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()