/*! \brief
* Initializes position calculation using the maximum possible input index.
*
* \param[in,out] pc Position calculation data structure.
* \param[in] g Maximum index group for the calculation.
* \param[in] bBase Whether \p pc will be used as a base or not.
*
* \p bBase affects on how the \p pc->gmax field is initialized.
*/
static void
set_poscalc_maxindex(gmx_ana_poscalc_t *pc, gmx_ana_index_t *g, bool bBase)
{
e_index_t ptype;
ptype = index_type_for_poscalc(pc->type);
gmx_ana_index_make_block(&pc->b, pc->coll->top, g, ptype, pc->flags & POS_COMPLWHOLE);
/* Set the type to POS_ATOM if the calculation in fact is such. */
if (pc->b.nr == pc->b.nra)
{
pc->type = POS_ATOM;
pc->flags &= ~(POS_MASS | POS_COMPLMAX | POS_COMPLWHOLE);
}
/* Set the POS_COMPLWHOLE flag if the calculation in fact always uses
* complete residues and molecules. */
if (!(pc->flags & POS_COMPLWHOLE)
&& (!(pc->flags & POS_DYNAMIC) || (pc->flags & POS_COMPLMAX))
&& (pc->type == POS_RES || pc->type == POS_MOL)
&& gmx_ana_index_has_complete_elems(g, ptype, pc->coll->top))
{
pc->flags &= ~POS_COMPLMAX;
pc->flags |= POS_COMPLWHOLE;
}
/* Setup the gmax field */
if ((pc->flags & POS_COMPLWHOLE) && !bBase && pc->b.nra > g->isize)
{
gmx_ana_index_copy(&pc->gmax, g, TRUE);
sfree(pc->gmax.name);
pc->gmax.name = NULL;
}
else
{
gmx_ana_index_set(&pc->gmax, pc->b.nra, pc->b.a, NULL, 0);
}
}
/*!
* \param[in,out] m Mapping structure to initialize.
* \param[in] g Index group to map
* (can be NULL if \p type is \ref INDEX_UNKNOWN).
* \param[in] top Topology structure
* (can be NULL if \p type is not \ref INDEX_RES or \ref INDEX_MOL).
* \param[in] type Type of mapping to construct.
*
* Initializes a new index group mapping.
* The index group provided to gmx_ana_indexmap_update() should always be a
* subset of the \p g given here.
*
* \p m should have been initialized somehow (calloc() is enough).
*/
void
gmx_ana_indexmap_init(gmx_ana_indexmap_t *m, gmx_ana_index_t *g,
t_topology *top, e_index_t type)
{
int i, ii, mi;
m->type = type;
gmx_ana_index_make_block(&m->b, top, g, type, false);
gmx_ana_indexmap_reserve(m, m->b.nr, m->b.nra);
for (i = mi = 0; i < m->b.nr; ++i)
{
ii = (type == INDEX_UNKNOWN ? 0 : m->b.a[m->b.index[i]]);
switch (type)
{
case INDEX_ATOM:
m->orgid[i] = ii;
break;
case INDEX_RES:
m->orgid[i] = top->atoms.atom[ii].resind;
break;
case INDEX_MOL:
while (top->mols.index[mi+1] <= ii)
{
++mi;
}
m->orgid[i] = mi;
break;
case INDEX_ALL:
case INDEX_UNKNOWN:
m->orgid[i] = 0;
break;
}
}
for (i = 0; i < m->b.nr; ++i)
{
m->refid[i] = i;
m->mapid[i] = m->orgid[i];
}
m->mapb.nr = m->b.nr;
m->mapb.nra = m->b.nra;
m->mapb.a = m->b.a;
std::memcpy(m->mapb.index, m->b.index, (m->b.nr+1)*sizeof(*(m->mapb.index)));
m->bStatic = true;
}
/*!
* \param[in,out] m Mapping structure to initialize.
* \param[in] g Index group to map
* (can be NULL if \p type is \ref INDEX_UNKNOWN).
* \param[in] top Topology structure
* (can be NULL if \p type is not \ref INDEX_RES or \ref INDEX_MOL).
* \param[in] type Type of mapping to construct.
*
* Initializes a new index group mapping.
* The index group provided to gmx_ana_indexmap_update() should always be a
* subset of the \p g given here.
*
* \p m should have been initialized somehow (calloc() is enough).
*/
void
gmx_ana_indexmap_init(gmx_ana_indexmap_t *m, gmx_ana_index_t *g,
t_topology *top, e_index_t type)
{
m->type = type;
gmx_ana_index_make_block(&m->b, top, g, type, false);
gmx_ana_indexmap_reserve(m, m->b.nr, m->b.nra);
int id = -1;
for (int i = 0; i < m->b.nr; ++i)
{
const int ii = (type == INDEX_UNKNOWN ? 0 : m->b.a[m->b.index[i]]);
next_group_index(ii, top, type, &id);
m->refid[i] = i;
m->mapid[i] = id;
m->orgid[i] = id;
}
m->mapb.nr = m->b.nr;
m->mapb.nra = m->b.nra;
m->mapb.a = m->b.a;
std::memcpy(m->mapb.index, m->b.index, (m->b.nr+1)*sizeof(*(m->mapb.index)));
m->bStatic = true;
}
