Rosetta Utilities  2014.35
Public Member Functions | Static Public Member Functions | List of all members
numeric::alignment::QCP_Kernel< Real > Class Template Reference

#include <QCP_Kernel.hh>

Public Member Functions

 QCP_Kernel ()
 
virtual ~QCP_Kernel ()
 

Static Public Member Functions

static void remove_center_of_mass (Real *coordinates, int number_of_atoms)
 
static Real inner_product (Real *A, Real *first_conformation_coords, Real *second_conformation_coords, int number_of_atoms)
 
static Real calc_rmsd_Theobald_method (Real *A, Real E0, int number_of_atoms, Real *rot_matrix)
 
static Real calc_coordinate_rmsd (Real *coords_a, Real *coords_b, int number_of_atoms, Real *rot_matrix)
 
static Real calc_centered_coordinate_rmsd (Real *coords_a, Real *coords_b, int number_of_atoms, Real *rot_matrix)
 

Constructor & Destructor Documentation

template<class Real>
numeric::alignment::QCP_Kernel< Real >::QCP_Kernel ( )
inline
template<class Real>
virtual numeric::alignment::QCP_Kernel< Real >::~QCP_Kernel ( )
inlinevirtual

Member Function Documentation

template<class Real>
static Real numeric::alignment::QCP_Kernel< Real >::calc_centered_coordinate_rmsd ( Real coords_a,
Real coords_b,
int  number_of_atoms,
Real rot_matrix 
)
inlinestatic
Remarks
Wrapping function for Douglas Theobald QCP superposition method to calculate the RMSD for two conformations.
Parameters
first_conformation_coords[In] Array containing the coordinates of the reference conformation.
second_conformation_coords[In] Array containing the coordinates of the conformation to be measured.
number_of_atoms[In] Number of atoms of both conformations.
rot_matrix[Out] 3x3 Output rotation matrix of superposition, if non-null.
Returns
The rmsd between both conformations.
Author
victor_gil
Date
05/10/2012
template<class Real>
static Real numeric::alignment::QCP_Kernel< Real >::calc_coordinate_rmsd ( Real coords_a,
Real coords_b,
int  number_of_atoms,
Real rot_matrix 
)
inlinestatic
Remarks
Wrapping function for Douglas Theobald QCP superposition method to calculate the RMSD for two conformations.
Parameters
first_conformation_coords[In] Array containing the coordinates of the reference conformation.
second_conformation_coords[In] Array containing the coordinates of the conformation to be measured.
number_of_atoms[In] Number of atoms of both conformations.
rot_matrix[Out] 3x3 Output rotation matrix of superposition, if non-null.
Returns
The rmsd between both conformations.
Author
victor_gil
Date
05/10/2012
template<class Real>
static Real numeric::alignment::QCP_Kernel< Real >::calc_rmsd_Theobald_method ( Real A,
Real  E0,
int  number_of_atoms,
Real rot_matrix 
)
inlinestatic
Remarks
This function ports the second part of Douglas Theobald's QCP superposition method.
Parameters
A[In] 3x3 coordinate inner product matrix, as computed via innerProduct.
E0[In] Upper bound for the maximum eigenvalue.
number_of_atoms[In] Number of atoms of conformations used to generate A and E0.
rot_matrix[Out] 3x3 Output rotation matrix of superposition, if non-null.
Returns
Rmsd between source conformations.
Author
victor_gil
Date
05/10/2012

Referenced by numeric::alignment::QCP_Kernel< double >::calc_centered_coordinate_rmsd(), and numeric::alignment::QCP_Kernel< double >::calc_coordinate_rmsd().

template<class Real>
static Real numeric::alignment::QCP_Kernel< Real >::inner_product ( Real A,
Real first_conformation_coords,
Real second_conformation_coords,
int  number_of_atoms 
)
inlinestatic
Remarks
Implements the 'inner product' operation of Douglas Theobald QCP superposition method (see : http://theobald.brandeis.edu/qcp/ and "Rapid calculation of RMSDs using a quaternion-based characteristic polynomial." Acta Crystallogr A 61(4):478-480 for more info).
Parameters
A[In/Out] 3x3 matrix for the coordinate inner product.
coords_a[In] Array containing centered coordinates.
coords_b[In] Array containing centered coordinates.
number_of_atoms[In] Number of atoms of both conformations.
Returns
The E0 parameter (upper bound for max Eigenvalue).
Author
victor_gil
Date
05/10/2012

Referenced by numeric::alignment::QCP_Kernel< double >::calc_centered_coordinate_rmsd(), and numeric::alignment::QCP_Kernel< double >::calc_coordinate_rmsd().

template<class Real>
static void numeric::alignment::QCP_Kernel< Real >::remove_center_of_mass ( Real coordinates,
int  number_of_atoms 
)
inlinestatic
Remarks
Removes center of mass from given coordinate array.
Parameters
coords[In] Array containing coordinates.
number_of_atoms[In] Number of atoms of both conformations.
Author
forda.nosp@m.s@uw.nosp@m..edu
Date
10/10/2013

Referenced by numeric::alignment::QCP_Kernel< double >::calc_coordinate_rmsd().


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