colvarmodule::rotation Class Reference

A rotation between two sets of coordinates (for the moment a wrapper for colvarmodule::quaternion) More...

#include <colvartypes.h>

Collaboration diagram for colvarmodule::rotation:

Public Member Functions
void	calc_optimal_rotation (std::vector< atom_pos > const &pos1, std::vector< atom_pos > const &pos2)
	Calculate the optimal rotation and store the corresponding eigenvalue and eigenvector in the arguments l0 and q0; if the gradients have been previously requested, calculate them as well. More...
void	calc_optimal_rotation (std::vector< cvm::atom > const &pos1, std::vector< atom_pos > const &pos2)
int	init ()
	Initialize member data.
	rotation ()
	Default constructor.
	rotation (cvm::quaternion const &qi)
	Constructor after a quaternion.
	rotation (cvm::real angle, cvm::rvector const &axis)
	Constructor after an axis of rotation and an angle (in radians)
	~rotation ()
	Destructor.
cvm::rvector	rotate (cvm::rvector const &v) const
	Return the rotated vector.
cvm::rotation	inverse () const
	Return the inverse of this rotation.
cvm::rmatrix	matrix () const
	Return the associated 3x3 matrix.
cvm::real	spin_angle (cvm::rvector const &axis) const
	Return the spin angle (in degrees) with respect to the provided axis (which MUST be normalized)
cvm::quaternion	dspin_angle_dq (cvm::rvector const &axis) const
	Return the derivative of the spin angle with respect to the quaternion.
cvm::real	cos_theta (cvm::rvector const &axis) const
	Return the projection of the orientation vector onto a predefined axis.
cvm::quaternion	dcos_theta_dq (cvm::rvector const &axis) const
	Return the derivative of the tilt wrt the quaternion.

Public Attributes
bool	b_debug_gradients
	Perform gradient tests.
cvm::quaternion	q
	The rotation itself (implemented as a quaternion)

Static Public Attributes
static bool	monitor_crossings = false
	Whether to test for eigenvalue crossing.
static cvm::real	crossing_threshold = 1.0E-02
	Threshold for the eigenvalue crossing test.

Protected Member Functions
void	build_correlation_matrix (std::vector< cvm::atom_pos > const &pos1, std::vector< cvm::atom_pos > const &pos2)
	Build the correlation matrix C (used by calc_optimal_rotation())
void	build_correlation_matrix (std::vector< cvm::atom > const &pos1, std::vector< cvm::atom_pos > const &pos2)
void	calc_optimal_rotation_impl ()
	Actual implementation of calc_optimal_rotation (and called by it)
void	compute_overlap_matrix ()
	Compute the overlap matrix S (used by calc_optimal_rotation())

Protected Attributes
cvm::quaternion	q_old
	Previous value of the rotation (used to warn the user when the structure changes too much, and there may be an eigenvalue crossing)
void *	jacobi
	Pointer to instance of Jacobi solver.

Private Attributes
cvm::rmatrix	C
	Correlation matrix C (3, 3)
cvm::real	S [4][4]
	Overlap matrix S (4, 4)
cvm::real	S_eigval [4]
	Eigenvalues of S.
cvm::real	S_eigvec [4][4]
	Eigenvectors of S.
cvm::real	S_backup [4][4]
	Used for debugging gradients.

Friends
template<typename T1 , typename T2 >
struct	rotation_derivative
template<typename T1 , typename T2 >
void	debug_gradients (cvm::rotation &rot, const std::vector< T1 > &pos1, const std::vector< T2 > &pos2)
	Function for debugging gradients (allow using either std::vector<cvm::atom_pos> or std::vector<cvm::atom> for pos1 and pos2) More...

Detailed Description

A rotation between two sets of coordinates (for the moment a wrapper for colvarmodule::quaternion)

Member Function Documentation

calc_optimal_rotation()

void colvarmodule::rotation::calc_optimal_rotation	(	std::vector< atom_pos > const &	pos1,
		std::vector< atom_pos > const &	pos2
	)

Calculate the optimal rotation and store the corresponding eigenvalue and eigenvector in the arguments l0 and q0; if the gradients have been previously requested, calculate them as well.

The method to derive the optimal rotation is defined in: Coutsias EA, Seok C, Dill KA. Using quaternions to calculate RMSD. J Comput Chem. 25(15):1849-57 (2004) DOI: 10.1002/jcc.20110 PubMed: 15376254

Friends And Related Function Documentation

debug_gradients

template<typename T1 , typename T2 >

void debug_gradients ( cvm::rotation &  rot, const std::vector< T1 > &  pos1, const std::vector< T2 > &  pos2  )

friend

Function for debugging gradients (allow using either std::vector<cvm::atom_pos> or std::vector<cvm::atom> for pos1 and pos2)

Parameters

[in]	pos1	Atom positions of group 1
[in]	pos2	Atom positions of group 2

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

• colvartypes.h
• colvartypes.cpp