src/tools/gmx_helix.c

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