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...

Inheritance diagram for CDPL.Pharm.ScreeningProcessor:

Classes
class	HitReportMode
	Specifies which conformer-level hits are reported per molecule. More...

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 Member Functions
None	__init__ (ScreeningDBAccessor db_acc)
	Constructs the `ScreeningProcessor` instance for the given screening database accessor db_acc. More...

int	getObjectID ()
	Returns the numeric identifier (ID) of the wrapped C++ class instance. More...

None	setDBAccessor (ScreeningDBAccessor db_acc)
	Specifies the screening database accessor. More...

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

None	setHitReportMode (HitReportMode mode)
	Sets the hit-report mode. More...

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

None	setMaxNumOmittedFeatures (int max_num)
	Sets the maximum number of query features that may remain unmatched in a valid hit. More...

int	getMaxNumOmittedFeatures ()
	Returns the currently configured maximum number of omitted features. More...

None	checkXVolumeClashes (bool check)
	Specifies whether the alignment shall check exclusion volume clashes between the query and the hit molecule. More...

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

None	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 ()
	Tells whether the alignment seeks the best-scoring rather than the first valid alignment. More...

None	setHitCallback (BoolSearchHitDoubleFunctor func)
	Specifies the hit-callback function. More...

BoolSearchHitDoubleFunctor	getHitCallback ()
	Returns the currently configured hit-callback function. More...

None	setProgressCallback (BoolSizeType2Functor func)
	Specifies the progress-reporting callback. More...

BoolSizeType2Functor	getProgressCallback ()
	Returns the currently configured progress-reporting callback. More...

None	setScoringFunction (DoubleSearchHitFunctor func)
	Specifies the function used to score a search hit. More...

DoubleSearchHitFunctor	getScoringFunction ()
	Returns the currently configured scoring function. More...

int	searchDB (FeatureContainer query, int mol_start_idx=0, int mol_end_idx=0)
	Screens the database with the supplied query pharmacophore. More...

Properties
	objectID = property(getObjectID)

	dbAcccessor = property(getDBAccessor, setDBAccessor)

	hitCallback = property(getHitCallback, setHitCallback)

	progressCallback = property(getProgressCallback, setProgressCallback)

	scoringFunction = property(getScoringFunction, setScoringFunction)

	hitReportMode = property(getHitReportMode, setHitReportMode)

	maxNumOmittedFeatures = property(getMaxNumOmittedFeatures, setMaxNumOmittedFeatures)

	checkXVolumes = property(xVolumeClashesChecked, checkXVolumeClashes)

	bestAlignments = property(bestAlignmentsSeeked, seekBestAlignments)

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.

Constructor & Destructor Documentation

◆ init()

None CDPL.Pharm.ScreeningProcessor.__init__ ( 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.

Member Function Documentation

◆ getObjectID()

int CDPL.Pharm.ScreeningProcessor.getObjectID ( )

Returns the numeric identifier (ID) of the wrapped C++ class instance.

Different Python ScreeningProcessor instances may reference the same underlying C++ class instance. The commonly used Python expression a is not b thus cannot tell reliably whether the two ScreeningProcessor instances a and b reference different C++ objects. The numeric identifier returned by this method allows to correctly implement such an identity test via the simple expression a.getObjectID() != b.getObjectID().

Returns: The numeric ID of the internally referenced C++ class instance.

◆ setDBAccessor()

None 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 ( )

Returns the currently configured screening database accessor.

Returns: A reference to the database accessor.

◆ setHitReportMode()

None CDPL.Pharm.ScreeningProcessor.setHitReportMode ( HitReportMode mode )

Sets the hit-report mode.

Parameters

mode	The new hit-report mode.

◆ getHitReportMode()

HitReportMode CDPL.Pharm.ScreeningProcessor.getHitReportMode ( )

Returns the currently configured hit-report mode.

Returns: The hit-report mode.

◆ setMaxNumOmittedFeatures()

None CDPL.Pharm.ScreeningProcessor.setMaxNumOmittedFeatures ( int 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()

int CDPL.Pharm.ScreeningProcessor.getMaxNumOmittedFeatures ( )

Returns the currently configured maximum number of omitted features.

Returns: The maximum number of omitted features.

◆ checkXVolumeClashes()

None 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 ( )

Tells whether exclusion volume clashes are checked during alignment.

Returns: True if the clash check is enabled, and False otherwise.

◆ seekBestAlignments()

None 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 ( )

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()

None CDPL.Pharm.ScreeningProcessor.setHitCallback ( BoolSearchHitDoubleFunctor func )

Specifies the hit-callback function.

Parameters

func	The hit-callback function.

◆ getHitCallback()

BoolSearchHitDoubleFunctor CDPL.Pharm.ScreeningProcessor.getHitCallback ( )

Returns the currently configured hit-callback function.

Returns: A reference to the hit-callback function.

◆ setProgressCallback()

None CDPL.Pharm.ScreeningProcessor.setProgressCallback ( BoolSizeType2Functor func )

Specifies the progress-reporting callback.

Parameters

func	The progress-callback function.

◆ getProgressCallback()

BoolSizeType2Functor CDPL.Pharm.ScreeningProcessor.getProgressCallback ( )

Returns the currently configured progress-reporting callback.

Returns: A reference to the progress-callback function.

◆ setScoringFunction()

None CDPL.Pharm.ScreeningProcessor.setScoringFunction ( DoubleSearchHitFunctor func )

Specifies the function used to score a search hit.

Parameters

func	The scoring function.

◆ getScoringFunction()

DoubleSearchHitFunctor CDPL.Pharm.ScreeningProcessor.getScoringFunction ( )

Returns the currently configured scoring function.

Returns: A reference to the scoring function.

◆ searchDB()

int CDPL.Pharm.ScreeningProcessor.searchDB	(	FeatureContainer	query,
		int	mol_start_idx = `0`,
		int	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.

Classes

Public Member Functions

Properties

Detailed Description

Constructor & Destructor Documentation

◆ __init__()

Member Function Documentation

◆ getObjectID()

◆ setDBAccessor()

◆ getDBAccessor()

◆ setHitReportMode()

◆ getHitReportMode()

◆ setMaxNumOmittedFeatures()

◆ getMaxNumOmittedFeatures()

◆ checkXVolumeClashes()

◆ xVolumeClashesChecked()

◆ seekBestAlignments()

◆ bestAlignmentsSeeked()

◆ setHitCallback()

◆ getHitCallback()

◆ setProgressCallback()

◆ getProgressCallback()

◆ setScoringFunction()

◆ getScoringFunction()

◆ searchDB()

◆ init()