static PyObject *contacts(PyObject *self, PyObject *args) {
int mol1, frame1, mol2, frame2;
PyObject *selected1, *selected2;
float cutoff;
if (!PyArg_ParseTuple(args, (char *)"iiO!iiO!f:atomselection.contacts",
&mol1, &frame1, &PyTuple_Type, &selected1,
&mol2, &frame2, &PyTuple_Type, &selected2,
&cutoff))
return NULL;
VMDApp *app = get_vmdapp();
AtomSel *sel1 = sel_from_py(mol1, frame1, selected1, app);
AtomSel *sel2 = sel_from_py(mol2, frame2, selected2, app);
if (!sel1 || !sel2) {
delete sel1;
delete sel2;
return NULL;
}
const float *ts1 = sel1->coordinates(app->moleculeList);
const float *ts2 = sel2->coordinates(app->moleculeList);
if (!ts1 || !ts2) {
PyErr_SetString(PyExc_ValueError, "No coordinates in selection");
delete sel1;
delete sel2;
return NULL;
}
Molecule *mol = app->moleculeList->mol_from_id(mol1);
GridSearchPair *pairlist = vmd_gridsearch3(
ts1, sel1->num_atoms, sel1->on,
ts2, sel2->num_atoms, sel2->on,
cutoff, -1, (sel1->num_atoms + sel2->num_atoms) * 27);
delete sel1;
delete sel2;
GridSearchPair *p, *tmp;
PyObject *list1 = PyList_New(0);
PyObject *list2 = PyList_New(0);
for (p=pairlist; p != NULL; p=tmp) {
// throw out pairs that are already bonded
MolAtom *a1 = mol->atom(p->ind1);
if (mol1 != mol2 || !a1->bonded(p->ind2)) {
PyList_Append(list1, PyInt_FromLong(p->ind1));
PyList_Append(list2, PyInt_FromLong(p->ind2));
}
tmp = p->next;
free(p);
}
PyObject *result = PyList_New(2);
PyList_SET_ITEM(result, 0, list1);
PyList_SET_ITEM(result, 1, list2);
return result;
}
static PyObject *contacts(PyObject *self, PyObject *args) {
int mol1, frame1, mol2, frame2;
PyObject *selected1, *selected2;
float cutoff;
if (!PyArg_ParseTuple(args, (char *)"iiO!iiO!f:atomselection.contacts",
&mol1, &frame1, &PyTuple_Type, &selected1,
&mol2, &frame2, &PyTuple_Type, &selected2,
&cutoff))
return NULL;
VMDApp *app = get_vmdapp();
AtomSel *sel1 = sel_from_py(mol1, frame1, selected1, app);
AtomSel *sel2 = sel_from_py(mol2, frame2, selected2, app);
if (!sel1 || !sel2) {
delete sel1;
delete sel2;
return NULL;
}
const float *ts1 = sel1->coordinates(app->moleculeList);
const float *ts2 = sel2->coordinates(app->moleculeList);
if (!ts1 || !ts2) {
PyErr_SetString(PyExc_ValueError, "No coordinates in selection");
delete sel1;
delete sel2;
return NULL;
}
Molecule *mol = app->moleculeList->mol_from_id(mol1);
GridSearchPair *pairlist = vmd_gridsearch3(
ts1, sel1->num_atoms, sel1->on,
ts2, sel2->num_atoms, sel2->on,
cutoff, -1, (sel1->num_atoms + sel2->num_atoms) * 27);
delete sel1;
delete sel2;
GridSearchPair *p, *tmp;
PyObject *list1 = PyList_New(0);
PyObject *list2 = PyList_New(0);
PyObject *tmp1;
PyObject *tmp2;
for (p=pairlist; p != NULL; p=tmp) {
// throw out pairs that are already bonded
MolAtom *a1 = mol->atom(p->ind1);
if (mol1 != mol2 || !a1->bonded(p->ind2)) {
// Needed to avoid a memory leak. Append increments the refcount
// of whatever gets added to it, but so does PyInt_FromLong.
// Without a decref, the integers created never have their refcount
// go to zero, and you leak memory.
tmp1 = PyInt_FromLong(p->ind1);
tmp2 = PyInt_FromLong(p->ind2);
PyList_Append(list1, tmp1);
PyList_Append(list2, tmp2);
Py_DECREF(tmp1);
Py_DECREF(tmp2);
}
tmp = p->next;
free(p);
}
PyObject *result = PyList_New(2);
PyList_SET_ITEM(result, 0, list1);
PyList_SET_ITEM(result, 1, list2);
return result;
}
