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