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