PROFASI  Version 1.5
Public Member Functions | List of all members
prf::RMSD Class Reference

Root Mean Square Deviation. More...

#include <rmsd.hh>

Public Member Functions

 RMSD ()
 Define an RMSD evaluator.
 
double operator() (Shape &sh1, Shape &sh2, bool sh1incms=false)
 Calculation of RMSD value between two shape objects.
 

Detailed Description

RMSD compares two Shape objects. One Shape is set as the reference structure. The other is the comparison Shape, which is passed as an argument to the value functions. The root mean square deviation is then defined as the minimum with respect to all possible rotations and translations, of the summed squares of displacements of corresponging points.

RMSD is evaluated using closed form analytic expressions based on Singular Value Decomposition.

Member Function Documentation

double RMSD::operator() ( Shape sh1,
Shape sh2,
bool  sh1incms = false 
)

Calculates the RMSD between two shape objects. The boolean variable sh1incms tells if the first shape is already in the centre of mass coordinates. If not, it is translated to the centre of mass coordinates during evaluation. If one of the structures is fixed and is used repeatedly for rmsd calculations, repeated translations of that shape to its centre of mass is unnecessary, and can be avoided by passing sh1incms as true. Only the first structure can be fixed.


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

PROFASI: Protein Folding and Aggregation Simulator, Version 1.5
© (2005-2016) Anders Irbäck and Sandipan Mohanty
Documentation generated on Mon Jul 18 2016 using Doxygen version 1.8.2