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