src/tools/gmx_dyndom.c

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  35 #ifdef HAVE_CONFIG_H
  36 #include <config.h>
  37 #endif
  38
  39 #include "3dview.h"
  40 #include "statutil.h"
  41 #include "smalloc.h"
  42 #include "copyrite.h"
  43 #include "index.h"
  44 #include "confio.h"
  45 #include "gmx_fatal.h"
  46 #include "vec.h"
  47 #include "physics.h"
  48 #include "random.h"
  49 #include "gmx_ana.h"
  50
  51
  52 static void rot_conf(t_atoms *atoms,rvec x[],rvec v[],real trans,real angle,
  53                      rvec head,rvec tail,matrix box,int isize,atom_id index[],
  54                      rvec xout[],rvec vout[])
  55 {
  56   rvec     arrow,center,xcm;
  57   real     theta,phi,arrow_len;
  58   mat4     Rx,Ry,Rz,Rinvy,Rinvz,Mtot,Tcm,Tinvcm,Tx;
  59   mat4     temp1,temp2,temp3,temp4,temp21,temp43;
  60   vec4     xv;
  61   int      i,j,ai;
  62
  63   rvec_sub(tail,head,arrow);
  64   arrow_len = norm(arrow);
  65   if (debug) {
  66     fprintf(debug,"Arrow vector:   %10.4f  %10.4f  %10.4f\n",
  67             arrow[XX],arrow[YY],arrow[ZZ]);
  68     fprintf(debug,"Effective translation %g nm\n",trans);
  69   }
  70   if (arrow_len == 0.0)
  71     gmx_fatal(FARGS,"Arrow vector not given");
  72
  73   /* Copy all aoms to output */
  74   for(i=0; (i<atoms->nr);i ++) {
  75     copy_rvec(x[i],xout[i]);
  76     copy_rvec(v[i],vout[i]);
  77   }
  78
  79   /* Compute center of mass and move atoms there */
  80   clear_rvec(xcm);
  81   for(i=0; (i<isize); i++)
  82     rvec_inc(xcm,x[index[i]]);
  83   for(i=0; (i<DIM); i++)
  84     xcm[i] /= isize;
  85   if (debug)
  86     fprintf(debug,"Center of mass: %10.4f  %10.4f  %10.4f\n",
  87             xcm[XX],xcm[YY],xcm[ZZ]);
  88   for(i=0; (i<isize); i++)
  89     rvec_sub(x[index[i]],xcm,xout[index[i]]);
  90
  91   /* Compute theta and phi that describe the arrow */
  92   theta = acos(arrow[ZZ]/arrow_len);
  93   phi   = atan2(arrow[YY]/arrow_len,arrow[XX]/arrow_len);
  94   if (debug)
  95     fprintf(debug,"Phi = %.1f, Theta = %.1f\n",RAD2DEG*phi,RAD2DEG*theta);
  96
  97   /* Now the total rotation matrix: */
  98   /* Rotate a couple of times */
  99   rotate(ZZ,-phi,Rz);
 100   rotate(YY,M_PI/2-theta,Ry);
 101   rotate(XX,angle*DEG2RAD,Rx);
 102   Rx[WW][XX] = trans;
 103   rotate(YY,theta-M_PI/2,Rinvy);
 104   rotate(ZZ,phi,Rinvz);
 105
 106   mult_matrix(temp1,Ry,Rz);
 107   mult_matrix(temp2,Rinvy,Rx);
 108   mult_matrix(temp3,temp2,temp1);
 109   mult_matrix(Mtot,Rinvz,temp3);
 110
 111   print_m4(debug,"Rz",Rz);
 112   print_m4(debug,"Ry",Ry);
 113   print_m4(debug,"Rx",Rx);
 114   print_m4(debug,"Rinvy",Rinvy);
 115   print_m4(debug,"Rinvz",Rinvz);
 116   print_m4(debug,"Mtot",Mtot);
 117
 118   for(i=0; (i<isize); i++) {
 119     ai = index[i];
 120     m4_op(Mtot,xout[ai],xv);
 121     rvec_add(xv,xcm,xout[ai]);
 122     m4_op(Mtot,v[ai],xv);
 123     copy_rvec(xv,vout[ai]);
 124   }
 125 }
 126
 127 int gmx_dyndom(int argc,char *argv[])
 128 {
 129   const char *desc[] = {
 130     "g_dyndom reads a pdb file output from DynDom",
 131     "http://www.cmp.uea.ac.uk/dyndom/",
 132     "It reads the coordinates, and the coordinates of the rotation axis",
 133     "furthermore it reads an index file containing the domains.",
 134     "Furthermore it takes the first and last atom of the arrow file",
 135     "as command line arguments (head and tail) and",
 136     "finally it takes the translation vector (given in DynDom info file)",
 137     "and the angle of rotation (also as command line arguments). If the angle",
 138     "determined by DynDom is given, one should be able to recover the",
 139     "second structure used for generating the DynDom output.",
 140     "Because of limited numerical accuracy this should be verified by",
 141     "computing an all-atom RMSD (using [TT]g_confrms[tt]) rather than by file",
 142     "comparison (using diff).[PAR]",
 143     "The purpose of this program is to interpolate and extrapolate the",
 144     "rotation as found by DynDom. As a result unphysical structures with",
 145     "long or short bonds, or overlapping atoms may be produced. Visual",
 146     "inspection, and energy minimization may be necessary to",
 147     "validate the structure."
 148   };
 149   static real trans0 = 0;
 150   static rvec head  = { 0,0,0 };
 151   static rvec tail  = { 0,0,0 };
 152   static real angle0 = 0,angle1 = 0, maxangle = 0;
 153   static int  label = 0,nframes=11;
 154   t_pargs pa[] = {
 155     { "-firstangle",    FALSE, etREAL, {&angle0},
 156       "Angle of rotation about rotation vector" },
 157     { "-lastangle",    FALSE, etREAL, {&angle1},
 158       "Angle of rotation about rotation vector" },
 159     { "-nframe",   FALSE, etINT,  {&nframes},
 160       "Number of steps on the pathway" },
 161     { "-maxangle", FALSE, etREAL, {&maxangle},
 162       "DymDom dtermined angle of rotation about rotation vector" },
 163     { "-trans",    FALSE, etREAL, {&trans0},
 164       "Translation (Aangstroem) along rotation vector (see DynDom info file)" },
 165     { "-head",     FALSE, etRVEC, {head},
 166       "First atom of the arrow vector" },
 167     { "-tail",     FALSE, etRVEC, {tail},
 168       "Last atom of the arrow vector" }
 169   };
 170   int     i,j,natoms,isize,status;
 171   atom_id *index=NULL,*index_all;
 172   char    title[256],*grpname;
 173   t_atoms atoms;
 174   real    angle,trans;
 175   rvec    *x,*v,*xout,*vout;
 176   matrix  box;
 177   output_env_t oenv;
 178
 179   t_filenm fnm[] = {
 180     { efPDB, "-f", "dyndom",  ffREAD },
 181     { efTRO, "-o", "rotated", ffWRITE },
 182     { efNDX, "-n", "domains", ffREAD }
 183   };
 184 #define NFILE asize(fnm)
 185
 186   CopyRight(stderr,argv[0]);
 187
 188   parse_common_args(&argc,argv,0,NFILE,fnm,asize(pa),pa,
 189                     asize(desc),desc,0,NULL,&oenv);
 190
 191   get_stx_coordnum (opt2fn("-f",NFILE,fnm),&natoms);
 192   init_t_atoms(&atoms,natoms,TRUE);
 193   snew(x,natoms);
 194   snew(v,natoms);
 195   read_stx_conf(opt2fn("-f",NFILE,fnm),title,&atoms,x,v,NULL,box);
 196   snew(xout,natoms);
 197   snew(vout,natoms);
 198
 199   printf("Select group to rotate:\n");
 200   rd_index(ftp2fn(efNDX,NFILE,fnm),1,&isize,&index,&grpname);
 201   printf("Going to rotate %s containg %d atoms\n",grpname,isize);
 202
 203   snew(index_all,atoms.nr);
 204   for(i=0; (i<atoms.nr); i++)
 205     index_all[i] = i;
 206
 207   status = open_trx(opt2fn("-o",NFILE,fnm),"w");
 208
 209   label = 'A';
 210   for(i=0; (i<nframes); i++,label++) {
 211     angle = angle0 + (i*(angle1-angle0))/(nframes-1);
 212     trans = trans0*0.1*angle/maxangle;
 213     printf("Frame: %2d (label %c), angle: %8.3f deg., trans: %8.3f nm\n",
 214            i,label,angle,trans);
 215     rot_conf(&atoms,x,v,trans,angle,head,tail,box,isize,index,xout,vout);
 216
 217     if (label > 'Z')
 218       label-=26;
 219     for(j=0; (j<atoms.nr); j++)
 220       atoms.resinfo[atoms.atom[j].resind].chain = label;
 221
 222     write_trx(status,atoms.nr,index_all,&atoms,i,angle,box,xout,vout,NULL);
 223   }
 224   close_trx(status);
 225
 226   thanx(stderr);
 227
 228   return 0;
 229 }