include/do_fit.h

   1 /*
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   4  *                This source code is part of
   5  *
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   8  *          GROningen MAchine for Chemical Simulations
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  10  *                        VERSION 3.1
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  12  * This program is free software; you can redistribute it and/or
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  32
  33 #ifndef _do_fit_h
  34 #define _do_fit_h
  35
  36 #ifdef HAVE_CONFIG_H
  37 #include <config.h>
  38 #endif
  39
  40
  41 extern real calc_similar_ind(bool bRho,int nind,atom_id *index,real mass[],
  42                              rvec x[],rvec xp[]);
  43 /* Returns RMSD or Rho (depending on bRho) over all atoms in index */
  44
  45 extern real rmsdev_ind(int nind,atom_id index[],real mass[],
  46                        rvec x[],rvec xp[]);
  47 /* Returns the RMS Deviation betweem x and xp over all atoms in index */
  48
  49 extern real rmsdev(int natoms,real mass[],rvec x[],rvec xp[]);
  50 /* Returns the RMS Deviation betweem x and xp over all atoms */
  51
  52 extern real rhodev_ind(int nind,atom_id index[],real mass[],rvec x[],rvec xp[]);
  53 /* Returns size-independent Rho similarity parameter over all atoms in index
  54  * Maiorov & Crippen, PROTEINS 22, 273 (1995).
  55  */
  56
  57 extern real rhodev(int natoms,real mass[],rvec x[],rvec xp[]);
  58 /* Returns size-independent Rho similarity parameter over all atoms
  59  * Maiorov & Crippen, PROTEINS 22, 273 (1995).
  60  */
  61
  62 extern void calc_fit_R(int natoms,real *w_rls,rvec *xp,rvec *x,matrix R);
  63 /* Calculates the rotation matrix R for which
  64  * sum_i w_rls_i (xp_i - R x_i).(xp_i - R x_i)
  65  * is minimal. This matrix is also used do_fit.
  66  * x_rotated[i] = sum R[i][j]*x[j]
  67  */
  68
  69 extern void do_fit(int natoms,real *w_rls,rvec *xp,rvec *x);
  70 /* Do a least squares fit of x to xp. Atoms which have zero mass
  71  * (w_rls[i]) are not taken into account in fitting.
  72  * This makes is possible to fit eg. on Calpha atoms and orient
  73  * all atoms. The routine only fits the rotational part,
  74  * therefore both xp and x should be centered round the origin.
  75  */
  76
  77 extern void reset_x(int ncm,atom_id ind_cm[],
  78                     int nreset,atom_id *ind_reset,rvec x[],real mass[]);
  79 /* Put the center of mass of atoms in the origin.
  80  * The center of mass is computed from the index ind_cm.
  81  * When ind_reset!=NULL the coordinates indexed by ind_reset are reset.
  82  * When ind_reset==NULL the coordinates up to nreset are reset.
  83  */
  84
  85 #endif  /* _do_fit_h */