align.h

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/**********************************************************************
align.h - Align two molecules or vectors of vector3

Copyright (C) 2010 by Noel M. O'Boyle

This file is part of the Open Babel project.
For more information, see <http://openbabel.org/>

This program is free software; you can redistribute it and/or modify
it under the terms of the GNU General Public License as published by
the Free Software Foundation version 2 of the License.

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 General Public License for more details.
***********************************************************************/

#ifndef OB_ALIGN_H
#define OB_ALIGN_H

#include <openbabel/mol.h>
#include <openbabel/math/vector3.h>
#include <openbabel/math/matrix3x3.h>
#include <openbabel/isomorphism.h>
#include <Eigen/Core>

namespace OpenBabel
{
 class OBAPI OBAlign {
 public:


 OBAlign(bool includeH=false, bool symmetry=true);
 OBAlign(const OBMol &refmol, const OBMol &targetmol, bool includeH=false, bool symmetry=true);
 OBAlign(const std::vector<vector3> &ref, const std::vector<vector3> &target);



 void SetRef(const std::vector<vector3> &ref);
 void SetTarget(const std::vector<vector3> &target);
 void SetRefMol(const OBMol &refmol);
 void SetTargetMol(const OBMol &targetmol);



 bool Align();

 enum AlignMethod {
 Kabsch = 0, // Returns matrix and RMSD
 QCP = 1 // Returns just RMSD (fast)
 };

 void SetMethod(enum AlignMethod method);



 double GetRMSD();
 matrix3x3 GetRotMatrix();
 std::vector<vector3> GetAlignment();
 bool UpdateCoords(OBMol* target);

 private:
 bool _ready;
 bool _fail;
 bool _symmetry;
 bool _includeH;
 enum AlignMethod _method;
 double _rmsd;
 OBBitVec _frag_atoms;
 Automorphisms _aut;
 const OBMol* _prefmol;
 const OBMol* _ptargetmol;
 Eigen::MatrixXd _rotMatrix;
 Eigen::Vector3d _ref_centr, _target_centr;
 const std::vector<vector3> *_pref;
 const std::vector<vector3> *_ptarget;
 std::vector<vector3> _refmol_coords;
 std::vector<vector3> _targetmol_coords;
 Eigen::MatrixXd _result;
 Eigen::MatrixXd _mref, _mtarget;
 void VectorsToMatrix(const std::vector<vector3> *pcoords, Eigen::MatrixXd &coords);
 Eigen::Vector3d MoveToOrigin(Eigen::MatrixXd &coords);
 void SimpleAlign(const Eigen::MatrixXd &mtarget);
 void TheobaldAlign(const Eigen::MatrixXd &mtarget);
 // Generate a mapping from the permutation map to the index of
 // correct column in _mtarget. Need to handle the fact that the
 // permutation group contains non-fragment atoms.
 // For example, map(213465) will be converted to newidx(102354).
 // If the atom with Idx=3 is not in the fragment, it will be
 // converted to newidx(10X243) instead.
 std::vector<unsigned int> _newidx;
 };
}

#endif // OB_ALIGN_H