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Add -tu option to g_hbond.
author
Justin Lemkul
<jalemkul@vt.edu>
Wed, 16 Feb 2011 15:38:39 +0000
(10:38 -0500)
committer
Justin Lemkul
<jalemkul@vt.edu>
Wed, 16 Feb 2011 15:38:39 +0000
(10:38 -0500)
IssueID #580
src/tools/gmx_hbond.c
patch
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blob
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diff --git
a/src/tools/gmx_hbond.c
b/src/tools/gmx_hbond.c
index 5f04157f4f8c2b8a3c442b944e9725dd56d77a91..dad3df7e47f6f4cc37b748a3cf1ec1c389409a3c 100644
(file)
--- a/
src/tools/gmx_hbond.c
+++ b/
src/tools/gmx_hbond.c
@@
-1823,9
+1823,9
@@
static void do_hblife(const char *fn,t_hbdata *hb,gmx_bool bMerge,gmx_bool bCont
}
fprintf(stderr,"\n");
if (bContact)
}
fprintf(stderr,"\n");
if (bContact)
- fp = xvgropen(fn,"Uninterrupted contact lifetime",
"Time (ps)"
,"()",oenv);
+ fp = xvgropen(fn,"Uninterrupted contact lifetime",
output_env_get_xvgr_tlabel(oenv)
,"()",oenv);
else
else
- fp = xvgropen(fn,"Uninterrupted hydrogen bond lifetime",
"Time (ps)"
,"()",
+ fp = xvgropen(fn,"Uninterrupted hydrogen bond lifetime",
output_env_get_xvgr_tlabel(oenv)
,"()",
oenv);
xvgr_legend(fp,asize(leg),leg,oenv);
oenv);
xvgr_legend(fp,asize(leg),leg,oenv);
@@
-2501,7
+2501,7
@@
static void do_hbac(const char *fn,t_hbdata *hb,
/* printf("\nNumber of data points is less than the number of parameters to fit\n." */
/* "The system is underdetermined, hence no ballistic term can be found.\n\n"); */
/* printf("\nNumber of data points is less than the number of parameters to fit\n." */
/* "The system is underdetermined, hence no ballistic term can be found.\n\n"); */
- fp = xvgropen(fn, "Hydrogen Bond Autocorrelation",
"Time (ps)"
,"C(t)");
+ fp = xvgropen(fn, "Hydrogen Bond Autocorrelation",
output_env_get_xvgr_tlabel(oenv)
,"C(t)");
xvgr_legend(fp,asize(legNN),legNN);
for(j=0; (j<nn); j++)
xvgr_legend(fp,asize(legNN),legNN);
for(j=0; (j<nn); j++)
@@
-2738,9
+2738,9
@@
static void do_hbac(const char *fn,t_hbdata *hb,
if (bContact)
if (bContact)
- fp = xvgropen(fn, "Contact Autocorrelation",
"Time (ps)"
,"C(t)",oenv);
+ fp = xvgropen(fn, "Contact Autocorrelation",
output_env_get_xvgr_tlabel(oenv)
,"C(t)",oenv);
else
else
- fp = xvgropen(fn, "Hydrogen Bond Autocorrelation",
"Time (ps)"
,"C(t)",oenv);
+ fp = xvgropen(fn, "Hydrogen Bond Autocorrelation",
output_env_get_xvgr_tlabel(oenv)
,"C(t)",oenv);
xvgr_legend(fp,asize(legGem),(const char**)legGem,oenv);
for(j=0; (j<nn); j++)
xvgr_legend(fp,asize(legGem),(const char**)legGem,oenv);
for(j=0; (j<nn); j++)
@@
-2877,9
+2877,9
@@
static void do_hbac(const char *fn,t_hbdata *hb,
if (bContact)
if (bContact)
- fp = xvgropen(fn, "Contact Autocorrelation",
"Time (ps)"
,"C(t)",oenv);
+ fp = xvgropen(fn, "Contact Autocorrelation",
output_env_get_xvgr_tlabel(oenv)
,"C(t)",oenv);
else
else
- fp = xvgropen(fn, "Hydrogen Bond Autocorrelation",
"Time (ps)"
,"C(t)",oenv);
+ fp = xvgropen(fn, "Hydrogen Bond Autocorrelation",
output_env_get_xvgr_tlabel(oenv)
,"C(t)",oenv);
xvgr_legend(fp,asize(legLuzar),legLuzar, oenv);
xvgr_legend(fp,asize(legLuzar),legLuzar, oenv);
@@
-2939,7
+2939,7
@@
static void analyse_donor_props(const char *fn,t_hbdata *hb,int nframes,real t,
if (!fn)
return;
if (!fp) {
if (!fn)
return;
if (!fp) {
- fp = xvgropen(fn,"Donor properties",
"Time (ps)"
,"Number",oenv);
+ fp = xvgropen(fn,"Donor properties",
output_env_get_xvgr_tlabel(oenv)
,"Number",oenv);
xvgr_legend(fp,asize(leg),leg,oenv);
}
nbound = 0;
xvgr_legend(fp,asize(leg),leg,oenv);
}
nbound = 0;
@@
-3265,7
+3265,7
@@
int gmx_hbond(int argc,char *argv[])
npargs = asize(pa);
ppa = add_acf_pargs(&npargs,pa);
npargs = asize(pa);
ppa = add_acf_pargs(&npargs,pa);
- parse_common_args(&argc,argv,PCA_CAN_TIME | PCA_BE_NICE,NFILE,fnm,npargs,
+ parse_common_args(&argc,argv,PCA_CAN_TIME | PCA_
TIME_UNIT | PCA_
BE_NICE,NFILE,fnm,npargs,
ppa,asize(desc),desc,asize(bugs),bugs,&oenv);
/* NN-loop? If so, what estimator to use ?*/
ppa,asize(desc),desc,asize(bugs),bugs,&oenv);
/* NN-loop? If so, what estimator to use ?*/
@@
-3363,7
+3363,7
@@
int gmx_hbond(int argc,char *argv[])
if (opt2bSet("-nhbdist",NFILE,fnm)) {
const char *leg[MAXHH+1] = { "0 HBs", "1 HB", "2 HBs", "3 HBs", "Total" };
fpnhb = xvgropen(opt2fn("-nhbdist",NFILE,fnm),
if (opt2bSet("-nhbdist",NFILE,fnm)) {
const char *leg[MAXHH+1] = { "0 HBs", "1 HB", "2 HBs", "3 HBs", "Total" };
fpnhb = xvgropen(opt2fn("-nhbdist",NFILE,fnm),
- "Number of donor-H with N HBs",
"Time (ps)"
,"N",oenv);
+ "Number of donor-H with N HBs",
output_env_get_xvgr_tlabel(oenv)
,"N",oenv);
xvgr_legend(fpnhb,asize(leg),leg,oenv);
}
xvgr_legend(fpnhb,asize(leg),leg,oenv);
}
@@
-3649,7
+3649,7
@@
int gmx_hbond(int argc,char *argv[])
dump_grid(debug, ngrid, grid);
add_frames(hb,nframes);
dump_grid(debug, ngrid, grid);
add_frames(hb,nframes);
- init_hbframe(hb,nframes,
t
);
+ init_hbframe(hb,nframes,
output_env_conv_time(oenv,t)
);
if (hb->bDAnr)
count_da_grid(ngrid, grid, hb->danr[nframes]);
if (hb->bDAnr)
count_da_grid(ngrid, grid, hb->danr[nframes]);
@@
-3930,7
+3930,7
@@
int gmx_hbond(int argc,char *argv[])
aver_nhb = 0;
aver_dist = 0;
fp = xvgropen(opt2fn("-num",NFILE,fnm),bContact ? "Contacts" :
aver_nhb = 0;
aver_dist = 0;
fp = xvgropen(opt2fn("-num",NFILE,fnm),bContact ? "Contacts" :
- "Hydrogen Bonds",
"Time"
,"Number",oenv);
+ "Hydrogen Bonds",
output_env_get_xvgr_tlabel(oenv)
,"Number",oenv);
snew(leg,2);
snew(leg[0],STRLEN);
snew(leg[1],STRLEN);
snew(leg,2);
snew(leg[0],STRLEN);
snew(leg[1],STRLEN);
@@
-3983,7
+3983,7
@@
int gmx_hbond(int argc,char *argv[])
/* Print HB in alpha-helix */
if (opt2bSet("-hx",NFILE,fnm)) {
fp = xvgropen(opt2fn("-hx",NFILE,fnm),
/* Print HB in alpha-helix */
if (opt2bSet("-hx",NFILE,fnm)) {
fp = xvgropen(opt2fn("-hx",NFILE,fnm),
- "Hydrogen Bonds",
"Time(ps)"
,"Count",oenv);
+ "Hydrogen Bonds",
output_env_get_xvgr_tlabel(oenv)
,"Count",oenv);
xvgr_legend(fp,NRHXTYPES,hxtypenames,oenv);
for(i=0; i<nframes; i++) {
fprintf(fp,"%10g",hb->time[i]);
xvgr_legend(fp,NRHXTYPES,hxtypenames,oenv);
for(i=0; i<nframes; i++) {
fprintf(fp,"%10g",hb->time[i]);
@@
-4064,7
+4064,7
@@
int gmx_hbond(int argc,char *argv[])
sprintf(mat.title,bContact ? "Contact Existence Map":
"Hydrogen Bond Existence Map");
sprintf(mat.legend,bContact ? "Contacts" : "Hydrogen Bonds");
sprintf(mat.title,bContact ? "Contact Existence Map":
"Hydrogen Bond Existence Map");
sprintf(mat.legend,bContact ? "Contacts" : "Hydrogen Bonds");
- sprintf(mat.label_x,
"Time (ps)"
);
+ sprintf(mat.label_x,
output_env_get_xvgr_tlabel(oenv)
);
sprintf(mat.label_y, bContact ? "Contact Index" : "Hydrogen Bond Index");
mat.bDiscrete=TRUE;
mat.nmap=2;
sprintf(mat.label_y, bContact ? "Contact Index" : "Hydrogen Bond Index");
mat.bDiscrete=TRUE;
mat.nmap=2;
@@
-4115,7
+4115,7
@@
int gmx_hbond(int argc,char *argv[])
#define USE_THIS_GROUP(j) ( (j == gr0) || (bTwo && (j == gr1)) )
fp = xvgropen(opt2fn("-dan",NFILE,fnm),
#define USE_THIS_GROUP(j) ( (j == gr0) || (bTwo && (j == gr1)) )
fp = xvgropen(opt2fn("-dan",NFILE,fnm),
- "Donors and Acceptors",
"Time(ps)"
,"Count",oenv);
+ "Donors and Acceptors",
output_env_get_xvgr_tlabel(oenv)
,"Count",oenv);
nleg = (bTwo?2:1)*2;
snew(legnames,nleg);
i=0;
nleg = (bTwo?2:1)*2;
snew(legnames,nleg);
i=0;