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