// del a new geometry object from the list with the given index. Return success.
// if n < 0, delete all markers
int GeometryList::del_geometry(int glindex, int n) {
// make sure the given GeometryMol object is OK
if(glindex >= 0 && glindex < num_lists()) {
// get the list of geometry objects for the given index
GeomListPtr glist = geom_list(glindex);
// make sure the geometry index is ok
if(n >= 0 && n < glist->num()) {
// delete and remove the geometry object
delete (*glist)[n];
glist->remove(n);
// indicate we were successful
return TRUE;
} else if(n < 0) {
// delete and remove all geometry objects
for(int j=(glist->num() - 1); j >= 0; j--) {
delete (*glist)[j];
glist->remove(j);
}
// indicate we were successful
return TRUE;
}
}
// if here, something did not work
return FALSE;
}
// delete(category, labeldict)
// XXX cut 'n paste from show...
static PyObject *label_delete(PyObject *self, PyObject *args) {
char *type;
PyObject *labeldict;
if (!PyArg_ParseTuple(args, (char *)"sO!:label.delete",
&type, &PyDict_Type, &labeldict))
return NULL;
VMDApp *app = get_vmdapp();
int cat = app->geometryList->geom_list_index(type);
if (cat < 0) {
PyErr_SetString(PyExc_ValueError, (char *)"Unknown label category");
return NULL;
}
GeomListPtr glist = app->geometryList->geom_list(cat);
int gnum = glist->num();
for (int i=0; i<gnum; i++) {
if (dict2geom(labeldict, (*glist)[i])) {
app->label_delete(type, i); // XXX check return code
Py_INCREF(Py_None);
return Py_None;
}
}
PyErr_SetString(PyExc_ValueError, "Invalid labeldict.");
return NULL;
}
const float *GeometryList::getTextOffset(const char *nm, int n) {
GeomListPtr glist = geom_list(nm);
if (!glist) return NULL;
if (n < 0 || n >= glist->num()) return NULL;
GeometryMol *g = (*glist)[n];
return g->text_offset();
}
int GeometryList::setTextFormat(const char *nm, int n, const char *format) {
GeomListPtr glist = geom_list(nm);
if (!glist) return FALSE;
if (n < 0 || n >= glist->num()) return FALSE;
GeometryMol *g = (*glist)[n];
g->set_text_format(format);
return TRUE;
}
const char *GeometryList::getTextFormat(const char *nm, int n) {
// XXX get/set Text Offset/Format duplicate their first four lines...
GeomListPtr glist = geom_list(nm);
if (!glist) return NULL;
if (n < 0 || n >= glist->num()) return NULL;
GeometryMol *g = (*glist)[n];
return g->text_format();
}
int GeometryList::setTextOffset(const char *nm, int n, const float delta[2]) {
GeomListPtr glist = geom_list(nm);
if (!glist) return FALSE;
if (n < 0 || n >= glist->num()) return FALSE;
GeometryMol *g = (*glist)[n];
g->set_text_offset(delta);
return TRUE;
}
void GeometryList::do_color_changed(int clr) {
if (clr == colorCat) {
for (int i=0; i<num_lists(); i++) {
GeomListPtr glist = geom_list(i);
GeomListStruct *s = geomLists.data(i);
int ind = scene->category_item_index(colorCat, geom_list_name(i));
int c = scene->category_item_value(colorCat, ind);
s->curColor = c;
for (int j=0; j<glist->num(); j++)
(*glist)[j]->set_color(c);
}
}
}
// prepare for drawing ... do any updates needed right before draw.
// For now, this always recreates the display list
void GeometryList::prepare() {
// go through all the geometry objects, recalculate, and find out if
// something is no longer 'ok'. If not, delete it.
for(int i=(num_lists() - 1); i >= 0; i--) {
GeomListPtr glist = geom_list(i);
for(int j=(glist->num() - 1); j >= 0; j--) {
GeometryMol *g = (*glist)[j];
if(!g->ok()) {
del_geometry(i, j);
}
}
}
}
int GeometryList::setTextThickness(float newthick) {
if (newthick <= 0)
return FALSE;
if (newthick == labelthickness) return TRUE;
labelthickness = newthick;
for(int i=(num_lists() - 1); i >= 0; i--) {
GeomListPtr glist = geom_list(i);
for(int j=(glist->num() - 1); j >= 0; j--) {
GeometryMol *g = (*glist)[j];
g->set_text_thickness(newthick);
}
}
return TRUE;
}
int GeometryList::setTextSize(float newsize) {
if (newsize <= 0)
return FALSE;
if (newsize == labelsize) return TRUE;
labelsize = newsize;
for(int i=(num_lists() - 1); i >= 0; i--) {
GeomListPtr glist = geom_list(i);
for(int j=(glist->num() - 1); j >= 0; j--) {
GeometryMol *g = (*glist)[j];
g->set_text_size(newsize);
}
}
return TRUE;
}
// getvalues(category, labeldict) -> list
// returns list containing value of label for every frame in the label
// if the label contains atoms from more than one molecule, only the first
// molecule is cycled (this the behavior of GeometryMol).
// XXX Note: this command is bad: the GeometryMol::calculate_all method
// twiddles the frame of the molecule, so this command isn't read only as
// its semantics would imply. But it should be possible to fix this
// in GeometryMol.
static PyObject *label_getvalues(PyObject *self, PyObject *args) {
char *type;
PyObject *labeldict;
if (!PyArg_ParseTuple(args, (char *)"sO!:label.getvalues",
&type, &PyDict_Type, &labeldict))
return NULL;
VMDApp *app = get_vmdapp();
int cat = app->geometryList->geom_list_index(type);
if (cat < 0) {
PyErr_SetString(PyExc_ValueError, (char *)"Unknown label category");
return NULL;
}
GeomListPtr glist = app->geometryList->geom_list(cat);
int gnum = glist->num();
for (int i=0; i<gnum; i++) {
if (dict2geom(labeldict, (*glist)[i]))
return getvalues((*glist)[i]);
}
PyErr_SetString(PyExc_ValueError, (char *)"Invalid label");
return NULL;
}
// delete the Nth category. Return success.
int GeometryList::del_geom_list(int n) {
GeomListStruct *oldlist = NULL;
// make sure we do have a category with this name
if(n >= 0 && n < num_lists()) {
// get data for Nth list
oldlist = geomLists.data(n);
GeomListPtr glist = oldlist->geomList;
// go through the list and delete all current GeometryMol objects
for(int i=(glist->num() - 1); i >= 0; i--) {
delete (*glist)[i];
}
// delete the old list storage and structure
delete glist;
delete oldlist;
geomLists.set_data(n, (GeomListStruct *) NULL);
}
// return whether we were successful
return (oldlist != NULL);
}
// toggle whether to show or hide a geometry monitor. If the monitor
// specified is < 0, does so for all monitors in the given category
int GeometryList::show_geometry(int glindex, int n, int s) {
// make sure the given GeometryMol object is OK
if(glindex >= 0 && glindex < num_lists()) {
// get the list of geometry objects for the given index
GeomListPtr glist = geom_list(glindex);
// make sure the geometry index is ok
if(n >= 0 && n < glist->num()) {
// hide or show the specified object
if (s)
(*glist)[n] -> on();
else
(*glist)[n] -> off();
// indicate we were successful
return TRUE;
} else if(n < 0) {
// delete and remove all geometry objects
for(int j=(glist->num() - 1); j >= 0; j--) {
if (s)
(*glist)[j] -> on();
else
(*glist)[j] -> off();
}
// indicate we were successful
return TRUE;
}
}
// if here, something did not work
return FALSE;
}
// listall(category) - return a list of labels for the given label category.
// labels will be returned as dictionary objects with the following keys:
// molid, atomid, value, on. molid and atomid will be tuples, value will
// be either a float or PyNone, and on will be 1 or 0.
static PyObject *listall(PyObject *self, PyObject *args) {
char *type;
if (!PyArg_ParseTuple(args, (char *)"s:label.listall", &type))
return NULL;
VMDApp *app = get_vmdapp();
int cat = app->geometryList->geom_list_index(type);
if (cat < 0) {
PyErr_SetString(PyExc_ValueError, (char *)"Unknown label category");
return NULL;
}
GeomListPtr glist = app->geometryList->geom_list(cat);
int gnum = glist->num();
PyObject *newlist = PyList_New(gnum);
for (int i=0; i<gnum; i++) {
PyObject *obj = geom2dict((*glist)[i]);
if (obj == NULL) {
Py_DECREF(newlist);
return NULL;
}
PyList_SET_ITEM(newlist, i, geom2dict((*glist)[i]));
}
return newlist;
}
int text_cmd_label(ClientData cd, Tcl_Interp *interp, int argc,
const char *argv[]) {
VMDApp *app = (VMDApp *)cd;
if (argc < 2) {
Tcl_SetResult(interp,
(char *)
"label add [Atoms|Bonds|Angles|Dihedrals] {atoms as <molid>/<atomid>}\n"
"label addspring <molid> <atomid> <atomid> <k>\n"
"label list -- return label categories\n"
"label list <category> -- return id's of labels in given category\n"
"label [show|hide|delete] <category> [index] -- \n\tControl specific label or all labels in category\n"
"label graph <category> <index> -- Return a list of values for the given label\n\tfor all animation frames\n"
"label textsize [<newsize>]\n" ,
TCL_STATIC);
return TCL_ERROR;
}
if(!strupncmp(argv[1], "add", CMDLEN)) {
if(argc > 3) {
int n = argc-3;
const char **items = argv+3;
int *molid= new int[n];
int *atmid = new int[n];
int i;
for(i=0; i < n; i++) {
if (find_atom_from_name(interp, items[i], molid+i, atmid+i))
break;
}
int rc = -1;
if(i == n) { // all successfully parsed
rc = app->label_add(argv[2], argc-3, molid, atmid, NULL, 0.0f, 1);
}
delete [] molid;
delete [] atmid;
if (rc < 0) {
Tcl_AppendResult(interp, "\nUnable to add label.", NULL);
return TCL_ERROR;
}
}
else
return TCL_ERROR;
}
else if(!strupncmp(argv[1],"addspring",CMDLEN)) { /* add a spring */
if(argc != 6) {
Tcl_AppendResult(interp, "usage: label addspring <molid> <atomid> <atomid> <k>", NULL);
return TCL_ERROR;
}
int molid[2];
int atomid[2];
float k;
sscanf(argv[2],"%d",molid); /* convert all of the args to numbers */
sscanf(argv[3],"%d",atomid);
sscanf(argv[4],"%d",atomid+1);
sscanf(argv[5],"%f",&k);
molid[1]=molid[0];
if (app->label_add("Springs", 2, molid, atomid, NULL, k, 1) < 0) {
Tcl_AppendResult(interp, "Unable to add spring.", NULL);
return TCL_ERROR;
}
}
else if(!strupncmp(argv[1], "list", CMDLEN)) {
if(argc == 3) {
int cat = app->geometryList->geom_list_index(argv[2]);
if (cat < 0) {
Tcl_AppendResult(interp, "graph list category '", argv[2],
"' was not found", NULL);
return TCL_ERROR;
}
// go through the list by hand
GeomListPtr glist = app->geometryList->geom_list(cat);
int gnum = glist->num();
char s[30];
GeometryMol *g;
for (int i=0; i<gnum; i++) {
g = (*glist)[i];
Tcl_AppendResult(interp, i==0 ? "" : " ", "{", NULL);
for (int j=0; j<g->items(); j++) {
// append the molecule id/atom index
sprintf(s, "%d %d", g -> obj_index(j), g -> com_index(j));
Tcl_AppendElement(interp, s);
}
// and the value and the status
sprintf(s, "%f", g->ok() ? g->calculate() : 0.0);
Tcl_AppendElement(interp, s);
Tcl_AppendElement(interp, g -> displayed() ? "show" : "hide");
Tcl_AppendResult(interp, "}", NULL);
}
return TCL_OK;
}
else if (argc == 2) {
// return the main categories
for (int i=0; i<app->geometryList -> num_lists(); i++) {
Tcl_AppendElement(interp, app->geometryList -> geom_list_name(i));
}
return TCL_OK;
} else
return TCL_ERROR;
} else if(!strupncmp(argv[1], "show", CMDLEN) ||
!strupncmp(argv[1], "hide", CMDLEN)) {
int item;
if(argc == 3 || (argc == 4 && !strupncmp(argv[3], "all", CMDLEN)))
item = (-1);
else if(argc == 4) {
if (Tcl_GetInt(interp, argv[3], &item) != TCL_OK) {
Tcl_AppendResult(interp, " in label ", argv[1], NULL);
return TCL_ERROR;
}
} else
return TCL_ERROR;
app->label_show(argv[2], item, !strupncmp(argv[1], "show", CMDLEN));
// XXX check return code
} else if(!strupncmp(argv[1], "delete", CMDLEN)) {
int item;
if(argc == 3 || (argc == 4 && !strupncmp(argv[3], "all", CMDLEN))) {
item = (-1);
} else if(argc == 4) {
if (Tcl_GetInt(interp, argv[3], &item) != TCL_OK) {
Tcl_AppendResult(interp, " in label ", argv[1], NULL);
return TCL_ERROR;
}
} else {
return TCL_ERROR;
}
app->label_delete(argv[2], item);
// XXX check return code
} else if(!strupncmp(argv[1], "graph", CMDLEN) && argc > 3) {
int item;
if (Tcl_GetInt(interp, argv[3], &item) != TCL_OK) {
return TCL_ERROR;
};
// find the geometry
int cat = app->geometryList->geom_list_index(argv[2]);
if (cat < 0) {
Tcl_AppendResult(interp, "Invalid geometry type: ", argv[2], NULL);
return TCL_ERROR;
}
// get the correct geometry pointer
GeomListPtr glist = app->geometryList -> geom_list(cat);
int gnum = glist -> num();
if (item < 0 || item >= gnum) {
sprintf(interp -> result, "label %s index %d out of range",
argv[2], item);
return TCL_ERROR;
}
// compute all the values
GeometryMol *g = (*glist)[item];
if (!g->has_value()) {
Tcl_AppendResult(interp, "Geometry type ", argv[2], " has no values to graph.", NULL);
return TCL_ERROR;
}
ResizeArray<float> gValues(1024);
if (!g->calculate_all(gValues)) {
interp->result = (char *) "label has no value";
return TCL_ERROR;
}
if (argc > 4) {
// save the values in the given filename
const char *filename = argv[4];
FILE *outfile = fopen(filename, "w");
if (!outfile) {
Tcl_AppendResult(interp, "Cannot write graph data to file ",
filename, NULL);
return TCL_ERROR;
}
for (int i=0; i<gValues.num(); i++) {
fprintf(outfile, "%f %f\n", float(i), gValues[i]);
}
fclose(outfile);
} else {
char s[20];
for (int count = 0; count < gValues.num(); count++) {
sprintf(s, "%f", gValues[count]);
Tcl_AppendElement(interp, s);
}
}
} else if (!strupncmp(argv[1], "textsize", CMDLEN)) {
if (argc == 2) {
// return the current size
Tcl_SetObjResult(interp, Tcl_NewDoubleObj(app->label_get_textsize()));
return TCL_OK;
} else if (argc == 3) {
// set new size
double newsize = 1;
if (Tcl_GetDouble(interp, argv[2], &newsize) != TCL_OK)
return TCL_ERROR;
if (!app->label_set_textsize((float) newsize)) {
Tcl_AppendResult(interp, "label textsize: Unable to set size to ",
argv[2], NULL);
return TCL_ERROR;
}
} else {
Tcl_SetResult(interp, "label textsize: wrong number of arguments",
TCL_STATIC);
return TCL_ERROR;
}
} else if (!strupncmp(argv[1], "textoffset", CMDLEN)) {
if (argc == 4) {
// return current offset;
const char *geomtype = argv[2];
int geom;
if (Tcl_GetInt(interp, argv[3], &geom) != TCL_OK) return TCL_ERROR;
const float *offset = app->geometryList->getTextOffset(geomtype, geom);
if (!offset) {
Tcl_SetResult(interp, "label textoffset: Invalid geometry specified", TCL_STATIC);
return TCL_ERROR;
}
Tcl_Obj *result = Tcl_NewListObj(0, NULL);
Tcl_ListObjAppendElement(interp, result, Tcl_NewDoubleObj(offset[0]));
Tcl_ListObjAppendElement(interp, result, Tcl_NewDoubleObj(offset[1]));
Tcl_SetObjResult(interp, result);
} else if (argc == 5) {
const char *geomtype = argv[2];
int geom;
if (Tcl_GetInt(interp, argv[3], &geom) != TCL_OK) return TCL_ERROR;
float x, y;
if (sscanf(argv[4], "%f %f", &x, &y) != 2) {
Tcl_AppendResult(interp, "Could not understand argument to label textoffset:", argv[2], NULL);
return TCL_ERROR;
}
if (!app->label_set_textoffset(geomtype, geom, x, y)) {
Tcl_SetResult(interp, "label textoffset: Invalid geometry specified", TCL_STATIC);
return TCL_ERROR;
}
} else {
Tcl_SetResult(interp, "label textoffset: wrong number of arguments",
TCL_STATIC);
return TCL_ERROR;
}
} else if (!strupncmp(argv[1], "textformat", CMDLEN)) {
if (argc == 4) {
// return current format
const char *geomtype = argv[2];
int geom;
if (Tcl_GetInt(interp, argv[3], &geom) != TCL_OK) return TCL_ERROR;
const char *format = app->geometryList->getTextFormat(geomtype, geom);
if (!format) {
Tcl_SetResult(interp, "label textformat: Invalid geometry specified", TCL_STATIC);
return TCL_ERROR;
}
Tcl_SetResult(interp, (char *)format, TCL_VOLATILE);
} else if (argc == 5) {
const char *geomtype = argv[2];
int geom;
if (Tcl_GetInt(interp, argv[3], &geom) != TCL_OK) return TCL_ERROR;
if (!app->label_set_textformat(geomtype, geom, argv[4])) {
Tcl_SetResult(interp, "label textformat failed.", TCL_STATIC);
return TCL_ERROR;
}
} else {
Tcl_SetResult(interp, "label textoffset: wrong number of arguments",
TCL_STATIC);
return TCL_ERROR;
}
}
return TCL_OK;
}
int GeometryList::add_geometry(const char *geomcatname, const int *molids,
const int *atomids, const int *cells, float k, int toggle) {
// check that geometry category name is valid
int geomcat = geom_list_index(geomcatname);
GeometryMol *g = NULL;
MoleculeList *mlist = app->moleculeList;
if (geomcat == geom_list_index("Atoms"))
g = new GeometryAtom(*molids, *atomids, cells, mlist, app->commandQueue, this);
else if (geomcat == geom_list_index("Bonds"))
g = new GeometryBond((int *)molids, (int *)atomids, cells, mlist, app->commandQueue, this);
else if (geomcat == geom_list_index("Angles"))
g = new GeometryAngle((int *)molids, (int *)atomids, cells, mlist, app->commandQueue, this);
else if (geomcat == geom_list_index("Dihedrals"))
g = new GeometryDihedral((int *)molids, (int *)atomids, cells, mlist, app->commandQueue, this);
else if (geomcat == geom_list_index("Springs"))
g = new GeometrySpring((int *)molids, (int *)atomids, mlist, app->commandQueue, k, this);
else {
msgErr << "Unknown geometry category '" << geomcatname << "'." << sendmsg;
return -1;
}
if(g && g->ok()) {
GeomListPtr glist = geom_list(geomcat);
// if there is already an identical label in the list,
// do not add this one, instead toggle the displayed
// status of the old one and return the index.
for(int i=(glist->num() - 1); i >= 0; i--) {
GeometryMol *g2 = (*glist)[i];
if(!strcmp(g2->unique_name(), g->unique_name())) {
// name matches
if (toggle) {
if (g2->displayed())
g2->off();
else
g2->on();
}
delete g;
return i;
}
}
// spam the console
msgInfo << "Added new " << geomcatname << " label " << g->name();
if (g->has_value())
msgInfo << " = " << g->calculate();
msgInfo << sendmsg;
// add the geometry object
glist->append(g);
// calculate the value for the first time
g->calculate();
// set the color, which also causes the display list to be generated
g->set_color(geomLists.data(geomcat)->curColor);
g->set_text_size(labelsize);
g->set_text_thickness(labelthickness);
// set the pick variables
g->set_pick();
// indicate we were successful; return index of this object
return glist->num() - 1;
}
// if here, something did not work
return -1;
}
