void
SelectionCollection::setTopology(t_topology *top, int natoms)
{
GMX_RELEASE_ASSERT(natoms > 0 || top != NULL,
"The number of atoms must be given if there is no topology");
// Get the number of atoms from the topology if it is not given.
if (natoms <= 0)
{
natoms = top->atoms.nr;
}
if (impl_->bExternalGroupsSet_)
{
ExceptionInitializer errors("Invalid index group references encountered");
SelectionTreeElementPointer root = impl_->sc_.root;
while (root)
{
checkExternalGroups(root, natoms, &errors);
root = root->next;
}
if (errors.hasNestedExceptions())
{
GMX_THROW(InconsistentInputError(errors));
}
}
gmx_ana_selcollection_t *sc = &impl_->sc_;
// Do this first, as it allocates memory, while the others don't throw.
gmx_ana_index_init_simple(&sc->gall, natoms);
sc->pcc.setTopology(top);
sc->top = top;
}
void
SelectionCollection::setTopology(t_topology *top, int natoms)
{
gmx_ana_selcollection_t *sc = &_impl->_sc;
gmx_ana_poscalc_coll_set_topology(sc->pcc, top);
sc->top = top;
/* Get the number of atoms from the topology if it is not given */
if (natoms <= 0)
{
if (sc->top == NULL)
{
GMX_THROW(APIError("Selections need either the topology or the number of atoms"));
}
natoms = sc->top->atoms.nr;
}
gmx_ana_index_init_simple(&sc->gall, natoms, NULL);
}
/*!
* \param[in,out] sc Selection collection to set the topology for.
* \param[in] top Topology data.
* \param[in] natoms Number of atoms. If <=0, the number of atoms in the
* topology is used.
* \returns 0 on success, EINVAL if \p top is NULL and \p natoms <= 0.
*
* The topology is also set for the position calculation collection
* associated with \p sc.
*
* \p natoms determines the largest atom index that can be selected by the
* selection: even if the topology contains more atoms, they will not be
* selected.
*/
int
gmx_ana_selcollection_set_topology(gmx_ana_selcollection_t *sc, t_topology *top,
int natoms)
{
gmx_ana_poscalc_coll_set_topology(sc->pcc, top);
sc->top = top;
/* Get the number of atoms from the topology if it is not given */
if (natoms <= 0)
{
if (!sc->top)
{
gmx_incons("selections need either the topology or the number of atoms");
return EINVAL;
}
natoms = sc->top->atoms.nr;
}
gmx_ana_index_init_simple(&sc->gall, natoms, NULL);
return 0;
}
