static void pr_html_files(FILE *out, int nfile, t_filenm fnm[],
const char *program, t_linkdata *links, gmx_bool bWiki)
{
int i;
char link[10], tmp[255];
if (bWiki)
{
fprintf(out, " %-10s %-12s %-12s %-s\n"
" -----------------------------------------------------\n",
"Option", "Filename", "Type", "Description");
}
else
{
fprintf(out,
"<TABLE BORDER=1 CELLSPACING=0 CELLPADDING=2>\n"
"<TR>"
"<TH>option</TH>"
"<TH>filename</TH>"
"<TH>type</TH>"
"<TH>description</TH>"
"</TR>\n");
}
for (i = 0; (i < nfile); i++)
{
strcpy(link, ftp2ext(fnm[i].ftp));
if (strcmp(link, "???") == 0)
{
strcpy(link, "files");
}
if (bWiki)
{
fprintf(out, " %-10s %-16s %-12s %-s\n",
fnm[i].opt,
NWR(fnm[i].fns[0]),
fileopt(fnm[i].flag, tmp, 255),
NWR(ftp2desc(fnm[i].ftp)));
}
else
{
fprintf(out,
"<TR>"
"<TD ALIGN=RIGHT> <b><tt>%s</tt></b> </TD>"
"<TD ALIGN=RIGHT> <tt><a href=\"%s.html\">%12s</a></tt> </TD>"
"<TD> %s </TD>"
"<TD> %s </TD>"
"</TR>\n",
fnm[i].opt, link, fnm[i].fns[0], fileopt(fnm[i].flag, tmp, 255),
NSR(ftp2desc(fnm[i].ftp)));
}
}
if (!bWiki)
{
fprintf(out, "</TABLE>\n");
}
}
static void write_texman(FILE *out,const char *program,
int nldesc,const char **desc,
int nfile,t_filenm *fnm,
int npargs,t_pargs *pa,
int nbug,const char **bugs,
t_linkdata *links)
{
int i;
char tmp[256];
fprintf(out,"\\section{\\normindex{%s}}\\label{%s}\n\n",check_tex(program),check_tex(program));
if (nldesc > 0)
for(i=0; (i<nldesc); i++)
fprintf(out,"%s\n",check_tex(desc[i]));
if (nfile > 0) {
fprintf(out,"\\vspace{-2ex}\\begin{tabbing}\n");
fprintf(out,"\n{\\normalsize \\bf Files}\\nopagebreak\\\\\n");
fprintf(out,"{\\tt ~~~~~~~} \\= {\\tt ~~~~~~~~~~~~~~} \\= "
"~~~~~~~~~~~~~~~~~~~~~~ \\= \\nopagebreak\\kill\n");
for(i=0; (i<nfile); i++)
fprintf(out,"\\>{\\tt %s} \\'\\> {\\tt %s} \\' %s \\> "
"\\parbox[t]{0.55\\linewidth}{%s} \\\\\n",
check_tex(fnm[i].opt),check_tex(fnm[i].fns[0]),
check_tex(fileopt(fnm[i].flag,tmp,255)),
check_tex(ftp2desc(fnm[i].ftp)));
fprintf(out,"\\end{tabbing}\\vspace{-4ex}\n");
}
if (npargs > 0) {
fprintf(out,"\\vspace{-2ex}\\begin{tabbing}\n");
fprintf(out,"\n{\\normalsize \\bf Other options}\\nopagebreak\\\\\n");
fprintf(out,"{\\tt ~~~~~~~~~~} \\= vector \\= "
"{\\tt ~~~~~~~} \\= \\nopagebreak\\kill\n");
for(i=0; (i<npargs); i++) {
if (strlen(check_tex(pa_val(&(pa[i]),tmp,255))) <= 8)
fprintf(out,"\\> {\\tt %s} \\'\\> %s \\'\\> {\\tt %s} \\' "
"\\parbox[t]{0.68\\linewidth}{%s}\\\\\n",
check_tex(pa[i].option),argtp[pa[i].type],
check_tex(pa_val(&(pa[i]),tmp,255)),
check_tex(pa[i].desc));
else
fprintf(out,"\\> {\\tt %s} \\'\\> %s \\'\\>\\\\\n"
"\\> \\'\\> \\'\\> {\\tt %s} \\' "
"\\parbox[t]{0.7\\linewidth}{%s}\\\\\n",
check_tex(pa[i].option),argtp[pa[i].type],
check_tex(pa_val(&(pa[i]),tmp,255)),
check_tex(pa[i].desc));
}
fprintf(out,"\\end{tabbing}\\vspace{-4ex}\n");
}
if (nbug > 0) {
fprintf(out,"\n");
fprintf(out,"\\begin{itemize}\n");
for(i=0; (i<nbug); i++)
fprintf(out,"\\item %s\n",check_tex(bugs[i]));
fprintf(out,"\\end{itemize}\n");
}
/* fprintf(out,"\n\\newpage\n"); */
}
void pr_htmldefs(FILE *fp)
{
int i;
fprintf(fp,"<title>GROMACS</title>\n");
fprintf(fp,"<h1>GROMACS Files</h1>\n");
fprintf(fp,"<b>GRO</b>ningen <b>MA</b>chine for <b>S</b>imulating <b>C</b>hemistry\n");
fprintf(fp,"<p>\n");
fprintf(fp,"The following %d filetypes are used by Gromacs:\n",efNR);
fprintf(fp,"<dl>\n");
for(i=0; (i<efNR); i++) {
fprintf(fp,"<dt><a href=\"%s.html\">%s.%s</a> (%s)<dd>%s\n",
ftp2ext(i),ftp2defnm(i),ftp2ext(i),ftp2ftype(i),
check_html(ftp2desc(i),NULL));
}
fprintf(fp,"</dl>\n");
}
int main(int argc,char *argv[])
{
const char *desc[] = {
"[TT]do_multiprot[tt] ",
"reads a trajectory file and aligns it to a reference structure ",
"each time frame",
"calling the multiprot program. This allows you to use a reference",
"structure whose sequence is different than that of the protein in the ",
"trajectory, since the alignment is based on the geometry, not sequence.",
"The output of [TT]do_multiprot[tt] includes the rmsd and the number of residues",
"on which it was calculated.",
"[PAR]",
"An aligned trajectory file is generated with the [TT]-ox[tt] option.[PAR]",
"With the [TT]-cr[tt] option, the number of hits in the alignment is given",
"per residue. This number can be between 0 and the number of frames, and",
"indicates the structural conservation of this residue.[PAR]",
"If you do not have the [TT]multiprot[tt] program, get it. [TT]do_multiprot[tt] assumes",
"that the [TT]multiprot[tt] executable is [TT]/usr/local/bin/multiprot[tt]. If this is ",
"not the case, then you should set an environment variable [BB]MULTIPROT[bb]",
"pointing to the [TT]multiprot[tt] executable, e.g.: [PAR]",
"[TT]setenv MULTIPROT /usr/MultiProtInstall/multiprot.Linux[tt][PAR]",
"Note that at the current implementation only binary alignment (your",
"molecule to a reference) is supported. In addition, note that the ",
"by default [TT]multiprot[tt] aligns the two proteins on their C-alpha carbons.",
"and that this depends on the [TT]multiprot[tt] parameters which are not dealt ",
"with here. Thus, the C-alpha carbons is expected to give the same "
"results as choosing the whole protein and will be slightly faster.[PAR]",
"For information about [TT]multiprot[tt], see:",
"http://bioinfo3d.cs.tau.ac.il/MultiProt/.[PAR]"
};
static bool bVerbose;
t_pargs pa[] = {
{ "-v", FALSE, etBOOL, {&bVerbose},
"HIDDENGenerate miles of useless information" }
};
const char *bugs[] = {
"The program is very slow, since multiprot is run externally"
};
t_trxstatus *status;
t_trxstatus *trxout=NULL;
FILE *tapein,*fo,*frc,*tmpf,*out=NULL,*fres=NULL;
const char *fnRef;
const char *fn="2_sol.res";
t_topology top;
int ePBC;
t_atoms *atoms,ratoms,useatoms;
t_trxframe fr;
t_pdbinfo p;
int nres,nres2,nr0;
real t;
int i,j,natoms,nratoms,nframe=0,model_nr=-1;
int cur_res,prev_res;
int nout;
t_countres *countres=NULL;
matrix box,rbox;
int gnx;
char *grpnm,*ss_str;
atom_id *index;
rvec *xp,*x,*xr;
char pdbfile[32],refpdb[256],title[256],rtitle[256],filemode[5];
char out_title[256];
char multiprot[256],*mptr;
int ftp;
int outftp=-1;
real rmsd;
bool bTrjout,bCountres;
const char *TrjoutFile=NULL;
output_env_t oenv;
static rvec translation={0,0,0},rotangles={0,0,0};
gmx_rmpbc_t gpbc=NULL;
t_filenm fnm[] = {
{ efTRX, "-f", NULL, ffREAD },
{ efTPS, NULL, NULL, ffREAD },
{ efNDX, NULL, NULL, ffOPTRD },
{ efSTX, "-r", NULL , ffREAD },
{ efXVG, "-o", "rmss", ffWRITE },
{ efXVG, "-rc", "rescount", ffWRITE},
{ efXVG, "-cr", "countres", ffOPTWR},
{ efTRX, "-ox", "aligned", ffOPTWR }
};
#define NFILE asize(fnm)
CopyRight(stderr,argv[0]);
parse_common_args(&argc,argv,PCA_CAN_TIME | PCA_CAN_VIEW | PCA_TIME_UNIT,
NFILE,fnm, asize(pa),pa, asize(desc),desc,
asize(bugs),bugs,&oenv
);
fnRef=opt2fn("-r",NFILE,fnm);
bTrjout = opt2bSet("-ox",NFILE,fnm);
bCountres= opt2bSet("-cr",NFILE,fnm);
if (bTrjout) {
TrjoutFile = opt2fn_null("-ox",NFILE,fnm);
}
read_tps_conf(ftp2fn(efTPS,NFILE,fnm),title,&top,&ePBC,&xp,NULL,box,FALSE);
gpbc = gmx_rmpbc_init(&top.idef,ePBC,top.atoms.nr,box);
atoms=&(top.atoms);
ftp=fn2ftp(fnRef);
get_stx_coordnum(fnRef,&nratoms);
init_t_atoms(&ratoms,nratoms,TRUE);
snew(xr,nratoms);
read_stx_conf(fnRef,rtitle,&ratoms,xr,NULL,&ePBC,rbox);
if (bVerbose) {
fprintf(stderr,"Read %d atoms\n",atoms->nr);
fprintf(stderr,"Read %d reference atoms\n",ratoms.nr);
}
if (bCountres) {
snew(countres,ratoms.nres);
j=0;
cur_res=0;
for (i=0;i<ratoms.nr;i++) {
prev_res=cur_res;
cur_res=ratoms.atom[i].resind;
if (cur_res != prev_res) {
countres[j].resnr=cur_res;
countres[j].count=0;
j++;
}
}
}
get_index(atoms,ftp2fn_null(efNDX,NFILE,fnm),1,&gnx,&index,&grpnm);
nres=0;
nr0=-1;
for(i=0; (i<gnx); i++) {
if (atoms->atom[index[i]].resind != nr0) {
nr0=atoms->atom[index[i]].resind;
nres++;
}
}
fprintf(stderr,"There are %d residues in your selected group\n",nres);
strcpy(pdbfile,"ddXXXXXX");
gmx_tmpnam(pdbfile);
if ((tmpf = fopen(pdbfile,"w")) == NULL) {
sprintf(pdbfile,"%ctmp%cfilterXXXXXX",DIR_SEPARATOR,DIR_SEPARATOR);
gmx_tmpnam(pdbfile);
if ((tmpf = fopen(pdbfile,"w")) == NULL) {
gmx_fatal(FARGS,"Can not open tmp file %s",pdbfile);
}
}
else {
gmx_ffclose(tmpf);
}
if (ftp != efPDB) {
strcpy(refpdb,"ddXXXXXX");
gmx_tmpnam(refpdb);
strcat(refpdb,".pdb");
write_sto_conf(refpdb,rtitle,&ratoms,xr,NULL,ePBC,rbox);
}
else {
strcpy(refpdb,fnRef);
}
if ((mptr=getenv("MULTIPROT")) == NULL) {
mptr="/usr/local/bin/multiprot";
}
if (!gmx_fexist(mptr)) {
gmx_fatal(FARGS,"MULTIPROT executable (%s) does not exist (use setenv MULTIPROT)",
mptr);
}
sprintf (multiprot,"%s %s %s > /dev/null %s",
mptr, refpdb, pdbfile, "2> /dev/null");
if (bVerbose)
fprintf(stderr,"multiprot cmd='%s'\n",multiprot);
if (!read_first_frame(oenv,&status,ftp2fn(efTRX,NFILE,fnm),&fr,TRX_READ_X))
gmx_fatal(FARGS,"Could not read a frame from %s",ftp2fn(efTRX,NFILE,fnm));
natoms = fr.natoms;
if (bTrjout) {
nout=natoms;
/* open file now */
outftp=fn2ftp(TrjoutFile);
if (bVerbose)
fprintf(stderr,"Will write %s: %s\n",ftp2ext(ftp),ftp2desc(outftp));
strcpy(filemode,"w");
switch (outftp) {
case efXTC:
case efG87:
case efTRR:
case efTRJ:
out=NULL;
trxout = open_trx(TrjoutFile,filemode);
break;
case efGRO:
case efG96:
case efPDB:
/* Make atoms struct for output in GRO or PDB files */
/* get memory for stuff to go in pdb file */
init_t_atoms(&useatoms,nout,FALSE);
sfree(useatoms.resinfo);
useatoms.resinfo=atoms->resinfo;
for(i=0;(i<nout);i++) {
useatoms.atomname[i]=atoms->atomname[i];
useatoms.atom[i]=atoms->atom[i];
useatoms.nres=max(useatoms.nres,useatoms.atom[i].resind+1);
}
useatoms.nr=nout;
out=gmx_ffopen(TrjoutFile,filemode);
break;
}
}
if (natoms > atoms->nr) {
gmx_fatal(FARGS,"\nTrajectory does not match topology!");
}
if (gnx > natoms) {
gmx_fatal(FARGS,"\nTrajectory does not match selected group!");
}
fo = xvgropen(opt2fn("-o",NFILE,fnm),"RMSD","Time (ps)","RMSD (nm)",oenv);
frc = xvgropen(opt2fn("-rc",NFILE,fnm),"Number of Residues in the alignment","Time (ps)","Residues",oenv);
do {
t = output_env_conv_time(oenv,fr.time);
gmx_rmpbc(gpbc,natoms,fr.box,fr.x);
tapein=gmx_ffopen(pdbfile,"w");
write_pdbfile_indexed(tapein,NULL,atoms,fr.x,ePBC,fr.box,' ',-1,gnx,index,NULL,TRUE);
gmx_ffclose(tapein);
system(multiprot);
remove(pdbfile);
process_multiprot_output(fn, &rmsd, &nres2,rotangles,translation,bCountres,countres);
fprintf(fo,"%12.7f",t);
fprintf(fo," %12.7f\n",rmsd);
fprintf(frc,"%12.7f",t);
fprintf(frc,"%12d\n",nres2);
if (bTrjout) {
rotate_conf(natoms,fr.x,NULL,rotangles[XX],rotangles[YY],rotangles[ZZ]);
for(i=0; i<natoms; i++) {
rvec_inc(fr.x[i],translation);
}
switch(outftp) {
case efTRJ:
case efTRR:
case efG87:
case efXTC:
write_trxframe(trxout,&fr,NULL);
break;
case efGRO:
case efG96:
case efPDB:
sprintf(out_title,"Generated by do_multiprot : %s t= %g %s",
title,output_env_conv_time(oenv,fr.time),output_env_get_time_unit(oenv));
switch(outftp) {
case efGRO:
write_hconf_p(out,out_title,&useatoms,prec2ndec(fr.prec),
fr.x,NULL,fr.box);
break;
case efPDB:
fprintf(out,"REMARK GENERATED BY DO_MULTIPROT\n");
sprintf(out_title,"%s t= %g %s",title,output_env_conv_time(oenv,fr.time),output_env_get_time_unit(oenv));
/* if reading from pdb, we want to keep the original
model numbering else we write the output frame
number plus one, because model 0 is not allowed in pdb */
if (ftp==efPDB && fr.step > model_nr) {
model_nr = fr.step;
}
else {
model_nr++;
}
write_pdbfile(out,out_title,&useatoms,fr.x,ePBC,fr.box,' ',model_nr,NULL,TRUE);
break;
case efG96:
fr.title = out_title;
fr.bTitle = (nframe == 0);
fr.bAtoms = FALSE;
fr.bStep = TRUE;
fr.bTime = TRUE;
write_g96_conf(out,&fr,-1,NULL);
}
break;
}
}
nframe++;
} while(read_next_frame(oenv,status,&fr));
if (bCountres) {
fres= xvgropen(opt2fn("-cr",NFILE,fnm),"Number of frames in which the residues are aligned to","Residue","Number",oenv);
for (i=0;i<ratoms.nres;i++) {
fprintf(fres,"%10d %12d\n",countres[i].resnr,countres[i].count);
}
gmx_ffclose(fres);
}
gmx_ffclose(fo);
gmx_ffclose(frc);
fprintf(stderr,"\n");
close_trj(status);
if (trxout != NULL) {
close_trx(trxout);
}
else if (out != NULL) {
gmx_ffclose(out);
}
view_all(oenv,NFILE, fnm);
sfree(xr);
if (bCountres) {
sfree(countres);
}
free_t_atoms(&ratoms,TRUE);
if (bTrjout) {
if (outftp==efPDB || outftp==efGRO || outftp==efG96) {
free_t_atoms(&useatoms,TRUE);
}
}
gmx_thanx(stderr);
return 0;
}
static void write_xmlman(FILE *out,
const char *program,
int nldesc,const char **desc,
int nfile,t_filenm *fnm,
int npargs,t_pargs *pa,
int nbug,const char **bugs,
t_linkdata *links)
{
int i;
char link[10],buf[256],opt[10];
#define NSR2(s) check_xml(s,program,links)
#define FLAG(w,f) (((w) & (f))==(f))
fprintf(out,"<gromacs-manual version=\"%s\" date=\"%s\" www=\"http://www.gromacs.org\">\n",GromacsVersion(),mydate(buf,255,FALSE));
/* fprintf(out,"<LINK rel=stylesheet href=\"style.css\" type=\"text/css\">\n"); */
fprintf(out,"<program name=\"%s\">",program);
if (nldesc > 0) {
fprintf(out,"\n<description>\n<par>\n");
for(i=0; (i<nldesc); i++)
fprintf(out,"%s\n",NSR2(desc[i]));
}
fprintf(out,"</par>\n</description>\n");
if (nfile > 0) {
fprintf(out,"\n<files>\n");
for(i=0; (i<nfile); i++) {
strcpy(link,ftp2ext(fnm[i].ftp));
if (strcmp(link,"???")==0)
strcpy(link,"files");
if (fnm[i].opt[0]=='-') strcpy(opt,fnm[i].opt+1);
else strcpy(opt,fnm[i].opt);
fprintf(out,
"<file type=\"%s\" typeid=\"%d\">\n"
"\t<flags read=\"%d\" write=\"%d\" optional=\"%d\"/>\n"
"\t<option>%s</option>\n"
"\t<default-name link=\"%s.html\">%s</default-name>\n"
"\t<description>%s</description>\n"
"</file>\n",
ftp2defnm(fnm[i].ftp), /* from gmxlib/filenm.c */
fnm[i].ftp,
FLAG(fnm[i].flag,ffREAD), FLAG(fnm[i].flag,ffWRITE), FLAG(fnm[i].flag,ffOPT),
opt,link,fnm[i].fn,/*fileopt(fnm[i].flag),*/
NSR(ftp2desc(fnm[i].ftp)));
}
fprintf(out,"</files>\n");
}
if (npargs > 0) {
fprintf(out,"\n<options>\n");
for(i=0; (i<npargs); i++)
fprintf(out,
"<option type=\"%s\" hidden=\"%d\">\n"
"\t<name >%s</name>\n"
"\t<default-value>%s</default-value>\n"
"\t<description>%s</description>\n"
"</option>\n",
argtp[pa[i].type], is_hidden(&pa[i]),
pa[i].option+1, /* +1 - with no trailing '-' */
pa_val(&(pa[i]),buf,255),pa[i].desc); /*argtp[pa[i].type],*/
fprintf(out,"</options>\n");
}
if (nbug > 0) {
fprintf(out,"\n<bugs>\n");
for(i=0; (i<nbug); i++)
fprintf(out,"\t<bug>%s</bug>\n",NSR(bugs[i]));
fprintf(out,"</bugs>\n");
}
fprintf(out,"\n</program>\n</gromacs-manual>\n");
#undef FLAG
}
static void write_nroffman(FILE *out,
const char *program,
int nldesc,const char **desc,
int nfile,t_filenm *fnm,
int npargs,t_pargs *pa,
int nbug,const char **bugs,
t_linkdata *links)
{
int i;
char tmp[256];
fprintf(out,".TH %s 1 \"%s\" \"\" \"GROMACS suite, %s\"\n",program,mydate(tmp,255,FALSE),GromacsVersion());
fprintf(out,".SH NAME\n");
fprintf(out,"%s\n",program);
fprintf(out,".B %s\n",GromacsVersion());
fprintf(out,".SH SYNOPSIS\n");
fprintf(out,"\\f3%s\\fP\n",program);
/* command line arguments */
if (nfile > 0) {
for(i=0; (i<nfile); i++)
fprintf(out,".BI \"%s\" \" %s \"\n",check_nroff(fnm[i].opt),
check_nroff(fnm[i].fns[0]));
}
if (npargs > 0) {
for(i=0; (i<npargs); i++)
if (pa[i].type == etBOOL)
fprintf(out,".BI \"\\-[no]%s\" \"\"\n",check_nroff(pa[i].option+1));
else
fprintf(out,".BI \"%s\" \" %s \"\n",check_nroff(pa[i].option),
check_nroff(argtp[pa[i].type]));
}
/* description */
if (nldesc > 0) {
fprintf(out,".SH DESCRIPTION\n");
for(i=0; (i<nldesc); i++)
fprintf(out,"\\&%s\n",check_nroff(desc[i]));
}
/* FILES */
if (nfile > 0) {
fprintf(out,".SH FILES\n");
for(i=0; (i<nfile); i++)
fprintf(out,".BI \"%s\" \" %s\" \n.B %s\n %s \n\n",
check_nroff(fnm[i].opt),
check_nroff(fnm[i].fns[0]),
check_nroff(fileopt(fnm[i].flag,tmp,255)),
check_nroff(ftp2desc(fnm[i].ftp)));
}
/* other options */
fprintf(out,".SH OTHER OPTIONS\n");
if ( npargs > 0 ) {
for(i=0; (i<npargs); i++) {
if (pa[i].type == etBOOL)
fprintf(out,".BI \"\\-[no]%s\" \"%s\"\n %s\n\n",
check_nroff(pa[i].option+1),
check_nroff(pa_val(&(pa[i]),tmp,255)),
check_nroff(pa[i].desc));
else
fprintf(out,".BI \"%s\" \" %s\" \" %s\" \n %s\n\n",
check_nroff(pa[i].option),
check_nroff(argtp[pa[i].type]),
check_nroff(pa_val(&(pa[i]),tmp,255)),
check_nroff(pa[i].desc));
}
}
if (nbug > 0) {
fprintf(out,".SH KNOWN PROBLEMS\n");
for(i=0; (i<nbug); i++)
fprintf(out,"\\- %s\n\n",check_nroff(bugs[i]));
}
fprintf(out,".SH SEE ALSO\n.BR gromacs(7)\n\n");
fprintf(out,"More information about \\fBGROMACS\\fR is available at <\\fIhttp://www.gromacs.org/\\fR>.\n");
}
static void write_htmlman(FILE *out,
char *program,
int nldesc,char **desc,
int nfile,t_filenm *fnm,
int npargs,t_pargs *pa,
int nbug,char **bugs)
{
int i;
char link[10];
#define NSR(s) check_html(s,program)
fprintf(out,"<HTML>\n<HEAD>\n<TITLE>%s</TITLE>\n",program);
fprintf(out,"<LINK rel=stylesheet href=\"style.css\" type=\"text/css\">\n");
fprintf(out,"<BODY text=\"#000000\" bgcolor=\"#FFFFFF\" link=\"#0000FF\" vlink=\"#990000\" alink=\"#FF0000\">\n");
fprintf(out,"<TABLE WIDTH=\"98%%\" NOBORDER >\n<TR><TD WIDTH=400>\n");
fprintf(out,"<TABLE WIDTH=400 NOBORDER>\n<TD WIDTH=116>\n");
fprintf(out,"<a href=\"http://www.gromacs.org/\">"
"<img SRC=\"../images/gmxlogo_small.jpg\""
"BORDER=0 height=133 width=116></a></td>\n");
fprintf(out,"<td ALIGN=LEFT VALIGN=TOP WIDTH=280>"
"<br><h2>%s</h2>",program);
fprintf(out,"<font size=-1><A HREF=\"../online.html\">Main Table of Contents</A></font><br>");
fprintf(out,"<br></td>\n</TABLE></TD><TD WIDTH=\"*\" ALIGN=RIGHT VALIGN=BOTTOM><p><B>%s<br>\n",GromacsVersion());
fprintf(out,"%s</B></td></tr></TABLE>\n<HR>\n",mydate());
if (nldesc > 0) {
fprintf(out,"<H3>Description</H3>\n<p>\n");
for(i=0; (i<nldesc); i++)
fprintf(out,"%s\n",NSR(desc[i]));
}
if (nfile > 0) {
fprintf(out,"<P>\n");
fprintf(out,"<H3>Files</H3>\n");
fprintf(out,
"<TABLE BORDER=1 CELLSPACING=0 CELLPADDING=2>\n"
"<TR>"
"<TH>option</TH>"
"<TH>filename</TH>"
"<TH>type</TH>"
"<TH>description</TH>"
"</TR>\n");
for(i=0; (i<nfile); i++) {
strcpy(link,ftp2ext(fnm[i].ftp));
if (strcmp(link,"???")==0)
strcpy(link,"files");
fprintf(out,
"<TR>"
"<TD ALIGN=RIGHT> <b><tt>%s</tt></b> </TD>"
"<TD ALIGN=RIGHT> <tt><a href=\"%s.html\">%12s</a></tt> </TD>"
"<TD> %s </TD>"
"<TD> %s </TD>"
"</TR>\n",
fnm[i].opt,link,fnm[i].fn,fileopt(fnm[i].flag),
NSR(ftp2desc(fnm[i].ftp)));
}
fprintf(out,"</TABLE>\n");
}
if (npargs > 0) {
fprintf(out,"<P>\n");
fprintf(out,"<H3>Other options</H3>\n");
fprintf(out,
"<TABLE BORDER=1 CELLSPACING=0 CELLPADDING=2>\n"
"<TR>"
"<TH>option</TH>"
"<TH>type</TH>"
"<TH>default</TH>"
"<TH>description</TH>"
"</TR>\n");
for(i=0; (i<npargs); i++)
fprintf(out,
"<TR>"
"<TD ALIGN=RIGHT> <b><tt>%s%s</tt></b> </TD>"
"<TD ALIGN=RIGHT> %s </TD>"
"<TD ALIGN=RIGHT> <tt>%s</tt> </TD>"
"<TD> %s </TD>"
"</TD>\n",
(pa[i].type == etBOOL)?"-[no]":"-",pa[i].option+1,
argtp[pa[i].type],pa_val(&(pa[i])),NSR(pa[i].desc));
fprintf(out,"</TABLE>\n");
}
if (nbug > 0) {
fprintf(out,"<P>\n");
fprintf(out,"<UL>\n");
for(i=0; (i<nbug); i++)
fprintf(out,"<LI>%s\n",NSR(bugs[i]));
fprintf(out,"</UL>\n");
}
fprintf(out,"<P>\n");
fprintf(out,"<hr>\n<div ALIGN=RIGHT>\n");
fprintf(out,"<font size=\"-1\"><a href=\"http://www.gromacs.org\">"
"http://www.gromacs.org</a></font><br>\n");
fprintf(out,"</div>\n");
fprintf(out,"</BODY>\n");
}
static void write_nroffman(FILE *out,
char *program,
int nldesc,char **desc,
int nfile,t_filenm *fnm,
int npargs,t_pargs *pa,
int nbug,char **bugs)
{
int i;
fprintf(out,".TH %s 1 \"%s\"\n",program,mydate());
fprintf(out,".SH NAME\n");
fprintf(out,"%s\n",program);
fprintf(out,".B %s\n",GromacsVersion());
fprintf(out,".SH SYNOPSIS\n");
fprintf(out,"\\f3%s\\fP\n",program);
/* command line arguments */
if (nfile > 0) {
for(i=0; (i<nfile); i++)
fprintf(out,".BI \"%s\" \" %s \"\n",fnm[i].opt,
fnm[i].fn);
}
if (npargs > 0) {
for(i=0; (i<npargs); i++)
if (pa[i].type == etBOOL)
fprintf(out,".BI \"-[no]%s\" \"\"\n",pa[i].option+1);
else
fprintf(out,".BI \"%s\" \" %s \"\n",pa[i].option,
argtp[pa[i].type]);
}
/* description */
if (nldesc > 0) {
fprintf(out,".SH DESCRIPTION\n");
for(i=0; (i<nldesc); i++)
fprintf(out,"%s\n",check_nroff(desc[i]));
}
/* FILES */
if (nfile > 0) {
fprintf(out,".SH FILES\n");
for(i=0; (i<nfile); i++)
fprintf(out,".BI \"%s\" \" %s\" \n.B %s\n %s \n\n",
fnm[i].opt,fnm[i].fn,fileopt(fnm[i].flag),
check_nroff(ftp2desc(fnm[i].ftp)));
}
/* other options */
fprintf(out,".SH OTHER OPTIONS\n");
if ( npargs > 0 ) {
for(i=0; (i<npargs); i++) {
if (pa[i].type == etBOOL)
fprintf(out,".BI \"-[no]%s\" \"%s\"\n %s\n\n",
check_nroff(pa[i].option+1),
pa_val(&(pa[i])),check_nroff(pa[i].desc));
else
fprintf(out,".BI \"%s\" \" %s\" \" %s\" \n %s\n\n",
check_nroff(pa[i].option),argtp[pa[i].type],
pa_val(&(pa[i])),check_nroff(pa[i].desc));
}
}
if (nbug > 0) {
for(i=0; (i<nbug); i++)
fprintf(out,"\\- %s\n\n",check_nroff(bugs[i]));
}
}