3 * This source code is part of
7 * GROningen MAchine for Chemical Simulations
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.
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.
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
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33 * Groningen Machine for Chemical Simulation
42 #include "gromacs/utility/cstringutil.h"
44 #include "gromacs/utility/smalloc.h"
45 #include "gromacs/commandline/pargs.h"
47 #include "gromacs/fileio/confio.h"
48 #include "gromacs/utility/fatalerror.h"
49 #include "gromacs/fileio/xvgr.h"
51 #include "gromacs/topology/index.h"
52 #include "gromacs/fileio/pdbio.h"
54 void cat(FILE *out,char *fn,real t)
60 double f1,f2,f3,f4,f5,f6;
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);
69 /*if ((int)strlen(buf) > 0)
70 fprintf(out,"%s\n",buf);*/
75 int main(int argc,char *argv[])
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."
92 { "-dt", FALSE, etREAL, { &dt }, "Time interval between frames." }
94 static char *bugs[] = {
95 "The program is very slow"
97 static char *OXYGEN="O";
103 int i,natoms,nframe=0;
109 char pdbfile[32],tmpfile[32];
110 char total[256],*dptr;
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 }
118 char *leg[] = { "shift","ring","anisCO","anisCN","sigmaE","sum" };
119 #define NFILE asize(fnm)
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);
125 top=read_top(ftp2fn(efTPX,NFILE,fnm));
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);
138 strcpy(pdbfile,"dsXXXXXX");
140 strcpy(tmpfile,"dsXXXXXX");
142 fprintf(stderr,"pdbfile = %s\ntmpfile = %s\n",pdbfile,tmpfile);
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);
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);
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);
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);
170 fprintf(tot,"%s\n",randf);
173 if (pclose(tot) != 0)
174 perror("closing pipe to total");
181 } while(read_next_x(status,&t,natoms,x,box));