5 #ifndef BALL_VIEW_WIDGETS_MOLECULARSTRUCTURE_H
6 #define BALL_VIEW_WIDGETS_MOLECULARSTRUCTURE_H
8 #ifndef BALL_VIEW_KERNEL_MODULARWIDGET_H
12 #ifndef BALL_MATHS_VECTOR3_H
16 #ifndef BALL_VIEW_DIALOGS_AMBERCONFIGURATIONDIALOG_H
20 #ifndef BALL_VIEW_DIALOGS_MINIMIZATIONDIALOG_H
24 #ifndef BALL_VIEW_DIALOGS_MOLECULARDYNAMICSDIALOG_H
28 #ifndef BALL_VIEW_DIALOGS_CHARMMCONFIGURATIONDIALOG_H
32 #ifndef BALL_VIEW_DIALOGS_MMFF94CONFIGURATIONDIALOG_H
36 #ifndef BALL_VIEW_DIALOGS_ASSIGNBONDORDERCONFIGURATIONDIALOG_H
40 #ifndef BALL_VIEW_DIALOGS_ASSIGNBONDORDERRESULTSDIALOG_H
44 #ifndef BALL_VIEW_DIALOGS_GENERaTECRYSTALDIALOG_H
48 #ifndef BALL_MOLMEC_AMBER_AMBER_H
52 #ifndef BALL_MOLMEC_CHARMM_CHARMM_H
56 #ifndef BALL_MOLMEC_MMFF94_MMFF94
61 #include <QtGui/QWidget>
150 virtual void onNotify(
Message *message);
166 virtual void initializeWidget(
MainControl& main_control);
199 virtual void fetchPreferences(
INIFile &inifile);
204 virtual void writePreferences(
INIFile &inifile);
234 void centerCamera(
Composite* composite = 0);
257 void runBondOrderAssignment(
bool show_dialog =
true);
280 virtual bool checkResidue();
283 virtual void createGridFromDistance();
286 virtual void createGridFromCameraDistance();
289 virtual void calculateSecondaryStructure();
292 virtual void mapProteins();
295 virtual void calculateRMSD();
301 bool generateCrystal(
bool show =
true);
304 void calculateHBonds();
307 void calculateRamachandranPlot();
313 void calculateForceFieldEnergy();
316 void runMinimization(
bool show_dialog_ =
true);
319 void MDSimulation(
bool show_dialog_ =
true);
322 void showAmberForceFieldOptions();
325 void showCharmmForceFieldOptions();
328 void showMMFF94ForceFieldOptions();
331 void chooseAmberFF();
334 void chooseCharmmFF();
343 void setupForceField();
346 bool calculateFDPB(
bool show =
true);
352 virtual void addComposite_(
Composite& composite,
const String& name,
bool normalize =
true);
354 void applyForceFieldSettings_();
356 void selectUnassignedForceFieldAtoms_();
358 bool setupForceField_(
System* system,
bool disable_selection =
false);
360 QAction* center_camera_id_;
361 QAction* build_bonds_id_;
362 QAction* build_endcaps_id_;
363 QAction* assign_bond_orders_id_;
364 QAction* add_hydrogens_id_;
365 QAction* check_structure_id_;
366 QAction* create_distance_grid_id_, *create_distance_grid_id2_;
367 QAction* calculate_ss_id_;
368 QAction* map_proteins_id_;
369 QAction* calculate_RMSD_id_;
370 QAction* assign_charges_id_;
372 QAction* minimization_id_;
373 QAction* mdsimulation_id_;
374 QAction* build_peptide_id_;
375 QAction* calculate_hbonds_id_;
376 QAction* amber_ff_id_;
377 QAction* charmm_ff_id_;
380 QAction* calculate_ramachandran_;
382 QAction* generate_crystal_;
402 #endif // BALL_VIEW_WIDGETS_MOLECULARSTRUCTURE_H
Assignment of bond orders from topology information.
AssignBondOrderResultsDialog & getBondOrderResultsDialog()
const AssignBondOrderConfigurationDialog & getBondOrderDialog() const
FDPBDialog * getFDPBDialog()
const AssignBondOrderResultsDialog & getBondOrderResultsDialog() const
#define BALL_EMBEDDABLE(TYPE, BASE)
MolecularDynamicsDialog & getMDSimulationDialog()
AssignBondOrderConfigurationDialog & getBondOrderDialog()
MinimizationDialog & getMinimizationDialog()
-*- Mode: C++; tab-width: 2; -*-