src/tools/g_helix.c

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  36 #ifdef HAVE_CONFIG_H
  37 #include <config.h>
  38 #endif
  39
  40 #include <math.h>
  41
  42 #include "confio.h"
  43 #include "copyrite.h"
  44 #include "fatal.h"
  45 #include "fitahx.h"
  46 #include "futil.h"
  47 #include "gstat.h"
  48 #include "wgms.h"
  49 #include "hxprops.h"
  50 #include "macros.h"
  51 #include "maths.h"
  52 #include "pbc.h"
  53 #include "tpxio.h"
  54 #include "physics.h"
  55 #include "index.h"
  56 #include "smalloc.h"
  57 #include "statutil.h"
  58 #include "string.h"
  59 #include "sysstuff.h"
  60 #include "txtdump.h"
  61 #include "typedefs.h"
  62 #include "vec.h"
  63 #include "xvgr.h"
  64
  65 void dump_ahx(int nres,
  66               t_bb bb[],rvec x[],matrix box,int teller)
  67 {
  68   FILE *fp;
  69   char buf[256];
  70   int  i;
  71
  72   sprintf(buf,"dump%d.gro",teller);
  73   fp=ffopen(buf,"w");
  74   fprintf(fp,"Dumping fitted helix frame %d\n",teller);
  75   fprintf(fp,"%5d\n",nres*5);
  76   for(i=0; (i<nres); i++) {
  77 #define PR(AA) fprintf(fp,"%5d%5s%5s%5d%8.3f%8.3f%8.3f\n",i+1,"GLY",#AA,bb[i].AA,x[bb[i].AA][XX],x[bb[i].AA][YY],x[bb[i].AA][ZZ]); fflush(fp)
  78     if (bb[i].bHelix) {
  79       PR(N);
  80       PR(H);
  81       PR(CA);
  82       PR(C);
  83       PR(O);
  84     }
  85   }
  86   for(i=0; (i<DIM); i++)
  87     fprintf(fp,"%10.5f",box[i][i]);
  88   fprintf(fp,"\n");
  89   fclose(fp);
  90 }
  91
  92 int get_prop(char prop[])
  93 {
  94   static char *ppp[efhNR] = {
  95     "RAD", "TWIST", "RISE", "LEN", "NHX", "DIP", "RMS", "CPHI",
  96     "RMSA", "PHI", "PSI", "HB3", "HB4", "HB5", "CD222"
  97   };
  98   int i,n;
  99
 100   fprintf(stderr,"Select something\n");
 101   for(i=0; (i<efhNR); ) {
 102     fprintf(stderr,"%2d: %10s",i,ppp[i]); i++;
 103     if (i<efhNR) {
 104       fprintf(stderr,"      %2d: %10s\n",i,ppp[i]);
 105       i++;
 106     }
 107     else
 108       fprintf(stderr,"\n");
 109   }
 110   do {
 111     scanf("%d",&n);
 112   } while ((n < 0) || (n >= efhNR));
 113
 114   strcpy(prop,ppp[n]);
 115
 116   return n;
 117 }
 118
 119
 120 void dump_otrj(FILE *otrj,int natoms,atom_id all_index[],rvec x[],
 121                real fac,rvec xav[])
 122 {
 123   static FILE *fp=NULL;
 124   static real fac0=1.0;
 125
 126   int  i,ai,m;
 127   real xa,xm;
 128
 129   if (fp==NULL) {
 130     fp=ffopen("WEDGAMMA10.DAT","w");
 131     fac0=fac;
 132   }
 133   fac/=fac0;
 134
 135   fprintf(fp,"%10g\n",fac);
 136
 137   for(i=0; (i<natoms); i++) {
 138     ai=all_index[i];
 139     for(m=0; (m<DIM); m++) {
 140       xa = xav[ai][m];
 141       xm = x[ai][m]*fac;
 142       xav[ai][m] = xa+xm;
 143       x[ai][m]   = xm;
 144     }
 145   }
 146   write_gms_ndx(otrj,natoms,all_index,x,NULL);
 147 }
 148
 149 int gmx_helix(int argc,char *argv[])
 150 {
 151   static char *desc[] = {
 152     "g_helix computes all kind of helix properties. First, the peptide",
 153     "is checked to find the longest helical part. This is determined by",
 154     "Hydrogen bonds and Phi/Psi angles.",
 155     "That bit is fitted",
 156     "to an ideal helix around the Z-axis and centered around the origin.",
 157     "Then the following properties are computed:[PAR]",
 158     "[BB]1.[bb] Helix radius (file radius.xvg). This is merely the",
 159     "RMS deviation in two dimensions for all Calpha atoms.",
 160     "it is calced as sqrt((SUM i(x^2(i)+y^2(i)))/N), where N is the number",
 161     "of backbone atoms. For an ideal helix the radius is 0.23 nm[BR]",
 162     "[BB]2.[bb] Twist (file twist.xvg). The average helical angle per",
 163     "residue is calculated. For alpha helix it is 100 degrees,",
 164     "for 3-10 helices it will be smaller,",
 165     "for 5-helices it will be larger.[BR]",
 166     "[BB]3.[bb] Rise per residue (file rise.xvg). The helical rise per",
 167     "residue is plotted as the difference in Z-coordinate between Ca",
 168     "atoms. For an ideal helix this is 0.15 nm[BR]",
 169     "[BB]4.[bb] Total helix length (file len-ahx.xvg). The total length",
 170     "of the",
 171     "helix in nm. This is simply the average rise (see above) times the",
 172     "number of helical residues (see below).[BR]",
 173     "[BB]5.[bb] Number of helical residues (file n-ahx.xvg). The title says",
 174     "it all.[BR]",
 175     "[BB]6.[bb] Helix Dipole, backbone only (file dip-ahx.xvg).[BR]",
 176     "[BB]7.[bb] RMS deviation from ideal helix, calculated for the Calpha",
 177     "atoms only (file rms-ahx.xvg).[BR]",
 178     "[BB]8.[bb] Average Calpha-Calpha dihedral angle (file phi-ahx.xvg).[BR]",
 179     "[BB]9.[bb] Average Phi and Psi angles (file phipsi.xvg).[BR]",
 180     "[BB]10.[bb] Ellipticity at 222 nm according to [IT]Hirst and Brooks[it]",
 181     "[PAR]"
 182   };
 183   static bool bCheck=FALSE,bFit=TRUE,bDBG=FALSE,bEV=FALSE;
 184   static int  rStart=0,rEnd=0,r0=1;
 185   t_pargs pa [] = {
 186     { "-r0", FALSE, etINT, {&r0},
 187       "The first residue number in the sequence" },
 188     { "-q",  FALSE, etBOOL,{&bCheck},
 189       "Check at every step which part of the sequence is helical" },
 190     { "-F",  FALSE, etBOOL,{&bFit},
 191       "Toggle fit to a perfect helix" },
 192     { "-db", FALSE, etBOOL,{&bDBG},
 193       "Print debug info" },
 194     { "-ev", FALSE, etBOOL,{&bEV},
 195       "Write a new 'trajectory' file for ED" },
 196     { "-ahxstart", FALSE, etINT, {&rStart},
 197       "First residue in helix" },
 198     { "-ahxend", FALSE, etINT, {&rEnd},
 199       "Last residue in helix" }
 200   };
 201
 202   typedef struct {
 203     FILE *fp,*fp2;
 204     bool bfp2;
 205     char *filenm;
 206     char *title;
 207     char *xaxis;
 208     char *yaxis;
 209     real val;
 210   } t_xvgrfile;
 211
 212   t_xvgrfile xf[efhNR] = {
 213     { NULL, NULL, TRUE,  "radius",  "Helix radius",               NULL, "r (nm)" , 0.0 },
 214     { NULL, NULL, TRUE,  "twist",   "Twist per residue",          NULL, "Angle (deg)", 0.0 },
 215     { NULL, NULL, TRUE,  "rise",    "Rise per residue",           NULL, "Rise (nm)", 0.0 },
 216     { NULL, NULL, FALSE, "len-ahx", "Length of the Helix",        NULL, "Length (nm)", 0.0 },
 217     { NULL, NULL, FALSE, "dip-ahx", "Helix Backbone Dipole",      NULL, "rq (nm e)", 0.0 },
 218     { NULL, NULL, TRUE,  "rms-ahx", "RMS Deviation from Ideal Helix", NULL, "RMS (nm)", 0.0 },
 219     { NULL, NULL, FALSE, "rmsa-ahx","Average RMSD per Residue",   "Residue", "RMS (nm)", 0.0 },
 220     { NULL, NULL,FALSE,  "cd222",   "Ellipticity at 222 nm", NULL, "nm", 0.0 },
 221     { NULL, NULL, TRUE,  "pprms",   "RMS Distance from \\8a\\4-helix", NULL, "deg" , 0.0 },
 222     { NULL, NULL, TRUE,  "caphi",   "Average Ca-Ca Dihedral",     NULL, "\\8F\\4(deg)", 0.0 },
 223     { NULL, NULL, TRUE,  "phi",     "Average \\8F\\4 angles", NULL, "deg" , 0.0 },
 224     { NULL, NULL, TRUE,  "psi",     "Average \\8Y\\4 angles", NULL, "deg" , 0.0 },
 225     { NULL, NULL, TRUE,  "hb3",     "Average n-n+3 hbond length", NULL, "nm" , 0.0 },
 226     { NULL, NULL, TRUE,  "hb4",     "Average n-n+4 hbond length", NULL, "nm" , 0.0 },
 227     { NULL, NULL, TRUE,  "hb5",     "Average n-n+5 hbond length", NULL, "nm" , 0.0 },
 228     { NULL, NULL,FALSE,  "JCaHa",   "J-Coupling Values",        "Residue", "Hz" , 0.0 },
 229     { NULL, NULL,FALSE,  "helicity","Helicity per Residue",     "Residue", "% of time" , 0.0 }
 230   };
 231
 232   FILE       *otrj;
 233   char       buf[54],prop[256];
 234   int        status;
 235   int        natoms,nre,nres,step;
 236   t_bb       *bb;
 237   int        i,j,ai,m,nall,nbb,nca,teller,nSel=0;
 238   atom_id    *bbindex,*caindex,*allindex;
 239   t_topology *top;
 240   rvec       *x,*xref,*xav;
 241   real       t,lambda;
 242   real       rms,fac;
 243   matrix     box;
 244   bool       bRange;
 245   t_filenm  fnm[] = {
 246     { efTPX, NULL,  NULL,   ffREAD  },
 247     { efNDX, NULL,  NULL,   ffREAD  },
 248     { efTRX, "-f",  NULL,   ffREAD  },
 249     { efG87, "-to", NULL,   ffOPTWR },
 250     { efSTO, "-cz", "zconf",ffWRITE },
 251     { efSTO, "-co", "waver",ffWRITE }
 252   };
 253 #define NFILE asize(fnm)
 254
 255   CopyRight(stderr,argv[0]);
 256   parse_common_args(&argc,argv,PCA_CAN_VIEW | PCA_CAN_TIME | PCA_BE_NICE,
 257                     NFILE,fnm,asize(pa),pa,asize(desc),desc,0,NULL);
 258
 259   bRange=(opt2parg_bSet("-ahxstart",asize(pa),pa) &&
 260           opt2parg_bSet("-ahxend",asize(pa),pa));
 261
 262   top=read_top(ftp2fn(efTPX,NFILE,fnm));
 263
 264   natoms=read_first_x(&status,opt2fn("-f",NFILE,fnm),&t,&x,box);
 265
 266   if (opt2bSet("-to",NFILE,fnm)) {
 267     otrj=opt2FILE("-to",NFILE,fnm,"w");
 268     nSel=get_prop(prop);
 269     fprintf(otrj,"%s Weighted Trajectory: %d atoms, NO box\n",prop,natoms);
 270   }
 271   else
 272     otrj=NULL;
 273
 274   if (natoms != top->atoms.nr)
 275     fatal_error(0,"Sorry can only run when the number of atoms in the run input file (%d) is equal to the number in the trajectory (%d)",
 276             top->atoms.nr,natoms);
 277
 278   bb=mkbbind(ftp2fn(efNDX,NFILE,fnm),&nres,&nbb,r0,&nall,&allindex,
 279              top->atoms.atomname,top->atoms.atom,top->atoms.resname);
 280   snew(bbindex,natoms);
 281   snew(caindex,nres);
 282
 283   fprintf(stderr,"nall=%d\n",nall);
 284
 285   /* Open output files, default x-axis is time */
 286   for(i=0; (i<efhNR); i++) {
 287     sprintf(buf,"%s.xvg",xf[i].filenm);
 288     remove(buf);
 289     xf[i].fp=xvgropen(buf,xf[i].title,xf[i].xaxis ? xf[i].xaxis : "Time (ps)",
 290                       xf[i].yaxis);
 291     if (xf[i].bfp2) {
 292       sprintf(buf,"%s.out",xf[i].filenm);
 293       remove(buf);
 294       xf[i].fp2=ffopen(buf,"w");
 295     }
 296   }
 297
 298   /* Read reference frame from tpx file to compute helix length */
 299   snew(xref,top->atoms.nr);
 300   read_tpx(ftp2fn(efTPX,NFILE,fnm),
 301            &step,&t,&lambda,NULL,NULL,
 302            &natoms,xref,NULL,NULL,NULL);
 303   calc_hxprops(nres,bb,xref,box);
 304   do_start_end(nres,bb,xref,&nbb,bbindex,&nca,caindex,bRange,rStart,rEnd);
 305   sfree(xref);
 306   if (bDBG) {
 307     fprintf(stderr,"nca=%d, nbb=%d\n",nca,nbb);
 308     pr_bb(stdout,nres,bb);
 309   }
 310
 311   snew(xav,natoms);
 312   teller=0;
 313   do {
 314     if ((teller++ % 10) == 0)
 315       fprintf(stderr,"\rt=%.2f",t);
 316     rm_pbc(&(top->idef),top->atoms.nr,box,x,x);
 317
 318     calc_hxprops(nres,bb,x,box);
 319     if (bCheck)
 320       do_start_end(nres,bb,x,&nbb,bbindex,&nca,caindex,FALSE,0,0);
 321
 322     if (nca >= 5) {
 323       rms=fit_ahx(nres,bb,natoms,nall,allindex,x,nca,caindex,box,bFit);
 324
 325       if (teller == 1) {
 326         write_sto_conf(opt2fn("-cz",NFILE,fnm),"Helix fitted to Z-Axis",
 327                        &(top->atoms),x,NULL,box);
 328       }
 329
 330       xf[efhRAD].val   = radius(xf[efhRAD].fp2,nca,caindex,x);
 331       xf[efhTWIST].val = twist(xf[efhTWIST].fp2,nca,caindex,x);
 332       xf[efhRISE].val  = rise(nca,caindex,x);
 333       xf[efhLEN].val   = ahx_len(nca,caindex,x,box);
 334       xf[efhCD222].val = ellipticity(nres,bb);
 335       xf[efhDIP].val   = dip(nbb,bbindex,x,top->atoms.atom);
 336       xf[efhRMS].val   = rms;
 337       xf[efhCPHI].val  = ca_phi(nca,caindex,x,box);
 338       xf[efhPPRMS].val = pprms(xf[efhPPRMS].fp2,nres,bb);
 339
 340       for(j=0; (j<=efhCPHI); j++)
 341         fprintf(xf[j].fp,   "%10g  %10g\n",t,xf[j].val);
 342
 343       av_phipsi(xf[efhPHI].fp,xf[efhPSI].fp,xf[efhPHI].fp2,xf[efhPSI].fp2,
 344                 t,nres,bb);
 345       av_hblen(xf[efhHB3].fp,xf[efhHB3].fp2,
 346                xf[efhHB4].fp,xf[efhHB4].fp2,
 347                xf[efhHB5].fp,xf[efhHB5].fp2,
 348                t,nres,bb);
 349
 350       if (otrj)
 351         dump_otrj(otrj,nall,allindex,x,xf[nSel].val,xav);
 352     }
 353   } while (read_next_x(status,&t,natoms,x,box));
 354   fprintf(stderr,"\n");
 355
 356   close_trj(status);
 357
 358   if (otrj) {
 359     fclose(otrj);
 360     fac=1.0/teller;
 361     for(i=0; (i<nall); i++) {
 362       ai=allindex[i];
 363       for(m=0; (m<DIM); m++)
 364         xav[ai][m]*=fac;
 365     }
 366     write_sto_conf_indexed(opt2fn("-co",NFILE,fnm),
 367                            "Weighted and Averaged conformation",
 368                            &(top->atoms),xav,NULL,box,nall,allindex);
 369   }
 370
 371   for(i=0; (i<nres); i++) {
 372     if (bb[i].nrms > 0) {
 373       fprintf(xf[efhRMSA].fp,"%10d  %10g\n",r0+i,bb[i].rmsa/bb[i].nrms);
 374     }
 375     fprintf(xf[efhAHX].fp,"%10d  %10g\n",r0+i,(bb[i].nhx*100.0)/(real )teller);
 376     fprintf(xf[efhJCA].fp,"%10d  %10g\n",
 377             r0+i,140.3+(bb[i].jcaha/(double)teller));
 378   }
 379
 380   for(i=0; (i<efhNR); i++) {
 381     fclose(xf[i].fp);
 382     if (xf[i].bfp2)
 383       fclose(xf[i].fp2);
 384     do_view(xf[i].filenm,"-nxy");
 385   }
 386
 387   thanx(stderr);
 388
 389   return 0;
 390 }
 391