src/local/mkyaw.c

   1 /*
   2  * $Id$
   3  *
   4  *       This source code is part of
   5  *
   6  *        G   R   O   M   A   C   S
   7  *
   8  * GROningen MAchine for Chemical Simulations
   9  *
  10  *               VERSION 2.0
  11  *
  12  * Copyright (c) 1991-1999
  13  * BIOSON Research Institute, Dept. of Biophysical Chemistry
  14  * University of Groningen, The Netherlands
  15  *
  16  * Please refer to:
  17  * GROMACS: A message-passing parallel molecular dynamics implementation
  18  * H.J.C. Berendsen, D. van der Spoel and R. van Drunen
  19  * Comp. Phys. Comm. 91, 43-56 (1995)
  20  *
  21  * Also check out our WWW page:
  22  * http://md.chem.rug.nl/~gmx
  23  * or e-mail to:
  24  * gromacs@chem.rug.nl
  25  *
  26  * And Hey:
  27  * Great Red Oystrich Makes All Chemists Sane
  28  */
  29 static char *SRCID_mkyaw_c = "$Id$";
  30
  31 #include <math.h>
  32 #include <string.h>
  33 #include <ctype.h>
  34 #include "pdbio.h"
  35 #include "confio.h"
  36 #include "symtab.h"
  37 #include "smalloc.h"
  38 #include "symtab.h"
  39 #include "macros.h"
  40 #include "copyrite.h"
  41 #include "statutil.h"
  42 #include "string2.h"
  43 #include "strdb.h"
  44 #include "rdgroup.h"
  45 #include "vec.h"
  46 #include "typedefs.h"
  47 #include "gbutil.h"
  48 #include "strdb.h"
  49 #include "rdgroup.h"
  50 #include "physics.h"
  51 #include "atomprop.h"
  52
  53 void copy_atom(t_symtab *tab,t_atoms *a1,int i1,t_atoms *a2,int i2,
  54                rvec xin[],rvec xout[],rvec vin[],rvec vout[])
  55 {
  56   a2->atom[i2]     = a1->atom[i1];
  57   a2->atomname[i2] = put_symtab(tab,*a1->atomname[i1]);
  58   a2->resname[a2->atom[i2].resnr] =
  59     put_symtab(tab,*a1->resname[a1->atom[i1].resnr]);
  60   copy_rvec(xin[i1],xout[i2]);
  61   copy_rvec(vin[i1],vout[i2]);
  62 }
  63
  64 int main(int argc, char *argv[])
  65 {
  66   t_symtab tab;
  67   static char *desc[] = {
  68     "mkyaw adds to an existing conf file for every OW atom an DW and SW",
  69     "after the hydrogens (or the inverse with the -back option)."
  70   };
  71   static bool bBack = FALSE;
  72   t_pargs pa[] = {
  73     { "-back",   FALSE, etBOOL, &bBack,
  74       "Remove SW and DW" }
  75   };
  76 #define NPA asize(pa)
  77   t_filenm fnm[] = {
  78     { efSTX, "-f", NULL, ffREAD },
  79     { efSTO, "-o", NULL, ffWRITE }
  80   };
  81 #define NFILE asize(fnm)
  82   int  i,iout,now,natom;
  83   rvec *xin,*vin,*xout,*vout;
  84   matrix box;
  85   t_atoms atoms,aout;
  86   char *infile,*outfile,title[256];
  87
  88   CopyRight(stderr,argv[0]);
  89   parse_common_args(&argc,argv,0,FALSE,NFILE,fnm,NPA,pa,
  90                     asize(desc),desc,0,NULL);
  91
  92   infile  = ftp2fn(efSTX,NFILE,fnm);
  93   outfile = ftp2fn(efSTO,NFILE,fnm);
  94
  95   get_stx_coordnum(infile,&natom);
  96   init_t_atoms(&atoms,natom,TRUE);
  97   snew(xin,natom);
  98   snew(vin,natom);
  99   read_stx_conf(infile,title,&atoms,xin,vin,box);
 100   printf("Read %d atoms\n",atoms.nr);
 101   open_symtab(&tab);
 102   if (!bBack) {
 103     now = 0;
 104     for(i=0; (i<natom-2); ) {
 105       if ((strstr(*atoms.atomname[i],"OW")   != NULL) &&
 106           (strstr(*atoms.atomname[i+1],"HW") != NULL) &&
 107           (strstr(*atoms.atomname[i+2],"HW") != NULL)) {
 108         now++;
 109         i+=3;
 110       }
 111       else
 112         i++;
 113     }
 114     fprintf(stderr,"There are %d water molecules\n",now);
 115     init_t_atoms(&aout,natom+2*now,TRUE);
 116     snew(xout,natom+2*now);
 117     snew(vout,natom+2*now);
 118     for(i=iout=0; (i<natom); i++) {
 119       copy_atom(&tab,&atoms,i,&aout,iout,xin,xout,vin,vout);
 120       iout++;
 121       if (i >= 2) {
 122         if (strstr(*atoms.atomname[i-2],"OW") != NULL) {
 123           copy_atom(&tab,&atoms,i-2,&aout,iout,xin,xout,vin,vout);
 124           aout.atomname[iout] = put_symtab(&tab,"DW");
 125           iout++;
 126           copy_atom(&tab,&atoms,i-2,&aout,iout,xin,xout,vin,vout);
 127           aout.atomname[iout] = put_symtab(&tab,"SW");
 128           iout++;
 129         }
 130       }
 131     }
 132     close_symtab(&tab);
 133     fprintf(stderr,"iout = %d\n",iout);
 134     write_sto_conf(outfile,"Gravity Sucks",&aout,xout,vout,box);
 135   }
 136
 137   thanx(stdout);
 138
 139   return 0;
 140 }
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