src/tools/fitahx.c

   1 /*
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  32 static char *SRCID_fitahx_c = "$Id$";
  33 #include "fitahx.h"
  34 #include "vec.h"
  35 #include "do_fit.h"
  36 #include "smalloc.h"
  37
  38 static void my_calc_xcm(int nbb,atom_id bbind[],rvec x[],rvec xcm)
  39 {
  40   int    i,m,ai;
  41
  42   clear_rvec(xcm);
  43   for(i=0; (i<nbb); i++) {
  44     ai=bbind[i];
  45     rvec_inc(xcm,x[ai]);
  46   }
  47   for(m=0; (m<DIM); m++)
  48     xcm[m]/=(nbb);
  49 }
  50
  51 static void my_sub_xcm(int nbb,atom_id bbind[],rvec x[],rvec xcm)
  52 {
  53   int i,ai;
  54
  55   for(i=0; (i<nbb); i++) {
  56     ai=bbind[i];
  57     rvec_dec(x[ai],xcm);
  58   }
  59 }
  60
  61 real fit_ahx(int nres,t_bb bb[],int natoms,int nall,atom_id allindex[],
  62              rvec x[],int nca,
  63              atom_id caindex[],matrix box,bool bFit)
  64 {
  65   static rvec *xref=NULL;
  66   static real *mass=NULL;
  67   const  real d=0.15;     /* Rise per residue (nm)    */
  68   const  real tw=1.745;   /* Twist per residue (rad)  */
  69   const  real rad=0.23;   /* Radius of the helix (nm) */
  70   real   phi0,trms,rms;
  71   rvec   dx,xcm;
  72   int    ai,i,nmass;
  73
  74   if (nca < 3)
  75     fatal_error(0,"Need at least 3 Calphas to fit to, (now %d)...\n",nca);
  76
  77   if (xref == NULL) {
  78     snew(xref,natoms);
  79     snew(mass,natoms);
  80   }
  81   phi0=0;
  82   for(i=0; (i<nca); i++) {
  83     ai=caindex[i];
  84     xref[ai][XX]=rad*cos(phi0);
  85     xref[ai][YY]=rad*sin(phi0);
  86     xref[ai][ZZ]=d*i;
  87
  88     /* Set the mass to select that this Calpha contributes to fitting */
  89     mass[ai]=10.0;
  90 /*#define DEBUG*/
  91 #ifdef DEBUG
  92     fprintf(stderr,"%5d  %8.3f  %8.3f  %8.3f  %8.3f  %8.3f  %8.3f\n",ai,
  93             x[ai][XX],x[ai][YY],x[ai][ZZ],
  94             xref[ai][XX],xref[ai][YY],xref[ai][ZZ]);
  95 #endif
  96     phi0+=tw;
  97   }
  98
  99   /* Center the referece around the origin */
 100   my_calc_xcm(nca,caindex,xref,xcm);
 101   my_sub_xcm(nca,caindex,xref,xcm);
 102
 103   if (bFit) {
 104     /* Now center the to-be-fitted coords around the origin */
 105     my_calc_xcm(nca,caindex,x,xcm);
 106     my_sub_xcm(nall,allindex,x,xcm);
 107   }
 108 #ifdef DEBUG
 109   dump_ahx(nres,bb,xref,box,0);
 110 #endif
 111
 112   nmass=0;
 113   for(i=0; (i<natoms); i++)
 114     if (mass[i] > 0)
 115       nmass++;
 116   if (nmass != nca)
 117     fatal_error(0,"nmass=%d, nca=%d\n",nmass,nca);
 118
 119   /* Now call the fitting routine */
 120   if (bFit)
 121     do_fit(natoms,mass,xref,x);
 122
 123   /* Reset masses and calc rms */
 124   trms=0.0;
 125   for(i=0; (i<nres); i++) {
 126     ai=bb[i].CA;
 127
 128     if (mass[ai] > 0.0) {
 129       rvec_sub(x[ai],xref[ai],dx);
 130       rms=iprod(dx,dx);
 131       bb[i].rmsa+=sqrt(rms);
 132       bb[i].nrms++;
 133       trms+=rms;
 134       mass[ai]=0.0;
 135     }
 136   }
 137   return sqrt(trms/nca);
 138 }
 139