High-level driver for pharmacophore-based screening of a Pharm::ScreeningDBAccessor-backed database against a query feature container, reporting alignment hits via a user-supplied callback. More...

#include <ScreeningProcessor.hpp>

Classes
class	SearchHit
	Data structure representing a single alignment hit produced by the screening processor, bundling the source pharmacophore/molecule, the alignment transformation and the source-database indices. More...

Public Types
enum	HitReportMode { FIRST_MATCHING_CONF , BEST_MATCHING_CONF , ALL_MATCHING_CONFS }
	Specifies which conformer-level hits are reported per molecule. More...

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

typedef std::function< bool(const SearchHit &, double)>	HitCallbackFunction
	Type of the callback invoked for every alignment hit (return: `true` to continue, `false` to abort the search). More...

typedef std::function< double(const SearchHit &)>	ScoringFunction
	Type of the function used to score a search hit. More...

typedef std::function< bool(std::size_t, std::size_t)>	ProgressCallbackFunction
	Type of the progress-reporting callback (arguments: current molecule index, total molecule count; return: `true` to continue, `false` to abort). More...

Public Member Functions
	ScreeningProcessor (ScreeningDBAccessor &db_acc)
	Constructs the `ScreeningProcessor` instance for the given screening database accessor db_acc. More...

	ScreeningProcessor (const ScreeningProcessor &proc)=delete

	~ScreeningProcessor ()
	Destructor. More...

ScreeningProcessor &	operator= (const ScreeningProcessor &proc)=delete

void	setDBAccessor (ScreeningDBAccessor &db_acc)
	Specifies the screening database accessor. More...

ScreeningDBAccessor &	getDBAccessor () const
	Returns the currently configured screening database accessor. More...

void	setHitReportMode (HitReportMode mode)
	Sets the hit-report mode. More...

HitReportMode	getHitReportMode () const
	Returns the currently configured hit-report mode. More...

void	setMaxNumOmittedFeatures (std::size_t max_num)
	Sets the maximum number of query features that may remain unmatched in a valid hit. More...

std::size_t	getMaxNumOmittedFeatures () const
	Returns the currently configured maximum number of omitted features. More...

void	checkXVolumeClashes (bool check)
	Specifies whether the alignment shall check exclusion-volume clashes between the query and the hit molecule. More...

bool	xVolumeClashesChecked () const
	Tells whether exclusion-volume clashes are checked during alignment. More...

void	seekBestAlignments (bool seek_best)
	Specifies whether the alignment shall search for the best-scoring rather than the first valid alignment per pose. More...

bool	bestAlignmentsSeeked () const
	Tells whether the alignment seeks the best-scoring rather than the first valid alignment. More...

void	setHitCallback (const HitCallbackFunction &func)
	Specifies the hit-callback function. More...

const HitCallbackFunction &	getHitCallback () const
	Returns the currently configured hit-callback function. More...

void	setProgressCallback (const ProgressCallbackFunction &func)
	Specifies the progress-reporting callback. More...

const ProgressCallbackFunction &	getProgressCallback () const
	Returns the currently configured progress-reporting callback. More...

void	setScoringFunction (const ScoringFunction &func)
	Specifies the function used to score a search hit. More...

const ScoringFunction &	getScoringFunction () const
	Returns the currently configured scoring function. More...

std::size_t	searchDB (const FeatureContainer &query, std::size_t mol_start_idx=0, std::size_t mol_end_idx=0)
	Screens the database with the supplied query pharmacophore. More...

Detailed Description

High-level driver for pharmacophore-based screening of a Pharm::ScreeningDBAccessor-backed database against a query feature container, reporting alignment hits via a user-supplied callback.

Member Typedef Documentation

◆ SharedPointer

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

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

◆ HitCallbackFunction

typedef std::function<bool(const SearchHit&, double)> CDPL::Pharm::ScreeningProcessor::HitCallbackFunction

Type of the callback invoked for every alignment hit (return: true to continue, false to abort the search).

◆ ScoringFunction

typedef std::function<double(const SearchHit&)> CDPL::Pharm::ScreeningProcessor::ScoringFunction

Type of the function used to score a search hit.

◆ ProgressCallbackFunction

typedef std::function<bool(std::size_t, std::size_t)> CDPL::Pharm::ScreeningProcessor::ProgressCallbackFunction

Type of the progress-reporting callback (arguments: current molecule index, total molecule count; return: true to continue, false to abort).

Member Enumeration Documentation

◆ HitReportMode

enum CDPL::Pharm::ScreeningProcessor::HitReportMode

Specifies which conformer-level hits are reported per molecule.

Enumerator
FIRST_MATCHING_CONF	Report the first conformer that matches the query.
BEST_MATCHING_CONF	Report only the best-scoring matching conformer.
ALL_MATCHING_CONFS	Report every conformer that matches the query.

Constructor & Destructor Documentation

◆ ScreeningProcessor() [1/2]

CDPL::Pharm::ScreeningProcessor::ScreeningProcessor ( ScreeningDBAccessor & db_acc )

Constructs the ScreeningProcessor instance for the given screening database accessor db_acc.

Parameters

db_acc An accessor for the database to screen.

◆ ScreeningProcessor() [2/2]

CDPL::Pharm::ScreeningProcessor::ScreeningProcessor ( const ScreeningProcessor & proc )

delete

◆ ~ScreeningProcessor()

CDPL::Pharm::ScreeningProcessor::~ScreeningProcessor ( )

Destructor.

Member Function Documentation

◆ operator=()

ScreeningProcessor& CDPL::Pharm::ScreeningProcessor::operator= ( const ScreeningProcessor & proc )

delete

◆ setDBAccessor()

void CDPL::Pharm::ScreeningProcessor::setDBAccessor ( ScreeningDBAccessor & db_acc )

Specifies the screening database accessor.

Parameters

db_acc The new database accessor.

◆ getDBAccessor()

ScreeningDBAccessor& CDPL::Pharm::ScreeningProcessor::getDBAccessor ( ) const

Returns the currently configured screening database accessor.

Returns: A reference to the database accessor.

◆ setHitReportMode()

void CDPL::Pharm::ScreeningProcessor::setHitReportMode ( HitReportMode mode )

Sets the hit-report mode.

Parameters

mode	The new hit-report mode.

◆ getHitReportMode()

HitReportMode CDPL::Pharm::ScreeningProcessor::getHitReportMode ( ) const

Returns the currently configured hit-report mode.

Returns: The hit-report mode.

◆ setMaxNumOmittedFeatures()

void CDPL::Pharm::ScreeningProcessor::setMaxNumOmittedFeatures ( std::size_t max_num )

Sets the maximum number of query features that may remain unmatched in a valid hit.

Parameters

max_num The new maximum number of omitted features.

◆ getMaxNumOmittedFeatures()

std::size_t CDPL::Pharm::ScreeningProcessor::getMaxNumOmittedFeatures ( ) const

Returns the currently configured maximum number of omitted features.

Returns: The maximum number of omitted features.

◆ checkXVolumeClashes()

void CDPL::Pharm::ScreeningProcessor::checkXVolumeClashes ( bool check )

Specifies whether the alignment shall check exclusion-volume clashes between the query and the hit molecule.

Parameters

check true to enable the clash check, and false to disable it.

◆ xVolumeClashesChecked()

bool CDPL::Pharm::ScreeningProcessor::xVolumeClashesChecked ( ) const

Tells whether exclusion-volume clashes are checked during alignment.

Returns: true if the clash check is enabled, and false otherwise.

◆ seekBestAlignments()

void CDPL::Pharm::ScreeningProcessor::seekBestAlignments ( bool seek_best )

Specifies whether the alignment shall search for the best-scoring rather than the first valid alignment per pose.

Parameters

seek_best true to seek the best alignment, and false to accept the first valid alignment.

◆ bestAlignmentsSeeked()

bool CDPL::Pharm::ScreeningProcessor::bestAlignmentsSeeked ( ) const

Tells whether the alignment seeks the best-scoring rather than the first valid alignment.

Returns: true if best-alignment seeking is enabled, and false otherwise.

◆ setHitCallback()

void CDPL::Pharm::ScreeningProcessor::setHitCallback ( const HitCallbackFunction & func )

Specifies the hit-callback function.

Parameters

func	The hit-callback function.

◆ getHitCallback()

const HitCallbackFunction& CDPL::Pharm::ScreeningProcessor::getHitCallback ( ) const

Returns the currently configured hit-callback function.

Returns: A const reference to the hit-callback function.

◆ setProgressCallback()

void CDPL::Pharm::ScreeningProcessor::setProgressCallback ( const ProgressCallbackFunction & func )

Specifies the progress-reporting callback.

Parameters

func	The progress-callback function.

◆ getProgressCallback()

const ProgressCallbackFunction& CDPL::Pharm::ScreeningProcessor::getProgressCallback ( ) const

Returns the currently configured progress-reporting callback.

Returns: A const reference to the progress-callback function.

◆ setScoringFunction()

void CDPL::Pharm::ScreeningProcessor::setScoringFunction ( const ScoringFunction & func )

Specifies the function used to score a search hit.

Parameters

func	The scoring function.

◆ getScoringFunction()

const ScoringFunction& CDPL::Pharm::ScreeningProcessor::getScoringFunction ( ) const

Returns the currently configured scoring function.

Returns: A const reference to the scoring function.

◆ searchDB()

std::size_t CDPL::Pharm::ScreeningProcessor::searchDB	(	const FeatureContainer &	query,
		std::size_t	mol_start_idx = `0`,
		std::size_t	mol_end_idx = `0`
	)

Screens the database with the supplied query pharmacophore.

Parameters

query	The query feature container.
mol_start_idx	The zero-based index of the first molecule to screen.
mol_end_idx	The exclusive upper bound of the molecule range; if 0, the search runs through the end of the database.

Returns: The number of accepted hits produced by the search.

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

Pharm/ScreeningProcessor.hpp

Classes

Public Types

Public Member Functions

Detailed Description

Member Typedef Documentation

◆ SharedPointer

◆ HitCallbackFunction

◆ ScoringFunction

◆ ProgressCallbackFunction

Member Enumeration Documentation

◆ HitReportMode

Constructor & Destructor Documentation

◆ ScreeningProcessor() [1/2]

◆ ScreeningProcessor() [2/2]

◆ ~ScreeningProcessor()

Member Function Documentation

◆ operator=()

◆ setDBAccessor()

◆ getDBAccessor()

◆ setHitReportMode()

◆ getHitReportMode()

◆ setMaxNumOmittedFeatures()

◆ getMaxNumOmittedFeatures()

◆ checkXVolumeClashes()

◆ xVolumeClashesChecked()

◆ seekBestAlignments()

◆ bestAlignmentsSeeked()

◆ setHitCallback()

◆ getHitCallback()

◆ setProgressCallback()

◆ getProgressCallback()

◆ setScoringFunction()

◆ getScoringFunction()

◆ searchDB()