src/gromacs/gmxana/fitahx.cpp

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  37 #include "gmxpre.h"
  38
  39 #include "fitahx.h"
  40
  41 #include <cmath>
  42
  43 #include "gromacs/math/do_fit.h"
  44 #include "gromacs/math/vec.h"
  45 #include "gromacs/utility/fatalerror.h"
  46 #include "gromacs/utility/smalloc.h"
  47
  48 static void my_calc_xcm(int nbb, atom_id bbind[], rvec x[], rvec xcm)
  49 {
  50     int    i, m, ai;
  51
  52     clear_rvec(xcm);
  53     for (i = 0; (i < nbb); i++)
  54     {
  55         ai = bbind[i];
  56         rvec_inc(xcm, x[ai]);
  57     }
  58     for (m = 0; (m < DIM); m++)
  59     {
  60         xcm[m] /= (nbb);
  61     }
  62 }
  63
  64 static void my_sub_xcm(int nbb, atom_id bbind[], rvec x[], rvec xcm)
  65 {
  66     int i, ai;
  67
  68     for (i = 0; (i < nbb); i++)
  69     {
  70         ai = bbind[i];
  71         rvec_dec(x[ai], xcm);
  72     }
  73 }
  74
  75 real fit_ahx(int nres, t_bb bb[], int natoms, int nall, atom_id allindex[],
  76              rvec x[], int nca,
  77              atom_id caindex[], gmx_bool bFit)
  78 {
  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) */
  84     real         phi0, trms, rms;
  85     rvec         dx, xcm;
  86     int          ai, i, nmass;
  87
  88     if (nca < 3)
  89     {
  90         gmx_fatal(FARGS, "Need at least 3 Calphas to fit to, (now %d)...\n", nca);
  91     }
  92
  93     if (xref == NULL)
  94     {
  95         snew(xref, natoms);
  96         snew(mass, natoms);
  97     }
  98     phi0 = 0;
  99     for (i = 0; (i < nca); i++)
 100     {
 101         ai           = caindex[i];
 102         xref[ai][XX] = rad*std::cos(phi0);
 103         xref[ai][YY] = rad*std::sin(phi0);
 104         xref[ai][ZZ] = d*i;
 105
 106         /* Set the mass to select that this Calpha contributes to fitting */
 107         mass[ai] = 10.0;
 108 /*#define DEBUG*/
 109 #ifdef DEBUG
 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]);
 113 #endif
 114         phi0 += tw;
 115     }
 116
 117     /* Center the referece around the origin */
 118     my_calc_xcm(nca, caindex, xref, xcm);
 119     my_sub_xcm(nca, caindex, xref, xcm);
 120
 121     if (bFit)
 122     {
 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);
 126     }
 127 #ifdef DEBUG
 128     dump_ahx(nres, bb, xref, box, 0);
 129 #endif
 130
 131     nmass = 0;
 132     for (i = 0; (i < natoms); i++)
 133     {
 134         if (mass[i] > 0)
 135         {
 136             nmass++;
 137         }
 138     }
 139     if (nmass != nca)
 140     {
 141         gmx_fatal(FARGS, "nmass=%d, nca=%d\n", nmass, nca);
 142     }
 143
 144     /* Now call the fitting routine */
 145     if (bFit)
 146     {
 147         do_fit(natoms, mass, xref, x);
 148     }
 149
 150     /* Reset masses and calc rms */
 151     trms = 0.0;
 152     for (i = 0; (i < nres); i++)
 153     {
 154         ai = bb[i].CA;
 155
 156         if (mass[ai] > 0.0)
 157         {
 158             rvec_sub(x[ai], xref[ai], dx);
 159             rms         = iprod(dx, dx);
 160             bb[i].rmsa += std::sqrt(rms);
 161             bb[i].nrms++;
 162             trms    += rms;
 163             mass[ai] = 0.0;
 164         }
 165     }
 166     return std::sqrt(trms/nca);
 167 }