src/contrib/do_multiprot.c

   1 /* -*- mode: c; tab-width: 4; indent-tabs-mode: nil; c-basic-offset: 4; c-file-style: "stroustrup"; -*-
   2  *
   3  *                This source code is NOT REALLY part of
   4  *
   5  *                 G   R   O   M   A   C   S
   6  *
   7  *          GROningen MAchine for Chemical Simulations
   8  *
   9  *                        VERSION 4.2.5
  10  * Written by David van der Spoel, Erik Lindahl, Berk Hess, and others.
  11  * Copyright (c) 1991-2000, University of Groningen, The Netherlands.
  12  * Copyright (c) 2001-2004, The GROMACS development team,
  13  * check out http://www.gromacs.org for more information.
  14
  15  * This program is free software; you can redistribute it and/or
  16  * modify it under the terms of the GNU General Public License
  17  * as published by the Free Software Foundation; either version 2
  18  * of the License, or (at your option) any later version.
  19  *
  20  * If you want to redistribute modifications, please consider that
  21  * scientific software is very special. Version control is crucial -
  22  * bugs must be traceable. We will be happy to consider code for
  23  * inclusion in the official distribution, but derived work must not
  24  * be called official GROMACS. Details are found in the README & COPYING
  25  * files - if they are missing, get the official version at www.gromacs.org.
  26  *
  27  * To help us fund GROMACS development, we humbly ask that you cite
  28  * the papers on the package - you can find them in the top README file.
  29  *
  30  * For more info, check our website at http://www.gromacs.org
  31  *
  32  * Author: do_multiprot was written by Ran Friedman <r.friedman@bioc.uzh.ch>
  33  *
  34  * And Hey:
  35  * Green Red Orange Magenta Azure Cyan Skyblue
  36  */
  37
  38 #ifdef HAVE_CONFIG_H
  39 #include <config.h>
  40 #endif
  41
  42 #include "typedefs.h"
  43 #include "macros.h"
  44 #include "gromacs/utility/smalloc.h"
  45 #include "gromacs/commandline/pargs.h"
  46 #include "copyrite.h"
  47 #include "gromacs/fileio/pdbio.h"
  48 #include "gromacs/utility/fatalerror.h"
  49 #include "gromacs/fileio/xvgr.h"
  50 #include "gromacs/topology/index.h"
  51 #include "gstat.h"
  52 #include "gromacs/fileio/tpxio.h"
  53 #include "viewit.h"
  54 #include "gbutil.h"
  55 #include "gromacs/math/vec.h"
  56 #include "gromacs/fileio/confio.h"
  57 #include "gromacs/fileio/gmxfio.h"
  58
  59 typedef struct {
  60     int resnr;
  61     int count;
  62 } t_countres;
  63
  64 static void process_multiprot_output(const char *fn, real *rmsd, int *nres, rvec rotangles,
  65                                      rvec translation, bool bCountres, t_countres *countres)
  66 {
  67     FILE       *mpoutput;
  68     char       line[256];
  69     char       *string;
  70     int        i=0,j=0,res;
  71
  72     (*rmsd)=-1;
  73     (*nres)=0;
  74     mpoutput=gmx_ffopen (fn,"r");
  75
  76     if (bCountres) {
  77         do {
  78             fgets(line, 256, mpoutput);
  79         } while (strstr(line,"Match List") == NULL);
  80         fgets(line, 256, mpoutput);
  81         do {
  82             string = strtok (line,".");
  83             while (i<2 && string != NULL) {
  84                 string = strtok (NULL,". ");
  85                 i++;
  86             }
  87             i=0;
  88             res=atoi(string);
  89             if (res > 0) {
  90                 while (countres[j].resnr!=res)
  91                     j++;
  92                 countres[j].count++;
  93             }
  94             fgets(line, 256, mpoutput);
  95         } while (strstr(line,"End of Match List") == NULL);
  96         rewind(mpoutput);
  97     }
  98     do {
  99         fgets(line, 256, mpoutput);
 100     } while (strstr(line,"Trans : ") == NULL);
 101
 102     string = strtok (line," :");
 103     string = strtok (NULL," ");
 104     while (i<3 && string != NULL) {
 105         string = strtok (NULL," ");
 106         rotangles[i]=atof(string);
 107         i++;
 108     }
 109     i=0;
 110     while (i<3 && string != NULL) {
 111         string = strtok (NULL," ");
 112         translation[i]=atof(string)/10;
 113         i++;
 114     }
 115     if (i!=3) {
 116         gmx_warning("Not enough values for rotation and translation vectors in the output of multiprot");
 117     }
 118
 119     rotangles[YY]=rotangles[YY]*(-1);
 120
 121     while ((*rmsd) <0) {
 122         fgets(line, 256, mpoutput);
 123         if (strstr(line,"RMSD : ") != NULL) {
 124             string = strtok (line,":");
 125             string = strtok (NULL,":");
 126             (*rmsd)=atof(string)/10;
 127         }
 128     }
 129     while (!(*nres)) {
 130         fgets(line,256, mpoutput);
 131         if (strstr(line,"Match List") != NULL) {
 132             string = strtok (line,":");
 133             string = strtok (NULL,":");
 134             (*nres) = atoi(string);
 135         }
 136     }
 137     gmx_ffclose(mpoutput);
 138 }
 139
 140 int main(int argc,char *argv[])
 141 {
 142     const char *desc[] = {
 143         "[TT]do_multiprot[tt] ",
 144         "reads a trajectory file and aligns it to a reference structure  ",
 145         "each time frame",
 146         "calling the multiprot program. This allows you to use a reference",
 147         "structure whose sequence is different than that of the protein in the ",
 148         "trajectory, since the alignment is based on the geometry, not sequence.",
 149         "The output of [TT]do_multiprot[tt] includes the rmsd and the number of residues",
 150         "on which it was calculated.",
 151         "[PAR]",
 152         "An aligned trajectory file is generated with the [TT]-ox[tt] option.[PAR]",
 153         "With the [TT]-cr[tt] option, the number of hits in the alignment is given",
 154         "per residue. This number can be between 0 and the number of frames, and",
 155         "indicates the structural conservation of this residue.[PAR]",
 156         "If you do not have the [TT]multiprot[tt] program, get it. [TT]do_multiprot[tt] assumes",
 157         "that the [TT]multiprot[tt] executable is [TT]/usr/local/bin/multiprot[tt]. If this is ",
 158         "not the case, then you should set an environment variable [BB]MULTIPROT[bb]",
 159         "pointing to the [TT]multiprot[tt] executable, e.g.: [PAR]",
 160         "[TT]setenv MULTIPROT /usr/MultiProtInstall/multiprot.Linux[tt][PAR]",
 161         "Note that at the current implementation only binary alignment (your",
 162         "molecule to a reference) is supported. In addition, note that the ",
 163         "by default [TT]multiprot[tt] aligns the two proteins on their C-alpha carbons.",
 164         "and that this depends on the [TT]multiprot[tt] parameters which are not dealt ",
 165         "with here. Thus, the C-alpha carbons is expected to give the same "
 166         "results as choosing the whole protein and will be slightly faster.[PAR]",
 167         "For information about [TT]multiprot[tt], see:",
 168         "http://bioinfo3d.cs.tau.ac.il/MultiProt/.[PAR]"
 169     };
 170     static bool bVerbose;
 171     t_pargs pa[] = {
 172         { "-v",  FALSE, etBOOL, {&bVerbose},
 173           "HIDDENGenerate miles of useless information" }
 174     };
 175
 176     const char *bugs[] = {
 177         "The program is very slow, since multiprot is run externally"
 178     };
 179
 180     t_trxstatus *status;
 181     t_trxstatus *trxout=NULL;
 182     FILE        *tapein,*fo,*frc,*tmpf,*out=NULL,*fres=NULL;
 183     const char  *fnRef;
 184     const char  *fn="2_sol.res";
 185     t_topology  top;
 186     int         ePBC;
 187     t_atoms     *atoms,ratoms,useatoms;
 188     t_trxframe  fr;
 189     t_pdbinfo   p;
 190     int         nres,nres2,nr0;
 191     real        t;
 192     int         i,j,natoms,nratoms,nframe=0,model_nr=-1;
 193     int         cur_res,prev_res;
 194     int         nout;
 195     t_countres  *countres=NULL;
 196     matrix      box,rbox;
 197     int         gnx;
 198     char        *grpnm,*ss_str;
 199     atom_id     *index;
 200     rvec        *xp,*x,*xr;
 201     char        pdbfile[32],refpdb[256],title[256],rtitle[256],filemode[5];
 202     char        out_title[256];
 203     char        multiprot[256],*mptr;
 204     int         ftp;
 205     int         outftp=-1;
 206     real        rmsd;
 207     bool        bTrjout,bCountres;
 208     const char  *TrjoutFile=NULL;
 209     output_env_t oenv;
 210     static rvec translation={0,0,0},rotangles={0,0,0};
 211     gmx_rmpbc_t gpbc=NULL;
 212
 213     t_filenm   fnm[] = {
 214         { efTRX, "-f",   NULL,      ffREAD },
 215         { efTPS, NULL,   NULL,      ffREAD },
 216         { efNDX, NULL,   NULL,      ffOPTRD },
 217         { efSTX, "-r",   NULL     , ffREAD },
 218         { efXVG, "-o",  "rmss",     ffWRITE },
 219         { efXVG, "-rc", "rescount", ffWRITE},
 220         { efXVG, "-cr", "countres", ffOPTWR},
 221         { efTRX, "-ox", "aligned",  ffOPTWR }
 222     };
 223 #define NFILE asize(fnm)
 224
 225     CopyRight(stderr,argv[0]);
 226     parse_common_args(&argc,argv,PCA_CAN_TIME | PCA_CAN_VIEW | PCA_TIME_UNIT,
 227                       NFILE,fnm, asize(pa),pa, asize(desc),desc,
 228                       asize(bugs),bugs,&oenv
 229         );
 230     fnRef=opt2fn("-r",NFILE,fnm);
 231     bTrjout = opt2bSet("-ox",NFILE,fnm);
 232     bCountres=  opt2bSet("-cr",NFILE,fnm);
 233
 234     if (bTrjout) {
 235         TrjoutFile = opt2fn_null("-ox",NFILE,fnm);
 236     }
 237
 238     read_tps_conf(ftp2fn(efTPS,NFILE,fnm),title,&top,&ePBC,&xp,NULL,box,FALSE);
 239     gpbc = gmx_rmpbc_init(&top.idef,ePBC,top.atoms.nr,box);
 240     atoms=&(top.atoms);
 241
 242     ftp=fn2ftp(fnRef);
 243
 244     get_stx_coordnum(fnRef,&nratoms);
 245     init_t_atoms(&ratoms,nratoms,TRUE);
 246     snew(xr,nratoms);
 247     read_stx_conf(fnRef,rtitle,&ratoms,xr,NULL,&ePBC,rbox);
 248
 249     if (bVerbose) {
 250         fprintf(stderr,"Read %d atoms\n",atoms->nr);
 251         fprintf(stderr,"Read %d reference atoms\n",ratoms.nr);
 252     }
 253     if (bCountres) {
 254         snew(countres,ratoms.nres);
 255         j=0;
 256         cur_res=0;
 257         for (i=0;i<ratoms.nr;i++) {
 258             prev_res=cur_res;
 259             cur_res=ratoms.atom[i].resind;
 260             if (cur_res != prev_res) {
 261                 countres[j].resnr=cur_res;
 262                 countres[j].count=0;
 263                 j++;
 264             }
 265         }
 266     }
 267     get_index(atoms,ftp2fn_null(efNDX,NFILE,fnm),1,&gnx,&index,&grpnm);
 268     nres=0;
 269     nr0=-1;
 270     for(i=0; (i<gnx); i++) {
 271         if (atoms->atom[index[i]].resind != nr0) {
 272             nr0=atoms->atom[index[i]].resind;
 273             nres++;
 274         }
 275     }
 276     fprintf(stderr,"There are %d residues in your selected group\n",nres);
 277
 278     strcpy(pdbfile,"ddXXXXXX");
 279     gmx_tmpnam(pdbfile);
 280     if ((tmpf = fopen(pdbfile,"w")) == NULL) {
 281         sprintf(pdbfile,"%ctmp%cfilterXXXXXX",DIR_SEPARATOR,DIR_SEPARATOR);
 282         gmx_tmpnam(pdbfile);
 283         if ((tmpf = fopen(pdbfile,"w")) == NULL) {
 284             gmx_fatal(FARGS,"Can not open tmp file %s",pdbfile);
 285         }
 286     }
 287     else {
 288         gmx_ffclose(tmpf);
 289     }
 290
 291     if (ftp != efPDB) {
 292         strcpy(refpdb,"ddXXXXXX");
 293         gmx_tmpnam(refpdb);
 294         strcat(refpdb,".pdb");
 295         write_sto_conf(refpdb,rtitle,&ratoms,xr,NULL,ePBC,rbox);
 296     }
 297     else {
 298         strcpy(refpdb,fnRef);
 299     }
 300
 301     if ((mptr=getenv("MULTIPROT")) == NULL) {
 302         mptr="/usr/local/bin/multiprot";
 303     }
 304     if (!gmx_fexist(mptr)) {
 305         gmx_fatal(FARGS,"MULTIPROT executable (%s) does not exist (use setenv MULTIPROT)",
 306                   mptr);
 307     }
 308     sprintf (multiprot,"%s %s %s > /dev/null %s",
 309              mptr, refpdb, pdbfile, "2> /dev/null");
 310
 311     if (bVerbose)
 312         fprintf(stderr,"multiprot cmd='%s'\n",multiprot);
 313
 314     if (!read_first_frame(oenv,&status,ftp2fn(efTRX,NFILE,fnm),&fr,TRX_READ_X))
 315         gmx_fatal(FARGS,"Could not read a frame from %s",ftp2fn(efTRX,NFILE,fnm));
 316     natoms = fr.natoms;
 317
 318     if (bTrjout) {
 319         nout=natoms;
 320         /* open file now */
 321         outftp=fn2ftp(TrjoutFile);
 322         if (bVerbose)
 323             fprintf(stderr,"Will write %s: %s\n",ftp2ext(ftp),ftp2desc(outftp));
 324         strcpy(filemode,"w");
 325         switch (outftp) {
 326             case efXTC:
 327             case efG87:
 328             case efTRR:
 329             case efTRJ:
 330                 out=NULL;
 331                 trxout = open_trx(TrjoutFile,filemode);
 332                 break;
 333             case efGRO:
 334             case efG96:
 335             case efPDB:
 336                 /* Make atoms struct for output in GRO or PDB files */
 337                 /* get memory for stuff to go in pdb file */
 338                 init_t_atoms(&useatoms,nout,FALSE);
 339                 sfree(useatoms.resinfo);
 340                 useatoms.resinfo=atoms->resinfo;
 341                 for(i=0;(i<nout);i++) {
 342                     useatoms.atomname[i]=atoms->atomname[i];
 343                     useatoms.atom[i]=atoms->atom[i];
 344                     useatoms.nres=max(useatoms.nres,useatoms.atom[i].resind+1);
 345                 }
 346                 useatoms.nr=nout;
 347                 out=gmx_ffopen(TrjoutFile,filemode);
 348                 break;
 349         }
 350     }
 351
 352     if (natoms > atoms->nr) {
 353         gmx_fatal(FARGS,"\nTrajectory does not match topology!");
 354     }
 355     if (gnx > natoms) {
 356         gmx_fatal(FARGS,"\nTrajectory does not match selected group!");
 357     }
 358
 359     fo = xvgropen(opt2fn("-o",NFILE,fnm),"RMSD","Time (ps)","RMSD (nm)",oenv);
 360     frc = xvgropen(opt2fn("-rc",NFILE,fnm),"Number of Residues in the alignment","Time (ps)","Residues",oenv);
 361
 362     do {
 363         t = output_env_conv_time(oenv,fr.time);
 364         gmx_rmpbc(gpbc,natoms,fr.box,fr.x);
 365         tapein=gmx_ffopen(pdbfile,"w");
 366         write_pdbfile_indexed(tapein,NULL,atoms,fr.x,ePBC,fr.box,' ',-1,gnx,index,NULL,TRUE);
 367         gmx_ffclose(tapein);
 368         system(multiprot);
 369         remove(pdbfile);
 370         process_multiprot_output(fn, &rmsd, &nres2,rotangles,translation,bCountres,countres);
 371         fprintf(fo,"%12.7f",t);
 372         fprintf(fo," %12.7f\n",rmsd);
 373         fprintf(frc,"%12.7f",t);
 374         fprintf(frc,"%12d\n",nres2);
 375         if (bTrjout) {
 376             rotate_conf(natoms,fr.x,NULL,rotangles[XX],rotangles[YY],rotangles[ZZ]);
 377             for(i=0; i<natoms; i++) {
 378                 rvec_inc(fr.x[i],translation);
 379             }
 380             switch(outftp) {
 381                 case efTRJ:
 382                 case efTRR:
 383                 case efG87:
 384                 case efXTC:
 385                     write_trxframe(trxout,&fr,NULL);
 386                     break;
 387                 case efGRO:
 388                 case efG96:
 389                 case efPDB:
 390                     sprintf(out_title,"Generated by do_multiprot : %s t= %g %s",
 391                             title,output_env_conv_time(oenv,fr.time),output_env_get_time_unit(oenv));
 392                     switch(outftp) {
 393                         case efGRO:
 394                             write_hconf_p(out,out_title,&useatoms,prec2ndec(fr.prec),
 395                                           fr.x,NULL,fr.box);
 396                             break;
 397                         case efPDB:
 398                             fprintf(out,"REMARK    GENERATED BY DO_MULTIPROT\n");
 399                             sprintf(out_title,"%s t= %g %s",title,output_env_conv_time(oenv,fr.time),output_env_get_time_unit(oenv));
 400                             /* if reading from pdb, we want to keep the original
 401                                model numbering else we write the output frame
 402                                number plus one, because model 0 is not allowed in pdb */
 403                             if (ftp==efPDB && fr.step > model_nr) {
 404                                 model_nr = fr.step;
 405                             }
 406                             else {
 407                                 model_nr++;
 408                             }
 409                             write_pdbfile(out,out_title,&useatoms,fr.x,ePBC,fr.box,' ',model_nr,NULL,TRUE);
 410                             break;
 411                         case efG96:
 412                             fr.title = out_title;
 413                             fr.bTitle = (nframe == 0);
 414                             fr.bAtoms = FALSE;
 415                             fr.bStep = TRUE;
 416                             fr.bTime = TRUE;
 417                             write_g96_conf(out,&fr,-1,NULL);
 418                     }
 419                     break;
 420             }
 421         }
 422         nframe++;
 423     } while(read_next_frame(oenv,status,&fr));
 424     if (bCountres) {
 425         fres=  xvgropen(opt2fn("-cr",NFILE,fnm),"Number of frames in which the residues are aligned to","Residue","Number",oenv);
 426         for (i=0;i<ratoms.nres;i++) {
 427             fprintf(fres,"%10d  %12d\n",countres[i].resnr,countres[i].count);
 428         }
 429         gmx_ffclose(fres);
 430     }
 431     gmx_ffclose(fo);
 432     gmx_ffclose(frc);
 433     fprintf(stderr,"\n");
 434     close_trj(status);
 435     if (trxout != NULL) {
 436         close_trx(trxout);
 437     }
 438     else if (out != NULL) {
 439         gmx_ffclose(out);
 440     }
 441     view_all(oenv,NFILE, fnm);
 442     sfree(xr);
 443     if (bCountres) {
 444         sfree(countres);
 445     }
 446     free_t_atoms(&ratoms,TRUE);
 447     if (bTrjout) {
 448         if (outftp==efPDB || outftp==efGRO || outftp==efG96) {
 449             free_t_atoms(&useatoms,TRUE);
 450         }
 451     }
 452     gmx_thanx(stderr);
 453     return 0;
 454 }