ContinuousMeasures.h File Reference

Continuous symmetry and shape measures. More...

#include "Molassembler/Shapes/PointGroupElements.h"
#include "Molassembler/Shapes/Data.h"

Include dependency graph for ContinuousMeasures.h:

Go to the source code of this file.

Data Structures
struct	Scine::Molassembler::Shapes::Continuous::ShapeResult
	Result of a continuous shape measure calculation. More...

Namespaces
	Scine
	Scine::Molassembler
	Central library namespace.
	Scine::Molassembler::Shapes
	Symmetry definitions and properties.
	Scine::Molassembler::Shapes::Continuous
	Symmetry element, point group, and polyhedral shape continuous metrics.
	Scine::Molassembler::Shapes::Continuous::Fixed
	Continuous symmetry measures for fixed symmetry elements.

Typedefs
using	Scine::Molassembler::Shapes::Continuous::PositionCollection = Eigen::Matrix< double, 3, Eigen::Dynamic >

Functions
PositionCollection	Scine::Molassembler::Shapes::Continuous::normalize (const PositionCollection &positions)
	Normalize positions for continuous symmetry measure analysis. More...
double	Scine::Molassembler::Shapes::Continuous::Fixed::element (const PositionCollection &normalizedPositions, const Elements::Rotation &rotation)
	Returns the CSM for a Rotation symmetry element along the rotation axis without optimizing the coordinates' rotation. More...
double	Scine::Molassembler::Shapes::Continuous::Fixed::element (const PositionCollection &normalizedPositions, const Elements::Reflection &reflection)
	Returns the CSM for a fixed reflection symmetry element. More...
double	Scine::Molassembler::Shapes::Continuous::Fixed::Cinf (const PositionCollection &normalizedPositions, const Eigen::Vector3d &axis)
	Returns the CSM for a fixed-axis infinite order rotation axis. More...
std::pair< double, Elements::Rotation >	Scine::Molassembler::Shapes::Continuous::element (const PositionCollection &normalizedPositions, Elements::Rotation rotation)
	Optimizes the axis of a rotational symmetry element and calculates the continuous symmetry measure.
std::pair< double, Elements::Reflection >	Scine::Molassembler::Shapes::Continuous::element (const PositionCollection &normalizedPositions, Elements::Reflection reflection)
	Optimizes the norm of a reflection symmetry element and calculates the continuous symmetry measure.
double	Scine::Molassembler::Shapes::Continuous::element (const PositionCollection &normalizedPositions, const Elements::Inversion &)
	Calculates the CSM for centroid inversion. More...
double	Scine::Molassembler::Shapes::Continuous::Cinf (const PositionCollection &normalizedPositions)
	Calculates the continuous symmetry measure for an infinite order rotation axis.
double	Scine::Molassembler::Shapes::Continuous::pointGroup (const PositionCollection &normalizedPositions, PointGroup pointGroup)
	Calculates the continuous symmetry measure for a set of particles and a particular point group. More...
ShapeResult	Scine::Molassembler::Shapes::Continuous::shapeFaithfulPaperImplementation (const PositionCollection &normalizedPositions, Shape shape)
	Faithful implementation of the continuous shape measure calculation algorithm from the paper. More...
ShapeResult	Scine::Molassembler::Shapes::Continuous::shapeAlternateImplementation (const PositionCollection &normalizedPositions, Shape shape)
	Slightly optimized implmentation of the continuous shape measure calculation algorithm. More...
ShapeResult	Scine::Molassembler::Shapes::Continuous::shapeAlternateImplementationCentroidLast (const PositionCollection &normalizedPositions, Shape shape)
	Like shapeAlternateImplementation, but the centroid is the last position.
ShapeResult	Scine::Molassembler::Shapes::Continuous::shapeHeuristics (const PositionCollection &normalizedPositions, Shape shape)
	Calculates the continuous shape measure of a set of coordinates with respect to a particular shape using heuristics. More...
ShapeResult	Scine::Molassembler::Shapes::Continuous::shapeHeuristicsCentroidLast (const PositionCollection &normalizedPositions, Shape shape)
	Same as shapeHeuristics(), except with set centroid mapping, so faster.
ShapeResult	Scine::Molassembler::Shapes::Continuous::shape (const PositionCollection &normalizedPositions, Shape shape)
	Forwarding function to calculate the continuous shape measure. More...
ShapeResult	Scine::Molassembler::Shapes::Continuous::shapeCentroidLast (const PositionCollection &normalizedPositions, const Shape shape)
	Same as shape(), except with set centroid mapping.
double	Scine::Molassembler::Shapes::Continuous::minimumDistortionAngle (Shape a, Shape b)
	Calculates minimum distortion angle in radians for shapes A and B. More...
double	Scine::Molassembler::Shapes::Continuous::minimalDistortionPathDeviation (const PositionCollection &positions, Shape a, Shape b, const double minimumDistortionAngle)
	Calculates deviation of positions from minimal distortion path between two shapes. More...
double	Scine::Molassembler::Shapes::Continuous::minimalDistortionPathDeviation (const PositionCollection &positions, Shape a, Shape b)
std::array< double, 4 >	Scine::Molassembler::Shapes::Continuous::randomCloudDistributionParameters (Shape shape, unsigned N, unsigned seed)
	Beta distribution parameters of shape measures of random point clouds. More...
boost::optional< double >	Scine::Molassembler::Shapes::Continuous::probabilityRandomCloud (double measure, Shape shape)
	Probability that shape measure in set of measures for random point clouds. More...

Detailed Description

Continuous symmetry and shape measures.

Copyright

This code is licensed under the 3-clause BSD license. Copyright ETH Zurich, Laboratory of Physical Chemistry, Reiher Group. See LICENSE.txt for details.