gmx_bool fflib_fexist(const char *file)
{
char *file_fullpath;
file_fullpath = low_gmxlibfn(file,TRUE,FALSE);
if (file_fullpath == NULL)
{
return FALSE;
}
else
{
sfree(file_fullpath);
return TRUE;
}
}
FILE *low_libopen(const char *file,gmx_bool bFatal)
{
FILE *ff;
char *fn;
fn=low_gmxlibfn(file,TRUE,bFatal);
if (fn==NULL) {
ff=NULL;
} else {
if (debug)
fprintf(debug,"Opening library file %s\n",fn);
ff=fopen(fn,"r");
}
sfree(fn);
return ff;
}
char *gmxlibfn(const char *file)
{
return low_gmxlibfn(file, TRUE, TRUE);
}
/* Open the file to be processed. The handle variable holds internal
info for the cpp emulator. Return integer status */
int cpp_open_file(const char *filenm, gmx_cpp_t *handle, char **cppopts)
{
gmx_cpp_t cpp;
char *buf, *pdum;
char *ptr, *ptr2;
int i;
unsigned int i1;
/* First process options, they might be necessary for opening files
(especially include statements). */
i = 0;
if (cppopts)
{
while (cppopts[i])
{
if (strstr(cppopts[i], "-I") == cppopts[i])
{
add_include(cppopts[i]+2);
}
if (strstr(cppopts[i], "-D") == cppopts[i])
{
/* If the option contains a =, split it into name and value. */
ptr = strchr(cppopts[i], '=');
if (ptr)
{
buf = gmx_strndup(cppopts[i] + 2, ptr - cppopts[i] - 2);
add_define(buf, ptr + 1);
sfree(buf);
}
else
{
add_define(cppopts[i] + 2, NULL);
}
}
i++;
}
}
if (debug)
{
fprintf(debug, "GMXCPP: added %d command line arguments\n", i);
}
snew(cpp, 1);
*handle = cpp;
cpp->fn = NULL;
/* Find the file. First check whether it is in the current directory. */
if (gmx_fexist(filenm))
{
cpp->fn = gmx_strdup(filenm);
}
else
{
/* If not, check all the paths given with -I. */
for (i = 0; i < nincl; ++i)
{
snew(buf, strlen(incl[i]) + strlen(filenm) + 2);
sprintf(buf, "%s/%s", incl[i], filenm);
if (gmx_fexist(buf))
{
cpp->fn = buf;
break;
}
sfree(buf);
}
/* If still not found, check the Gromacs library search path. */
if (!cpp->fn)
{
cpp->fn = low_gmxlibfn(filenm, FALSE, FALSE);
}
}
if (!cpp->fn)
{
gmx_fatal(FARGS, "Topology include file \"%s\" not found", filenm);
}
if (NULL != debug)
{
fprintf(debug, "GMXCPP: cpp file open %s\n", cpp->fn);
}
/* If the file name has a path component, we need to change to that
* directory. Note that we - just as C - always use UNIX path separators
* internally in include file names.
*/
ptr = strrchr(cpp->fn, '/');
ptr2 = strrchr(cpp->fn, DIR_SEPARATOR);
if (ptr == NULL || (ptr2 != NULL && ptr2 > ptr))
{
ptr = ptr2;
}
if (ptr == NULL)
{
cpp->path = NULL;
cpp->cwd = NULL;
}
else
{
cpp->path = cpp->fn;
*ptr = '\0';
cpp->fn = gmx_strdup(ptr+1);
snew(cpp->cwd, STRLEN);
gmx_getcwd(cpp->cwd, STRLEN);
if (NULL != debug)
{
fprintf(debug, "GMXCPP: cwd %s\n", cpp->cwd);
}
gmx_chdir(cpp->path);
if (NULL != debug)
{
fprintf(debug, "GMXCPP: chdir to %s\n", cpp->path);
}
}
cpp->line_len = 0;
cpp->line = NULL;
cpp->line_nr = 0;
cpp->nifdef = 0;
cpp->ifdefs = NULL;
cpp->child = NULL;
cpp->parent = NULL;
if (cpp->fp == NULL)
{
if (NULL != debug)
{
fprintf(debug, "GMXCPP: opening file %s\n", cpp->fn);
}
cpp->fp = fopen(cpp->fn, "r");
}
if (cpp->fp == NULL)
{
switch (errno)
{
case EINVAL:
default:
return eCPP_UNKNOWN;
}
}
return eCPP_OK;
}
void
choose_ff(const char *ffsel,
char *forcefield, int ff_maxlen,
char *ffdir, int ffdir_maxlen)
{
int nff;
char **ffdirs,**ffs,**ffs_dir,*ptr;
int i,j,sel,cwdsel,nfound;
char buf[STRLEN],**desc;
FILE *fp;
char *pret;
nff = fflib_search_file_in_dirend(fflib_forcefield_itp(),
fflib_forcefield_dir_ext(),
&ffdirs);
if (nff == 0)
{
gmx_fatal(FARGS,"No force fields found (files with name '%s' in subdirectories ending on '%s')",
fflib_forcefield_itp(),fflib_forcefield_dir_ext());
}
/* Replace with unix path separators */
if(DIR_SEPARATOR!='/')
{
for(i=0;i<nff;i++)
{
while( (ptr=strchr(ffdirs[i],DIR_SEPARATOR))!=NULL )
{
*ptr='/';
}
}
}
/* Store the force field names in ffs */
snew(ffs,nff);
snew(ffs_dir,nff);
for(i=0; i<nff; i++)
{
/* Remove the path from the ffdir name - use our unix standard here! */
ptr = strrchr(ffdirs[i],'/');
if (ptr == NULL)
{
ffs[i] = strdup(ffdirs[i]);
ffs_dir[i] = low_gmxlibfn(ffdirs[i],FALSE,FALSE);
if (ffs_dir[i] == NULL)
{
gmx_fatal(FARGS,"Can no longer find file '%s'",ffdirs[i]);
}
}
else
{
ffs[i] = strdup(ptr+1);
ffs_dir[i] = strdup(ffdirs[i]);
}
ffs_dir[i][strlen(ffs_dir[i])-strlen(ffs[i])-1] = '\0';
/* Remove the extension from the ffdir name */
ffs[i][strlen(ffs[i])-strlen(fflib_forcefield_dir_ext())] = '\0';
}
if (ffsel != NULL)
{
sel = -1;
cwdsel = -1;
nfound = 0;
for(i=0; i<nff; i++)
{
if ( strcmp(ffs[i],ffsel)==0 )
{
/* Matching ff name */
sel = i;
nfound++;
if( strncmp(ffs_dir[i],".",1)==0 )
{
cwdsel = i;
}
}
}
if(cwdsel != -1)
{
sel = cwdsel;
}
if(nfound>1)
{
if(cwdsel!=-1)
{
fprintf(stderr,
"Force field '%s' occurs in %d places. pdb2gmx is using the one in the\n"
"current directory. Use interactive selection (not the -ff option) if\n"
"you would prefer a different one.\n",ffsel,nfound);
}
else
{
gmx_fatal(FARGS,
"Force field '%s' occurs in %d places, but not in the current directory.\n"
"Run without the -ff switch and select the force field interactively.",ffsel,nfound);
}
}
else if (nfound==0)
{
gmx_fatal(FARGS,"Could not find force field '%s' in current directory, install tree or GMXDATA path.",ffsel);
}
}
else if (nff > 1)
{
snew(desc,nff);
for(i=0; (i<nff); i++)
{
sprintf(buf,"%s%c%s%s%c%s",
ffs_dir[i],DIR_SEPARATOR,
ffs[i],fflib_forcefield_dir_ext(),DIR_SEPARATOR,
fflib_forcefield_doc());
if (gmx_fexist(buf))
{
/* We don't use fflib_open, because we don't want printf's */
fp = ffopen(buf,"r");
snew(desc[i],STRLEN);
get_a_line(fp,desc[i],STRLEN);
ffclose(fp);
}
else
{
desc[i] = strdup(ffs[i]);
}
}
/* Order force fields from the same dir alphabetically
* and put deprecated force fields at the end.
*/
for(i=0; (i<nff); i++)
{
for(j=i+1; (j<nff); j++)
{
if (strcmp(ffs_dir[i],ffs_dir[j]) == 0 &&
((desc[i][0] == '[' && desc[j][0] != '[') ||
((desc[i][0] == '[' || desc[j][0] != '[') &&
gmx_strcasecmp(desc[i],desc[j]) > 0)))
{
swap_strings(ffdirs,i,j);
swap_strings(ffs ,i,j);
swap_strings(desc ,i,j);
}
}
}
printf("\nSelect the Force Field:\n");
for(i=0; (i<nff); i++)
{
if (i == 0 || strcmp(ffs_dir[i-1],ffs_dir[i]) != 0)
{
if( strcmp(ffs_dir[i],".")==0 )
{
printf("From current directory:\n");
}
else
{
printf("From '%s':\n",ffs_dir[i]);
}
}
printf("%2d: %s\n",i+1,desc[i]);
sfree(desc[i]);
}
sfree(desc);
do
{
pret = fgets(buf,STRLEN,stdin);
if (pret != NULL)
{
sscanf(buf,"%d",&sel);
sel--;
}
}
while ( pret==NULL || (sel < 0) || (sel >= nff));
}
else
{
sel = 0;
}
if (strlen(ffs[sel]) >= (size_t)ff_maxlen)
{
gmx_fatal(FARGS,"Length of force field name (%d) >= maxlen (%d)",
strlen(ffs[sel]),ff_maxlen);
}
strcpy(forcefield,ffs[sel]);
if (strlen(ffdirs[sel]) >= (size_t)ffdir_maxlen)
{
gmx_fatal(FARGS,"Length of force field dir (%d) >= maxlen (%d)",
strlen(ffdirs[sel]),ffdir_maxlen);
}
strcpy(ffdir,ffdirs[sel]);
for(i=0; (i<nff); i++)
{
sfree(ffdirs[i]);
sfree(ffs[i]);
sfree(ffs_dir[i]);
}
sfree(ffdirs);
sfree(ffs);
sfree(ffs_dir);
}
