gint core_undelete(struct model_pak *model, GSList *list)
{
struct core_pak *core;
struct shel_pak *shell;
g_assert(model != NULL);
g_assert(list != NULL);
core = list->data;
core->status &= ~DELETED;
model->cores = g_slist_prepend(model->cores, core);
if (core->shell)
{
shell = core->shell;
shell->status &= ~DELETED;
model->shels = g_slist_prepend(model->shels, core->shell);
}
/* FIXME - this doesnt work */
/*
connect_atom_compute(core, model);
*/
/* TODO - more fine grained molecule recalc (ie recalc of affected molecules only) */
connect_bonds(model);
connect_molecules(model);
return(TRUE);
}
void delete_commit(struct model_pak *data)
{
gint flag1=FALSE, flag2=FALSE;
gpointer m;
GSList *list1, *list2;
struct core_pak *core;
struct shel_pak *shell;
struct bond_pak *bond;
g_assert(data != NULL);
/* delete flaged cores in list */
list1 = data->cores;
while (list1)
{
core = list1->data;
list1 = g_slist_next(list1);
if (core->status & DELETED)
{
#if DEBUG_DELETE_COMMIT
printf("Deleting %s core [%p] ...\n", core->label, core);
#endif
flag1 = TRUE;
/* flag assoc. shell */
if (core->shell)
{
shell = core->shell;
shell->status |= DELETED;
}
/* update connectivity */
connect_atom_clear(core, data);
list2 = data->ubonds;
while (list2)
{
bond = list2->data;
list2 = g_slist_next(list2);
if (bond->atom1 == core || bond->atom2 == core)
{
data->ubonds = g_slist_remove(data->ubonds, bond);
g_free(bond);
}
}
/* update selection */
data->selection = g_slist_remove(data->selection, core);
/* delete any labels that reference the deleted core */
list2 = data->measure_list;
while (list2)
{
m = list2->data;
list2 = g_slist_next(list2);
if (measure_has_core(core, m))
measure_free(m, data);
}
/* update main list */
data->cores = g_slist_remove(data->cores, core);
g_free(core);
}
}
/* delete flaged shells in list */
list1 = data->shels;
while (list1)
{
shell = list1->data;
list1 = g_slist_next(list1);
if (shell->status & DELETED)
{
flag2 = TRUE;
/* update main list */
data->shels = g_slist_remove(data->shels, shell);
g_free(shell);
}
}
/* refresh totals */
data->num_atoms = g_slist_length(data->cores);
data->num_shells = g_slist_length(data->shels);
/* refresh spatial partitioning */
/* it's probably best to refresh the partitioning here, rather than */
/* incrementally as it's speedups for large models we're targeting */
zone_init(data);
/* cope with deleted bonds - expensive, so only do if required */
if (flag1)
{
connect_bonds(data);
connect_molecules(data);
}
/* refresh net charge calc */
calc_emp(data);
/* refresh unique atom list */
g_slist_free(data->unique_atom_list);
data->unique_atom_list = find_unique(ELEMENT, data);
/* refresh widgets */
meas_graft_model(data);
gui_refresh(GUI_MODEL_PROPERTIES);
/* reset functions with static pointers to cores */
data->state = 0;
}
gint read_frame(FILE *fp, gint n, struct model_pak *model)
{
gint status;
gdouble rmax, v1[3], v2[3];
gpointer camera=NULL;
GString *err_text;
g_assert(model != NULL);
rmax = model->rmax;
/* conventional or transformation style animation */
if (model->transform_list)
{
/* NEW - process transformation list as an animation */
status = read_transform(n, model);
}
else
{
g_assert(fp != NULL);
ARR3SET(v1, model->centroid);
ARR3SET(v2, model->offset);
status = read_raw_frame(fp, n, model);
if (status)
{
err_text = g_string_new("");
g_string_printf(err_text, "Error reading frame: %d\n", n);
gui_text_show(ERROR, err_text->str);
g_string_free(err_text, TRUE);
return(1);
}
/* setup (have to save camera) */
camera = camera_dup(model->camera);
model_prep(model);
model->camera = camera;
g_free(model->camera_default);
model->camera_default = camera;
ARR3SET(model->centroid, v1);
ARR3SET(model->offset, v2);
}
/* apply desired constraint */
if (model->periodic && !model->anim_fix)
{
switch (model->anim_confine)
{
case PBC_CONFINE_ATOMS:
coords_confine_cores(model->cores, model);
case PBC_CONFINE_MOLS:
coords_compute(model);
connect_bonds(model);
connect_molecules(model);
break;
}
}
if (model->anim_noscale)
model->rmax = rmax;
return(0);
}
