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#ifndef _princ_h
#define _princ_h
#include "visibility.h"
#include "typedefs.h"

#ifdef __cplusplus
extern "C" {
#endif

void rotate_atoms(int gnx, atom_id index[], rvec x[], matrix trans);
/* Rotate all atoms in index using matrix trans */

GMX_LIBGMX_EXPORT
void principal_comp(int n, atom_id index[], t_atom atom[], rvec x[],
                    matrix trans, rvec d);
/* Calculate the principal components of atoms in index. Atoms are
 * mass weighted. It is assumed that the center of mass is in the origin!
 */

GMX_LIBGMX_EXPORT
void orient_princ(t_atoms *atoms, int isize, atom_id *index,
                  int natoms, rvec x[], rvec *v, rvec d);
/* rotates molecule to align principal axes with coordinate axes */

GMX_LIBGMX_EXPORT
real calc_xcm(rvec x[], int gnx, atom_id *index, t_atom *atom, rvec xcm,
              gmx_bool bQ);
/* Calculate the center of mass of the atoms in index. if bQ then the atoms
 * will be charge weighted rather than mass weighted.
 * Returns the total mass/charge.
 */

GMX_LIBGMX_EXPORT
real sub_xcm(rvec x[], int gnx, atom_id *index, t_atom atom[], rvec xcm,
             gmx_bool bQ);
/* Calc. the center of mass and subtract it from all coordinates.
 * Returns the original center of mass in xcm
 * Returns the total mass
 */

void add_xcm(rvec x[], int gnx, atom_id *index, rvec xcm);
/* Increment all atoms in index with xcm */

#ifdef __cplusplus
}
#endif

#endif
