/*!
* \param[out] dest Destination index groups.
* \param[in] src Source index groups.
*
* A deep copy is made for all fields, including the group names.
*/
void
gmx_ana_indexgrps_clone(gmx_ana_indexgrps_t **dest, gmx_ana_indexgrps_t *src)
{
int g;
gmx_ana_indexgrps_alloc(dest, src->nr);
for (g = 0; g < src->nr; ++g)
{
gmx_ana_index_copy(&(*dest)->g[g], &src->g[g], TRUE);
}
}
/*!
* \param[out] g Index group structure.
* \param[in] ngrps Number of index groups.
* \param[in] isize Array of index group sizes.
* \param[in] index Array of pointers to indices of each group.
* \param[in] name Array of names of the groups.
* \param[in] bFree If TRUE, the \p isize, \p index and \p name arrays
* are freed after they have been copied.
*/
void
gmx_ana_indexgrps_set(gmx_ana_indexgrps_t **g, int ngrps, int *isize,
atom_id **index, char **name, bool bFree)
{
int i;
gmx_ana_indexgrps_alloc(g, ngrps);
for (i = 0; i < ngrps; ++i)
{
gmx_ana_index_set(&(*g)->g[i], isize[i], index[i], name[i], isize[i]);
}
if (bFree)
{
sfree(isize);
sfree(index);
sfree(name);
}
}
/*!
* \param[out] g Index group structure.
* \param[in] top Topology structure.
* \param[in] fnm File name for the index file.
* Memory is automatically allocated.
*
* One or both of \p top or \p fnm can be NULL.
* If \p top is NULL, an index file is required and the groups are read
* from the file (uses Gromacs routine init_index()).
* If \p fnm is NULL, default groups are constructed based on the
* topology (uses Gromacs routine analyse()).
* If both are null, the index group structure is initialized empty.
*/
void
gmx_ana_indexgrps_init(gmx_ana_indexgrps_t **g, t_topology *top,
const char *fnm)
{
t_blocka *block = NULL;
char **names = NULL;
int i, j;
if (fnm)
{
block = init_index(fnm, &names);
}
else if (top)
{
block = new_blocka();
analyse(&top->atoms, block, &names, FALSE, FALSE);
}
else
{
snew(*g, 1);
(*g)->nr = 0;
(*g)->g = NULL;
return;
}
gmx_ana_indexgrps_alloc(g, block->nr);
for (i = 0; i < block->nr; ++i)
{
gmx_ana_index_t *grp = &(*g)->g[i];
grp->isize = block->index[i+1] - block->index[i];
snew(grp->index, grp->isize);
for (j = 0; j < grp->isize; ++j)
{
grp->index[j] = block->a[block->index[i]+j];
}
grp->name = names[i];
grp->nalloc_index = grp->isize;
}
done_blocka(block);
sfree(block);
sfree(names);
}
