src/tools/gmx_rotmat.c

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  36 #ifdef HAVE_CONFIG_H
  37 #include <config.h>
  38 #endif
  39
  40 #include <math.h>
  41 #include <string.h>
  42
  43 #include "statutil.h"
  44 #include "sysstuff.h"
  45 #include "typedefs.h"
  46 #include "smalloc.h"
  47 #include "macros.h"
  48 #include "vec.h"
  49 #include "pbc.h"
  50 #include "copyrite.h"
  51 #include "futil.h"
  52 #include "statutil.h"
  53 #include "index.h"
  54 #include "mshift.h"
  55 #include "xvgr.h"
  56 #include "rmpbc.h"
  57 #include "tpxio.h"
  58 #include "do_fit.h"
  59 #include "gmx_ana.h"
  60
  61
  62 static void get_refx(output_env_t oenv,const char *trxfn,int nfitdim,int skip,
  63                      int gnx,int *index,
  64                      bool bMW,t_topology *top,int ePBC,rvec *x_ref)
  65 {
  66     int    natoms,nfr_all,nfr,i,j,a,r,c,min_fr;
  67     int    status;
  68     real   *ti,min_t;
  69     double tot_mass,msd,*srmsd,min_srmsd,srmsd_tot;
  70     rvec   *x,**xi;
  71     real   xf;
  72     matrix box,R;
  73     real   *w_rls;
  74
  75     nfr_all = 0;
  76     nfr     = 0;
  77     snew(ti,100);
  78     snew(xi,100);
  79     natoms = read_first_x(oenv,&status,trxfn,&ti[nfr],&x,box);
  80
  81     snew(w_rls,gnx);
  82     tot_mass = 0;
  83     for(a=0; a<gnx; a++)
  84     {
  85         if (index[a] >= natoms)
  86         {
  87             gmx_fatal(FARGS,"Atom index (%d) is larger than the number of atoms in the trajecory (%d)",index[a]+1,natoms);
  88         }
  89         w_rls[a] = (bMW ? top->atoms.atom[index[a]].m : 1.0);
  90         tot_mass += w_rls[a];
  91     }
  92
  93     do
  94     {
  95         if (nfr_all % skip == 0)
  96         {
  97             rm_pbc(&top->idef,ePBC,natoms,box,x,x);
  98             snew(xi[nfr],gnx);
  99             for(i=0; i<gnx; i++)
 100             {
 101                 copy_rvec(x[index[i]],xi[nfr][i]);
 102             }
 103             reset_x(gnx,NULL,gnx,NULL,xi[nfr],w_rls);
 104             nfr++;
 105             if (nfr % 100 == 0)
 106             {
 107                 srenew(ti,nfr+100);
 108                 srenew(xi,nfr+100);
 109             }
 110         }
 111         nfr_all++;
 112     }
 113     while(read_next_x(oenv,status,&ti[nfr],natoms,x,box));
 114     close_trj(status);
 115     sfree(x);
 116
 117     snew(srmsd,nfr);
 118     for(i=0; i<nfr; i++)
 119     {
 120         printf("\rProcessing frame %d of %d",i,nfr);
 121         for(j=i+1; j<nfr; j++)
 122         {
 123             calc_fit_R(nfitdim,gnx,w_rls,xi[i],xi[j],R);
 124
 125             msd = 0;
 126             for(a=0; a<gnx; a++)
 127             {
 128                 for(r=0; r<DIM; r++)
 129                 {
 130                     xf = 0;
 131                     for(c=0; c<DIM; c++)
 132                     {
 133                         xf += R[r][c]*xi[j][a][c];
 134                     }
 135                     msd += w_rls[a]*sqr(xi[i][a][r] - xf);
 136                 }
 137             }
 138             msd /= tot_mass;
 139             srmsd[i] += sqrt(msd);
 140             srmsd[j] += sqrt(msd);
 141         }
 142         sfree(xi[i]);
 143     }
 144     printf("\n");
 145     sfree(w_rls);
 146
 147     min_srmsd = GMX_REAL_MAX;
 148     min_fr    = -1;
 149     min_t     = -1;
 150     srmsd_tot = 0;
 151     for(i=0; i<nfr; i++)
 152     {
 153         srmsd[i] /= (nfr - 1);
 154         if (srmsd[i] < min_srmsd)
 155         {
 156             min_srmsd = srmsd[i];
 157             min_fr    = i;
 158             min_t     = ti[i];
 159         }
 160         srmsd_tot += srmsd[i];
 161     }
 162     sfree(srmsd);
 163
 164     printf("Average RMSD between all structures: %.3f\n",srmsd_tot/nfr);
 165     printf("Structure with lowest RMSD to all others: time %g, av. RMSD %.3f\n",
 166            min_t,min_srmsd);
 167
 168     for(a=0; a<gnx; a++)
 169     {
 170         copy_rvec(xi[min_fr][a],x_ref[index[a]]);
 171     }
 172
 173     sfree(xi);
 174 }
 175
 176 int gmx_rotmat(int argc,char *argv[])
 177 {
 178     const char *desc[] = {
 179         "g_rotmat plots the rotation matrix required for least squares fitting",
 180         "a conformation onto the reference conformation provided with",
 181         "[TT]-s[tt]. Translation is removed before fitting.",
 182         "The output are the three vectors that give the new directions",
 183         "of the x, y and z directions of the reference conformation,",
 184         "for example: (zx,zy,zz) is the orientation of the reference",
 185         "z-axis in the trajectory frame.",
 186         "[PAR]",
 187         "This tool is useful for, for instance,",
 188         "determining the orientation of a molecule",
 189         "at an interface, possibly on a trajectory produced with",
 190         "[TT]trjconv -fit rotxy+transxy[tt] to remove the rotation",
 191         "in the xy-plane.",
 192         "[PAR]",
 193         "Option [TT]-ref[tt] determines a reference structure for fitting,",
 194         "instead of using the structure from [TT]-s[tt]. The structure with",
 195         "the lowest sum of RMSD's to all other structures is used.",
 196         "Since the computational cost of this procedure grows with",
 197         "the square of the number of frames, the [TT]-skip[tt] option",
 198         "can be useful. A full fit or only a fit in the x/y plane can",
 199         "be performed.",
 200         "[PAR]",
 201         "Option [TT]-fitxy[tt] fits in the x/y plane before determining",
 202         "the rotation matrix."
 203     };
 204     const char *reffit[] =
 205         { NULL, "none", "xyz", "xy", NULL };
 206     static int  skip=1;
 207     static bool bFitXY=FALSE,bMW=TRUE;
 208     t_pargs pa[] = {
 209         { "-ref", FALSE, etENUM, {reffit},
 210           "Determine the optimal reference structure" },
 211         { "-skip", FALSE, etINT, {&skip},
 212           "Use every nr-th frame for -ref" },
 213         { "-fitxy", FALSE, etBOOL, {&bFitXY},
 214           "Fit the x/y rotation before determining the rotation" },
 215         { "-mw", FALSE, etBOOL, {&bMW},
 216           "Use mass weighted fitting" }
 217     };
 218     FILE       *out;
 219     int        status;
 220     t_topology top;
 221     int        ePBC;
 222     rvec       *x_ref,*x;
 223     matrix     box,R;
 224     real       t;
 225     int        natoms,i;
 226     char       *grpname,title[256];
 227     int        gnx;
 228     atom_id    *index;
 229     output_env_t oenv;
 230     real       *w_rls;
 231     char *leg[]  = { "xx", "xy", "xz", "yx", "yy", "yz", "zx", "zy", "zz" };
 232 #define NLEG asize(leg)
 233     t_filenm fnm[] = {
 234         { efTRX, "-f",   NULL,       ffREAD },
 235         { efTPS, NULL,   NULL,       ffREAD },
 236         { efNDX, NULL,   NULL,       ffOPTRD },
 237         { efXVG, NULL,   "rotmat",   ffWRITE }
 238     };
 239 #define NFILE asize(fnm)
 240
 241     CopyRight(stderr,argv[0]);
 242
 243     parse_common_args(&argc,argv,PCA_CAN_TIME | PCA_CAN_VIEW | PCA_BE_NICE,
 244                       NFILE,fnm,asize(pa),pa,asize(desc),desc,0,NULL,&oenv);
 245
 246     read_tps_conf(ftp2fn(efTPS,NFILE,fnm),title,&top,&ePBC,&x_ref,NULL,box,bMW);
 247
 248     rm_pbc(&top.idef,ePBC,top.atoms.nr,box,x_ref,x_ref);
 249     get_index(&top.atoms,ftp2fn_null(efNDX,NFILE,fnm),1,&gnx,&index,&grpname);
 250
 251     if (reffit[0][0] != 'n')
 252     {
 253         get_refx(oenv,ftp2fn(efTRX,NFILE,fnm),reffit[0][2]=='z' ? 3 : 2,skip,
 254                  gnx,index,bMW,&top,ePBC,x_ref);
 255     }
 256
 257     natoms = read_first_x(oenv,&status,ftp2fn(efTRX,NFILE,fnm),&t,&x,box);
 258
 259     snew(w_rls,natoms);
 260     for(i=0; i<gnx; i++)
 261     {
 262         if (index[i] >= natoms)
 263         {
 264             gmx_fatal(FARGS,"Atom index (%d) is larger than the number of atoms in the trajecory (%d)",index[i]+1,natoms);
 265         }
 266         w_rls[index[i]] = (bMW ? top.atoms.atom[index[i]].m : 1.0);
 267     }
 268
 269     if (reffit[0][0] == 'n')
 270     {
 271         reset_x(gnx,index,natoms,NULL,x_ref,w_rls);
 272     }
 273
 274     out = xvgropen(ftp2fn(efXVG,NFILE,fnm),
 275                    "Fit matrix","Time (ps)","",oenv);
 276     xvgr_legend(out,NLEG,leg,oenv);
 277
 278     do
 279     {
 280         rm_pbc(&top.idef,ePBC,natoms,box,x,x);
 281
 282         reset_x(gnx,index,natoms,NULL,x,w_rls);
 283
 284         if (bFitXY)
 285         {
 286             do_fit_ndim(2,natoms,w_rls,x_ref,x);
 287         }
 288
 289         calc_fit_R(DIM,natoms,w_rls,x_ref,x,R);
 290
 291         fprintf(out,
 292                 "%7g %7.4f %7.4f %7.4f %7.4f %7.4f %7.4f %7.4f %7.4f %7.4f\n",
 293                 t,
 294                 R[XX][XX],R[XX][YY],R[XX][ZZ],
 295                 R[YY][XX],R[YY][YY],R[YY][ZZ],
 296                 R[ZZ][XX],R[ZZ][YY],R[ZZ][ZZ]);
 297     }
 298     while(read_next_x(oenv,status,&t,natoms,x,box));
 299
 300     close_trj(status);
 301
 302     ffclose(out);
 303
 304     do_view(oenv,ftp2fn(efXVG,NFILE,fnm),"-nxy");
 305
 306     thanx(stderr);
 307
 308     return 0;
 309 }