src/math/RMSD.hpp

/*
 *  *******************************************************************
 *
 *  rmsd.h 
 *  (c) 2005 Bosco K Ho
 * 
 *  Implementation of the Kabsch algorithm to find the RMSD, and 
 *  the least-squares rotation matrix for a superposition between 
 *  two sets of vectors.
 *
 *  This implementation is completely self-contained. No other dependencies.
 *
 *  **************************************************************************
 *
 *  This program is free software; you can redistribute it and/or modify
 *  it under the terms of the GNU Lesser General Public License as published
 *  by the Free Software Foundation; either version 2.1 of the License, or (at
 *  your option) any later version.
 *  
 *  This program is distributed in the hope that it will be useful,  but
 *  WITHOUT ANY WARRANTY; without even the implied warranty of
 *  MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the GNU
 *  Lesser General Public License for more details. 
 *  
 *  You should have received a copy of the GNU Lesser General Public License 
 *  along with this program; if not, write to the Free Software Foundation, 
 *  Inc., 59 Temple Place - Suite 330, Boston, MA  02111-1307, USA.
 *
 *  **************************************************************************
 * 
 */

#ifndef MATH_RMSD_HPP
#define MATH_RMSD_HPP

#include <vector>

#include "config.h"
#include "math/SquareMatrix3.hpp"

namespace OpenMD {

  class RMSD{
  public:
    RMSD();
    RMSD(std::vector<Vector3d> ref) {
      set_reference_structure(ref);
    }
    virtual ~RMSD() { };

    void set_reference_structure(std::vector<Vector3d> ref) {
      ref_ = ref;
      ref_com = V3Zero;
      
      for (unsigned int n = 0; n < ref_.size(); n++) {
        ref_com += ref_[n];
      }
      ref_com /= (RealType)ref.size();      
    }
    
    /*
     * calculate_rmsd()
     *
     *   given a vector of Vector3 coordinates, constructs
     *    - mov_com: the centre of mass of the mov list
     *    - mov_to_ref: vector between the com of mov and ref
     *    - U: the rotation matrix for least-squares, usage of
     *
     *   returns
     *    - rmsd: measures similarity between the vectors
     */
    RealType calculate_rmsd(std::vector<Vector3d> mov,
                            Vector3d mov_com,
                            Vector3d mov_to_ref);
    
    /* 
     * optimal_superposition()
     *
     *   Returns best-fit rotation matrix 
     */
    RotMat3x3d optimal_superposition(std::vector<Vector3d> mov,
                            Vector3d mov_com,
                            Vector3d mov_to_ref);

    
  protected:
    std::vector<Vector3d> ref_;
    Vector3d ref_com;

  };
}
    

#endif
Revision:	1782
Committed:	Wed Aug 22 02:28:28 2012 UTC (13 years, 2 months ago) by gezelter
File size:	2703 byte(s)
Log Message:	MERGE OpenMD development branch 1465:1781 into trunk
#	User	Rev	Content
1	gezelter	1335	/*
2			* *******************************************************************
3			*
4			* rmsd.h
5			* (c) 2005 Bosco K Ho
6			*
7			* Implementation of the Kabsch algorithm to find the RMSD, and
8			* the least-squares rotation matrix for a superposition between
9			* two sets of vectors.
10			*
11			* This implementation is completely self-contained. No other dependencies.
12			*
13			* **************************************************************************
14			*
15			* This program is free software; you can redistribute it and/or modify
16			* it under the terms of the GNU Lesser General Public License as published
17			* by the Free Software Foundation; either version 2.1 of the License, or (at
18			* your option) any later version.
19			*
20			* This program is distributed in the hope that it will be useful, but
21			* WITHOUT ANY WARRANTY; without even the implied warranty of
22			* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
23			* Lesser General Public License for more details.
24			*
25			* You should have received a copy of the GNU Lesser General Public License
26			* along with this program; if not, write to the Free Software Foundation,
27			* Inc., 59 Temple Place - Suite 330, Boston, MA 02111-1307, USA.
28			*
29			* **************************************************************************
30			*
31			*/
32
33			#ifndef MATH_RMSD_HPP
34			#define MATH_RMSD_HPP
35
36			#include <vector>
37
38			#include "config.h"
39			#include "math/SquareMatrix3.hpp"
40
41	gezelter	1390	namespace OpenMD {
42	gezelter	1335
43			class RMSD{
44			public:
45			RMSD();
46			RMSD(std::vector<Vector3d> ref) {
47			set_reference_structure(ref);
48			}
49			virtual ~RMSD() { };
50
51			void set_reference_structure(std::vector<Vector3d> ref) {
52			ref_ = ref;
53			ref_com = V3Zero;
54
55	gezelter	1782	for (unsigned int n = 0; n < ref_.size(); n++) {
56	gezelter	1335	ref_com += ref_[n];
57			}
58			ref_com /= (RealType)ref.size();
59			}
60
61			/*
62			* calculate_rmsd()
63			*
64			* given a vector of Vector3 coordinates, constructs
65			* - mov_com: the centre of mass of the mov list
66			* - mov_to_ref: vector between the com of mov and ref
67			* - U: the rotation matrix for least-squares, usage of
68			*
69			* returns
70			* - rmsd: measures similarity between the vectors
71			*/
72			RealType calculate_rmsd(std::vector<Vector3d> mov,
73			Vector3d mov_com,
74	cli2	1349	Vector3d mov_to_ref);
75	gezelter	1335
76			/*
77			* optimal_superposition()
78			*
79			* Returns best-fit rotation matrix
80			*/
81	cli2	1349	RotMat3x3d optimal_superposition(std::vector<Vector3d> mov,
82			Vector3d mov_com,
83			Vector3d mov_to_ref);
84	gezelter	1335
85	cli2	1349
86	gezelter	1335	protected:
87			std::vector<Vector3d> ref_;
88			Vector3d ref_com;
89
90			};
91			}
92
93
94			#endif