include/do_fit.h

   1 /*
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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 #include "typedefs.h"
  44
  45 #ifdef __cplusplus
  46 extern "C" {
  47 #endif
  48
  49 extern real calc_similar_ind(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 extern 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 extern real rmsdev(int natoms,real mass[],rvec x[],rvec xp[]);
  58 /* Returns the RMS Deviation betweem x and xp over all atoms */
  59
  60 extern 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 extern 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 extern 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 extern 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 extern 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 extern 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 extern 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  /* _do_fit_h */