// add(category, (molids), (atomids))
static PyObject *label_add(PyObject *self, PyObject *args) {
char *type;
PyObject *molids, *atomids;
int i;
if (!PyArg_ParseTuple(args, (char *)"sO!O!:label.add",
&type, &PyTuple_Type, &molids, &PyTuple_Type, &atomids))
return NULL;
VMDApp *app = get_vmdapp();
MoleculeList *mlist = app->moleculeList;
int cat = app->geometryList->geom_list_index(type);
if (cat < 0) {
PyErr_SetString(PyExc_ValueError, (char *)"Unknown label category");
return NULL;
}
int numitems;
if (PyTuple_Size(molids) == 1 && PyTuple_Size(atomids) == 1)
numitems = 1;
else if (PyTuple_Size(molids) == 2 && PyTuple_Size(atomids) == 2)
numitems = 2;
else if (PyTuple_Size(molids) == 3 && PyTuple_Size(atomids) == 3)
numitems = 3;
else if (PyTuple_Size(molids) == 4 && PyTuple_Size(atomids) == 4)
numitems = 4;
else {
PyErr_SetString(PyExc_TypeError, (char *)"label.add: 2nd and 3rd arguments"
" must be tuples of size 1, 2, 3, or 4");
return NULL;
}
int m[4], a[4];
for (i=0; i<numitems; i++) {
m[i] = PyInt_AsLong(PyTuple_GET_ITEM(molids, i));
a[i] = PyInt_AsLong(PyTuple_GET_ITEM(atomids, i));
if (PyErr_Occurred())
return NULL;
Molecule *mol = mlist->mol_from_id(m[i]);
if (!mol) {
PyErr_SetString(PyExc_ValueError, (char *)"Invalid molecule id");
return NULL;
}
if (a[i] < 0 || a[i] >= mol->nAtoms) {
PyErr_SetString(PyExc_ValueError, (char *)"Invalid atom id");
return NULL;
}
}
// Add the label, but don't toggle the on/off status.
int ind = app->label_add(type, numitems, m, a, NULL, 0.0f, 0);
if (ind < 0) {
Py_INCREF(Py_None);
return Py_None;
}
// Get the dict corresponding to this label. The dict we return
// corresponds to either the label we just created, or to an existing
// label whose state we have not changed. This makes it safe to use
// label.add to get a proxy to a VMD label.
GeomListPtr glist = app->geometryList->geom_list(cat);
return geom2dict((*glist)[ind]);
}
// helper function to get a molecule. Raises a ValueError exception on error
static MoleculeGraphics *mol_from_id(int id) {
VMDApp *app = get_vmdapp();
MoleculeList *mlist = app->moleculeList;
Molecule *mol = mlist->mol_from_id(id);
if (!mol) {
PyErr_SetString(PyExc_ValueError, (char *)"Invalid graphics molecule");
return NULL;
}
return mol->moleculeGraphics();
}
MoleculeList molecules(const AtomContainer& fragment, bool selected_only)
{
// iterate over all molecules
AtomContainerConstIterator it = fragment.beginAtomContainer();
MoleculeList result;
for (; +it; ++it)
{
const Molecule* molecule = dynamic_cast<const Molecule*>(&*it);
if ((molecule != 0) && (it->isSelected() || !selected_only))
{
// store the molecule pointer in the list
result.push_back(const_cast<Molecule*>(molecule));
}
}
return result;
}
void MolBrowser::update() {
MoleculeList *mlist = app->moleculeList;
int nummols = mlist->num();
char buf[256], molnamebuf[81];
int need_full_regen = 0;
#if 1
// If the browser is larger than needed, we have to
// re-create it from scratch since some molecule was
// potentially deleted from the middle.
// If the size remains fixed, then we need to regenerate
// because we are getting called to rename an existing molecule...
if (size() > nummols || size() == nummols) {
need_full_regen = 1;
}
#else
need_full_regen = 1;
#endif
if (need_full_regen) {
clear();
for (int i=0; i<nummols; i++) {
Molecule *mol = mlist->molecule(i);
// prevent string length overflows
strncpy(molnamebuf, mol->molname(), sizeof(molnamebuf)-1);
// display state of active/displayed/fixed by toggling the text color
sprintf(buf, "%d\t%s\t%s\t%s\t%s\t%-13s\t%-9d\t%-7d\t%-3d",
mol->id(),
mlist->is_top(i) ? "T" : " ",
mlist->active(i) ? VMDMENU_MOL_ACTIVE : VMDMENU_MOL_INACTIVE,
mlist->displayed(i) ? VMDMENU_MOL_DISPLAYED : VMDMENU_MOL_NONDISPLAYED,
mlist->fixed(i) ? VMDMENU_MOL_FIXED : VMDMENU_MOL_NONFIXED,
molnamebuf, mol->nAtoms, mol->numframes(), mol->num_volume_data()
);
if (i < size())
text(i+1, buf);
else
add(buf);
}
} else {
// we just need to add one new molecule...
int i = nummols - 1;
Molecule *mol = mlist->molecule(i);
// prevent string length overflows
strncpy(molnamebuf, mol->molname(), sizeof(molnamebuf)-1);
// display state of active/displayed/fixed by toggling the text color
sprintf(buf, "%d\t%s\t%s\t%s\t%s\t%-13s\t%-9d\t%-7d\t%-3d",
mol->id(),
mlist->is_top(i) ? "T" : " ",
mlist->active(i) ? VMDMENU_MOL_ACTIVE : VMDMENU_MOL_INACTIVE,
mlist->displayed(i) ? VMDMENU_MOL_DISPLAYED : VMDMENU_MOL_NONDISPLAYED,
mlist->fixed(i) ? VMDMENU_MOL_FIXED : VMDMENU_MOL_NONFIXED,
molnamebuf, mol->nAtoms, mol->numframes(), mol->num_volume_data()
);
if (i < size())
text(i+1, buf); // this shouldn't happen here...
else
add(buf);
}
if (mainmenu) mainmenu->update_gui_state();
}
void MolBrowser::update() {
MoleculeList *mlist = app->moleculeList;
int nummols = mlist->num();
#if 1
//
// XXX this code updates the state of all of the molecules reliably, but
// creates a huge performance cost when thousands of molecules are
// loaded. We really need a scheme to create a changelist and apply
// the changelist to only those molecule browser lines that need updates.
//
if (size() > nummols)
clear();
for (int i=0; i<nummols; i++) {
char buf[256], molnamebuf[81];
Molecule *mol = mlist->molecule(i);
// prevent string length overflows
strncpy(molnamebuf, mol->molname(), sizeof(molnamebuf)-1);
// display state of active/displayed/fixed by toggling the text color
sprintf(buf, "%d\t%s\t%s\t%s\t%s\t%-13s\t%-9d\t%-7d\t%-3d",
mol->id(),
mlist->is_top(i) ? "T" : " ",
mlist->active(i) ? VMDMENU_MOL_ACTIVE : VMDMENU_MOL_INACTIVE,
mlist->displayed(i) ? VMDMENU_MOL_DISPLAYED : VMDMENU_MOL_NONDISPLAYED,
mlist->fixed(i) ? VMDMENU_MOL_FIXED : VMDMENU_MOL_NONFIXED,
molnamebuf, mol->nAtoms, mol->numframes(), mol->num_volume_data()
);
if (i < size())
text(i+1, buf); // update existing browser line
else
add(buf); // add a new browser line
}
#else
//
// XXX this code addresses the performance issues associated with the
// full-update code above, but breaks molecule browser's handling
// of operations multi-molecule selections.
//
char buf[256], molnamebuf[81];
int need_full_regen = 0;
#if 1
// If the browser is larger than needed, we have to
// re-create it from scratch since some molecule was
// potentially deleted from the middle.
// If the size remains fixed, then we need to regenerate
// because we are getting called to rename an existing molecule...
if (size() > nummols || size() == nummols) {
need_full_regen = 1;
}
#else
need_full_regen = 1;
#endif
if (need_full_regen) {
clear();
for (int i=0; i<nummols; i++) {
Molecule *mol = mlist->molecule(i);
// prevent string length overflows
strncpy(molnamebuf, mol->molname(), sizeof(molnamebuf)-1);
// display state of active/displayed/fixed by toggling the text color
sprintf(buf, "%d\t%s\t%s\t%s\t%s\t%-13s\t%-9d\t%-7d\t%-3d",
mol->id(),
mlist->is_top(i) ? "T" : " ",
mlist->active(i) ? VMDMENU_MOL_ACTIVE : VMDMENU_MOL_INACTIVE,
mlist->displayed(i) ? VMDMENU_MOL_DISPLAYED : VMDMENU_MOL_NONDISPLAYED,
mlist->fixed(i) ? VMDMENU_MOL_FIXED : VMDMENU_MOL_NONFIXED,
molnamebuf, mol->nAtoms, mol->numframes(), mol->num_volume_data()
);
if (i < size())
text(i+1, buf); // update existing browser line
else
add(buf); // add a new browser line
}
} else {
// we just need to add one new molecule...
int i = nummols - 1;
Molecule *mol = mlist->molecule(i);
// prevent string length overflows
strncpy(molnamebuf, mol->molname(), sizeof(molnamebuf)-1);
// display state of active/displayed/fixed by toggling the text color
sprintf(buf, "%d\t%s\t%s\t%s\t%s\t%-13s\t%-9d\t%-7d\t%-3d",
mol->id(),
mlist->is_top(i) ? "T" : " ",
mlist->active(i) ? VMDMENU_MOL_ACTIVE : VMDMENU_MOL_INACTIVE,
mlist->displayed(i) ? VMDMENU_MOL_DISPLAYED : VMDMENU_MOL_NONDISPLAYED,
mlist->fixed(i) ? VMDMENU_MOL_FIXED : VMDMENU_MOL_NONFIXED,
molnamebuf, mol->nAtoms, mol->numframes(), mol->num_volume_data()
);
if (i < size())
text(i+1, buf); // update existing browser line
else
add(buf); // add a new browser line
}
#endif
if (mainmenu) mainmenu->update_gui_state();
}