src/kernel/g_protonate.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 3.2.0
  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
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  33  * Gallium Rubidium Oxygen Manganese Argon Carbon Silicon
  34  */
  35 #ifdef HAVE_CONFIG_H
  36 #include <config.h>
  37 #endif
  38
  39 #include <math.h>
  40 #include "typedefs.h"
  41 #include "macros.h"
  42 #include "copyrite.h"
  43 #include "smalloc.h"
  44 #include "statutil.h"
  45 #include "confio.h"
  46 #include "genhydro.h"
  47 #include "tpxio.h"
  48 #include "index.h"
  49 #include "vec.h"
  50 #include "hackblock.h"
  51
  52 int main (int argc,char *argv[])
  53 {
  54   const char *desc[] = {
  55     "[TT]protonate[tt] reads (a) conformation(s) and adds all missing",
  56     "hydrogens as defined in [TT]ffgmx2.hdb[tt]. If only [TT]-s[tt] is",
  57     "specified, this conformation will be protonated, if also [TT]-f[tt]",
  58     "is specified, the conformation(s) will be read from this file",
  59     "which can be either a single conformation or a trajectory.",
  60     "[PAR]",
  61     "If a pdb file is supplied, residue names might not correspond to",
  62     "to the GROMACS naming conventions, in which case these residues will",
  63     "probably not be properly protonated.",
  64     "[PAR]",
  65     "If an index file is specified, please note that the atom numbers",
  66     "should correspond to the [BB]protonated[bb] state."
  67   };
  68
  69   char        title[STRLEN+1];
  70   const char  *infile;
  71   char        *grpnm;
  72   t_topology  top;
  73   int         ePBC;
  74   t_atoms     *atoms,*iatoms;
  75   t_protonate protdata;
  76   atom_id     *index;
  77   t_trxstatus *status;
  78   t_trxstatus *out;
  79   t_trxframe  fr,frout;
  80   rvec        *x,*ix;
  81   int         nidx,natoms,natoms_out;
  82   matrix      box;
  83   int         i,frame,resind;
  84   gmx_bool        bReadMultiple;
  85   output_env_t oenv;
  86
  87   t_filenm fnm[] = {
  88     { efTPS, NULL, NULL,         ffREAD  },
  89     { efTRX, "-f", NULL,         ffOPTRD },
  90     { efNDX, NULL, NULL,         ffOPTRD },
  91     { efTRO, "-o", "protonated", ffWRITE }
  92   };
  93 #define NFILE asize(fnm)
  94
  95   CopyRight(stderr,argv[0]);
  96   parse_common_args(&argc,argv,PCA_CAN_TIME,
  97                     NFILE,fnm,0,NULL,asize(desc),desc,0,NULL,&oenv);
  98
  99   infile=opt2fn("-s",NFILE,fnm);
 100   read_tps_conf(infile,title,&top,&ePBC,&x,NULL,box,FALSE);
 101   atoms=&(top.atoms);
 102   printf("Select group to process:\n");
 103   get_index(atoms,ftp2fn_null(efNDX,NFILE,fnm),1,&nidx,&index,&grpnm);
 104   bReadMultiple = opt2bSet("-f",NFILE,fnm);
 105   if (bReadMultiple) {
 106     infile = opt2fn("-f",NFILE,fnm);
 107     if ( !read_first_frame(oenv,&status, infile, &fr, TRX_NEED_X ) )
 108       gmx_fatal(FARGS,"cannot read coordinate file %s",infile);
 109     natoms = fr.natoms;
 110   } else {
 111     clear_trxframe(&fr,TRUE);
 112     fr.natoms = atoms->nr;
 113     fr.bTitle = TRUE;
 114     fr.title  = title;
 115     fr.bX     = TRUE;
 116     fr.x      = x;
 117     fr.bBox   = TRUE;
 118     copy_mat(box, fr.box);
 119     natoms = fr.natoms;
 120   }
 121
 122   /* check input */
 123   if ( natoms == 0 )
 124     gmx_fatal(FARGS,"no atoms in coordinate file %s",infile);
 125   if ( natoms > atoms->nr )
 126     gmx_fatal(FARGS,"topology with %d atoms does not match "
 127                 "coordinates with %d atoms",atoms->nr,natoms);
 128   for(i=0; i<nidx; i++)
 129     if (index[i] > natoms)
 130       gmx_fatal(FARGS,"An atom number in group %s is larger than the number of "
 131                   "atoms (%d) in the coordinate file %s",grpnm,natoms,infile);
 132
 133   /* get indexed copy of atoms */
 134   snew(iatoms,1);
 135   init_t_atoms(iatoms,nidx,FALSE);
 136   snew(iatoms->atom, iatoms->nr);
 137   resind = 0;
 138   for(i=0; i<nidx; i++) {
 139     iatoms->atom[i] = atoms->atom[index[i]];
 140     iatoms->atomname[i] = atoms->atomname[index[i]];
 141     if ( i>0 && (atoms->atom[index[i]].resind!=atoms->atom[index[i-1]].resind) )
 142       resind++;
 143     iatoms->atom[i].resind = resind;
 144     iatoms->resinfo[resind] = atoms->resinfo[atoms->atom[index[i]].resind];
 145     iatoms->nres = max(iatoms->nres, iatoms->atom[i].resind+1);
 146   }
 147
 148   init_t_protonate(&protdata);
 149
 150   out = open_trx(opt2fn("-o",NFILE,fnm),"w");
 151   snew(ix, nidx);
 152   frame=0;
 153   do {
 154     if (debug) fprintf(debug,"FRAME %d (%d %g)\n",frame,fr.step,fr.time);
 155     /* get indexed copy of x */
 156     for(i=0; i<nidx; i++)
 157       copy_rvec(fr.x[index[i]], ix[i]);
 158     /* protonate */
 159     natoms_out = protonate(&iatoms, &ix, &protdata);
 160
 161     /* setup output frame */
 162     frout = fr;
 163     frout.natoms = natoms_out;
 164     frout.bAtoms = TRUE;
 165     frout.atoms  = iatoms;
 166     frout.bV     = FALSE;
 167     frout.bF     = FALSE;
 168     frout.x      = ix;
 169
 170     /* write output */
 171     write_trxframe(out,&frout,NULL);
 172     frame++;
 173   } while ( bReadMultiple && read_next_frame(oenv,status, &fr) );
 174
 175   thanx(stderr);
 176
 177   return 0;
 178 }
 179