include/do_fit.h

   1 /*
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  35
  36 #ifndef _do_fit_h
  37 #define _do_fit_h
  38
  39 #include "typedefs.h"
  40
  41 #ifdef __cplusplus
  42 extern "C" {
  43 #endif
  44
  45 real calc_similar_ind(gmx_bool bRho,int nind,atom_id *index,real mass[],
  46                              rvec x[],rvec xp[]);
  47 /* Returns RMSD or Rho (depending on bRho) over all atoms in index */
  48
  49 real rmsdev_ind(int nind,atom_id index[],real mass[],
  50                        rvec x[],rvec xp[]);
  51 /* Returns the RMS Deviation betweem x and xp over all atoms in index */
  52
  53 real rmsdev(int natoms,real mass[],rvec x[],rvec xp[]);
  54 /* Returns the RMS Deviation betweem x and xp over all atoms */
  55
  56 real rhodev_ind(int nind,atom_id index[],real mass[],rvec x[],rvec xp[]);
  57 /* Returns size-independent Rho similarity parameter over all atoms in index
  58  * Maiorov & Crippen, PROTEINS 22, 273 (1995).
  59  */
  60
  61 real rhodev(int natoms,real mass[],rvec x[],rvec xp[]);
  62 /* Returns size-independent Rho similarity parameter over all atoms
  63  * Maiorov & Crippen, PROTEINS 22, 273 (1995).
  64  */
  65
  66 void calc_fit_R(int ndim,int natoms,real *w_rls,rvec *xp,rvec *x,
  67                        matrix R);
  68 /* Calculates the rotation matrix R for which
  69  * sum_i w_rls_i (xp_i - R x_i).(xp_i - R x_i)
  70  * is minimal. ndim=3 gives full fit, ndim=2 gives xy fit.
  71  * This matrix is also used do_fit.
  72  * x_rotated[i] = sum R[i][j]*x[j]
  73  */
  74
  75 void do_fit_ndim(int ndim,int natoms,real *w_rls,rvec *xp,rvec *x);
  76 /* Do a least squares fit of x to xp. Atoms which have zero mass
  77  * (w_rls[i]) are not taken into account in fitting.
  78  * This makes is possible to fit eg. on Calpha atoms and orient
  79  * all atoms. The routine only fits the rotational part,
  80  * therefore both xp and x should be centered round the origin.
  81  */
  82
  83 void do_fit(int natoms,real *w_rls,rvec *xp,rvec *x);
  84 /* Calls do_fit with ndim=3, thus fitting in 3D */
  85
  86 void reset_x_ndim(int ndim,int ncm,const atom_id *ind_cm,
  87                          int nreset,const atom_id *ind_reset,
  88                          rvec x[],const real mass[]);
  89 /* Put the center of mass of atoms in the origin for dimensions 0 to ndim.
  90  * The center of mass is computed from the index ind_cm.
  91  * When ind_cm!=NULL the COM is determined using ind_cm.
  92  * When ind_cm==NULL the COM is determined for atoms 0 to ncm.
  93  * When ind_reset!=NULL the coordinates indexed by ind_reset are reset.
  94  * When ind_reset==NULL the coordinates up to nreset are reset.
  95  */
  96
  97 void reset_x(int ncm,const atom_id *ind_cm,
  98                     int nreset,const atom_id *ind_reset,
  99                     rvec x[],const real mass[]);
 100 /* Calls reset_x with ndim=3, thus resetting all dimesions */
 101
 102 #ifdef __cplusplus
 103 }
 104 #endif
 105
 106 #endif  /* _do_fit_h */