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/* |
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* ******************************************************************* |
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* |
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* rmsd.h |
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* (c) 2005 Bosco K Ho |
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* |
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* Implementation of the Kabsch algorithm to find the RMSD, and |
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* the least-squares rotation matrix for a superposition between |
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* two sets of vectors. |
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* |
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* This implementation is completely self-contained. No other dependencies. |
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* |
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* ************************************************************************** |
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* |
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* This program is free software; you can redistribute it and/or modify |
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* it under the terms of the GNU Lesser General Public License as published |
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* by the Free Software Foundation; either version 2.1 of the License, or (at |
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* your option) any later version. |
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* |
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* This program is distributed in the hope that it will be useful, but |
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* WITHOUT ANY WARRANTY; without even the implied warranty of |
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* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU |
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* Lesser General Public License for more details. |
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* |
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* You should have received a copy of the GNU Lesser General Public License |
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* along with this program; if not, write to the Free Software Foundation, |
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* Inc., 59 Temple Place - Suite 330, Boston, MA 02111-1307, USA. |
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* |
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* ************************************************************************** |
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* |
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*/ |
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|
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#ifndef MATH_RMSD_HPP |
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#define MATH_RMSD_HPP |
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|
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#include <vector> |
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|
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#include "config.h" |
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#include "math/SquareMatrix3.hpp" |
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|
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namespace oopse { |
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|
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class RMSD{ |
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public: |
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RMSD(); |
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RMSD(std::vector<Vector3d> ref) { |
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set_reference_structure(ref); |
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} |
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virtual ~RMSD() { }; |
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|
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void set_reference_structure(std::vector<Vector3d> ref) { |
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ref_ = ref; |
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ref_com = V3Zero; |
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|
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for (int n=0; n<ref_.size(); n++) { |
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ref_com += ref_[n]; |
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} |
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ref_com /= (RealType)ref.size(); |
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} |
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|
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/* |
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* calculate_rmsd() |
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* |
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* given a vector of Vector3 coordinates, constructs |
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* - mov_com: the centre of mass of the mov list |
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* - mov_to_ref: vector between the com of mov and ref |
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* - U: the rotation matrix for least-squares, usage of |
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* |
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* returns |
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* - rmsd: measures similarity between the vectors |
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*/ |
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RealType calculate_rmsd(std::vector<Vector3d> mov, |
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Vector3d mov_com, |
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Vector3d mov_to_ref, |
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RotMat3x3d U); |
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|
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|
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/* |
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* optimal_superposition() |
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* |
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* Returns best-fit rotation matrix |
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*/ |
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RotMat3x3d optimal_superposition(std::vector<Vector3d> mov); |
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|
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|
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protected: |
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std::vector<Vector3d> ref_; |
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Vector3d ref_com; |
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|
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}; |
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} |
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|
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|
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#endif |
