Scine::Molassembler::DistanceGeometry::EigenRefinementProblem< dimensionality, FloatType, SIMD > Class Template Reference

Eigen-based refinement error function. More...

#include <EigenRefinement.h>

Data Structures
struct	DefaultTermVisitor
	Visitor that can be passed to visit all terms. More...

Public Types
Public types
using	VectorType = Eigen::Matrix< FloatType, Eigen::Dynamic, 1 >
	Vector layout of positions.
using	ThreeDimensionalVector = Eigen::Matrix< FloatType, 3, 1 >
	Three dimensional vector.
using	FullDimensionalVector = Eigen::Matrix< FloatType, dimensionality, 1 >
	Three or four dimensional vector (depending on dimensionality)
using	ThreeDimensionalMatrixType = Eigen::Matrix< FloatType, 3, Eigen::Dynamic >
	Three-row dynamic column matrix.
using	FullDimensionalMatrixType = Eigen::Matrix< FloatType, dimensionality, Eigen::Dynamic >
	Three or four-row dynamic column matrix.
using	FloatingPointType = FloatType
	Template argument specifying floating-point type.

Public Member Functions
void	operator() (const VectorType &parameters, FloatType &value, Eigen::Ref< VectorType > gradient) const
	Calculates the error value and gradient for all contributions. More...
double	calculateProportionChiralConstraintsCorrectSign (const VectorType &positions) const
	Calculates the number of chiral constraints with correct sign. More...
template<typename Visitor >
auto	visitTerms (const VectorType &positions, Visitor &&visitor) const
template<typename Visitor >
auto	visitUnfulfilledConstraints (const DistanceBoundsMatrix &bounds, const VectorType &positions, Visitor &&visitor) const
	Visit all unfulfilled constraints. More...
Constructors
	EigenRefinementProblem (const Eigen::MatrixXd &squaredBounds, std::vector< ChiralConstraint > passChiralConstraints, std::vector< DihedralConstraint > passDihedralConstraints)
Contribution functions
void	distanceContributions (const VectorType &positions, FloatType &error, Eigen::Ref< VectorType > gradient) const
	Adds pairwise distance error and gradient contributions. More...
void	chiralContributions (const VectorType &positions, FloatType &error, Eigen::Ref< VectorType > gradient) const
	Adds chiral error and gradient contributions. More...
void	dihedralContributions (const VectorType &positions, FloatType &error, Eigen::Ref< VectorType > gradient) const
	Adds dihedral error and gradient contributions. More...
void	fourthDimensionContributions (const VectorType &positions, FloatType &error, Eigen::Ref< VectorType > gradient) const
	Adds pairwise distance error and gradient contributions. More...

Static Public Member Functions
Static member functions
static std::string	name ()
	Get a string representation of the type name. More...
static FullDimensionalVector	getPosition (const VectorType &positions, const AtomIndex index)
	Copy a full dimensional position of an atom. More...
static ThreeDimensionalVector	getPosition3D (const VectorType &positions, const AtomIndex index)
	Copy a three-dimensional position of an atom. More...
static FullDimensionalVector	getAveragePosition (const VectorType &positions, const ChiralConstraint::AtomListType &atomList)
	Calculate the average full-dimensional position of several atoms. More...
static ThreeDimensionalVector	getAveragePosition3D (const VectorType &positions, const ChiralConstraint::AtomListType &atomList)
	Calculate the average three-dimensional position of several atoms. More...

Data Fields
Public members
VectorType	upperDistanceBoundsSquared
	Upper distance bounds squared, linearized in i < j.
VectorType	lowerDistanceBoundsSquared
	Lower distance bounds squared, linearized in i < j.
VectorType	chiralUpperConstraints
	Chiral upper constraints, in sequence of chiralConstraints.
VectorType	chiralLowerConstraints
	Chiral lower constraints, in sequence of chiralConstraints.
VectorType	dihedralConstraintSumsHalved
	Dihedral bounds' averages, in sequence of dihedralConstraints.
VectorType	dihedralConstraintDiffsHalved
	Dihedral bounds upper minus lower, halved, in sequence.
std::vector< ChiralConstraint >	chiralConstraints
	List of chiral constraints.
std::vector< DihedralConstraint >	dihedralConstraints
	List of dihedral constraints.
bool	compressFourthDimension = false
	Whether to compress the fourth dimension.
bool	dihedralTerms = false
	Whether to enable dihedral terms.
Signaling members
double	proportionChiralConstraintsCorrectSign = 0.0

Private Member Functions
Contribution implementations
template<class Visitor >
void	distanceContributionsImpl (const VectorType &positions, FloatType &error, Eigen::Ref< VectorType > gradient, Visitor &&visitor) const
	Adds distance error and gradient contributions (non-SIMD)
template<typename Visitor >
void	chiralContributionsImpl (const VectorType &positions, FloatType &error, Eigen::Ref< VectorType > gradient, Visitor &&visitor) const
	Adds chiral error and gradient contributions.
template<class Visitor >
void	dihedralContributionsImpl (const VectorType &positions, FloatType &error, Eigen::Ref< VectorType > gradient, Visitor &&visitor) const
	Adds dihedral error and gradient contributions.
template<class Visitor = DefaultTermVisitor>
void	fourthDimensionContributionsImpl (const VectorType &positions, FloatType &error, Eigen::Ref< VectorType > gradient, Visitor &&visitor={}) const
	Adds fourth dimension error and gradient contributions. More...

Detailed Description

template<unsigned dimensionality, typename FloatType, bool SIMD>
class Scine::Molassembler::DistanceGeometry::EigenRefinementProblem< dimensionality, FloatType, SIMD >

Eigen-based refinement error function.

Template Parameters

dimensionality	3 or 4 spatial dimensions to refine in
FloatType	float or double
SIMD	Whether to use rewritten implementations that try to take advantage of Eigen's SIMD capabilities

Member Function Documentation

template<unsigned dimensionality, typename FloatType , bool SIMD>

double Scine::Molassembler::DistanceGeometry::EigenRefinementProblem< dimensionality, FloatType, SIMD >::calculateProportionChiralConstraintsCorrectSign ( const VectorType &  positions ) const

inline

Calculates the number of chiral constraints with correct sign.

Complexity \(\Theta(C)\) where \(C\) is the number of chiral constraints

template<unsigned dimensionality, typename FloatType , bool SIMD>

void Scine::Molassembler::DistanceGeometry::EigenRefinementProblem< dimensionality, FloatType, SIMD >::chiralContributions ( const VectorType &  positions, FloatType &  error, Eigen::Ref< VectorType >  gradient  ) const

inline

Adds chiral error and gradient contributions.

Complexity \(\Omega(C)\)

template<unsigned dimensionality, typename FloatType , bool SIMD>

void Scine::Molassembler::DistanceGeometry::EigenRefinementProblem< dimensionality, FloatType, SIMD >::dihedralContributions ( const VectorType &  positions, FloatType &  error, Eigen::Ref< VectorType >  gradient  ) const

inline

Adds dihedral error and gradient contributions.

Complexity \(\Omega(D)\)

template<unsigned dimensionality, typename FloatType , bool SIMD>

void Scine::Molassembler::DistanceGeometry::EigenRefinementProblem< dimensionality, FloatType, SIMD >::distanceContributions ( const VectorType &  positions, FloatType &  error, Eigen::Ref< VectorType >  gradient  ) const

inline

Adds pairwise distance error and gradient contributions.

Complexity \(\Omega(N^2)\)

template<unsigned dimensionality, typename FloatType , bool SIMD>

void Scine::Molassembler::DistanceGeometry::EigenRefinementProblem< dimensionality, FloatType, SIMD >::fourthDimensionContributions ( const VectorType &  positions, FloatType &  error, Eigen::Ref< VectorType >  gradient  ) const

inline

Adds pairwise distance error and gradient contributions.

Complexity \(\Omega(N^2)\)

template<unsigned dimensionality, typename FloatType , bool SIMD>

template<class Visitor = DefaultTermVisitor>

void Scine::Molassembler::DistanceGeometry::EigenRefinementProblem< dimensionality, FloatType, SIMD >::fourthDimensionContributionsImpl ( const VectorType &  positions, FloatType &  error, Eigen::Ref< VectorType >  gradient, Visitor &&  visitor = {}  ) const

inlineprivate

Adds fourth dimension error and gradient contributions.

Complexity \(\Theta(N)\)

template<unsigned dimensionality, typename FloatType , bool SIMD>

static FullDimensionalVector Scine::Molassembler::DistanceGeometry::EigenRefinementProblem< dimensionality, FloatType, SIMD >::getAveragePosition ( const VectorType &  positions, const ChiralConstraint::AtomListType &  atomList  )

inlinestatic

Calculate the average full-dimensional position of several atoms.

Complexity \(\Theta(A)\) where A is the number of atoms whose positions to average

template<unsigned dimensionality, typename FloatType , bool SIMD>

static ThreeDimensionalVector Scine::Molassembler::DistanceGeometry::EigenRefinementProblem< dimensionality, FloatType, SIMD >::getAveragePosition3D ( const VectorType &  positions, const ChiralConstraint::AtomListType &  atomList  )

inlinestatic

Calculate the average three-dimensional position of several atoms.

Complexity \(\Theta(A)\) where A is the number of atoms whose positions to average

template<unsigned dimensionality, typename FloatType , bool SIMD>

static FullDimensionalVector Scine::Molassembler::DistanceGeometry::EigenRefinementProblem< dimensionality, FloatType, SIMD >::getPosition ( const VectorType &  positions, const AtomIndex  index  )

inlinestatic

Copy a full dimensional position of an atom.

Complexity \(\Theta(1)\)

template<unsigned dimensionality, typename FloatType , bool SIMD>

static ThreeDimensionalVector Scine::Molassembler::DistanceGeometry::EigenRefinementProblem< dimensionality, FloatType, SIMD >::getPosition3D ( const VectorType &  positions, const AtomIndex  index  )

inlinestatic

Copy a three-dimensional position of an atom.

Complexity \(\Theta(1)\)

template<unsigned dimensionality, typename FloatType , bool SIMD>

static std::string Scine::Molassembler::DistanceGeometry::EigenRefinementProblem< dimensionality, FloatType, SIMD >::name ( )

inlinestatic

Get a string representation of the type name.

Complexity \(\Theta(1)\)

template<unsigned dimensionality, typename FloatType , bool SIMD>

void Scine::Molassembler::DistanceGeometry::EigenRefinementProblem< dimensionality, FloatType, SIMD >::operator() ( const VectorType &  parameters, FloatType &  value, Eigen::Ref< VectorType >  gradient  ) const

inline

Calculates the error value and gradient for all contributions.

Parameters

[in]	parameters	The linearized positions of all particles
[out]	value	The error function value for the given positional parameters
[out]	gradient	The gradient for the given positional parameters

Precondition

parameters must be evenly divisible by the dimensionality

Postcondition

Error is stored in value and gradient in gradient

template<unsigned dimensionality, typename FloatType , bool SIMD>

template<typename Visitor >

auto Scine::Molassembler::DistanceGeometry::EigenRefinementProblem< dimensionality, FloatType, SIMD >::visitUnfulfilledConstraints ( const DistanceBoundsMatrix &  bounds, const VectorType &  positions, Visitor &&  visitor  ) const

inline

Visit all unfulfilled constraints.

Template Parameters

Visitor

Type containing a deviationThreshold and result member variable and implementing the following methods: distanceOverThreshold: (unsigned, unsigned, double) -> void chiralOverThreshold: (ChiralConstraint, double) -> void dihedralOverThreshold: (DihedralConstraint, double) -> void

Parameters

bounds	distance bounds instance
positions	parameter positions to the error function
visitor	Instance of VisitorType

This function is very helpful in implementing multiple behaviors, like debug or error information on unsatisfied bonds or checking whether all constraints are within their bounds.

Returns

visitor.result

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

• Molassembler/DistanceGeometry/EigenRefinement.h