void get_structure(t_atoms *atoms, const char *IndexFile,
const char *StructureFile, struct edix *edx, int nfit,
atom_id ifit[], int nav, atom_id index[])
{
atom_id *igro; /*index corresponding to target or origin structure*/
int ngro;
int ntar;
rvec *xtar;
char title[STRLEN];
char * grpname;
ntar = read_conffile(StructureFile, title, &xtar);
printf("Select an index group of %d elements that corresponds to the atoms in the structure file %s\n",
ntar, StructureFile);
get_index(atoms, IndexFile, 1, &ngro, &igro, &grpname);
if (ngro != ntar)
{
gmx_fatal(FARGS, "You selected an index group with %d elements instead of %d", ngro, ntar);
}
init_edx(edx);
filter2edx(edx, nfit, ifit, ngro, igro, xtar, StructureFile);
/* If average and reference/fitting structure differ, append the average structure as well */
if (ifit != index) /*if fit structure is different append these coordinates, too -- don't mind duplicates*/
{
filter2edx(edx, nav, index, ngro, igro, xtar, StructureFile);
}
}
/**
* This is the main entry point of the program
*
* @param argc The number of elements in `argv`
* @param argv Command line arguments
* @return Zero on success
*/
int main(int argc, char** argv)
{
int continuous = 0;
int quickly = 0;
int i;
FILE* f;
conffile_t* data;
conffile_t* data_;
char* env;
struct passwd* pw;
for (i = 0; i < argc; i++)
{
char* arg = *(argv + i);
#define __(opt) (!strcmp(arg, opt))
if (__("-c") || __("-cq") || __("-qc") || __("--continuous"))
continuous = 1;
if (__("-q") || __("-cq") || __("-qc") || __("--quickly"))
quickly = 1;
#undef __
}
if ((env = getenv("HOME")) && *env && !chdir(env));
else if ((pw = getpwuid(getuid())) && pw->pw_dir)
if (chdir(pw->pw_dir))
fprintf(stderr, "%s: cannot change directory to your home directory", *argv);
retry:
init_coordination(continuous, quickly);
f = get_conffile(NULL);
if (f != NULL)
{
data_ = data = read_conffile(f);
fclose(f);
}
else
{
/* If there are not configurion use use: */
data_ = data = malloc(3 * sizeof(conffile_t));
#define __use1(INDEX, METHOD) \
({ \
data[INDEX].argc = 1; \
data[INDEX].argv = malloc(sizeof(char*)); \
data[INDEX].argv[0] = malloc(strlen(METHOD ".") * sizeof(char)); \
memcpy(data[INDEX].argv[0], METHOD, strlen(METHOD ".") * sizeof(char)); \
})
#define __use2(INDEX, METHOD, ARGV1) \
({ \
data[INDEX].argc = 2; \
data[INDEX].argv = malloc(2 * sizeof(char*)); \
data[INDEX].argv[0] = malloc(strlen(METHOD ".") * sizeof(char)); \
memcpy(data[INDEX].argv[0], METHOD, strlen(METHOD ".") * sizeof(char)); \
data[INDEX].argv[1] = malloc(strlen(METHOD ".") * sizeof(char)); \
memcpy(data[INDEX].argv[1], ARGV1, strlen(ARGV1 ".") * sizeof(char)); \
})
__use1(0, "cache");
__use2(1, "read", ".config/geolocation");
__use2(2, "read", "/etc/geolocation");
__use1(3, "timezone-offset");
#undef __use1
#undef __use2
data[4].argc = -1;
data[4].argv = NULL;
}
for (; data->argc > 0; data++)
run(data->argc, data->argv);
free(data_);
if (already_done())
abort_coordination();
if (!term_coordination())
{
if (quickly && !continuous)
return 1;
quickly = 1;
continuous = 0;
goto retry;
}
return 0;
}
