Properties.h File Reference

Run-time shape property calculations. More...

#include "Molassembler/Shapes/Data.h"
#include <set>

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Data Structures
struct	Scine::Molassembler::Shapes::Properties::DistortionInfo
	Data type grouping distortions between shapes. More...
struct	Scine::Molassembler::Shapes::Properties::ShapeTransitionGroup
	A grouping of index mappings of equal angular and chiral distortion. More...

Namespaces
	Scine
	Scine::Molassembler
	Central library namespace.
	Scine::Molassembler::Shapes
	Symmetry definitions and properties.
	Scine::Molassembler::Shapes::Properties
	Runtime-computed properties of shapes.

Functions
Permutation	Scine::Molassembler::Shapes::Properties::applyPermutation (const Permutation &occupation, const Permutation &permutation)
	Rotates a passed list of indices with a specified rotation vector. More...
std::vector< Vertex >	Scine::Molassembler::Shapes::Properties::applyRotation (const Permutation &occupation, Shape shape, unsigned rotationFunctionIndex)
	Rotates a passed list of indices of a specific shape. More...
unsigned	Scine::Molassembler::Shapes::Properties::rotationPeriodicity (Shape shape, const Permutation &rotation)
	Calculate the periodicty of a shape's index rotation. More...
PURITY_WEAK std::vector < std::vector< Vertex > >	Scine::Molassembler::Shapes::Properties::positionGroups (Shape shape)
	Group shape vertices according to whether they can be interconverted by rotation. More...
std::vector< char >	Scine::Molassembler::Shapes::Properties::positionGroupCharacters (Shape shape)
	Generate a character representation of a shape's position groups. More...
Permutation	Scine::Molassembler::Shapes::Properties::inverseRotation (const Permutation &rotation)
	Generate the inverse rotation to a shape's rotation. More...
Eigen::Vector3d	Scine::Molassembler::Shapes::Properties::getCoordinates (Shape shape, const boost::optional< Vertex > &vertexOption)
	Gets the coordinates of an indexOptional for a specific shape. More...
double	Scine::Molassembler::Shapes::Properties::getTetrahedronVolume (const Eigen::Vector3d &i, const Eigen::Vector3d &j, const Eigen::Vector3d &k, const Eigen::Vector3d &l)
	Tetrahedron volume spanned by four positions. More...
double	Scine::Molassembler::Shapes::Properties::calculateAngleDistortion (Shape from, Shape to, const std::vector< Vertex > &indexMapping)
	Calculates angular distorition for an index mapping between shapes. More...
boost::optional< Vertex >	Scine::Molassembler::Shapes::Properties::propagateIndexOptionalThroughMapping (const boost::optional< Vertex > &indexOptional, const std::vector< Vertex > &indexMapping)
	Propagates an index optional through an index mapping. More...
double	Scine::Molassembler::Shapes::Properties::calculateChiralDistortion (Shape from, Shape to, const std::vector< Vertex > &indexMapping)
	Calculates chiral distortion for a transition between shapes. More...
std::set< std::vector< Vertex >>	Scine::Molassembler::Shapes::Properties::generateAllRotations (Shape shape, const std::vector< Vertex > &indices)
	Generates all rotations of a sequence of indices within a shape. More...
std::vector< Vertex >	Scine::Molassembler::Shapes::Properties::applyIndexMapping (Shape to, const std::vector< Vertex > &mapping)
	Transform shape positions through a mapping. More...
std::vector< DistortionInfo >	Scine::Molassembler::Shapes::Properties::shapeTransitionMappings (Shape from, Shape to)
	Calculates ideal index mappings for +1, 0 size transitions. More...
std::vector< DistortionInfo >	Scine::Molassembler::Shapes::Properties::ligandLossTransitionMappings (Shape from, Shape to, Vertex positionInSourceShape)
	Calculates ideal index mappings for ligand loss transitions. More...
ShapeTransitionGroup	Scine::Molassembler::Shapes::Properties::selectBestTransitionMappings (const std::vector< DistortionInfo > &distortions)
	Selects the best transition mapping from many DistortionInfos. More...
PURITY_WEAK unsigned	Scine::Molassembler::Shapes::Properties::numUnlinkedStereopermutations (Shape shape, unsigned nIdenticalLigands)
	Calculates the number of stereopermutations in a specific shape and a number of identical ligands. More...
PURITY_WEAK bool	Scine::Molassembler::Shapes::Properties::hasMultipleUnlinkedStereopermutations (Shape shape, unsigned nIdenticalLigands)
	Calculates if there are multiple unlinked stereopermutations in a specific shape for a number of identical ligands. More...
PURITY_WEAK Shape	Scine::Molassembler::Shapes::Properties::mostSymmetric (std::vector< Shape > selection)
	Yields the shape with the most rotations from a selection. More...
PURITY_WEAK Shape	Scine::Molassembler::Shapes::Properties::mostSymmetric (unsigned shapeSize)
	Yields the shape with the most rotations of a particular size. More...

Variables
constexpr double	Scine::Molassembler::Shapes::Properties::floatingPointEqualityThreshold [[gnu::unused]] = 1e-4

Detailed Description

Run-time shape property calculations.

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. Contains a suite of property calculations on the dynamic shape data.