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                      gmx_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     t_trxstatus *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     gmx_rmpbc_t  gpbc=NULL;
  75
  76
  77     nfr_all = 0;
  78     nfr     = 0;
  79     snew(ti,100);
  80     snew(xi,100);
  81     natoms = read_first_x(oenv,&status,trxfn,&ti[nfr],&x,box);
  82
  83     snew(w_rls,gnx);
  84     tot_mass = 0;
  85     for(a=0; a<gnx; a++)
  86     {
  87         if (index[a] >= natoms)
  88         {
  89             gmx_fatal(FARGS,"Atom index (%d) is larger than the number of atoms in the trajecory (%d)",index[a]+1,natoms);
  90         }
  91         w_rls[a] = (bMW ? top->atoms.atom[index[a]].m : 1.0);
  92         tot_mass += w_rls[a];
  93     }
  94     gpbc = gmx_rmpbc_init(&top->idef,ePBC,natoms,box);
  95
  96     do
  97     {
  98         if (nfr_all % skip == 0)
  99         {
 100             gmx_rmpbc(gpbc,natoms,box,x);
 101             snew(xi[nfr],gnx);
 102             for(i=0; i<gnx; i++)
 103             {
 104                 copy_rvec(x[index[i]],xi[nfr][i]);
 105             }
 106             reset_x(gnx,NULL,gnx,NULL,xi[nfr],w_rls);
 107             nfr++;
 108             if (nfr % 100 == 0)
 109             {
 110                 srenew(ti,nfr+100);
 111                 srenew(xi,nfr+100);
 112             }
 113         }
 114         nfr_all++;
 115     }
 116     while(read_next_x(oenv,status,&ti[nfr],natoms,x,box));
 117     close_trj(status);
 118     sfree(x);
 119
 120     gmx_rmpbc_done(gpbc);
 121
 122     snew(srmsd,nfr);
 123     for(i=0; i<nfr; i++)
 124     {
 125         printf("\rProcessing frame %d of %d",i,nfr);
 126         for(j=i+1; j<nfr; j++)
 127         {
 128             calc_fit_R(nfitdim,gnx,w_rls,xi[i],xi[j],R);
 129
 130             msd = 0;
 131             for(a=0; a<gnx; a++)
 132             {
 133                 for(r=0; r<DIM; r++)
 134                 {
 135                     xf = 0;
 136                     for(c=0; c<DIM; c++)
 137                     {
 138                         xf += R[r][c]*xi[j][a][c];
 139                     }
 140                     msd += w_rls[a]*sqr(xi[i][a][r] - xf);
 141                 }
 142             }
 143             msd /= tot_mass;
 144             srmsd[i] += sqrt(msd);
 145             srmsd[j] += sqrt(msd);
 146         }
 147         sfree(xi[i]);
 148     }
 149     printf("\n");
 150     sfree(w_rls);
 151
 152     min_srmsd = GMX_REAL_MAX;
 153     min_fr    = -1;
 154     min_t     = -1;
 155     srmsd_tot = 0;
 156     for(i=0; i<nfr; i++)
 157     {
 158         srmsd[i] /= (nfr - 1);
 159         if (srmsd[i] < min_srmsd)
 160         {
 161             min_srmsd = srmsd[i];
 162             min_fr    = i;
 163             min_t     = ti[i];
 164         }
 165         srmsd_tot += srmsd[i];
 166     }
 167     sfree(srmsd);
 168
 169     printf("Average RMSD between all structures: %.3f\n",srmsd_tot/nfr);
 170     printf("Structure with lowest RMSD to all others: time %g, av. RMSD %.3f\n",
 171            min_t,min_srmsd);
 172
 173     for(a=0; a<gnx; a++)
 174     {
 175         copy_rvec(xi[min_fr][a],x_ref[index[a]]);
 176     }
 177
 178     sfree(xi);
 179 }
 180
 181 int gmx_rotmat(int argc,char *argv[])
 182 {
 183     const char *desc[] = {
 184         "g_rotmat plots the rotation matrix required for least squares fitting",
 185         "a conformation onto the reference conformation provided with",
 186         "[TT]-s[tt]. Translation is removed before fitting.",
 187         "The output are the three vectors that give the new directions",
 188         "of the x, y and z directions of the reference conformation,",
 189         "for example: (zx,zy,zz) is the orientation of the reference",
 190         "z-axis in the trajectory frame.",
 191         "[PAR]",
 192         "This tool is useful for, for instance,",
 193         "determining the orientation of a molecule",
 194         "at an interface, possibly on a trajectory produced with",
 195         "[TT]trjconv -fit rotxy+transxy[tt] to remove the rotation",
 196         "in the xy-plane.",
 197         "[PAR]",
 198         "Option [TT]-ref[tt] determines a reference structure for fitting,",
 199         "instead of using the structure from [TT]-s[tt]. The structure with",
 200         "the lowest sum of RMSD's to all other structures is used.",
 201         "Since the computational cost of this procedure grows with",
 202         "the square of the number of frames, the [TT]-skip[tt] option",
 203         "can be useful. A full fit or only a fit in the x/y plane can",
 204         "be performed.",
 205         "[PAR]",
 206         "Option [TT]-fitxy[tt] fits in the x/y plane before determining",
 207         "the rotation matrix."
 208     };
 209     const char *reffit[] =
 210         { NULL, "none", "xyz", "xy", NULL };
 211     static int  skip=1;
 212     static gmx_bool bFitXY=FALSE,bMW=TRUE;
 213     t_pargs pa[] = {
 214         { "-ref", FALSE, etENUM, {reffit},
 215           "Determine the optimal reference structure" },
 216         { "-skip", FALSE, etINT, {&skip},
 217           "Use every nr-th frame for -ref" },
 218         { "-fitxy", FALSE, etBOOL, {&bFitXY},
 219           "Fit the x/y rotation before determining the rotation" },
 220         { "-mw", FALSE, etBOOL, {&bMW},
 221           "Use mass weighted fitting" }
 222     };
 223     FILE       *out;
 224     t_trxstatus *status;
 225     t_topology top;
 226     int        ePBC;
 227     rvec       *x_ref,*x;
 228     matrix     box,R;
 229     real       t;
 230     int        natoms,i;
 231     char       *grpname,title[256];
 232     int        gnx;
 233     gmx_rmpbc_t  gpbc=NULL;
 234     atom_id    *index;
 235     output_env_t oenv;
 236     real       *w_rls;
 237     const char *leg[]  = { "xx", "xy", "xz", "yx", "yy", "yz", "zx", "zy", "zz" };
 238 #define NLEG asize(leg)
 239     t_filenm fnm[] = {
 240         { efTRX, "-f",   NULL,       ffREAD },
 241         { efTPS, NULL,   NULL,       ffREAD },
 242         { efNDX, NULL,   NULL,       ffOPTRD },
 243         { efXVG, NULL,   "rotmat",   ffWRITE }
 244     };
 245 #define NFILE asize(fnm)
 246
 247     CopyRight(stderr,argv[0]);
 248
 249     parse_common_args(&argc,argv,PCA_CAN_TIME | PCA_CAN_VIEW | PCA_BE_NICE,
 250                       NFILE,fnm,asize(pa),pa,asize(desc),desc,0,NULL,&oenv);
 251
 252     read_tps_conf(ftp2fn(efTPS,NFILE,fnm),title,&top,&ePBC,&x_ref,NULL,box,bMW);
 253
 254     gpbc = gmx_rmpbc_init(&top.idef,ePBC,top.atoms.nr,box);
 255
 256     gmx_rmpbc(gpbc,top.atoms.nr,box,x_ref);
 257
 258     get_index(&top.atoms,ftp2fn_null(efNDX,NFILE,fnm),1,&gnx,&index,&grpname);
 259
 260     if (reffit[0][0] != 'n')
 261     {
 262         get_refx(oenv,ftp2fn(efTRX,NFILE,fnm),reffit[0][2]=='z' ? 3 : 2,skip,
 263                  gnx,index,bMW,&top,ePBC,x_ref);
 264     }
 265
 266     natoms = read_first_x(oenv,&status,ftp2fn(efTRX,NFILE,fnm),&t,&x,box);
 267
 268     snew(w_rls,natoms);
 269     for(i=0; i<gnx; i++)
 270     {
 271         if (index[i] >= natoms)
 272         {
 273             gmx_fatal(FARGS,"Atom index (%d) is larger than the number of atoms in the trajecory (%d)",index[i]+1,natoms);
 274         }
 275         w_rls[index[i]] = (bMW ? top.atoms.atom[index[i]].m : 1.0);
 276     }
 277
 278     if (reffit[0][0] == 'n')
 279     {
 280         reset_x(gnx,index,natoms,NULL,x_ref,w_rls);
 281     }
 282
 283     out = xvgropen(ftp2fn(efXVG,NFILE,fnm),
 284                    "Fit matrix","Time (ps)","",oenv);
 285     xvgr_legend(out,NLEG,leg,oenv);
 286
 287     do
 288     {
 289         gmx_rmpbc(gpbc,natoms,box,x);
 290
 291         reset_x(gnx,index,natoms,NULL,x,w_rls);
 292
 293         if (bFitXY)
 294         {
 295             do_fit_ndim(2,natoms,w_rls,x_ref,x);
 296         }
 297
 298         calc_fit_R(DIM,natoms,w_rls,x_ref,x,R);
 299
 300         fprintf(out,
 301                 "%7g %7.4f %7.4f %7.4f %7.4f %7.4f %7.4f %7.4f %7.4f %7.4f\n",
 302                 t,
 303                 R[XX][XX],R[XX][YY],R[XX][ZZ],
 304                 R[YY][XX],R[YY][YY],R[YY][ZZ],
 305                 R[ZZ][XX],R[ZZ][YY],R[ZZ][ZZ]);
 306     }
 307     while(read_next_x(oenv,status,&t,natoms,x,box));
 308
 309     gmx_rmpbc_done(gpbc);
 310
 311     close_trj(status);
 312
 313     ffclose(out);
 314
 315     do_view(oenv,ftp2fn(efXVG,NFILE,fnm),"-nxy");
 316
 317     thanx(stderr);
 318
 319     return 0;
 320 }