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/*
 * This file is part of the GROMACS molecular simulation package.
 *
 * Copyright (c) 1991-2000, University of Groningen, The Netherlands.
 * Copyright (c) 2001-2004, The GROMACS development team.
 * Copyright (c) 2010,2014,2015,2016, by the GROMACS development team, led by
 * Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
 * and including many others, as listed in the AUTHORS file in the
 * top-level source directory and at http://www.gromacs.org.
 *
 * GROMACS 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.
 *
 * GROMACS 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 GROMACS; if not, see
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 */
#ifndef GMX_MATH_DO_FIT_H
#define GMX_MATH_DO_FIT_H

#include "gromacs/math/vectypes.h"
#include "gromacs/utility/basedefinitions.h"
#include "gromacs/utility/real.h"

#ifdef __cplusplus
extern "C" {
#endif

real calc_similar_ind(gmx_bool bRho, int nind, int *index, real mass[],
                      rvec x[], rvec xp[]);
/* Returns RMSD or Rho (depending on bRho) over all atoms in index */

real rmsdev_ind(int nind, int index[], real mass[],
                rvec x[], rvec xp[]);
/* Returns the RMS Deviation betweem x and xp over all atoms in index */

real rmsdev(int natoms, real mass[], rvec x[], rvec xp[]);
/* Returns the RMS Deviation betweem x and xp over all atoms */

real rhodev_ind(int nind, int index[], real mass[], rvec x[], rvec xp[]);
/* Returns size-independent Rho similarity parameter over all atoms in index
 * Maiorov & Crippen, PROTEINS 22, 273 (1995).
 */

real rhodev(int natoms, real mass[], rvec x[], rvec xp[]);
/* Returns size-independent Rho similarity parameter over all atoms
 * Maiorov & Crippen, PROTEINS 22, 273 (1995).
 */

void calc_fit_R(int ndim, int natoms, real *w_rls, const rvec *xp, rvec *x,
                matrix R);
/* Calculates the rotation matrix R for which
 * sum_i w_rls_i (xp_i - R x_i).(xp_i - R x_i)
 * is minimal. ndim=3 gives full fit, ndim=2 gives xy fit.
 * This matrix is also used do_fit.
 * x_rotated[i] = sum R[i][j]*x[j]
 */

void do_fit_ndim(int ndim, int natoms, real *w_rls, const rvec *xp, rvec *x);
/* Do a least squares fit of x to xp. Atoms which have zero mass
 * (w_rls[i]) are not taken into account in fitting.
 * This makes is possible to fit eg. on Calpha atoms and orient
 * all atoms. The routine only fits the rotational part,
 * therefore both xp and x should be centered round the origin.
 */

void do_fit(int natoms, real *w_rls, const rvec *xp, rvec *x);
/* Calls do_fit with ndim=3, thus fitting in 3D */

void reset_x_ndim(int ndim, int ncm, const int *ind_cm,
                  int nreset, const int *ind_reset,
                  rvec x[], const real mass[]);
/* Put the center of mass of atoms in the origin for dimensions 0 to ndim.
 * The center of mass is computed from the index ind_cm.
 * When ind_cm!=NULL the COM is determined using ind_cm.
 * When ind_cm==NULL the COM is determined for atoms 0 to ncm.
 * When ind_reset!=NULL the coordinates indexed by ind_reset are reset.
 * When ind_reset==NULL the coordinates up to nreset are reset.
 */

void reset_x(int ncm, const int *ind_cm,
             int nreset, const int *ind_reset,
             rvec x[], const real mass[]);
/* Calls reset_x with ndim=3, thus resetting all dimesions */

#ifdef __cplusplus
}
#endif

#endif