Bundle of configuration parameters for Shape.ScreeningProcessor. More...

Inheritance diagram for CDPL.Shape.ScreeningSettings:

Classes
class	AlignmentMode
	Bitmask flags specifying the strategies used to seed alignment starting transformations. More...

class	ColorFeatureType
	Specifies which kind of color (pharmacophore) features are used during shape alignment. More...

class	ScreeningMode
	Specifies which alignment hits are reported by the screening processor. More...

Public Member Functions
None	__init__ ()
	Constructs a `ScreeningSettings` instance with default values.

None	__init__ (ScreeningSettings settings)
	Initializes a copy of the `ScreeningSettings` instance settings. More...

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

ScreeningSettings	assign (ScreeningSettings settings)
	Replaces the current state of self with a copy of the state of the `ScreeningSettings` instance settings. More...

None	setScoringFunction (DoubleAlignmentResultFunctor func)
	Sets the scoring function used to rank alignment results. More...

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

None	setScoreCutoff (float cutoff)
	Sets the minimum score below which alignment hits are discarded (or NO_CUTOFF). More...

float	getScoreCutoff ()
	Returns the currently configured score cutoff (or NO_CUTOFF). More...

None	setColorFeatureType (ColorFeatureType type)
	Sets the color feature type to use during alignment. More...

ColorFeatureType	getColorFeatureType ()
	Returns the currently configured color feature type. More...

None	setScreeningMode (ScreeningMode mode)
	Sets the screening mode. More...

ScreeningMode	getScreeningMode ()
	Returns the currently configured screening mode. More...

None	setAlignmentMode (AlignmentMode mode)
	Sets the alignment-mode bitmask (see AlignmentMode). More...

AlignmentMode	getAlignmentMode ()
	Returns the currently configured alignment-mode bitmask. More...

None	setNumRandomStarts (int num_starts)
	Sets the number of random starting transformations when AlignmentMode.RANDOM is enabled. More...

int	getNumRandomStarts ()
	Returns the currently configured number of random starts. More...

None	allCarbonMode (bool all_c)
	Enables or disables the all-carbon mode (treats every heavy atom as carbon for shape generation). More...

bool	allCarbonMode ()
	Tells whether the all-carbon mode is enabled. More...

None	singleConformerSearch (bool all_c)

bool	singleConformerSearch ()
	Tells whether only a single conformer of each molecule is considered. More...

None	setMaxNumOptimizationIterations (int max_iter)
	Sets the maximum number of overlap-optimization iterations. More...

int	getMaxNumOptimizationIterations ()
	Returns the currently configured maximum number of overlap-optimization iterations. More...

None	setOptimizationStopGradient (float grad_norm)
	Sets the gradient norm at which the overlap optimization is stopped. More...

float	getOptimizationStopGradient ()
	Returns the currently configured overlap-optimization stop gradient. More...

None	optimizeOverlap (bool optimize)
	Specifies whether the overlap shall be optimized iteratively after the initial alignment. More...

bool	optimizeOverlap ()
	Tells whether the overlap is optimized iteratively. More...

None	greedyOptimization (bool greedy)
	Specifies whether the overlap optimization shall use a greedy strategy that stops at the first local maximum. More...

bool	greedyOptimization ()
	Tells whether the overlap optimization uses a greedy strategy. More...

Static Public Attributes
	DEFAULT = _HIDDEN_VALUE_
	A static instance with default-initialized values.

	NO_CUTOFF = nan
	Sentinel value (NaN) used to disable the score cutoff.

Properties
	objectID = property(getObjectID)

	scoringFunction = property(getScoringFunction, setScoringFunction)

	scoreCutoff = property(getScoreCutoff, setScoreCutoff)

	screeningMode = property(getScreeningMode, setScreeningMode)

	alignmentMode = property(getAlignmentMode, setAlignmentMode)

	numRandomStarts = property(getNumRandomStarts, setNumRandomStarts)

	allCarbon = property(allCarbonMode, allCarbonMode)

	singleConfSearch = property(singleConformerSearch, singleConformerSearch)

	colorFeatureType = property(getColorFeatureType, setColorFeatureType)

	maxNumOptIterations = property(getMaxNumOptimizationIterations, setMaxNumOptimizationIterations)

	optStopGradient = property(getOptimizationStopGradient, setOptimizationStopGradient)

	optOverlap = property(optimizeOverlap, optimizeOverlap)

	greedyOpt = property(greedyOptimization, greedyOptimization)

Detailed Description

Bundle of configuration parameters for Shape.ScreeningProcessor.

The settings select the scoring function, the type of color (pharmacophore) features used, the screening mode (e.g. best-overall vs. best-per-query), the alignment-start strategy, and the parameters of the iterative overlap optimization.

Constructor & Destructor Documentation

◆ init()

None CDPL.Shape.ScreeningSettings.__init__ ( ScreeningSettings settings )

Initializes a copy of the ScreeningSettings instance settings.

Parameters

settings The ScreeningSettings instance to copy.

Member Function Documentation

◆ getObjectID()

int CDPL.Shape.ScreeningSettings.getObjectID ( )

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

Different Python ScreeningSettings 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 ScreeningSettings 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.

◆ assign()

ScreeningSettings CDPL.Shape.ScreeningSettings.assign ( ScreeningSettings settings )

Replaces the current state of self with a copy of the state of the ScreeningSettings instance settings.

Parameters

settings The ScreeningSettings instance to copy.

Returns: self

◆ setScoringFunction()

None CDPL.Shape.ScreeningSettings.setScoringFunction ( DoubleAlignmentResultFunctor func )

Sets the scoring function used to rank alignment results.

Parameters

func	The scoring function.

◆ getScoringFunction()

DoubleAlignmentResultFunctor CDPL.Shape.ScreeningSettings.getScoringFunction ( )

Returns the currently configured scoring function.

Returns: A reference to the scoring function.

◆ setScoreCutoff()

None CDPL.Shape.ScreeningSettings.setScoreCutoff ( float cutoff )

Sets the minimum score below which alignment hits are discarded (or NO_CUTOFF).

Parameters

cutoff The new score cutoff (or NO_CUTOFF to disable cutoff filtering).

◆ getScoreCutoff()

float CDPL.Shape.ScreeningSettings.getScoreCutoff ( )

Returns the currently configured score cutoff (or NO_CUTOFF).

Returns: The score cutoff (or NO_CUTOFF if cutoff filtering is disabled).

◆ setColorFeatureType()

None CDPL.Shape.ScreeningSettings.setColorFeatureType ( ColorFeatureType type )

Sets the color feature type to use during alignment.

Parameters

type	The new color-feature type.

◆ getColorFeatureType()

ColorFeatureType CDPL.Shape.ScreeningSettings.getColorFeatureType ( )

Returns the currently configured color feature type.

Returns: The color-feature type.

◆ setScreeningMode()

None CDPL.Shape.ScreeningSettings.setScreeningMode ( ScreeningMode mode )

Sets the screening mode.

Parameters

mode	The new screening mode.

◆ getScreeningMode()

ScreeningMode CDPL.Shape.ScreeningSettings.getScreeningMode ( )

Returns the currently configured screening mode.

Returns: The screening mode.

◆ setAlignmentMode()

None CDPL.Shape.ScreeningSettings.setAlignmentMode ( AlignmentMode mode )

Sets the alignment-mode bitmask (see AlignmentMode).

Parameters

mode	The new alignment-mode bitmask.

◆ getAlignmentMode()

AlignmentMode CDPL.Shape.ScreeningSettings.getAlignmentMode ( )

Returns the currently configured alignment-mode bitmask.

Returns: The alignment-mode bitmask.

◆ setNumRandomStarts()

None CDPL.Shape.ScreeningSettings.setNumRandomStarts ( int num_starts )

Sets the number of random starting transformations when AlignmentMode.RANDOM is enabled.

Parameters

num_starts The new number of random starts.

◆ getNumRandomStarts()

int CDPL.Shape.ScreeningSettings.getNumRandomStarts ( )

Returns the currently configured number of random starts.

Returns: The number of random starts.

◆ allCarbonMode() [1/2]

None CDPL.Shape.ScreeningSettings.allCarbonMode ( bool all_c )

Enables or disables the all-carbon mode (treats every heavy atom as carbon for shape generation).

Parameters

all_c True to enable the all-carbon mode, and False to use the actual atom types.

◆ allCarbonMode() [2/2]

bool CDPL.Shape.ScreeningSettings.allCarbonMode ( )

Tells whether the all-carbon mode is enabled.

Returns: True if the all-carbon mode is enabled, and False otherwise.

◆ singleConformerSearch() [1/2]

None CDPL.Shape.ScreeningSettings.singleConformerSearch ( bool all_c )

Parameters

all_c

◆ singleConformerSearch() [2/2]

bool CDPL.Shape.ScreeningSettings.singleConformerSearch ( )

Tells whether only a single conformer of each molecule is considered.

Returns: True if only a single conformer is considered, and False otherwise.

◆ setMaxNumOptimizationIterations()

None CDPL.Shape.ScreeningSettings.setMaxNumOptimizationIterations ( int max_iter )

Sets the maximum number of overlap-optimization iterations.

Parameters

max_iter The new maximum number of iterations.

◆ getMaxNumOptimizationIterations()

int CDPL.Shape.ScreeningSettings.getMaxNumOptimizationIterations ( )

Returns the currently configured maximum number of overlap-optimization iterations.

Returns: The maximum number of iterations.

◆ setOptimizationStopGradient()

None CDPL.Shape.ScreeningSettings.setOptimizationStopGradient ( float grad_norm )

Sets the gradient norm at which the overlap optimization is stopped.

Parameters

grad_norm The new stop gradient norm.

◆ getOptimizationStopGradient()

float CDPL.Shape.ScreeningSettings.getOptimizationStopGradient ( )

Returns the currently configured overlap-optimization stop gradient.

Returns: The stop gradient norm.

◆ optimizeOverlap() [1/2]

None CDPL.Shape.ScreeningSettings.optimizeOverlap ( bool optimize )

Specifies whether the overlap shall be optimized iteratively after the initial alignment.

Parameters

optimize True to optimize the overlap, and False to skip optimization.

◆ optimizeOverlap() [2/2]

bool CDPL.Shape.ScreeningSettings.optimizeOverlap ( )

Tells whether the overlap is optimized iteratively.

Returns: True if the overlap is optimized, and False otherwise.

◆ greedyOptimization() [1/2]

None CDPL.Shape.ScreeningSettings.greedyOptimization ( bool greedy )

Specifies whether the overlap optimization shall use a greedy strategy that stops at the first local maximum.

Parameters

greedy True to use the greedy strategy, and False to use the full optimization.

◆ greedyOptimization() [2/2]

bool CDPL.Shape.ScreeningSettings.greedyOptimization ( )

Tells whether the overlap optimization uses a greedy strategy.

Returns: True if the greedy strategy is used, and False otherwise.

Classes

Public Member Functions

Static Public Attributes

Properties

Detailed Description

Constructor & Destructor Documentation

◆ __init__()

Member Function Documentation

◆ getObjectID()

◆ assign()

◆ setScoringFunction()

◆ getScoringFunction()

◆ setScoreCutoff()

◆ getScoreCutoff()

◆ setColorFeatureType()

◆ getColorFeatureType()

◆ setScreeningMode()

◆ getScreeningMode()

◆ setAlignmentMode()

◆ getAlignmentMode()

◆ setNumRandomStarts()

◆ getNumRandomStarts()

◆ allCarbonMode() [1/2]

◆ allCarbonMode() [2/2]

◆ singleConformerSearch() [1/2]

◆ singleConformerSearch() [2/2]

◆ setMaxNumOptimizationIterations()

◆ getMaxNumOptimizationIterations()

◆ setOptimizationStopGradient()

◆ getOptimizationStopGradient()

◆ optimizeOverlap() [1/2]

◆ optimizeOverlap() [2/2]

◆ greedyOptimization() [1/2]

◆ greedyOptimization() [2/2]

◆ init()