Extracts the solvent-accessible surface atoms of a set of atoms. More...

#include <SurfaceAtomExtractor.hpp>

Public Member Functions
	SurfaceAtomExtractor ()
	Constructs the `SurfaceAtomExtractor` instance. More...

	SurfaceAtomExtractor (const AtomContainer &cntnr, const MolecularGraph &parent_molgraph, Fragment &frag)
	Perceives the surface accessible atoms of cntnr and adds them to the fragment frag. More...

void	setProbeRadius (double radius)
	Specifies the radius of the probe sphere that determines the accessibility of the surface atoms. More...

double	getProbeRadius () const
	Returns the radius of the probe sphere that determines the accessibility of the surface atoms. More...

void	setGridStepSize (double size)
	Specifies the distance between the grid-points in space which store lists of atoms with proximal positions. More...

double	getGridStepSize () const
	Return the distance between the grid-points for proximal atom lookup. More...

void	setGridOversize (double size)
	Specifies the margin that gets added to each side of the molecular graph's bounding-box for the calculation of the final atom-lookup grid dimensions. More...

double	getGridOversize () const
	Returns the margin that gets added to each side of the molecular graph's bounding-box for the calculation of the final atom-lookup grid dimensions. More...

void	setMinSurfaceAccessibility (double min_acc)
	Specifies the minimum fraction of test points that have to be accessible by the probe sphere to consider an atom as a surface atom. More...

double	getMinSurfaceAccessibility () const
	Returns the minimum fraction of test points that have to be accessible by the probe sphere to consider an atom as a surface atom. More...

void	setNumTestPoints (std::size_t num_points)
	Specifies the number of points on the atom surface at which a test for surface accessibility is carried out. More...

std::size_t	getNumTestPoints () const
	Returns the number of points on the atom surface at which a test for surface accessibility is carried out. More...

void	setAtom3DCoordinatesFunction (const Atom3DCoordinatesFunction &func)
	Specifies a function for the retrieval of atom 3D-coordinates. More...

const Atom3DCoordinatesFunction &	getAtom3DCoordinatesFunction () const
	Returns the function that was registered for the retrieval of atom 3D-coordinates. More...

void	extract (const AtomContainer &cntnr, const MolecularGraph &parent_molgraph, Fragment &frag)
	Perceives the surface accessible atoms of cntnr that are part of molgraph and adds them to the fragment frag. More...

Static Public Attributes
static constexpr double	DEF_PROBE_RADIUS = 1.2
	The default probe sphere radius (in Å). More...

static constexpr double	DEF_GRID_OVERSIZE = 5.0
	The default margin (in Å) added to each side of the bounding box for the atom-lookup grid. More...

static constexpr double	DEF_GRID_STEP_SIZE = 0.75
	The default distance between grid points (in Å) along each axis of the atom-lookup grid. More...

static constexpr double	DEF_MIN_SURFACE_ACC = 0.01
	The default minimum fraction of accessible test points required to classify an atom as surface-accessible. More...

static constexpr std::size_t	DEF_NUM_TEST_POINTS = 250
	The default number of test points generated per atom on its van-der-Waals surface. More...

Detailed Description

Extracts the solvent-accessible surface atoms of a set of atoms.

For each candidate atom, a configurable number of probe-sphere test points is generated on the atom's van-der-Waals surface and tested against the surrounding atoms (looked up via an internal 3D grid for efficiency). An atom is reported as surface-accessible when at least the minimum required fraction of its test points is reachable by the probe sphere. The probe radius, accessibility threshold, test-point count, and grid parameters can be tuned via the setters; atom 3D coordinates are obtained through a user-replaceable accessor function.

Constructor & Destructor Documentation

◆ SurfaceAtomExtractor() [1/2]

CDPL::Chem::SurfaceAtomExtractor::SurfaceAtomExtractor ( )

Constructs the SurfaceAtomExtractor instance.

◆ SurfaceAtomExtractor() [2/2]

CDPL::Chem::SurfaceAtomExtractor::SurfaceAtomExtractor	(	const AtomContainer &	cntnr,
		const MolecularGraph &	parent_molgraph,
		Fragment &	frag
	)

Perceives the surface accessible atoms of cntnr and adds them to the fragment frag.

Parameters

cntnr	The set of atoms for which to perceive the surface accessibility.
parent_molgraph	The parent molecular graph which embeds the atoms in cntnr.
frag	The output fragment where to store the perceived surface atoms.

Member Function Documentation

◆ setProbeRadius()

void CDPL::Chem::SurfaceAtomExtractor::setProbeRadius ( double radius )

Specifies the radius of the probe sphere that determines the accessibility of the surface atoms.

Parameters

radius The radius of the probe sphere.

Note: The default value is specified by the constant SurfaceAtomExtractor::DEF_PROBE_RADIUS.

◆ getProbeRadius()

double CDPL::Chem::SurfaceAtomExtractor::getProbeRadius ( ) const

Returns the radius of the probe sphere that determines the accessibility of the surface atoms.

Returns: The used probe sphere radius.

◆ setGridStepSize()

void CDPL::Chem::SurfaceAtomExtractor::setGridStepSize ( double size )

Specifies the distance between the grid-points in space which store lists of atoms with proximal positions.

Parameters

size	The distance between the grid-points along each axis.

Note: The default value is specified by the constant SurfaceAtomExtractor::DEF_GRID_STEP_SIZE.

◆ getGridStepSize()

double CDPL::Chem::SurfaceAtomExtractor::getGridStepSize ( ) const

Return the distance between the grid-points for proximal atom lookup.

Returns: The used distance between the grid-points along each axis.

◆ setGridOversize()

void CDPL::Chem::SurfaceAtomExtractor::setGridOversize ( double size )

Specifies the margin that gets added to each side of the molecular graph's bounding-box for the calculation of the final atom-lookup grid dimensions.

Parameters

size	The margin that gets added to the molecular graph's bounding-box.

Note: The default value is specified by the constant SurfaceAtomExtractor::DEF_GRID_OVERSIZE.

◆ getGridOversize()

double CDPL::Chem::SurfaceAtomExtractor::getGridOversize ( ) const

Returns the margin that gets added to each side of the molecular graph's bounding-box for the calculation of the final atom-lookup grid dimensions.

Returns: The margin that gets added to the molecular graph's bounding-box.

◆ setMinSurfaceAccessibility()

void CDPL::Chem::SurfaceAtomExtractor::setMinSurfaceAccessibility ( double min_acc )

Specifies the minimum fraction of test points that have to be accessible by the probe sphere to consider an atom as a surface atom.

Parameters

min_acc The minimum required fraction of accessible test points.

Note: The default value is specified by the constant SurfaceAtomExtractor::DEF_MIN_SURFACE_ACC.

◆ getMinSurfaceAccessibility()

double CDPL::Chem::SurfaceAtomExtractor::getMinSurfaceAccessibility ( ) const

Returns the minimum fraction of test points that have to be accessible by the probe sphere to consider an atom as a surface atom.

Returns: The minimum required fraction of accessible test points.

◆ setNumTestPoints()

void CDPL::Chem::SurfaceAtomExtractor::setNumTestPoints ( std::size_t num_points )

Specifies the number of points on the atom surface at which a test for surface accessibility is carried out.

Parameters

num_points The number of test points.

Note: The default value is specified by the constant SurfaceAtomExtractor::DEF_NUM_TEST_POINTS.

◆ getNumTestPoints()

std::size_t CDPL::Chem::SurfaceAtomExtractor::getNumTestPoints ( ) const

Returns the number of points on the atom surface at which a test for surface accessibility is carried out.

Returns: The number of test points.

◆ setAtom3DCoordinatesFunction()

void CDPL::Chem::SurfaceAtomExtractor::setAtom3DCoordinatesFunction ( const Atom3DCoordinatesFunction & func )

Specifies a function for the retrieval of atom 3D-coordinates.

Parameters

func	The atom 3D-coordinates function.

◆ getAtom3DCoordinatesFunction()

const Atom3DCoordinatesFunction& CDPL::Chem::SurfaceAtomExtractor::getAtom3DCoordinatesFunction ( ) const

Returns the function that was registered for the retrieval of atom 3D-coordinates.

Returns: The registered atom 3D-coordinates function.

◆ extract()

void CDPL::Chem::SurfaceAtomExtractor::extract	(	const AtomContainer &	cntnr,
		const MolecularGraph &	parent_molgraph,
		Fragment &	frag
	)

Perceives the surface accessible atoms of cntnr that are part of molgraph and adds them to the fragment frag.

Parameters

cntnr	The set of atoms for which to perceive the surface accessibility.
parent_molgraph	The parent molecular graph which embeds the atoms in cntnr.
frag	The output fragment where to store the perceived surface atoms.

Member Data Documentation

◆ DEF_PROBE_RADIUS

constexpr double CDPL::Chem::SurfaceAtomExtractor::DEF_PROBE_RADIUS = 1.2

staticconstexpr

The default probe sphere radius (in Å).

◆ DEF_GRID_OVERSIZE

constexpr double CDPL::Chem::SurfaceAtomExtractor::DEF_GRID_OVERSIZE = 5.0

staticconstexpr

The default margin (in Å) added to each side of the bounding box for the atom-lookup grid.

◆ DEF_GRID_STEP_SIZE

constexpr double CDPL::Chem::SurfaceAtomExtractor::DEF_GRID_STEP_SIZE = 0.75

staticconstexpr

The default distance between grid points (in Å) along each axis of the atom-lookup grid.

◆ DEF_MIN_SURFACE_ACC

constexpr double CDPL::Chem::SurfaceAtomExtractor::DEF_MIN_SURFACE_ACC = 0.01

staticconstexpr

The default minimum fraction of accessible test points required to classify an atom as surface-accessible.

◆ DEF_NUM_TEST_POINTS

constexpr std::size_t CDPL::Chem::SurfaceAtomExtractor::DEF_NUM_TEST_POINTS = 250

staticconstexpr

The default number of test points generated per atom on its van-der-Waals surface.

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

SurfaceAtomExtractor.hpp

Public Member Functions

Static Public Attributes

Detailed Description

Constructor & Destructor Documentation

◆ SurfaceAtomExtractor() [1/2]

◆ SurfaceAtomExtractor() [2/2]

Member Function Documentation

◆ setProbeRadius()

◆ getProbeRadius()

◆ setGridStepSize()

◆ getGridStepSize()

◆ setGridOversize()

◆ getGridOversize()

◆ setMinSurfaceAccessibility()

◆ getMinSurfaceAccessibility()

◆ setNumTestPoints()

◆ getNumTestPoints()

◆ setAtom3DCoordinatesFunction()

◆ getAtom3DCoordinatesFunction()

◆ extract()

Member Data Documentation

◆ DEF_PROBE_RADIUS

◆ DEF_GRID_OVERSIZE

◆ DEF_GRID_STEP_SIZE

◆ DEF_MIN_SURFACE_ACC

◆ DEF_NUM_TEST_POINTS