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47 real calc_similar_ind(gmx_bool bRho, int nind, atom_id *index, real mass[],
49 /* Returns RMSD or Rho (depending on bRho) over all atoms in index */
51 real rmsdev_ind(int nind, atom_id index[], real mass[],
53 /* Returns the RMS Deviation betweem x and xp over all atoms in index */
55 real rmsdev(int natoms, real mass[], rvec x[], rvec xp[]);
56 /* Returns the RMS Deviation betweem x and xp over all atoms */
58 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).
63 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).
68 void calc_fit_R(int ndim, int natoms, real *w_rls, rvec *xp, rvec *x,
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]
77 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.
85 void do_fit(int natoms, real *w_rls, rvec *xp, rvec *x);
86 /* Calls do_fit with ndim=3, thus fitting in 3D */
88 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.
99 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 */
108 #endif /* _do_fit_h */