include/do_fit.h

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  35
  36 #ifndef _do_fit_h
  37 #define _do_fit_h
  38
  39 #ifdef HAVE_CONFIG_H
  40 #include <config.h>
  41 #endif
  42
  43 #ifdef __cplusplus
  44 extern "C" {
  45 #endif
  46
  47 extern real calc_similar_ind(bool bRho,int nind,atom_id *index,real mass[],
  48                              rvec x[],rvec xp[]);
  49 /* Returns RMSD or Rho (depending on bRho) over all atoms in index */
  50
  51 extern real rmsdev_ind(int nind,atom_id index[],real mass[],
  52                        rvec x[],rvec xp[]);
  53 /* Returns the RMS Deviation betweem x and xp over all atoms in index */
  54
  55 extern real rmsdev(int natoms,real mass[],rvec x[],rvec xp[]);
  56 /* Returns the RMS Deviation betweem x and xp over all atoms */
  57
  58 extern real rhodev_ind(int nind,atom_id index[],real mass[],rvec x[],rvec xp[]);
  59 /* Returns size-independent Rho similarity parameter over all atoms in index
  60  * Maiorov & Crippen, PROTEINS 22, 273 (1995).
  61  */
  62
  63 extern real rhodev(int natoms,real mass[],rvec x[],rvec xp[]);
  64 /* Returns size-independent Rho similarity parameter over all atoms
  65  * Maiorov & Crippen, PROTEINS 22, 273 (1995).
  66  */
  67
  68 extern void calc_fit_R(int ndim,int natoms,real *w_rls,rvec *xp,rvec *x,
  69                        matrix R);
  70 /* Calculates the rotation matrix R for which
  71  * sum_i w_rls_i (xp_i - R x_i).(xp_i - R x_i)
  72  * is minimal. ndim=3 gives full fit, ndim=2 gives xy fit.
  73  * This matrix is also used do_fit.
  74  * x_rotated[i] = sum R[i][j]*x[j]
  75  */
  76
  77 extern void do_fit_ndim(int ndim,int natoms,real *w_rls,rvec *xp,rvec *x);
  78 /* Do a least squares fit of x to xp. Atoms which have zero mass
  79  * (w_rls[i]) are not taken into account in fitting.
  80  * This makes is possible to fit eg. on Calpha atoms and orient
  81  * all atoms. The routine only fits the rotational part,
  82  * therefore both xp and x should be centered round the origin.
  83  */
  84
  85 extern void do_fit(int natoms,real *w_rls,rvec *xp,rvec *x);
  86 /* Calls do_fit with ndim=3, thus fitting in 3D */
  87
  88 extern void reset_x_ndim(int ndim,int ncm,const atom_id *ind_cm,
  89                          int nreset,const atom_id *ind_reset,
  90                          rvec x[],const real mass[]);
  91 /* Put the center of mass of atoms in the origin for dimensions 0 to ndim.
  92  * The center of mass is computed from the index ind_cm.
  93  * When ind_cm!=NULL the COM is determined using ind_cm.
  94  * When ind_cm==NULL the COM is determined for atoms 0 to ncm.
  95  * When ind_reset!=NULL the coordinates indexed by ind_reset are reset.
  96  * When ind_reset==NULL the coordinates up to nreset are reset.
  97  */
  98
  99 extern void reset_x(int ncm,const atom_id *ind_cm,
 100                     int nreset,const atom_id *ind_reset,
 101                     rvec x[],const real mass[]);
 102 /* Calls reset_x with ndim=3, thus resetting all dimesions */
 103
 104 #ifdef __cplusplus
 105 }
 106 #endif
 107
 108 #endif  /* _do_fit_h */