SurfaceAtomExtractor.
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#include <SurfaceAtomExtractor.hpp>
◆ SurfaceAtomExtractor() [1/2]
CDPL::Chem::SurfaceAtomExtractor::SurfaceAtomExtractor |
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Constructs the SurfaceAtomExtractor
instance.
◆ SurfaceAtomExtractor() [2/2]
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. |
◆ setProbeRadius()
void CDPL::Chem::SurfaceAtomExtractor::setProbeRadius |
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double |
radius | ) |
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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 |
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const |
◆ setGridStepSize()
void CDPL::Chem::SurfaceAtomExtractor::setGridStepSize |
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double |
size | ) |
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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 |
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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 |
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double |
size | ) |
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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
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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 |
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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 |
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double |
min_acc | ) |
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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 |
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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 |
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std::size_t |
num_points | ) |
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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 |
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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()
Specifies a function for the retrieval of atom 3D-coordinates.
- Parameters
-
func | The atom 3D-coordinates function. |
◆ getAtom3DCoordinatesFunction()
Returns the function that was registered for the retrieval of atom 3D-coordinates.
- Returns
- The registered atom 3D-coordinates function.
◆ extract()
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. |
◆ DEF_PROBE_RADIUS
constexpr double CDPL::Chem::SurfaceAtomExtractor::DEF_PROBE_RADIUS = 1.2 |
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staticconstexpr |
◆ DEF_GRID_OVERSIZE
constexpr double CDPL::Chem::SurfaceAtomExtractor::DEF_GRID_OVERSIZE = 5.0 |
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staticconstexpr |
◆ DEF_GRID_STEP_SIZE
constexpr double CDPL::Chem::SurfaceAtomExtractor::DEF_GRID_STEP_SIZE = 0.75 |
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staticconstexpr |
◆ DEF_MIN_SURFACE_ACC
constexpr double CDPL::Chem::SurfaceAtomExtractor::DEF_MIN_SURFACE_ACC = 0.01 |
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staticconstexpr |
◆ DEF_NUM_TEST_POINTS
constexpr std::size_t CDPL::Chem::SurfaceAtomExtractor::DEF_NUM_TEST_POINTS = 250 |
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staticconstexpr |
The documentation for this class was generated from the following file: