src/tools/fitahx.c

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  35 #ifdef HAVE_CONFIG_H
  36 #include <config.h>
  37 #endif
  38
  39 #include "fitahx.h"
  40 #include "vec.h"
  41 #include "do_fit.h"
  42 #include "smalloc.h"
  43
  44 static void my_calc_xcm(int nbb,atom_id bbind[],rvec x[],rvec xcm)
  45 {
  46   int    i,m,ai;
  47
  48   clear_rvec(xcm);
  49   for(i=0; (i<nbb); i++) {
  50     ai=bbind[i];
  51     rvec_inc(xcm,x[ai]);
  52   }
  53   for(m=0; (m<DIM); m++)
  54     xcm[m]/=(nbb);
  55 }
  56
  57 static void my_sub_xcm(int nbb,atom_id bbind[],rvec x[],rvec xcm)
  58 {
  59   int i,ai;
  60
  61   for(i=0; (i<nbb); i++) {
  62     ai=bbind[i];
  63     rvec_dec(x[ai],xcm);
  64   }
  65 }
  66
  67 real fit_ahx(int nres,t_bb bb[],int natoms,int nall,atom_id allindex[],
  68              rvec x[],int nca,
  69              atom_id caindex[],matrix box,gmx_bool bFit)
  70 {
  71   static rvec *xref=NULL;
  72   static real *mass=NULL;
  73   const  real d=0.15;     /* Rise per residue (nm)    */
  74   const  real tw=1.745;   /* Twist per residue (rad)  */
  75   const  real rad=0.23;   /* Radius of the helix (nm) */
  76   real   phi0,trms,rms;
  77   rvec   dx,xcm;
  78   int    ai,i,nmass;
  79
  80   if (nca < 3)
  81     gmx_fatal(FARGS,"Need at least 3 Calphas to fit to, (now %d)...\n",nca);
  82
  83   if (xref == NULL) {
  84     snew(xref,natoms);
  85     snew(mass,natoms);
  86   }
  87   phi0=0;
  88   for(i=0; (i<nca); i++) {
  89     ai=caindex[i];
  90     xref[ai][XX]=rad*cos(phi0);
  91     xref[ai][YY]=rad*sin(phi0);
  92     xref[ai][ZZ]=d*i;
  93
  94     /* Set the mass to select that this Calpha contributes to fitting */
  95     mass[ai]=10.0;
  96 /*#define DEBUG*/
  97 #ifdef DEBUG
  98     fprintf(stderr,"%5d  %8.3f  %8.3f  %8.3f  %8.3f  %8.3f  %8.3f\n",ai,
  99             x[ai][XX],x[ai][YY],x[ai][ZZ],
 100             xref[ai][XX],xref[ai][YY],xref[ai][ZZ]);
 101 #endif
 102     phi0+=tw;
 103   }
 104
 105   /* Center the referece around the origin */
 106   my_calc_xcm(nca,caindex,xref,xcm);
 107   my_sub_xcm(nca,caindex,xref,xcm);
 108
 109   if (bFit) {
 110     /* Now center the to-be-fitted coords around the origin */
 111     my_calc_xcm(nca,caindex,x,xcm);
 112     my_sub_xcm(nall,allindex,x,xcm);
 113   }
 114 #ifdef DEBUG
 115   dump_ahx(nres,bb,xref,box,0);
 116 #endif
 117
 118   nmass=0;
 119   for(i=0; (i<natoms); i++)
 120     if (mass[i] > 0)
 121       nmass++;
 122   if (nmass != nca)
 123     gmx_fatal(FARGS,"nmass=%d, nca=%d\n",nmass,nca);
 124
 125   /* Now call the fitting routine */
 126   if (bFit)
 127     do_fit(natoms,mass,xref,x);
 128
 129   /* Reset masses and calc rms */
 130   trms=0.0;
 131   for(i=0; (i<nres); i++) {
 132     ai=bb[i].CA;
 133
 134     if (mass[ai] > 0.0) {
 135       rvec_sub(x[ai],xref[ai],dx);
 136       rms=iprod(dx,dx);
 137       bb[i].rmsa+=sqrt(rms);
 138       bb[i].nrms++;
 139       trms+=rms;
 140       mass[ai]=0.0;
 141     }
 142   }
 143   return sqrt(trms/nca);
 144 }
 145