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 oopse {

  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 (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:	3509
Committed:	Wed May 20 19:35:05 2009 UTC (15 years, 1 month ago) by cli2
File size:	2689 byte(s)
Log Message:	Modifications to support RMSD calculations, removing classes we aren't using.
#	Content
1	/*
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	namespace oopse {
42
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	for (int n=0; n<ref_.size(); n++) {
56	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	Vector3d mov_to_ref);
75
76	/*
77	* optimal_superposition()
78	*
79	* Returns best-fit rotation matrix
80	*/
81	RotMat3x3d optimal_superposition(std::vector<Vector3d> mov,
82	Vector3d mov_com,
83	Vector3d mov_to_ref);
84
85
86	protected:
87	std::vector<Vector3d> ref_;
88	Vector3d ref_com;
89
90	};
91	}
92
93
94	#endif