int gmx_rama(int argc,char *argv[])
{
const char *desc[] = {
"[TT]g_rama[tt] selects the [GRK]phi[grk]/[GRK]psi[grk] dihedral combinations from your topology file",
"and computes these as a function of time.",
"Using simple Unix tools such as [IT]grep[it] you can select out",
"specific residues."
};
FILE *out;
t_xrama *xr;
int j;
output_env_t oenv;
t_filenm fnm[] = {
{ efTRX, "-f", NULL, ffREAD },
{ efTPX, NULL, NULL, ffREAD },
{ efXVG, NULL, "rama",ffWRITE }
};
#define NFILE asize(fnm)
parse_common_args(&argc,argv,PCA_CAN_VIEW | PCA_CAN_TIME | PCA_BE_NICE,
NFILE,fnm,0,NULL,asize(desc),desc,0,NULL,&oenv);
snew(xr,1);
init_rama(oenv,ftp2fn(efTRX,NFILE,fnm),ftp2fn(efTPX,NFILE,fnm),xr,3);
out=xvgropen(ftp2fn(efXVG,NFILE,fnm),"Ramachandran Plot","Phi","Psi",oenv);
xvgr_line_props(out,0,elNone,ecFrank,oenv);
xvgr_view(out,0.2,0.2,0.8,0.8,oenv);
xvgr_world(out,-180,-180,180,180,oenv);
fprintf(out,"@ xaxis tick on\n@ xaxis tick major 60\n@ xaxis tick minor 30\n");
fprintf(out,"@ yaxis tick on\n@ yaxis tick major 60\n@ yaxis tick minor 30\n");
fprintf(out,"@ s0 symbol 2\n@ s0 symbol size 0.4\n@ s0 symbol fill 1\n");
j=0;
do {
plot_rama(out,xr);
j++;
} while (new_data(xr));
fprintf(stderr,"\n");
ffclose(out);
do_view(oenv,ftp2fn(efXVG,NFILE,fnm),NULL);
thanx(stderr);
return 0;
}
int main(int argc, char *argv[])
{
const char *desc[] = {
"[TT]g_xrama[tt] shows a Ramachandran movie, that is, it shows",
"the Phi/Psi angles as a function of time in an X-Window.[PAR]"
"Static Phi/Psi plots for printing can be made with [TT]g_rama[tt].[PAR]",
"Some of the more common X command line options can be used:[BR]",
"[TT]-bg[tt], [TT]-fg[tt] change colors, [TT]-font fontname[tt], changes the font."
};
output_env_t oenv;
t_x11 *x11;
t_topology *ramatop;
t_app *app;
t_filenm fnm[] = {
{ efTRX, "-f", NULL, ffREAD },
{ efTPX, NULL, NULL, ffREAD }
};
#define NFILE asize(fnm)
CopyRight(stderr, argv[0]);
parse_common_args(&argc, argv, PCA_CAN_TIME, NFILE, fnm, 0, NULL,
asize(desc), desc, 0, NULL, &oenv);
if ((x11 = GetX11(&argc, argv)) == NULL)
{
fprintf(stderr, "Can't open display, set your DISPLAY environment variable\n");
exit(1);
}
XSetForeground(x11->disp, x11->gc, x11->fg);
app = init_app(x11, argc, argv);
ramatop = init_rama(oenv, ftp2fn(efTRX, NFILE, fnm), ftp2fn(efTPX, NFILE, fnm),
app->xr, 3);
mk_gly(app);
XMapWindow(x11->disp, app->wd.self);
XMapSubwindows(x11->disp, app->wd.self);
x11->MainLoop(x11);
x11->CleanUp(x11);
thanx(stderr);
return 0;
}
int gmx_dih(int argc,char *argv[])
{
const char *desc[] = {
"g_dih can do two things. The default is to analyze dihedral transitions",
"by merely computing all the dihedral angles defined in your topology",
"for the whole trajectory. When a dihedral flips over to another minimum",
"an angle/time plot is made.[PAR]",
"The opther option is to discretize the dihedral space into a number of",
"bins, and group each conformation in dihedral space in the",
"appropriate bin. The output is then given as a number of dihedral",
"conformations sorted according to occupancy."
};
static int mult = -1;
static bool bSA = FALSE;
t_pargs pa[] = {
{ "-sa", FALSE, etBOOL, {&bSA},
"Perform cluster analysis in dihedral space instead of analysing dihedral transitions." },
{ "-mult", FALSE, etINT, {&mult},
"mulitiplicity for dihedral angles (by default read from topology)" }
};
FILE *out;
t_xrama *xr;
t_topology *top;
real **dih,*time;
real dd;
int i,nframes,maxframes=1000;
t_filenm fnm[] = {
{ efTRX, "-f", NULL, ffREAD },
{ efTPX, NULL, NULL, ffREAD },
{ efOUT, NULL, NULL, ffWRITE }
};
#define NFILE asize(fnm)
CopyRight(stderr,argv[0]);
parse_common_args(&argc,argv,PCA_CAN_VIEW | PCA_CAN_TIME | PCA_BE_NICE,
NFILE,fnm,asize(pa),pa,asize(desc),desc,0,NULL);
if (mult != -1)
fprintf(stderr,"Using %d for dihedral multiplicity rather than topology values\n",mult);
snew(xr,1);
init_rama(ftp2fn(efTRX,NFILE,fnm),
ftp2fn(efTPX,NFILE,fnm),xr,3);
top=read_top(ftp2fn(efTPX,NFILE,fnm),NULL);
/* Brute force malloc, may be too big... */
snew(dih,xr->ndih);
for(i=0; (i<xr->ndih); i++)
snew(dih[i],maxframes);
snew(time,maxframes);
fprintf(stderr,"\n");
nframes = 0;
while (new_data(xr)) {
for(i=0; (i<xr->ndih); i++) {
dd=xr->dih[i].ang*RAD2DEG;
while (dd < 0)
dd+=360;
while (dd > 360)
dd-=360;
dih[i][nframes]=dd;
}
time[nframes]=xr->t;
nframes++;
if (nframes > maxframes) {
maxframes += 1000;
for(i=0; (i<xr->ndih); i++)
srenew(dih[i],maxframes);
srenew(time,maxframes);
}
}
fprintf(stderr,"\nCalculated all dihedrals, now analysing...\n");
out=ftp2FILE(efOUT,NFILE,fnm,"w");
if (bSA) {
/* Cluster and structure analysis */
ana_cluster(out,xr,dih,time,top,nframes,mult);
}
else {
/* Analyse transitions... */
ana_trans(out,xr,dih,time,top,nframes);
}
fclose(out);
thanx(stderr);
return 0;
}
