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42 #include "gromacs/math/vec.h"
44 #include "gromacs/math/do_fit.h"
45 #include "gromacs/utility/fatalerror.h"
46 #include "gromacs/utility/smalloc.h"
48 static void my_calc_xcm(int nbb, atom_id bbind[], rvec x[], rvec xcm)
53 for (i = 0; (i < nbb); i++)
58 for (m = 0; (m < DIM); m++)
64 static void my_sub_xcm(int nbb, atom_id bbind[], rvec x[], rvec xcm)
68 for (i = 0; (i < nbb); i++)
75 real fit_ahx(int nres, t_bb bb[], int natoms, int nall, atom_id allindex[],
77 atom_id caindex[], gmx_bool bFit)
79 static rvec *xref = NULL;
80 static real *mass = NULL;
81 const real d = 0.15; /* Rise per residue (nm) */
82 const real tw = 1.745; /* Twist per residue (rad) */
83 const real rad = 0.23; /* Radius of the helix (nm) */
90 gmx_fatal(FARGS, "Need at least 3 Calphas to fit to, (now %d)...\n", nca);
99 for (i = 0; (i < nca); i++)
102 xref[ai][XX] = rad*cos(phi0);
103 xref[ai][YY] = rad*sin(phi0);
106 /* Set the mass to select that this Calpha contributes to fitting */
110 fprintf(stderr, "%5d %8.3f %8.3f %8.3f %8.3f %8.3f %8.3f\n", ai,
111 x[ai][XX], x[ai][YY], x[ai][ZZ],
112 xref[ai][XX], xref[ai][YY], xref[ai][ZZ]);
117 /* Center the referece around the origin */
118 my_calc_xcm(nca, caindex, xref, xcm);
119 my_sub_xcm(nca, caindex, xref, xcm);
123 /* Now center the to-be-fitted coords around the origin */
124 my_calc_xcm(nca, caindex, x, xcm);
125 my_sub_xcm(nall, allindex, x, xcm);
128 dump_ahx(nres, bb, xref, box, 0);
132 for (i = 0; (i < natoms); i++)
141 gmx_fatal(FARGS, "nmass=%d, nca=%d\n", nmass, nca);
144 /* Now call the fitting routine */
147 do_fit(natoms, mass, xref, x);
150 /* Reset masses and calc rms */
152 for (i = 0; (i < nres); i++)
158 rvec_sub(x[ai], xref[ai], dx);
160 bb[i].rmsa += sqrt(rms);
166 return sqrt(trms/nca);