Rosetta Utilities  2014.35
Namespaces | Functions
rms.cc File Reference

RMS functions imported from rosetta++. More...

#include <numeric/xyzVector.hh>
#include <numeric/xyz.functions.hh>
#include <numeric/numeric.functions.hh>
#include <numeric/model_quality/rms.hh>
#include <numeric/model_quality/maxsub.hh>
#include <numeric/types.hh>
#include <utility/vector1.hh>
#include <ObjexxFCL/FArray1D.hh>
#include <ObjexxFCL/FArray2D.hh>
#include <complex>

Namespaces

 numeric
 Unit headers.
 
 numeric::model_quality
 

Functions

numeric::Real numeric::model_quality::calc_rms (utility::vector1< xyzVector< Real > > p1_coords, utility::vector1< xyzVector< Real > > p2_coords)
 
numeric::Real numeric::model_quality::rms_wrapper_slow_and_correct (int natoms, FArray2D< numeric::Real > p1a, FArray2D< numeric::Real > p2a)
 
bool numeric::model_quality::close_enough (numeric::Real val1, numeric::Real val2, numeric::Real TOL=1e-5)
 
bool numeric::model_quality::is_identity_matrix (ObjexxFCL::FArray2D< numeric::Real > uu)
 
numeric::Real numeric::model_quality::rms_wrapper (int natoms, FArray2D< numeric::Real > p1a, FArray2D< numeric::Real > p2a)
 
void numeric::model_quality::calc_rms_fast (float &rms_out, FArray2A< numeric::Real > xx, FArray2A< numeric::Real > yy, FArray1A< numeric::Real > ww, int npoints, numeric::Real ctx)
 companion function for findUU ( it is optional ) computes the minimum RMS deviation beteen XX and YY as though it rotated the arrays, without actually rotating them. More...
 
void numeric::model_quality::findUU (FArray2< numeric::Real > &XX, FArray2< numeric::Real > &YY, FArray1< numeric::Real > const &WW, int Npoints, FArray2< numeric::Real > &UU, numeric::Real &sigma3)
 intended to rotate one protein xyz array onto another one such that the point-by-point rms is minimized. More...
 
void numeric::model_quality::findUU (utility::vector1< numeric::xyzVector< numeric::Real > > &XX, utility::vector1< numeric::xyzVector< numeric::Real > > &YY, utility::vector1< numeric::Real > const &WW, int Npoints, numeric::xyzMatrix< numeric::Real > &UU, numeric::Real &sigma3)
 This is a helper function for using the above implementation of findUU. There is some cost to the conversion but everything else is probably slower and also you don't have to use FArrays everywhere. More...
 
void numeric::model_quality::BlankMatrixMult (FArray2A< numeric::Real > A, int n, int np, int transposeA, FArray2A< numeric::Real > B, int m, int transposeB, FArray2A< numeric::Real > AxB_out)
 
void numeric::model_quality::MatrixMult (FArray2A< numeric::Real > A, int n, int np, int transposeA, FArray2A< numeric::Real > B, int m, int transposeB, FArray2A< numeric::Real > AxB_out)
 
void numeric::model_quality::fixEigenvector (FArray2A< numeric::Real > m_v)
 
void numeric::model_quality::rmsfitca2 (int npoints, ObjexxFCL::FArray2A< double > xx, ObjexxFCL::FArray2A< double > yy, ObjexxFCL::FArray1A< double > ww, int natsel, double &esq)
 computes the rms between two weighted point vectors. More...
 
void numeric::model_quality::rmsfitca3 (int npoints, ObjexxFCL::FArray2A< double > xx0, ObjexxFCL::FArray2A< double > xx, ObjexxFCL::FArray2A< double > yy0, ObjexxFCL::FArray2A< double > yy, double &esq)
 
double numeric::model_quality::det3 (FArray2A< double > m)
 
void numeric::model_quality::rsym_eigenval (ObjexxFCL::FArray2A< double > m, ObjexxFCL::FArray1A< double > ev)
 computes the eigen values of a real symmetric 3x3 matrix More...
 
void numeric::model_quality::rsym_rotation (ObjexxFCL::FArray2A< double > mm, ObjexxFCL::FArray2A< double > m, ObjexxFCL::FArray1A< double > ev, ObjexxFCL::FArray2A< double > rot)
 finds a (proper) rotation matrix that minimizes the rms. More...
 
void numeric::model_quality::rsym_evector (ObjexxFCL::FArray2A< double > m, ObjexxFCL::FArray1A< double > ev, ObjexxFCL::FArray2A< double > mvec)
 Author: charlie strauss (cems) 2001 given original matrix plus its eigen values compute the eigen vectors. USAGE notice: for computing min rms rotations be sure to call this with the lowest eigen value in Ev(3). More...
 

Detailed Description

RMS functions imported from rosetta++.

Author
James Thompson
Date
Wed Aug 22 12:10:37 2007