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

#include <ScreeningSettings.hpp>

Public Types
enum	ScreeningMode { BEST_OVERALL_MATCH , BEST_MATCH_PER_QUERY , BEST_MATCH_PER_QUERY_CONF }
	Specifies which alignment hits are reported by the screening processor. More...

enum	ColorFeatureType { NO_FEATURES , PHARMACOPHORE_EXP_CHARGES , PHARMACOPHORE_IMP_CHARGES }
	Specifies which kind of color (pharmacophore) features are used during shape alignment. More...

enum	AlignmentMode { NO_ALIGNMENT = 0x0 , SHAPE_CENTROID = 0x1 , ATOM_CENTERS = 0x2 , COLOR_FEATURE_CENTERS = 0x4 , RANDOM = 0x8 }
	Bitmask flags specifying the strategies used to seed alignment starting transformations. More...

typedef std::function< double(const AlignmentResult &)>	ScoringFunction
	Type of the function used to score an alignment result. More...

Public Member Functions
	ScreeningSettings ()
	Constructs a `ScreeningSettings` instance with default values. More...

void	setScoringFunction (const ScoringFunction &func)
	Sets the scoring function used to rank alignment results. More...

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

void	setColorFeatureType (ColorFeatureType type)
	Sets the color feature type to use during alignment. More...

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

void	setScreeningMode (ScreeningMode mode)
	Sets the screening mode. More...

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

void	setAlignmentMode (AlignmentMode mode)
	Sets the alignment-mode bitmask (see AlignmentMode). More...

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

void	setNumRandomStarts (std::size_t num_starts)
	Sets the number of random starting transformations when AlignmentMode::RANDOM is enabled. More...

std::size_t	getNumRandomStarts () const
	Returns the currently configured number of random starts. More...

void	allCarbonMode (bool all_c)
	Enables or disables the all-carbon mode (treats every heavy atom as carbon for shape generation). More...

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

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

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

void	optimizeOverlap (bool optimize)
	Specifies whether the overlap shall be optimized iteratively after the initial alignment. More...

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

void	greedyOptimization (bool greedy)
	Specifies whether the overlap optimization shall use a greedy strategy that stops at the first local maximum. More...

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

void	setMaxNumOptimizationIterations (std::size_t max_iter)
	Sets the maximum number of overlap-optimization iterations. More...

std::size_t	getMaxNumOptimizationIterations () const
	Returns the currently configured maximum number of overlap-optimization iterations. More...

void	setOptimizationStopGradient (double grad_norm)
	Sets the gradient norm at which the overlap optimization is stopped. More...

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

void	setScoreCutoff (double cutoff)
	Sets the minimum score below which alignment hits are discarded (or NO_CUTOFF). More...

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

Static Public Attributes
static const ScreeningSettings	DEFAULT
	A static instance with default-initialized values. More...

static constexpr double	NO_CUTOFF = std::numeric_limits<double>::quiet_NaN()
	Sentinel value (NaN) used to disable the score cutoff. More...

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.

Member Typedef Documentation

◆ ScoringFunction

typedef std::function<double(const AlignmentResult&)> CDPL::Shape::ScreeningSettings::ScoringFunction

Type of the function used to score an alignment result.

Member Enumeration Documentation

◆ ScreeningMode

enum CDPL::Shape::ScreeningSettings::ScreeningMode

Specifies which alignment hits are reported by the screening processor.

Enumerator
BEST_OVERALL_MATCH	Report only the single best-scoring alignment hit across all queries.
BEST_MATCH_PER_QUERY	Report the best-scoring alignment hit per query molecule.
BEST_MATCH_PER_QUERY_CONF	Report the best-scoring alignment hit per (query, query conformer) pair.

◆ ColorFeatureType

enum CDPL::Shape::ScreeningSettings::ColorFeatureType

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

Enumerator
NO_FEATURES	Disable color features (shape-only alignment).
PHARMACOPHORE_EXP_CHARGES	Use pharmacophore features derived from explicit charges.
PHARMACOPHORE_IMP_CHARGES	Use pharmacophore features derived from perceived (implicit) charges.

◆ AlignmentMode

enum CDPL::Shape::ScreeningSettings::AlignmentMode

Bitmask flags specifying the strategies used to seed alignment starting transformations.

Enumerator
NO_ALIGNMENT	Disable alignment entirely (overlap is computed in the input pose only).
SHAPE_CENTROID	Place the aligned shape at the centroid of the reference shape.
ATOM_CENTERS	Seed alignments by superimposing pairs of atom centers.
COLOR_FEATURE_CENTERS	Seed alignments by superimposing pairs of color (pharmacophore) feature centers.
RANDOM	Seed alignments with random rotations.

Constructor & Destructor Documentation

◆ ScreeningSettings()

CDPL::Shape::ScreeningSettings::ScreeningSettings ( )

Constructs a ScreeningSettings instance with default values.

Member Function Documentation

◆ setScoringFunction()

void CDPL::Shape::ScreeningSettings::setScoringFunction ( const ScoringFunction & func )

Sets the scoring function used to rank alignment results.

Parameters

func	The scoring function.

◆ getScoringFunction()

const ScoringFunction& CDPL::Shape::ScreeningSettings::getScoringFunction ( ) const

Returns the currently configured scoring function.

Returns: A const reference to the scoring function.

◆ setColorFeatureType()

void 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 ( ) const

Returns the currently configured color feature type.

Returns: The color-feature type.

◆ setScreeningMode()

void CDPL::Shape::ScreeningSettings::setScreeningMode ( ScreeningMode mode )

Sets the screening mode.

Parameters

mode	The new screening mode.

◆ getScreeningMode()

ScreeningMode CDPL::Shape::ScreeningSettings::getScreeningMode ( ) const

Returns the currently configured screening mode.

Returns: The screening mode.

◆ setAlignmentMode()

void 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 ( ) const

Returns the currently configured alignment-mode bitmask.

Returns: The alignment-mode bitmask.

◆ setNumRandomStarts()

void CDPL::Shape::ScreeningSettings::setNumRandomStarts ( std::size_t num_starts )

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

Parameters

num_starts The new number of random starts.

◆ getNumRandomStarts()

std::size_t CDPL::Shape::ScreeningSettings::getNumRandomStarts ( ) const

Returns the currently configured number of random starts.

Returns: The number of random starts.

◆ allCarbonMode() [1/2]

void 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 ( ) const

Tells whether the all-carbon mode is enabled.

Returns: true if the all-carbon mode is enabled, and false otherwise.

◆ singleConformerSearch() [1/2]

void CDPL::Shape::ScreeningSettings::singleConformerSearch ( bool single_conf )

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

Parameters

single_conf true to consider only a single conformer, and false to consider all conformers.

◆ singleConformerSearch() [2/2]

bool CDPL::Shape::ScreeningSettings::singleConformerSearch ( ) const

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

Returns: true if only a single conformer is considered, and false otherwise.

◆ optimizeOverlap() [1/2]

void 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 ( ) const

Tells whether the overlap is optimized iteratively.

Returns: true if the overlap is optimized, and false otherwise.

◆ greedyOptimization() [1/2]

void 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 ( ) const

Tells whether the overlap optimization uses a greedy strategy.

Returns: true if the greedy strategy is used, and false otherwise.

◆ setMaxNumOptimizationIterations()

void CDPL::Shape::ScreeningSettings::setMaxNumOptimizationIterations ( std::size_t max_iter )

Sets the maximum number of overlap-optimization iterations.

Parameters

max_iter The new maximum number of iterations.

◆ getMaxNumOptimizationIterations()

std::size_t CDPL::Shape::ScreeningSettings::getMaxNumOptimizationIterations ( ) const

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

Returns: The maximum number of iterations.

◆ setOptimizationStopGradient()

void CDPL::Shape::ScreeningSettings::setOptimizationStopGradient ( double grad_norm )

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

Parameters

grad_norm The new stop gradient norm.

◆ getOptimizationStopGradient()

double CDPL::Shape::ScreeningSettings::getOptimizationStopGradient ( ) const

Returns the currently configured overlap-optimization stop gradient.

Returns: The stop gradient norm.

◆ setScoreCutoff()

void CDPL::Shape::ScreeningSettings::setScoreCutoff ( double 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()

double CDPL::Shape::ScreeningSettings::getScoreCutoff ( ) const

Returns the currently configured score cutoff (or NO_CUTOFF).

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

Member Data Documentation

◆ DEFAULT

const ScreeningSettings CDPL::Shape::ScreeningSettings::DEFAULT

static

A static instance with default-initialized values.

◆ NO_CUTOFF

constexpr double CDPL::Shape::ScreeningSettings::NO_CUTOFF = std::numeric_limits<double>::quiet_NaN()

staticconstexpr

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

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

ScreeningSettings.hpp

Public Types

Public Member Functions

Static Public Attributes

Detailed Description

Member Typedef Documentation

◆ ScoringFunction

Member Enumeration Documentation

◆ ScreeningMode

◆ ColorFeatureType

◆ AlignmentMode

Constructor & Destructor Documentation

◆ ScreeningSettings()

Member Function Documentation

◆ setScoringFunction()

◆ getScoringFunction()

◆ setColorFeatureType()

◆ getColorFeatureType()

◆ setScreeningMode()

◆ getScreeningMode()

◆ setAlignmentMode()

◆ getAlignmentMode()

◆ setNumRandomStarts()

◆ getNumRandomStarts()

◆ allCarbonMode() [1/2]

◆ allCarbonMode() [2/2]

◆ singleConformerSearch() [1/2]

◆ singleConformerSearch() [2/2]

◆ optimizeOverlap() [1/2]

◆ optimizeOverlap() [2/2]

◆ greedyOptimization() [1/2]

◆ greedyOptimization() [2/2]

◆ setMaxNumOptimizationIterations()

◆ getMaxNumOptimizationIterations()

◆ setOptimizationStopGradient()

◆ getOptimizationStopGradient()

◆ setScoreCutoff()

◆ getScoreCutoff()

Member Data Documentation

◆ DEFAULT

◆ NO_CUTOFF