// Retrieve desired value
bool BasisShellVariable::retrieveAccessor(int i, ReturnValue& rv, bool hasArrayIndex, int arrayIndex)
{
Messenger::enter("BasisShellVariable::retrieveAccessor");
// Cast 'i' into Accessors enum value
if ((i < 0) || (i >= nAccessors))
{
printf("Internal Error: Accessor id %i is out of range for BasisShell type.\n", i);
Messenger::exit("BasisShellVariable::retrieveAccessor");
return false;
}
Accessors acc = (Accessors) i;
// Check for correct lack/presence of array index given
if ((accessorData[i].arraySize == 0) && hasArrayIndex)
{
Messenger::print("Error: Unnecessary array index provided for member '%s'.", qPrintable(accessorData[i].name));
Messenger::exit("BasisShellVariable::retrieveAccessor");
return false;
}
else if ((accessorData[i].arraySize > 0) && (hasArrayIndex))
{
if ((arrayIndex < 1) || (arrayIndex > accessorData[i].arraySize))
{
Messenger::print("Error: Array index out of bounds for member '%s' (%i, range is 1-%i).", qPrintable(accessorData[i].name), arrayIndex, accessorData[i].arraySize);
Messenger::exit("BasisShellVariable::retrieveAccessor");
return false;
}
}
// Get current data from ReturnValue
bool result = true;
BasisShell* ptr = (BasisShell*) rv.asPointer(VTypes::BasisShellData, result);
if ((!result) || (ptr == NULL))
{
Messenger::print("Invalid (NULL) %s reference encountered.", VTypes::dataType(VTypes::BasisShellData));
result = false;
}
if (result) switch (acc)
{
case (BasisShellVariable::AtomId):
rv.set(ptr->atomId()+1);
break;
case (BasisShellVariable::Primitives):
if ((arrayIndex < 1) || (arrayIndex > ptr->nPrimitives()))
{
Messenger::print("Array index [%i] is out of range for 'primitives' member.", arrayIndex);
result = false;
}
else rv.set(VTypes::BasisPrimitiveData, ptr->primitive(arrayIndex-1));
break;
case (BasisShellVariable::Type):
rv.set(BasisShell::basisShellType(ptr->type()));
break;
default:
printf("Internal Error: Access to member '%s' has not been defined in BasisShellVariable.\n", qPrintable(accessorData[i].name));
result = false;
break;
}
Messenger::exit("BasisShellVariable::retrieveAccessor");
return result;
}
ATEN_USING_NAMESPACE
// Get part of string before specified character/string
bool Commands::function_AfterStr(CommandNode* c, Bundle& obj, ReturnValue& rv)
{
rv.set(c->argc(0).section(c->argc(1), 1)); // ATEN2 TODO Test this
if (c->hasArg(2) && c->argb(2) && (rv.asString()[0] == '\0')) rv.set(c->argc(0));
return true;
}
// Retrieve desired value
bool WidgetVariable::retrieveAccessor(int i, ReturnValue& rv, bool hasArrayIndex, int arrayIndex)
{
Messenger::enter("WidgetVariable::retrieveAccessor");
// Cast 'i' into Accessors enum value
if ((i < 0) || (i >= nAccessors))
{
printf("Internal Error: Accessor id %i is out of range for Aten type.\n", i);
Messenger::exit("WidgetVariable::retrieveAccessor");
return false;
}
Accessors acc = (Accessors) i;
// Check for correct lack/presence of array index given
if ((accessorData[i].arraySize == 0) && hasArrayIndex)
{
Messenger::print("Error: Unnecessary array index provided for member '%s'.", qPrintable(accessorData[i].name));
Messenger::exit("WidgetVariable::retrieveAccessor");
return false;
}
else if ((accessorData[i].arraySize > 0) && (hasArrayIndex))
{
if ((arrayIndex < 1) || (arrayIndex > accessorData[i].arraySize))
{
Messenger::print("Error: Array index out of bounds for member '%s' (%i, range is 1-%i).", qPrintable(accessorData[i].name), arrayIndex, accessorData[i].arraySize);
Messenger::exit("WidgetVariable::retrieveAccessor");
return false;
}
}
// Variables used in retrieval
bool result = true;
TreeGuiWidget* ptr = (TreeGuiWidget*) rv.asPointer(VTypes::WidgetData, result);
if ((!result) || (ptr == NULL))
{
Messenger::print("Invalid (NULL) %s reference encountered.", VTypes::dataType(VTypes::WidgetData));
result = false;
}
if (result) switch (acc)
{
case (WidgetVariable::Enabled):
rv.set(ptr->enabled());
break;
case (WidgetVariable::VerticalFill):
rv.set(ptr->qtWidgetObject() == NULL ? false : ptr->qtWidgetObject()->autoFillVertical());
break;
case (WidgetVariable::Visible):
rv.set(ptr->visible());
break;
default:
printf("Internal Error: Access to member '%s' has not been defined in WidgetVariable.\n", qPrintable(accessorData[i].name));
result = false;
break;
}
Messenger::exit("WidgetVariable::retrieveAccessor");
return result;
}
// Retrieve desired value
bool MatrixVariable::retrieveAccessor(int i, ReturnValue& rv, bool hasArrayIndex, int arrayIndex)
{
Messenger::enter("MatrixVariable::retrieveAccessor");
// Cast 'i' into Accessors enum value
if ((i < 0) || (i >= nAccessors))
{
printf("Internal Error: Accessor id %i is out of range for Matrix type.\n", i);
Messenger::exit("MatrixVariable::retrieveAccessor");
return false;
}
Accessors acc = (Accessors) i;
// Check for correct lack/presence of array index given
if (hasArrayIndex)
{
Messenger::print("Error: Unnecessary array index provided for member '%s'.", qPrintable(accessorData[i].name));
Messenger::exit("MatrixVariable::retrieveAccessor");
return false;
}
// Get current data from ReturnValue
bool result = true;
Matrix m = rv.asMatrix(result);
if (result) switch (acc)
{
case (MatrixVariable::Determinant):
rv.set(m.determinant());
break;
case (MatrixVariable::XX):
case (MatrixVariable::XY):
case (MatrixVariable::XZ):
case (MatrixVariable::XW):
case (MatrixVariable::YX):
case (MatrixVariable::YY):
case (MatrixVariable::YZ):
case (MatrixVariable::YW):
case (MatrixVariable::ZX):
case (MatrixVariable::ZY):
case (MatrixVariable::ZZ):
case (MatrixVariable::ZW):
case (MatrixVariable::WX):
case (MatrixVariable::WY):
case (MatrixVariable::WZ):
case (MatrixVariable::WW):
rv.set(m[acc-MatrixVariable::XX]);
break;
default:
printf("Internal Error: Access to member '%s' has not been defined in MatrixVariable.\n", qPrintable(accessorData[i].name));
result = false;
break;
}
Messenger::exit("MatrixVariable::retrieveAccessor");
return result;
}
// Perform desired function
bool ForcefieldBoundVariable::performFunction(int i, ReturnValue& rv, TreeNode* node)
{
Messenger::enter("ForcefieldBoundVariable::performFunction");
// Cast 'i' into Accessors enum value
if ((i < 0) || (i >= nFunctions))
{
printf("Internal Error: FunctionAccessor id %i is out of range for ForcefieldBound type.\n", i);
Messenger::exit("ForcefieldBoundVariable::performFunction");
return false;
}
// Get current data from ReturnValue
bool result = true;
ForcefieldBound* ptr = (ForcefieldBound*) rv.asPointer(VTypes::ForcefieldBoundData, result);
int id;
if (result) switch (i)
{
case (ForcefieldBoundVariable::Parameter):
switch (ptr->type())
{
case (ForcefieldBound::BondInteraction):
case (ForcefieldBound::UreyBradleyInteraction):
id = BondFunctions::bondParameter(ptr->bondForm(), node->argc(0), true);
if (id == BondFunctions::functionData[ptr->bondForm()].nParameters) result = false;
else rv.set(ptr->parameter(id));
break;
case (ForcefieldBound::AngleInteraction):
id = AngleFunctions::angleParameter(ptr->angleForm(), node->argc(0), true);
if (id == AngleFunctions::functionData[ptr->angleForm()].nParameters) result = false;
else rv.set(ptr->parameter(id));
break;
case (ForcefieldBound::TorsionInteraction):
case (ForcefieldBound::ImproperInteraction):
id = TorsionFunctions::torsionParameter(ptr->torsionForm(), node->argc(0), true);
if (id == TorsionFunctions::functionData[ptr->torsionForm()].nParameters) result = false;
else rv.set(ptr->parameter(id));
break;
default:
break;
}
break;
default:
printf("Internal Error: Access to function '%s' has not been defined in ForcefieldBoundVariable.\n", qPrintable(functionData[i].name));
result = false;
break;
}
Messenger::exit("ForcefieldBoundVariable::performFunction");
return result;
}
void List<T>::splice(ContextType ctx, ObjectType this_object, size_t argc, const ValueType arguments[], ReturnValue &return_value) {
validate_argument_count_at_least(argc, 1);
auto list = get_internal<T, ListClass<T>>(this_object);
size_t size = list->size();
long index = std::min<long>(Value::to_number(ctx, arguments[0]), size);
if (index < 0) {
index = std::max<long>(size + index, 0);
}
size_t remove;
if (argc < 2) {
remove = size - index;
}
else {
remove = std::max<long>(Value::to_number(ctx, arguments[1]), 0);
remove = std::min<long>(remove, size - index);
}
std::vector<ValueType> removed_objects;
removed_objects.reserve(remove);
for (size_t i = 0; i < remove; i++) {
auto realm_object = realm::Object(list->get_realm(), list->get_object_schema(), list->get(index));
removed_objects.push_back(RealmObject<T>::create_instance(ctx, realm_object));
list->remove(index);
}
for (size_t i = 2; i < argc; i++) {
list->insert(ctx, arguments[i], index + i - 2);
}
return_value.set(Object::create_array(ctx, removed_objects));
}
// Set whether 2D grid uses data value as height component
bool Commands::function_GridUseZ(CommandNode* c, Bundle& obj, ReturnValue& rv)
{
if (obj.notifyNull(Bundle::GridPointer)) return false;
if (c->hasArg(0)) obj.g->setUseDataForZ(c->argb(0));
rv.set(obj.g->useDataForZ());
return true;
}
// Replace characters in supplied string
bool Commands::function_ReplaceChars(CommandNode* c, Bundle& obj, ReturnValue& rv)
{
QString result = c->argc(0);
for (int n=0; n<c->argc(1).length(); ++n) result = result.replace(c->argc(1).at(n), c->argc(2));
rv.set(result);
return true;
}
// Perform desired function
bool BasisShellVariable::performFunction(int i, ReturnValue& rv, TreeNode* node)
{
Messenger::enter("BasisShellVariable::performFunction");
// Cast 'i' into Accessors enum value
if ((i < 0) || (i >= nFunctions))
{
printf("Internal Error: FunctionAccessor id %i is out of range for BasisShell type.\n", i);
Messenger::exit("BasisShellVariable::performFunction");
return false;
}
// Get current data from ReturnValue
bool result = true;
BasisShell* ptr = (BasisShell*) rv.asPointer(VTypes::BasisShellData, result);
BasisPrimitive* prim;
int n;
if (result) switch (i)
{
case (BasisShellVariable::AddPrimitive):
prim = ptr->addPrimitive();
prim->setExponent( node->argd(0) );
for (n=1; n<node->nArgs(); ++n) prim->addCoefficient(node->argd(n));
rv.set(VTypes::BasisPrimitiveData, prim);
break;
default:
printf("Internal Error: Access to function '%s' has not been defined in BasisShellVariable.\n", qPrintable(functionData[i].name));
result = false;
break;
}
Messenger::exit("BasisShellVariable::performFunction");
return result;
}
// Set view percentage for secondary surface
bool Commands::function_GridViewPercentageSecondary(CommandNode* c, Bundle& obj, ReturnValue& rv)
{
if (obj.notifyNull(Bundle::GridPointer)) return false;
if (c->hasArg(0)) obj.g->setSecondaryCutoffAsViewPercentage(c->argd(0), c->hasArg(1) ? c->argb(1) : false);
rv.set((obj.g->partialSecondarySum() / obj.g->totalAbsoluteSum())*100.0);
return true;
}
// Set visibility of grid data
bool Commands::function_GridVisible(CommandNode* c, Bundle& obj, ReturnValue& rv)
{
if (obj.notifyNull(Bundle::GridPointer)) return false;
if (c->hasArg(0)) obj.g->setVisible(c->argb(0));
rv.set(obj.g->isVisible());
return true;
}
// Return value of node
bool MatrixVariable::execute(ReturnValue& rv)
{
// If this matrix is a constant, read the nine stored expressions to recreate it
if (readOnly_) reCreate();
rv.set(matrixData_);
return true;
}
// Perform desired function
bool BondVariable::performFunction(int i, ReturnValue& rv, TreeNode* node)
{
Messenger::enter("BondVariable::performFunction");
// Cast 'i' into Accessors enum value
if ((i < 0) || (i >= nFunctions))
{
printf("Internal Error: FunctionAccessor id %i is out of range for Bond type.\n", i);
Messenger::exit("BondVariable::performFunction");
return false;
}
// Get current data from ReturnValue
bool result = true;
Bond* ptr = (Bond*) rv.asPointer(VTypes::BondData, result);
if (result) switch (i)
{
case (BondVariable::Partner):
rv.set(VTypes::AtomData, ptr->partner( (Atom*) node->argp(0, VTypes::AtomData)));
break;
default:
printf("Internal Error: Access to function '%s' has not been defined in BondVariable.\n", qPrintable(functionData[i].name));
result = false;
break;
}
Messenger::exit("BondVariable::performFunction");
return result;
}
// Initialise grid, setting extent of grid (number of points in each direction)
bool Commands::function_InitialiseGrid(CommandNode* c, Bundle& obj, ReturnValue& rv)
{
if (obj.notifyNull(Bundle::GridPointer)) return false;
Grid::GridType gt = Grid::gridType(c->argc(0), true);
if (gt == Grid::nGridTypes) return false;
rv.set(obj.g->initialise(gt, c->arg3i(1)));
return true;
}
// Create new grid in the current model
bool Commands::function_NewGrid(CommandNode* c, Bundle& obj, ReturnValue& rv)
{
if (obj.notifyNull(Bundle::ModelPointer)) return false;
obj.g = aten_.currentModel()->addGrid();
obj.g->setName(c->argc(0).trimmed());
rv.set(VTypes::GridData, obj.g);
return true;
}
void RealmObjectClass<T>::get_property(ContextType ctx, ObjectType object, const String &property, ReturnValue &return_value) {
try {
auto realm_object = get_internal<T, RealmObjectClass<T>>(object);
auto result = realm_object->template get_property_value<ValueType>(ctx, property);
return_value.set(result);
} catch (InvalidPropertyException &ex) {
// getters for nonexistent properties in JS should always return undefined
}
}
void List<T>::unshift(ContextType ctx, ObjectType this_object, size_t argc, const ValueType arguments[], ReturnValue &return_value) {
validate_argument_count_at_least(argc, 1);
auto list = get_internal<T, ListClass<T>>(this_object);
for (size_t i = 0; i < argc; i++) {
list->insert(ctx, arguments[i], i);
}
return_value.set((uint32_t)list->size());
}
// Return value of node as array
bool MatrixArrayVariable::executeAsArray(ReturnValue& rv, int arrayIndex)
{
// Check bounds
if ((arrayIndex < 0) || (arrayIndex >= arraySize_))
{
Messenger::print("Error: Array index %i is out of bounds for array '%s'.", arrayIndex+1, qPrintable(name_));
return false;
}
rv.set( matrixArrayData_[arrayIndex] );
return true;
}
void ListClass<T>::unshift(ContextType ctx, FunctionType, ObjectType this_object, size_t argc, const ValueType arguments[], ReturnValue &return_value) {
validate_argument_count_at_least(argc, 1);
auto list = get_internal<T, ListClass<T>>(this_object);
NativeAccessor<T> accessor(ctx, list->get_realm(), list->get_object_schema());
for (size_t i = 0; i < argc; i++) {
list->insert(accessor, i, arguments[i]);
}
return_value.set((uint32_t)list->size());
}
// Load grid ('loadgrid <filename>')
bool Commands::function_LoadGrid(CommandNode* c, Bundle& obj, ReturnValue& rv)
{
if (obj.notifyNull(Bundle::ModelPointer)) return false;
Grid* g = NULL;
if (aten_.importGrid(obj.rs(), c->argc(0))) g = obj.g;
else return false;
// Set return value
rv.set(VTypes::GridData, g);
return true;
}
// Convert string to integer number
bool Commands::function_AToI(CommandNode* c, Bundle& obj, ReturnValue& rv)
{
static QRegularExpression re("[\\d.\\-eE]+");
QRegularExpressionMatch match = re.match(c->argc(0));
if (match.hasMatch()) rv.set( match.captured(0).toInt() );
else
{
Messenger::warn("Couldn't convert '%s' to an integer number.\n", qPrintable(c->argc(0)));
rv.reset();
}
return true;
}
// Return string based on supplied format and arguments
bool Commands::function_ToA(CommandNode* c, Bundle& obj, ReturnValue& rv)
{
Format* fmt = c->createFormat(0,1);
if (fmt == NULL)
{
printf("Error - No format defined in 'toa' command.\n");
return false;
}
bool result = fmt->writeToString();
if (result) rv.set(fmt->string());
else rv.reset();
return result;
}
void List<T>::shift(ContextType ctx, ObjectType this_object, size_t argc, const ValueType arguments[], ReturnValue &return_value) {
validate_argument_count(argc, 0);
auto list = get_internal<T, ListClass<T>>(this_object);
if (list->size() == 0) {
list->verify_in_transaction();
return_value.set_undefined();
}
else {
auto realm_object = realm::Object(list->get_realm(), list->get_object_schema(), list->get(0));
return_value.set(RealmObject<T>::create_instance(ctx, realm_object));
list->remove(0);
}
}
void ListClass<T>::pop(ContextType ctx, FunctionType, ObjectType this_object, size_t argc, const ValueType arguments[], ReturnValue &return_value) {
validate_argument_count(argc, 0);
auto list = get_internal<T, ListClass<T>>(this_object);
size_t size = list->size();
if (size == 0) {
list->verify_in_transaction();
return_value.set_undefined();
}
else {
size_t index = size - 1;
auto realm_object = realm::Object(list->get_realm(), list->get_object_schema(), list->get(index));
return_value.set(RealmObjectClass<T>::create_instance(ctx, std::move(realm_object)));
list->remove(index);
}
}
// Return nth grid of model
bool Commands::function_GetGrid(CommandNode* c, Bundle& obj, ReturnValue& rv)
{
if (obj.notifyNull(Bundle::ModelPointer)) return false;
Grid* g = NULL;
switch (c->argType(0))
{
case (VTypes::IntegerData):
g = obj.rs()->grid(c->argi(0)-1);
break;
case (VTypes::GridData):
g = (Grid*) c->argp(0, VTypes::GridData);
break;
default:
Messenger::print("Can't convert a variable of type '%s' to a Grid.", VTypes::dataType(c->argType(0)));
break;
}
if (g == NULL) return false;
rv.set(VTypes::GridData, g);
return true;
}
ATEN_USING_NAMESPACE
// Assign charge to selected atoms in model ('charge <q>'), or get charge of current selection
bool Commands::function_Charge(CommandNode* c, Bundle& obj, ReturnValue& rv)
{
if (obj.notifyNull(Bundle::ModelPointer)) return false;
double q = 0.0;
if (c->hasArg(0))
{
obj.rs()->beginUndoState("Charge selected atoms");
for (RefListItem<Atom,int>* ri = obj.rs()->selection(); ri != NULL; ri = ri->next) obj.rs()->atomSetCharge(ri->item, c->argd(0));
obj.rs()->endUndoState();
}
else
{
q = 0.0;
for (RefListItem<Atom,int>* ri = obj.rs()->selection(); ri != NULL; ri = ri->next) q += ri->item->charge();
}
rv.set(q);
return true;
}
void List<T>::get_index(ContextType ctx, ObjectType object, uint32_t index, ReturnValue &return_value) {
auto list = get_internal<T, ListClass<T>>(object);
auto realm_object = realm::Object(list->get_realm(), list->get_object_schema(), list->get(index));
return_value.set(RealmObject<T>::create_instance(ctx, realm_object));
}
void List<T>::get_length(ContextType ctx, ObjectType object, ReturnValue &return_value) {
auto list = get_internal<T, ListClass<T>>(object);
return_value.set((uint32_t)list->size());
}
void List<T>::sorted(ContextType ctx, ObjectType this_object, size_t argc, const ValueType arguments[], ReturnValue &return_value) {
validate_argument_count(argc, 1, 2);
auto list = get_internal<T, ListClass<T>>(this_object);
return_value.set(Results<T>::create_sorted(ctx, *list, argc, arguments));
}
void List<T>::snapshot(ContextType ctx, ObjectType this_object, size_t argc, const ValueType arguments[], ReturnValue &return_value) {
validate_argument_count(argc, 0);
auto list = get_internal<T, ListClass<T>>(this_object);
return_value.set(Results<T>::create_instance(ctx, *list, false));
}
