src/contrib/do_shift.c

   1 /*
   2  *
   3  *                This source code is part of
   4  *
   5  *                 G   R   O   M   A   C   S
   6  *
   7  *          GROningen MAchine for Chemical Simulations
   8  *
   9  *                        VERSION 3.3.99_development_20071104
  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) 2001-2006, 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  * And Hey:
  33  * Groningen Machine for Chemical Simulation
  34  */
  35 #ifdef HAVE_CONFIG_H
  36 #include <config.h>
  37 #endif
  38
  39 #include <stdlib.h>
  40 #include "errno.h"
  41 #include "typedefs.h"
  42 #include "gromacs/utility/cstringutil.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/confio.h"
  48 #include "gromacs/utility/fatalerror.h"
  49 #include "gromacs/fileio/xvgr.h"
  50 #include "gstat.h"
  51 #include "gromacs/topology/index.h"
  52 #include "gromacs/fileio/pdbio.h"
  53
  54 void cat(FILE *out,char *fn,real t)
  55 {
  56   FILE *in;
  57   char *ptr,buf[256];
  58   int    anr,rnr;
  59   char   anm[24],rnm[24];
  60   double f1,f2,f3,f4,f5,f6;
  61
  62   in=gmx_ffopen(fn,"r");
  63   while ((ptr=fgets2(buf,255,in)) != NULL) {
  64     sscanf(buf,"%d%d%s%s%lf%lf%lf%lf%lf%lf",
  65            &anr,&rnr,rnm,anm,&f1,&f2,&f3,&f4,&f5,&f6);
  66     fprintf(out,"%8g  %10g  %10g  %10g  %10g  %10g  %10g  %s%d-%s%d\n",
  67             t,f6,f1,f2,f3,f4,f5,rnm,rnr,anm,anr);
  68   }
  69   /*if ((int)strlen(buf) > 0)
  70     fprintf(out,"%s\n",buf);*/
  71   fflush(out);
  72   gmx_ffclose(in);
  73 }
  74
  75 int main(int argc,char *argv[])
  76 {
  77   static char *desc[] = {
  78     "[TT]do_shift[tt] reads a trajectory file and computes the chemical",
  79     "shift for each time frame (or every [BB]dt[bb] ps) by",
  80     "calling the 'total' program. If you do not have the total program,",
  81     "get it. do_shift assumes that the total executable is in",
  82     "[TT]/home/mdgroup/total/total[tt]. If that is not the case, then you should",
  83     "set an environment variable [BB]GMX_TOTAL[bb] as in: [PAR]",
  84     "[TT]setenv GMX_TOTAL /usr/local/bin/total[tt][PAR]",
  85     "where the right hand side should point to the total executable.[PAR]",
  86     "Output is printed in files [TT]shift.out[tt] where t is the time of the frame.[PAR]",
  87     "The program also needs an input file called [BB]random.dat[bb] which",
  88     "contains the random coil chemical shifts of all protons."
  89   };
  90   static real dt=0.0;
  91   t_pargs pa[] = {
  92     { "-dt", FALSE, etREAL, { &dt }, "Time interval between frames." }
  93   };
  94   static char *bugs[] = {
  95     "The program is very slow"
  96   };
  97   static     char *OXYGEN="O";
  98   FILE       *out,*tot,*fp;
  99   t_topology *top;
 100   t_atoms    *atoms;
 101   int        status,nres;
 102   real       t,nt;
 103   int        i,natoms,nframe=0;
 104   matrix     box;
 105   int        gnx;
 106   char       *grpnm,*randf;
 107   atom_id    *index;
 108   rvec       *x,*x_s;
 109   char       pdbfile[32],tmpfile[32];
 110   char       total[256],*dptr;
 111   t_filenm   fnm[] = {
 112     { efTRX, "-f",   NULL,     ffREAD },
 113     { efTPX, NULL,   NULL,     ffREAD },
 114     { efNDX, NULL,   NULL,     ffREAD },
 115     { efOUT, "-o",   "shift",  ffWRITE },
 116     { efDAT, "-d",   "random", ffREAD }
 117   };
 118   char *leg[] = { "shift","ring","anisCO","anisCN","sigmaE","sum" };
 119 #define NFILE asize(fnm)
 120
 121   CopyRight(stdout,argv[0]);
 122   parse_common_args(&argc,argv,PCA_CAN_TIME,NFILE,fnm,
 123                     asize(pa),pa,asize(desc),desc,asize(bugs),bugs);
 124
 125   top=read_top(ftp2fn(efTPX,NFILE,fnm));
 126   atoms=&(top->atoms);
 127   nres=atoms->nres;
 128   for(i=0; (i<atoms->nr); i++)
 129     if ((strcmp(*atoms->atomname[i],"O1") == 0) ||
 130         (strcmp(*atoms->atomname[i],"O2") == 0) ||
 131         (strcmp(*atoms->atomname[i],"OXT") == 0) ||
 132         (strcmp(*atoms->atomname[i],"OT") == 0))
 133       atoms->atomname[i]=&OXYGEN;
 134   rd_index(ftp2fn(efNDX,NFILE,fnm),1,&gnx,&index,&grpnm);
 135
 136   snew(x_s,atoms->nr);
 137
 138   strcpy(pdbfile,"dsXXXXXX");
 139   gmx_tmpnam(pdbfile);
 140   strcpy(tmpfile,"dsXXXXXX");
 141   gmx_tmpnam(tmpfile);
 142   fprintf(stderr,"pdbfile = %s\ntmpfile = %s\n",pdbfile,tmpfile);
 143
 144   if ((dptr=getenv("GMX_TOTAL")) == NULL)
 145     dptr="/home/mdgroup/total/total";
 146   sprintf(total,"%s > /dev/null",dptr);
 147   fprintf(stderr,"total cmd='%s'\n",total);
 148   randf=ftp2fn(efDAT,NFILE,fnm);
 149
 150   natoms=read_first_x(&status,ftp2fn(efTRX,NFILE,fnm),&t,&x,box);
 151   if (natoms != atoms->nr)
 152     gmx_fatal(FARGS,"Trajectory does not match topology!");
 153   out=ftp2FILE(efOUT,NFILE,fnm,"w");
 154   xvgr_legend(out,asize(leg),leg);
 155   nt=t;
 156   do {
 157     if (t >= nt) {
 158       rm_pbc(&(top->idef),top->atoms.nr,box,x,x_s);
 159       fp=gmx_ffopen(pdbfile,"w");
 160       write_pdbfile_indexed(fp,"Generated by do_shift",
 161                             atoms,x_s,box,0,-1,gnx,index);
 162       gmx_ffclose(fp);
 163
 164       if ((tot=popen(total,"w")) == NULL)
 165         perror("opening pipe to total");
 166       fprintf(tot,"%s\n",pdbfile);
 167       fprintf(tot,"%s\n",tmpfile);
 168       fprintf(tot,"3\n");
 169       fprintf(tot,"N\n");
 170       fprintf(tot,"%s\n",randf);
 171       fprintf(tot,"N\n");
 172       fprintf(tot,"N\n");
 173       if (pclose(tot) != 0)
 174         perror("closing pipe to total");
 175       cat(out,tmpfile,t);
 176       remove(pdbfile);
 177       remove(tmpfile);
 178       nt+=dt;
 179       nframe++;
 180     }
 181   } while(read_next_x(status,&t,natoms,x,box));
 182   close_trj(status);
 183   gmx_ffclose(out);
 184
 185   gmx_thanx(stderr);
 186
 187   return 0;
 188 }