/*************************************************************************
* FUNCTION : RPMPRoblem_Obj::Get_Obj *
* ARGUMENTS : none *
* RETURNS : Object with refcount of 0 *
* EXCEPTIONS : none *
* PURPOSE : Create a Tcl_Obj from a problem *
*************************************************************************/
Tcl_Obj *RPMPRoblem_Obj::Get_obj(void)
{
Tcl_Obj *obj = Tcl_NewObj();
obj->typePtr = &mytype;
obj->internalRep.otherValuePtr = Dup();
Tcl_InvalidateStringRep(obj);
return obj;
}
/*************************************************************************
* FUNCTION : RPMPRoblem_Obj::Create_from_problem *
* ARGUMENTS : ref to problem *
* RETURNS : none *
* EXCEPTIONS : none *
* PURPOSE : Create a problem Tcl_Obj *
*************************************************************************/
Tcl_Obj *RPMPRoblem_Obj::Create_from_problem(const rpmProblem_s &x)
{
Tcl_Obj *y = Tcl_NewObj();
assert(y);
Tcl_IncrRefCount(y);
Tcl_InvalidateStringRep(y);
y->typePtr = &mytype;
y->internalRep.otherValuePtr = new RPMPRoblem_Obj(x);
return y;
}
Tcl_Obj *Ttk_NewStateSpecObj(unsigned int onbits, unsigned int offbits)
{
Tcl_Obj *objPtr = Tcl_NewObj();
Tcl_InvalidateStringRep(objPtr);
objPtr->typePtr = &StateSpecObjType;
objPtr->internalRep.longValue = (onbits << 16) | offbits;
return objPtr;
}
int
Tcljson_JsonObjToTclObj(struct json_object *joPtr, Tcl_Obj **objPtr)
{
TclJsonObject *tjPtr;
*objPtr = NULL;
tjPtr = (TclJsonObject *) Tcl_Alloc(sizeof(TclJsonObject));
tjPtr->joPtr = joPtr;
*objPtr = Tcl_NewObj();
(*objPtr)->internalRep.otherValuePtr = (VOID *) tjPtr;
(*objPtr)->typePtr = &tclJsonObjectType;
Tcl_InvalidateStringRep(*objPtr);
return TCL_OK;
}
TWAPI_EXTERN Tcl_Obj *ObjFromWinCharsN(const WCHAR *wsP, int nchars)
{
Tcl_Obj *objP;
WinChars *rep;
if (wsP == NULL)
return ObjFromEmptyString();
if (! gBaseSettings.use_unicode_obj)
return TwapiUtf8ObjFromWinChars(wsP, -1);
rep = WinCharsNew(wsP, nchars);
objP = Tcl_NewObj();
Tcl_InvalidateStringRep(objP);
WinCharsSet(objP, rep);
return objP;
}
/*************************************************************************
* FUNCTION : RPMPRoblem_ObjL::Problem *
* ARGUMENTS : interp, tcl args, *
* Problem object *
* index in objv of first tag we need *
* RETURNS : 0 if OK, else error *
* EXCEPTIONS : none *
* PURPOSE : Manipulate a problem entry *
* NOTES : format for this is *
* RPM [<prob>] [part [value]]* *
* where <prob> is an existing problem object - if not given, then the *
* command will create a new problem object. *
* [part] is one of the defined problem tags for a problem *
* [value] if given will set the defined part *
* *
* *
*************************************************************************/
int RPMPRoblem_Obj::Problem(Tcl_Interp *interp,int objc, Tcl_Obj *const objv[],
Tcl_Obj *prob,int first_tag
)
{
// Now, we have one of 2 possibilities here - they gave us a single tag
// to query, or a list of (tag,value) pairs
if (objc == (first_tag+1))
{
// Single tag - return the value of the tag.
int which = 0;
if (Tcl_GetIndexFromObj(interp,objv[first_tag],prob_parts,"tag",0,&which) != TCL_OK)
return TCL_ERROR;
Tcl_SetObjResult(interp,Get_part((PARTS)which)); // Return value to TCL
return TCL_OK;
}
Tcl_InvalidateStringRep(prob);
// OK, so this should be a set of (tag,value) pairs - parse them
for (int i = first_tag; i < objc; i += 2)
{
// Make sure we actually HAVE a value
if ((i+1)>objc)
return Cmd_base::Error(interp,"Need a value");
// what tag is it?
int which = 0;
if (Tcl_GetIndexFromObj(interp,objv[i],prob_parts,"tag",0,&which) != TCL_OK)
return TCL_ERROR;
switch ((PARTS)which)
{
case PACKAGE:
{
int len = 0;
char *x = Tcl_GetStringFromObj(objv[i+1],&len);
char *p = new char[len+1];
strncpy(p,x,len);
p[len] = 0;
if (problem.pkgNEVR)
delete [] problem.pkgNEVR;
problem.pkgNEVR = p;
}
break;
case ALT:
{
int len = 0;
char *x = Tcl_GetStringFromObj(objv[i+1],&len);
char *p = new char[len+1];
strncpy(p,x,len);
p[len] = 0;
if (problem.altNEVR)
delete [] problem.altNEVR;
problem.altNEVR = p;
}
break;
case KEY:
{
int value = 0;
if (Tcl_GetIntFromObj(interp,objv[i+1],&value) != TCL_OK)
return TCL_ERROR;
problem.key = (fnpyKey)value;
}
break;
case TYPE:
{
int which = 0;
if (Tcl_GetIndexFromObjStruct(interp,objv[i+1],(char **)&prob_strings[0].name,sizeof(prob_strings[0]),
"type",0,&which
) != TCL_OK)
return TCL_ERROR;
problem.type = (rpmProblemType)prob_strings[which].code;
}
break;
case IGNORE:
{
int value = 0;
if (Tcl_GetIntFromObj(interp,objv[i+1],&value) != TCL_OK)
return TCL_ERROR;
problem.ignoreProblem = value;
}
break;
case STRING:
{
int len = 0;
char *x = Tcl_GetStringFromObj(objv[i+1],&len);
char *p = new char[len+1];
strncpy(p,x,len);
p[len] = 0;
if (problem.str1)
delete [] problem.str1;
problem.str1 = p;
}
break;
case INT:
{
int value = 0;
if (Tcl_GetIntFromObj(interp,objv[i+1],&value) != TCL_OK)
return TCL_ERROR;
problem.ulong1 = value;
}
break;
}
}
Tcl_SetObjResult(interp,prob); // Return value to TCL
return TCL_OK;
}
static int
TestobjCmd(
ClientData clientData, /* Not used. */
Tcl_Interp *interp, /* Current interpreter. */
int objc, /* Number of arguments. */
Tcl_Obj *const objv[]) /* Argument objects. */
{
int varIndex, destIndex, i;
const char *index, *subCmd, *string;
const Tcl_ObjType *targetType;
if (objc < 2) {
wrongNumArgs:
Tcl_WrongNumArgs(interp, 1, objv, "option arg ?arg ...?");
return TCL_ERROR;
}
subCmd = Tcl_GetString(objv[1]);
if (strcmp(subCmd, "assign") == 0) {
if (objc != 4) {
goto wrongNumArgs;
}
index = Tcl_GetString(objv[2]);
if (GetVariableIndex(interp, index, &varIndex) != TCL_OK) {
return TCL_ERROR;
}
if (CheckIfVarUnset(interp, varIndex)) {
return TCL_ERROR;
}
string = Tcl_GetString(objv[3]);
if (GetVariableIndex(interp, string, &destIndex) != TCL_OK) {
return TCL_ERROR;
}
SetVarToObj(destIndex, varPtr[varIndex]);
Tcl_SetObjResult(interp, varPtr[destIndex]);
} else if (strcmp(subCmd, "convert") == 0) {
const char *typeName;
if (objc != 4) {
goto wrongNumArgs;
}
index = Tcl_GetString(objv[2]);
if (GetVariableIndex(interp, index, &varIndex) != TCL_OK) {
return TCL_ERROR;
}
if (CheckIfVarUnset(interp, varIndex)) {
return TCL_ERROR;
}
typeName = Tcl_GetString(objv[3]);
if ((targetType = Tcl_GetObjType(typeName)) == NULL) {
Tcl_AppendStringsToObj(Tcl_GetObjResult(interp),
"no type ", typeName, " found", NULL);
return TCL_ERROR;
}
if (Tcl_ConvertToType(interp, varPtr[varIndex], targetType)
!= TCL_OK) {
return TCL_ERROR;
}
Tcl_SetObjResult(interp, varPtr[varIndex]);
} else if (strcmp(subCmd, "duplicate") == 0) {
if (objc != 4) {
goto wrongNumArgs;
}
index = Tcl_GetString(objv[2]);
if (GetVariableIndex(interp, index, &varIndex) != TCL_OK) {
return TCL_ERROR;
}
if (CheckIfVarUnset(interp, varIndex)) {
return TCL_ERROR;
}
string = Tcl_GetString(objv[3]);
if (GetVariableIndex(interp, string, &destIndex) != TCL_OK) {
return TCL_ERROR;
}
SetVarToObj(destIndex, Tcl_DuplicateObj(varPtr[varIndex]));
Tcl_SetObjResult(interp, varPtr[destIndex]);
} else if (strcmp(subCmd, "freeallvars") == 0) {
if (objc != 2) {
goto wrongNumArgs;
}
for (i = 0; i < NUMBER_OF_OBJECT_VARS; i++) {
if (varPtr[i] != NULL) {
Tcl_DecrRefCount(varPtr[i]);
varPtr[i] = NULL;
}
}
} else if (strcmp(subCmd, "invalidateStringRep") == 0) {
if (objc != 3) {
goto wrongNumArgs;
}
index = Tcl_GetString(objv[2]);
if (GetVariableIndex(interp, index, &varIndex) != TCL_OK) {
return TCL_ERROR;
}
if (CheckIfVarUnset(interp, varIndex)) {
return TCL_ERROR;
}
Tcl_InvalidateStringRep(varPtr[varIndex]);
Tcl_SetObjResult(interp, varPtr[varIndex]);
} else if (strcmp(subCmd, "newobj") == 0) {
if (objc != 3) {
goto wrongNumArgs;
}
index = Tcl_GetString(objv[2]);
if (GetVariableIndex(interp, index, &varIndex) != TCL_OK) {
return TCL_ERROR;
}
SetVarToObj(varIndex, Tcl_NewObj());
Tcl_SetObjResult(interp, varPtr[varIndex]);
} else if (strcmp(subCmd, "objtype") == 0) {
const char *typeName;
/*
* Return an object containing the name of the argument's type of
* internal rep. If none exists, return "none".
*/
if (objc != 3) {
goto wrongNumArgs;
}
if (objv[2]->typePtr == NULL) {
Tcl_SetObjResult(interp, Tcl_NewStringObj("none", -1));
} else {
typeName = objv[2]->typePtr->name;
Tcl_SetObjResult(interp, Tcl_NewStringObj(typeName, -1));
}
} else if (strcmp(subCmd, "refcount") == 0) {
if (objc != 3) {
goto wrongNumArgs;
}
index = Tcl_GetString(objv[2]);
if (GetVariableIndex(interp, index, &varIndex) != TCL_OK) {
return TCL_ERROR;
}
if (CheckIfVarUnset(interp, varIndex)) {
return TCL_ERROR;
}
Tcl_SetObjResult(interp, Tcl_NewIntObj(varPtr[varIndex]->refCount));
} else if (strcmp(subCmd, "type") == 0) {
if (objc != 3) {
goto wrongNumArgs;
}
index = Tcl_GetString(objv[2]);
if (GetVariableIndex(interp, index, &varIndex) != TCL_OK) {
return TCL_ERROR;
}
if (CheckIfVarUnset(interp, varIndex)) {
return TCL_ERROR;
}
if (varPtr[varIndex]->typePtr == NULL) { /* a string! */
Tcl_AppendToObj(Tcl_GetObjResult(interp), "string", -1);
} else {
Tcl_AppendToObj(Tcl_GetObjResult(interp),
varPtr[varIndex]->typePtr->name, -1);
}
} else if (strcmp(subCmd, "types") == 0) {
if (objc != 2) {
goto wrongNumArgs;
}
if (Tcl_AppendAllObjTypes(interp,
Tcl_GetObjResult(interp)) != TCL_OK) {
return TCL_ERROR;
}
} else {
Tcl_AppendStringsToObj(Tcl_GetObjResult(interp),
"bad option \"", Tcl_GetString(objv[1]),
"\": must be assign, convert, duplicate, freeallvars, "
"newobj, objcount, objtype, refcount, type, or types", NULL);
return TCL_ERROR;
}
return TCL_OK;
}
static int obj_Cgmap(ClientData /*UNUSED*/, Tcl_Interp *interp, int argc, Tcl_Obj * const objv[])
{
Tcl_Obj *atomselect = NULL;
Tcl_Obj *object = NULL;
Tcl_Obj *bytes = NULL;
Tcl_Obj *bytes_append = NULL;
Tcl_Obj *sel = NULL;
float *coords = NULL;
float *coords_append = NULL;
const char *blockid_field = "user";
const char *order_field = "user2";
const char *weight_field= "user3";
int nframes, natoms, ncoords, result, length;
int first, last, stride;
int molid, append_molid;
natoms = ncoords = result = 0;
molid = append_molid = 0;
first = last = 0;
stride = 1;
nframes = 1;
std::vector<float> weight;
std::vector<int> bead;
std::vector<int> index;
// Parse Arguments
int n = 1;
while (n < argc) {
const char *cmd = Tcl_GetString(objv[n]);
if (!strncmp(cmd, "-molid", 7)) {
if (Tcl_GetIntFromObj(interp,objv[n+1], &molid) != TCL_OK) {return TCL_ERROR;}
n += 2;
} else if (!strncmp(cmd, "-append", 8)) {
if (Tcl_GetIntFromObj(interp,objv[n+1], &append_molid) != TCL_OK) {return TCL_ERROR;}
n += 2;
} else if (!strncmp(cmd, "-sel", 5)) {
sel = objv[n+1];
n += 2;
} else if (!strncmp(cmd, "-first", 5)) {
if (Tcl_GetIntFromObj(interp,objv[n+1], &first) != TCL_OK) {return TCL_ERROR;}
n += 2;
} else if (!strncmp(cmd, "-last", 4)) {
if (Tcl_GetIntFromObj(interp,objv[n+1], &last) != TCL_OK) {return TCL_ERROR;}
n += 2;
} else if (!strncmp(cmd, "-stride", 6)) {
if (Tcl_GetIntFromObj(interp,objv[n+1], &stride) != TCL_OK) {return TCL_ERROR;}
n += 2;
} else if (!strncmp(cmd, "-weight", 7)) {
weight_field = Tcl_GetString(objv[n+1]);
n += 2;
} else if (!strncmp(cmd, "-blockid", 7)) {
blockid_field = Tcl_GetString(objv[n+1]);
n += 2;
} else if (!strncmp(cmd, "-order", 6)) {
order_field = Tcl_GetString(objv[n+1]);
n += 2;
} else {
Tcl_WrongNumArgs(interp,1,objv, (char *)"molid");
return TCL_ERROR;
}
}
// Create an internal selection that we can manipulate if none was defined
// Note that a passed selection overides the passed molid
if (!sel) {
Tcl_Obj *script = Tcl_ObjPrintf("atomselect %i all", molid);
if (Tcl_EvalObjEx(interp, script, TCL_EVAL_DIRECT) != TCL_OK) {
Tcl_SetResult(interp, (char *) "Cgmap: error calling atomselect", TCL_STATIC);
return TCL_ERROR;
}
atomselect = Tcl_GetObjResult(interp);
Tcl_IncrRefCount(atomselect);
} else {
// Create a internal selection that is a COPY of the passed selection
atomselect = Tcl_DuplicateObj(sel);
Tcl_IncrRefCount(atomselect);
// Get the molid
Tcl_Obj *script = Tcl_DuplicateObj(sel);
Tcl_AppendToObj(script, " molid", -1);
if(Tcl_EvalObjEx(interp, script, TCL_EVAL_DIRECT) != TCL_OK) {
Tcl_SetResult(interp, (char *) "Cgmap: error calling atomselect", TCL_STATIC);
return TCL_ERROR;
}
Tcl_Obj *molid_result = Tcl_GetObjResult(interp);
if (Tcl_GetIntFromObj(interp, molid_result, &molid) != TCL_OK) {return TCL_ERROR;}
}
// Get the number of frames
Tcl_Obj *script = Tcl_ObjPrintf("molinfo %i get numframes", molid);
if (Tcl_EvalObjEx(interp, script, TCL_EVAL_DIRECT) != TCL_OK) {
Tcl_SetResult(interp, (char *) "Cgmap: error calling molinfo for nframes", TCL_STATIC);
return TCL_ERROR;
}
object = Tcl_GetObjResult(interp);
if (Tcl_GetIntFromObj(interp, object, &nframes) != TCL_OK) {
Tcl_SetResult(interp, (char *) "Cgmap: error parsing number of frames", TCL_STATIC);
return TCL_ERROR;
}
if ( first < 0 || first >= nframes ) {
Tcl_SetResult(interp, (char *) "Cgmap: illegal value of first_frame", TCL_STATIC);
return TCL_ERROR;
}
if ( last == -1 || last > nframes || last < first ) last = nframes;
// Get the number of atoms from selection
script = Tcl_DuplicateObj(atomselect);
Tcl_AppendToObj(script, " num", -1);
if (Tcl_EvalObjEx(interp, script, TCL_EVAL_DIRECT) != TCL_OK) {
Tcl_SetResult(interp, (char *) "Cgmap: error calling atomselect", TCL_STATIC);
return TCL_ERROR;
}
object = Tcl_GetObjResult(interp);
if (Tcl_GetIntFromObj(interp, object, &natoms) != TCL_OK) {
Tcl_SetResult(interp, (char *) "Cgmap: error parsing number of atoms", TCL_STATIC);
return TCL_ERROR;
}
// Make sure we actually have some atoms
if (natoms == 0) {
Tcl_SetResult(interp, (char *) "Cgmap: Selection or molecule contains no atoms", TCL_STATIC);
return TCL_ERROR;
}
// Get the weights (mass)
script = Tcl_DuplicateObj(atomselect);
Tcl_AppendPrintfToObj (script, " get %s", weight_field);
if (Tcl_EvalObjEx(interp, script, TCL_EVAL_DIRECT) != TCL_OK) {
Tcl_SetResult(interp, (char *) "Cgmap: error calling atomselect for weights", TCL_STATIC);
return TCL_ERROR;
}
ncoords = parse_vector(Tcl_GetObjResult(interp), weight, interp);
if (ncoords == -1) {
Tcl_SetResult(interp, (char *) "Cgmap: error parsing atomselect result", TCL_STATIC);
return TCL_ERROR;
}
// Get the bead IDs
script = Tcl_DuplicateObj(atomselect);
Tcl_AppendPrintfToObj (script, " get %s", blockid_field);
if (Tcl_EvalObjEx(interp, script, TCL_EVAL_DIRECT) != TCL_OK) {
Tcl_SetResult(interp, (char *) "Cgmap: error calling atomselect for blocks", TCL_STATIC);
return TCL_ERROR;
}
ncoords = parse_ivector(Tcl_GetObjResult(interp), bead, interp, true);
if (ncoords == -1) {
Tcl_SetResult(interp, (char *) "Cgmap: error parsing atomselect result", TCL_STATIC);
return TCL_ERROR;
}
// Get the atom IDs, we use these as a map when accessing the coordinate array
// user2 is set via ::CGit::setBeadID
script = Tcl_DuplicateObj(atomselect);
Tcl_AppendPrintfToObj (script, " get %s", order_field);
if (Tcl_EvalObjEx(interp, script, TCL_EVAL_DIRECT) != TCL_OK) {
Tcl_SetResult(interp, (char *) "Cgmap: error calling atomselect for order", TCL_STATIC);
return TCL_ERROR;
}
ncoords = parse_ivector(Tcl_GetObjResult(interp), index, interp, true);
if (ncoords == -1) {
Tcl_SetResult(interp, (char *) "Cgmap: error parsing atomselect result", TCL_STATIC);
return TCL_ERROR;
}
// Get current frame of the target mol
script = Tcl_ObjPrintf("molinfo %d get frame", append_molid);
if (Tcl_EvalObjEx(interp, script, TCL_EVAL_DIRECT) != TCL_OK) {
Tcl_SetResult(interp, (char *) "Cgmap: error getting append mol's current frame", TCL_STATIC);
return TCL_ERROR;
}
int append_frame = 0;
object = Tcl_GetObjResult(interp);
if (Tcl_GetIntFromObj(interp, object, &append_frame) != TCL_OK) {
Tcl_SetResult(interp, (char *) "Cgmap: error parsing append mol's current frame", TCL_STATIC);
return TCL_ERROR;
}
//Get number of atoms in target (append) mol
script = Tcl_ObjPrintf("molinfo %i get numatoms", append_molid);
if (Tcl_EvalObjEx(interp, script, TCL_EVAL_DIRECT) != TCL_OK) {
Tcl_SetResult(interp, (char *) "Cgmap: error getting append mol's number of atoms", TCL_STATIC);
return TCL_ERROR;
}
int append_natoms = 0;
object = Tcl_GetObjResult(interp);
if (Tcl_GetIntFromObj(interp, object, &append_natoms) != TCL_OK) {
Tcl_SetResult(interp, (char *) "Cgmap: error parsing append mol's number of atoms", TCL_STATIC);
return TCL_ERROR;
}
int print = ((last - first) / 10);
if (print < 10) print = 10;
if (print > 100) print = 100;
//Loop over frames, calculate COMS, set coordinates in target mol
for (int frame = first;
frame <= last && frame < nframes;
frame += stride) {
if (frame % print == 0) {
//Tcl_Obj *msg = Tcl_ObjPrintf ("puts \"Mapping frame %i\"", frame);
Tcl_Obj *msg = Tcl_ObjPrintf ("vmdcon -info \"CGit> Mapping frame %i\"", frame);
result = Tcl_EvalObjEx(interp, msg, TCL_EVAL_DIRECT);
if (result != TCL_OK) { return TCL_ERROR; }
}
//Update the frames
Tcl_Obj *mol_chgframe = Tcl_ObjPrintf ("molinfo top set frame %i", frame);
if (Tcl_EvalObjEx(interp, mol_chgframe, TCL_EVAL_DIRECT) != TCL_OK)
return TCL_ERROR;
// Get the coordinates of the molecules in the reference mol
Tcl_Obj *get_ts = Tcl_ObjPrintf("gettimestep %d %i", molid, frame);
if (Tcl_EvalObjEx(interp, get_ts, TCL_EVAL_DIRECT) != TCL_OK) {
Tcl_SetResult(interp, (char *) "Cgmap: error getting coordinates", TCL_STATIC);
return TCL_ERROR;
}
bytes = Tcl_GetObjResult(interp);
Tcl_IncrRefCount(bytes);
Tcl_InvalidateStringRep (bytes);
coords = reinterpret_cast<float *> (Tcl_GetByteArrayFromObj(bytes, &length));
/** Create a new frame for append_mol **/
Tcl_ObjPrintf("animate dup %i", append_molid);
if (Tcl_EvalObjEx(interp, get_ts, TCL_EVAL_DIRECT) != TCL_OK) {
Tcl_SetResult(interp, (char *) "Cgmap: error adding frame to append mol", TCL_STATIC);
return TCL_ERROR;
}
append_frame++;
Tcl_Obj *setframe = Tcl_ObjPrintf("molinfo %i set frame %i; display update", molid, frame);
if (Tcl_EvalObjEx(interp, setframe, TCL_EVAL_DIRECT) != TCL_OK) {
Tcl_SetResult(interp, (char *) "Cgmap: error updating source frame", TCL_STATIC);
return TCL_ERROR;
}
// Copy PBC conditions
Tcl_Obj *setpbc = Tcl_ObjPrintf("molinfo %i set {a b c} [molinfo %i get {a b c}]", append_molid, molid);
if (Tcl_EvalObjEx(interp, setpbc, TCL_EVAL_DIRECT) != TCL_OK) {
Tcl_SetResult(interp, (char *) "Cgmap: error updating PBC", TCL_STATIC);
return TCL_ERROR;
}
// Get the coordinates of the molecules in the target (append) mol
get_ts = Tcl_ObjPrintf("gettimestep %d %i", append_molid, append_frame);
if (Tcl_EvalObjEx(interp, get_ts, TCL_EVAL_DIRECT) != TCL_OK) {
Tcl_SetResult(interp, (char *) "Cgmap: error getting coordinates", TCL_STATIC);
return TCL_ERROR;
}
bytes_append = Tcl_GetObjResult(interp);
Tcl_IncrRefCount(bytes_append);
Tcl_InvalidateStringRep(bytes_append);
coords_append = reinterpret_cast<float *> (Tcl_GetByteArrayFromObj(bytes_append, &length));
//loop over coordinates and beads, calculate COMs
int current_bead, current_atom;
current_bead = current_atom = 0;
// Nested loop to work on each bead at a time
float w,x,y,z;
int j = 0;
for (int start_atom = 0; start_atom < natoms; ) {
current_bead = bead[start_atom];
w = x = y = z = 0;
// Calculate COM for each bead
for ( current_atom = start_atom;
current_atom < natoms && bead[current_atom] == current_bead;
current_atom++) {
//Lookup the atom index from the selection
unsigned int idx = index[current_atom];
float tw = weight[current_atom];
w += tw;
x += tw * coords[3*idx];
y += tw * coords[3*idx+1];
z += tw * coords[3*idx+2];
}
if (w == 0) {
Tcl_SetResult(interp, (char *) "Cgmap: Bad weight can't total zero", TCL_STATIC);
return TCL_ERROR;
}
// Insert calculated COMS into append_mols coordinate array
// Need to figure out some kind of bounds checking here...
coords_append[3 * j ] = x / w;
coords_append[3 * j + 1] = y / w;
coords_append[3 * j + 2] = z / w;
start_atom = current_atom;
j++;
} // bead loop
// call rawtimestep to set byte array for append_mol
Tcl_Obj *set_ts[5];
set_ts[0] = Tcl_NewStringObj("rawtimestep", -1);
set_ts[1] = Tcl_ObjPrintf("%d",append_molid);
set_ts[2] = bytes_append;
set_ts[3] = Tcl_NewStringObj("-frame", -1);
set_ts[4] = Tcl_NewIntObj(append_frame);
if (Tcl_EvalObjv (interp, 5, set_ts, 0) != TCL_OK)
return TCL_ERROR;
//Cleanup
Tcl_DecrRefCount(bytes);
Tcl_DecrRefCount(bytes_append);
} // Frame loop
//Cleanup
Tcl_DecrRefCount(atomselect);
Tcl_SetResult(interp, (char *) "", TCL_STATIC);
return TCL_OK;
}
Tcl_Obj*
TnmSnmpNorm(Tcl_Interp *interp, Tcl_Obj *objPtr, int flags)
{
int i, code, objc;
Tcl_Obj **objv;
Tcl_Obj *vbListPtr = NULL;
/*
* The following Tcl_Objs are allocated once and reused whenever
* we need to expand a varbind list containing object identifiers
* without any value or type elements.
*/
static Tcl_Obj *nullType = NULL;
static Tcl_Obj *zeroValue = NULL;
static Tcl_Obj *nullValue = NULL;
if (! nullType) {
nullType = Tcl_NewStringObj("NULL", 4);
Tcl_IncrRefCount(nullType);
}
if (! zeroValue) {
zeroValue = Tcl_NewIntObj(0);
Tcl_IncrRefCount(zeroValue);
}
if (! nullValue) {
nullValue = Tcl_NewStringObj(NULL, 0);
Tcl_IncrRefCount(nullValue);
}
/*
* Split the varbind list into a list of varbinds. Create a
* new Tcl list to hold the expanded varbind list.
*/
code = Tcl_ListObjGetElements(interp, objPtr, &objc, &objv);
if (code != TCL_OK) {
goto errorExit;
}
vbListPtr = Tcl_NewListObj(0, NULL);
for (i = 0; i < objc; i++) {
int vbc, type;
Tcl_Obj **vbv, *vbPtr;
TnmOid* oidPtr;
Tcl_Obj *oidObjPtr, *typeObjPtr, *valueObjPtr;
TnmMibNode *nodePtr = NULL;
/*
* Create a new varbind element in the expanded result list
* for each varbind.
*/
vbPtr = Tcl_NewListObj(0, NULL);
Tcl_ListObjAppendElement(interp, vbListPtr, vbPtr);
code = Tcl_ListObjGetElements(interp, objv[i], &vbc, &vbv);
if (code != TCL_OK) {
goto errorExit;
}
/*
* Get the object identifier value from the first list
* element. Check the number of list elements and assign
* them to the oid, type and value variables.
*/
switch (vbc) {
case 1:
oidObjPtr = vbv[0];
typeObjPtr = nullType;
valueObjPtr = nullValue;
break;
case 2:
oidObjPtr = vbv[0];
typeObjPtr = NULL;
valueObjPtr = vbv[1];
break;
case 3:
oidObjPtr = vbv[0];
typeObjPtr = vbv[1];
valueObjPtr = vbv[2];
break;
default: {
char msg[80];
sprintf(msg, "illegal number of elements in varbind %d", i);
Tcl_ResetResult(interp);
Tcl_AppendStringsToObj(Tcl_GetObjResult(interp),
msg, (char *) NULL);
goto errorExit;
}
}
/*
* Check/resolve the object identifier and assign it to the
* result list. Make sure to make a deep copy if the object
* identifier value is shared since the string representation
* must be invalidated to ensure that hexadecimal
* sub-identifier are converted into decimal sub-identifier.
*/
oidPtr = TnmGetOidFromObj(interp, oidObjPtr);
if (! oidPtr) {
goto errorExit;
}
if (Tcl_IsShared(oidObjPtr)) {
oidObjPtr = Tcl_DuplicateObj(oidObjPtr);
}
TnmOidObjSetRep(oidObjPtr, TNM_OID_AS_OID);
Tcl_InvalidateStringRep(oidObjPtr);
Tcl_ListObjAppendElement(interp, vbPtr, oidObjPtr);
/*
* Lookup the type in the MIB if there is no type given in the
* varbind element.
*/
if (! typeObjPtr) {
int syntax;
nodePtr = TnmMibNodeFromOid(oidPtr, NULL);
if (! nodePtr) {
char msg[80];
sprintf(msg, "failed to lookup the type for varbind %d", i);
Tcl_ResetResult(interp);
Tcl_AppendStringsToObj(Tcl_GetObjResult(interp),
msg, (char *) NULL);
goto errorExit;
}
syntax = (nodePtr->typePtr && nodePtr->typePtr->name)
? nodePtr->typePtr->syntax : nodePtr->syntax;
typeObjPtr = Tcl_NewStringObj(
TnmGetTableValue(tnmSnmpTypeTable, (unsigned) syntax), -1);
}
type = TnmGetTableKeyFromObj(NULL, tnmSnmpTypeTable,
typeObjPtr, NULL);
if (type == -1) {
type = TnmGetTableKeyFromObj(NULL, tnmSnmpExceptionTable,
typeObjPtr, NULL);
if (type == -1) {
char msg[80];
invalidType:
sprintf(msg, "illegal type in varbind %d", i);
Tcl_ResetResult(interp);
Tcl_AppendStringsToObj(Tcl_GetObjResult(interp),
msg, (char *) NULL);
goto errorExit;
}
}
Tcl_ListObjAppendElement(interp, vbPtr, typeObjPtr);
/*
* Check the value and perform any conversions needed to
* convert the value into the base type representation.
*/
switch (type) {
case ASN1_INTEGER: {
long longValue;
code = Tcl_GetLongFromObj(interp, valueObjPtr, &longValue);
if (code != TCL_OK) {
if (! nodePtr) {
nodePtr = TnmMibNodeFromOid(oidPtr, NULL);
}
if (nodePtr) {
Tcl_Obj *value;
value = TnmMibScanValue(nodePtr->typePtr, nodePtr->syntax,
valueObjPtr);
if (! value) {
goto errorExit;
}
Tcl_ResetResult(interp);
code = Tcl_GetLongFromObj(interp, value, &longValue);
}
if (code != TCL_OK) {
goto errorExit;
}
valueObjPtr = Tcl_NewLongObj(longValue);
}
if (flags & TNM_SNMP_NORM_INT) {
if (! nodePtr) {
nodePtr = TnmMibNodeFromOid(oidPtr, NULL);
}
if (nodePtr && nodePtr->typePtr) {
Tcl_Obj *newPtr;
newPtr = TnmMibFormatValue(nodePtr->typePtr,
nodePtr->syntax,
valueObjPtr);
if (newPtr) {
valueObjPtr = newPtr;
}
}
}
break;
}
case ASN1_COUNTER32:
case ASN1_GAUGE32:
case ASN1_TIMETICKS: {
TnmUnsigned32 u;
code = TnmGetUnsigned32FromObj(interp, valueObjPtr, &u);
if (code != TCL_OK) {
goto errorExit;
}
break;
}
case ASN1_COUNTER64: {
TnmUnsigned64 u;
code = TnmGetUnsigned64FromObj(interp, valueObjPtr, &u);
if (code != TCL_OK) {
goto errorExit;
}
break;
}
case ASN1_IPADDRESS: {
if (TnmGetIpAddressFromObj(interp, valueObjPtr) == NULL) {
goto errorExit;
}
Tcl_InvalidateStringRep(valueObjPtr);
break;
}
case ASN1_OBJECT_IDENTIFIER:
if (! TnmGetOidFromObj(interp, valueObjPtr)) {
goto errorExit;
}
if (Tcl_IsShared(valueObjPtr)) {
valueObjPtr = Tcl_DuplicateObj(valueObjPtr);
}
if (flags & TNM_SNMP_NORM_OID) {
TnmOidObjSetRep(valueObjPtr, TNM_OID_AS_NAME);
} else {
TnmOidObjSetRep(valueObjPtr, TNM_OID_AS_OID);
}
Tcl_InvalidateStringRep(valueObjPtr);
break;
case ASN1_OCTET_STRING: {
int len;
if (! nodePtr) {
nodePtr = TnmMibNodeFromOid(oidPtr, NULL);
}
if (nodePtr) {
Tcl_Obj *scan;
scan = TnmMibScanValue(nodePtr->typePtr, nodePtr->syntax,
valueObjPtr);
if (scan) {
valueObjPtr = scan;
}
}
if (TnmGetOctetStringFromObj(interp, valueObjPtr, &len) == NULL) {
goto errorExit;
}
Tcl_InvalidateStringRep(valueObjPtr);
break;
}
case ASN1_NULL:
valueObjPtr = nullValue;
break;
default:
goto invalidType;
}
Tcl_ListObjAppendElement(interp, vbPtr, valueObjPtr);
}
return vbListPtr;
errorExit:
if (vbListPtr) {
Tcl_DecrRefCount(vbListPtr);
}
return NULL;
}