the molecule at index mol_idx into mol.

Parameters

mol_idx	The zero-based molecule index.
mol	The output molecule.
overwrite	If `true`, mol is cleared before reading; if `false`, the atoms/bonds are appended.

Implemented in CDPL::Pharm::PSDScreeningDBAccessor.

◆ getPharmacophore() [1/2]

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

pure virtual

Reads the pharmacophore at index pharm_idx into pharm.

Parameters

pharm_idx	The zero-based pharmacophore index (across all molecules).
pharm	The output pharmacophore.
overwrite	If `true`, pharm is cleared before reading; if `false`, the features are appended.

Implemented in CDPL::Pharm::PSDScreeningDBAccessor.

◆ getPharmacophore() [2/2]

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

pure virtual

Reads the pharmacophore corresponding to conformer mol_conf_idx of molecule mol_idx into 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`, pharm is cleared before reading; if `false`, the features are appended.

Implemented in CDPL::Pharm::PSDScreeningDBAccessor.

◆ getMoleculeIndex()

virtual std::size_t CDPL::Pharm::ScreeningDBAccessor::getMoleculeIndex ( std::size_t pharm_idx ) const

pure virtual

Returns the molecule index of the pharmacophore at index pharm_idx.

Parameters

pharm_idx The zero-based pharmacophore index.

Returns: The zero-based molecule index.

Implemented in CDPL::Pharm::PSDScreeningDBAccessor.

◆ getConformationIndex()

virtual std::size_t CDPL::Pharm::ScreeningDBAccessor::getConformationIndex ( std::size_t pharm_idx ) const

pure virtual

Returns the conformer index within the parent molecule of the pharmacophore at index pharm_idx.

Parameters

pharm_idx The zero-based pharmacophore index.

Returns: The zero-based conformer index.

Implemented in CDPL::Pharm::PSDScreeningDBAccessor.

◆ getFeatureCounts() [1/2]

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

pure virtual

Returns the cached per Pharm::FeatureType frequency histogram of the pharmacophore at index pharm_idx.

Parameters

pharm_idx The zero-based pharmacophore index.

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

Implemented in CDPL::Pharm::PSDScreeningDBAccessor.

◆ getFeatureCounts() [2/2]

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

pure virtual

Returns the cached per Pharm::FeatureType frequency histogram of conformer mol_conf_idx of molecule mol_idx.

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.

Implemented in CDPL::Pharm::PSDScreeningDBAccessor.

◆ operator=()

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

inlineprotected

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

ScreeningDBAccessor.hpp

Public Types

Public Member Functions

Protected Member Functions

Detailed Description

Member Typedef Documentation

◆ SharedPointer

Constructor & Destructor Documentation

◆ ~ScreeningDBAccessor()

Member Function Documentation

◆ 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]

◆ operator=()