src/gromacs/math/do_fit.h

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  37 #ifndef GMX_MATH_DO_FIT_H
  38 #define GMX_MATH_DO_FIT_H
  39
  40 #include "gromacs/math/vectypes.h"
  41 #include "gromacs/utility/basedefinitions.h"
  42 #include "gromacs/utility/real.h"
  43
  44 #ifdef __cplusplus
  45 extern "C" {
  46 #endif
  47
  48 real calc_similar_ind(gmx_bool bRho, int nind, int *index, real mass[],
  49                       rvec x[], rvec xp[]);
  50 /* Returns RMSD or Rho (depending on bRho) over all atoms in index */
  51
  52 real rmsdev_ind(int nind, int index[], real mass[],
  53                 rvec x[], rvec xp[]);
  54 /* Returns the RMS Deviation betweem x and xp over all atoms in index */
  55
  56 real rmsdev(int natoms, real mass[], rvec x[], rvec xp[]);
  57 /* Returns the RMS Deviation betweem x and xp over all atoms */
  58
  59 real rhodev_ind(int nind, int index[], real mass[], rvec x[], rvec xp[]);
  60 /* Returns size-independent Rho similarity parameter over all atoms in index
  61  * Maiorov & Crippen, PROTEINS 22, 273 (1995).
  62  */
  63
  64 real rhodev(int natoms, real mass[], rvec x[], rvec xp[]);
  65 /* Returns size-independent Rho similarity parameter over all atoms
  66  * Maiorov & Crippen, PROTEINS 22, 273 (1995).
  67  */
  68
  69 void calc_fit_R(int ndim, int natoms, real *w_rls, const rvec *xp, rvec *x,
  70                 matrix R);
  71 /* Calculates the rotation matrix R for which
  72  * sum_i w_rls_i (xp_i - R x_i).(xp_i - R x_i)
  73  * is minimal. ndim=3 gives full fit, ndim=2 gives xy fit.
  74  * This matrix is also used do_fit.
  75  * x_rotated[i] = sum R[i][j]*x[j]
  76  */
  77
  78 void do_fit_ndim(int ndim, int natoms, real *w_rls, const rvec *xp, rvec *x);
  79 /* Do a least squares fit of x to xp. Atoms which have zero mass
  80  * (w_rls[i]) are not taken into account in fitting.
  81  * This makes is possible to fit eg. on Calpha atoms and orient
  82  * all atoms. The routine only fits the rotational part,
  83  * therefore both xp and x should be centered round the origin.
  84  */
  85
  86 void do_fit(int natoms, real *w_rls, const rvec *xp, rvec *x);
  87 /* Calls do_fit with ndim=3, thus fitting in 3D */
  88
  89 void reset_x_ndim(int ndim, int ncm, const int *ind_cm,
  90                   int nreset, const int *ind_reset,
  91                   rvec x[], const real mass[]);
  92 /* Put the center of mass of atoms in the origin for dimensions 0 to ndim.
  93  * The center of mass is computed from the index ind_cm.
  94  * When ind_cm!=NULL the COM is determined using ind_cm.
  95  * When ind_cm==NULL the COM is determined for atoms 0 to ncm.
  96  * When ind_reset!=NULL the coordinates indexed by ind_reset are reset.
  97  * When ind_reset==NULL the coordinates up to nreset are reset.
  98  */
  99
 100 void reset_x(int ncm, const int *ind_cm,
 101              int nreset, const int *ind_reset,
 102              rvec x[], const real mass[]);
 103 /* Calls reset_x with ndim=3, thus resetting all dimesions */
 104
 105 #ifdef __cplusplus
 106 }
 107 #endif
 108
 109 #endif