static PyObject *setbonds(PyObject *self, PyObject *args) {
int molid;
PyObject *atomlist, *bondlist;
if (!PyArg_ParseTuple(args, (char *)"iO!O!:setbonds", &molid,
&PyTuple_Type, &atomlist, &PyList_Type, &bondlist))
return NULL; // bad args
Molecule *mol = get_vmdapp()->moleculeList->mol_from_id(molid);
if (!mol) {
PyErr_SetString(PyExc_ValueError, "molecule no longer exists");
return NULL;
}
int num_atoms = mol->nAtoms;
int num_selected = PyTuple_Size(atomlist);
if (PyList_Size(bondlist) != num_selected) {
PyErr_SetString(PyExc_ValueError,
(char *)"setbonds: atomlist and bondlist must have the same size");
return NULL;
}
mol->force_recalc(DrawMolItem::MOL_REGEN); // many reps ignore bonds
for (int i=0; i<num_selected; i++) {
int id = PyInt_AsLong(PyTuple_GET_ITEM(atomlist, i));
if (PyErr_Occurred()) {
return NULL;
}
if (id < 0 || id >= num_atoms) {
PyErr_SetString(PyExc_ValueError, (char *)"invalid atom id found");
return NULL;
}
MolAtom *atom = mol->atom(id);
PyObject *atomids = PyList_GET_ITEM(bondlist, i);
if (!PyList_Check(atomids)) {
PyErr_SetString(PyExc_TypeError,
(char *)"bondlist must contain lists");
return NULL;
}
int numbonds = PyList_Size(atomids);
int k=0;
for (int j=0; j<numbonds; j++) {
int bond = PyInt_AsLong(PyList_GET_ITEM(atomids, j));
if (PyErr_Occurred())
return NULL;
if (bond >= 0 && bond < mol->nAtoms) {
atom->bondTo[k++] = bond;
} else {
char buf[40];
sprintf(buf, "Invalid atom id in bondlist: %d", bond);
PyErr_SetString(PyExc_ValueError, buf);
return NULL;
}
}
atom->bonds = k;
}
Py_INCREF(Py_None);
return Py_None;
}
static PyObject *py_align(PyObject *self, PyObject *args) {
int selmol, selframe, refmol, refframe, movemol, moveframe;
PyObject *selobj, *refobj, *moveobj, *weightobj = NULL;
if (!PyArg_ParseTuple(args, (char *)"iiO!iiO!iiO!O:atomselection.align",
&selmol, &selframe, &PyTuple_Type, &selobj,
&refmol, &refframe, &PyTuple_Type, &refobj,
&movemol, &moveframe, &PyTuple_Type, &moveobj,
&weightobj))
return NULL;
// check if movemol is -1. If so, use the sel molecule and timestep instead
if (movemol == -1) {
movemol = selmol;
moveobj = NULL;
}
VMDApp *app = get_vmdapp();
AtomSel *sel=NULL, *ref=NULL, *move=NULL;
if (!(sel = sel_from_py(selmol, selframe, selobj, app)) ||
!(ref = sel_from_py(refmol, refframe, refobj, app)) ||
!(move = sel_from_py(movemol, moveframe, moveobj, app))) {
delete sel;
delete ref;
delete move;
return NULL;
}
const float *selts, *refts;
float *movets;
if (!(selts = sel->coordinates(app->moleculeList)) ||
!(refts = ref->coordinates(app->moleculeList)) ||
!(movets = move->coordinates(app->moleculeList))) {
delete sel;
delete ref;
delete move;
PyErr_SetString(PyExc_ValueError, "No coordinates in selection");
return NULL;
}
float *weight = parse_weight(sel, weightobj);
if (!weight) {
delete sel;
delete ref;
delete move;
return NULL;
}
// Find the matrix that aligns sel with ref. Apply the transformation to
// the atoms in move.
// XXX need to add support for the "order" parameter as in Tcl.
Matrix4 mat;
int rc = measure_fit(sel, ref, selts, refts, weight, NULL, &mat);
delete [] weight;
delete sel;
delete ref;
if (rc < 0) {
delete move;
PyErr_SetString(PyExc_ValueError, (char *)measure_error(rc));
return NULL;
}
for (int i=0; i<move->num_atoms; i++) {
if (move->on[i]) {
float *pos = movets+3*i;
mat.multpoint3d(pos, pos);
}
}
Molecule *mol = app->moleculeList->mol_from_id(move->molid());
mol->force_recalc(DrawMolItem::MOL_REGEN);
delete move;
Py_INCREF(Py_None);
return Py_None;
}
static PyObject *set(PyObject *self, PyObject *args) {
int i, molid, frame;
PyObject *selected, *val;
char *attr = 0;
//
// get molid, frame, list, attribute, and value
//
if (!PyArg_ParseTuple(args, (char *)"iiO!sO!", &molid, &frame,
&PyTuple_Type, &selected,
&attr, &PyTuple_Type, &val ))
return NULL; // bad args
//
// check that we have been given either one value or one for each selected
// atom
//
int num_selected = PyTuple_Size(selected);
int tuplesize = PyTuple_Size(val);
if (tuplesize != 1 && tuplesize != num_selected) {
PyErr_SetString(PyExc_ValueError, "wrong number of items");
return NULL;
}
//
// check molecule
//
VMDApp *app = get_vmdapp();
Molecule *mol = app->moleculeList->mol_from_id(molid);
if (!mol) {
PyErr_SetString(PyExc_ValueError, "molecule no longer exists");
return NULL;
}
const int num_atoms = mol->nAtoms;
//
// Check for a valid attribute
//
SymbolTable *table = app->atomSelParser;
int attrib_index = table->find_attribute(attr);
if (attrib_index == -1) {
PyErr_SetString(PyExc_ValueError, "unknown atom attribute");
return NULL;
}
SymbolTableElement *elem = table->fctns.data(attrib_index);
if (elem->is_a != SymbolTableElement::KEYWORD &&
elem->is_a != SymbolTableElement::SINGLEWORD) {
PyErr_SetString(PyExc_ValueError, "attribute is not a keyword or singleword");
return NULL;
}
if (!table->is_changeable(attrib_index)) {
PyErr_SetString(PyExc_ValueError, "attribute is not modifiable");
return NULL;
}
//
// convert the list of selected atoms into an array of integer flags
//
// XXX should check that selected contains valid indices
int *flgs = new int[num_atoms];
memset(flgs,0,num_atoms*sizeof(int));
for (i=0; i<num_selected; i++)
flgs[PyInt_AsLong(PyTuple_GET_ITEM(selected,i))] = 1;
//
// set the data
//
// singlewords can never be set, so macro is NULL.
atomsel_ctxt context(table, mol, frame, NULL);
if (elem->returns_a == SymbolTableElement::IS_INT) {
int *list = new int[num_atoms];
if (tuplesize > 1) {
int j=0;
for (int i=0; i<num_atoms; i++) {
if (flgs[i])
list[i] = PyInt_AsLong(PyTuple_GET_ITEM(val, j++));
}
} else {
for (int i=0; i<num_atoms; i++) {
if (flgs[i])
list[i] = PyInt_AsLong(PyTuple_GET_ITEM(val, 0));
}
}
elem->set_keyword_int(&context, num_atoms, list, flgs);
delete [] list;
} else if (elem->returns_a == SymbolTableElement::IS_FLOAT) {
double *list = new double[num_atoms];
if (tuplesize > 1) {
int j=0;
for (int i=0; i<num_atoms; i++) {
if (flgs[i])
list[i] = PyFloat_AsDouble(PyTuple_GET_ITEM(val, j++));
}
} else {
for (int i=0; i<num_atoms; i++) {
if (flgs[i])
list[i] = PyFloat_AsDouble(PyTuple_GET_ITEM(val, 0));
}
}
elem->set_keyword_double(&context, num_atoms, list, flgs);
delete [] list;
} else if (elem->returns_a == SymbolTableElement::IS_STRING) {
const char **list = new const char *[num_atoms];
if (tuplesize > 1) {
int j=0;
for (int i=0; i<num_atoms; i++) {
if (flgs[i])
list[i] = PyString_AsString(PyTuple_GET_ITEM(val, j++));
}
} else {
for (int i=0; i<num_atoms; i++) {
if (flgs[i])
list[i] = PyString_AsString(PyTuple_GET_ITEM(val, 0));
}
}
elem->set_keyword_string(&context, num_atoms, list, flgs);
delete [] list;
}
// Recompute the color assignments if certain atom attributes are changed.
if (!strcmp(attr, "name") ||
!strcmp(attr, "type") ||
!strcmp(attr, "resname") ||
!strcmp(attr, "chain") ||
!strcmp(attr, "segid") ||
!strcmp(attr, "segname"))
app->moleculeList->add_color_names(molid);
mol->force_recalc(DrawMolItem::SEL_REGEN | DrawMolItem::COL_REGEN);
delete [] flgs;
Py_INCREF(Py_None);
return Py_None;
}
