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);
203 virtual void fetchPreferences(
INIFile &inifile);
208 virtual void writePreferences(
INIFile &inifile);
238 void centerCamera(
Composite* composite = 0);
261 void runBondOrderAssignment(
bool show_dialog =
true);
284 virtual bool checkResidue();
287 virtual void createGridFromDistance();
290 virtual void createGridFromCameraDistance();
293 virtual void calculateSecondaryStructure();
296 virtual void mapProteins();
299 virtual void calculateRMSD();
305 bool generateCrystal(
bool show =
true);
308 void calculateHBonds();
311 void calculateRamachandranPlot();
317 void calculateForceFieldEnergy();
320 void runMinimization(
bool show_dialog_ =
true);
323 void MDSimulation(
bool show_dialog_ =
true);
326 void showAmberForceFieldOptions();
329 void showCharmmForceFieldOptions();
332 void showMMFF94ForceFieldOptions();
335 void chooseAmberFF();
338 void chooseCharmmFF();
347 void setupForceField();
350 bool calculateFDPB(
bool show =
true);
356 virtual void addComposite_(
Composite& composite,
const String& name,
bool normalize =
true);
358 void applyForceFieldSettings_();
360 void selectUnassignedForceFieldAtoms_();
362 bool setupForceField_(
System* system,
bool disable_selection =
false);
364 QAction* center_camera_id_;
365 QAction* build_bonds_id_;
366 QAction* build_endcaps_id_;
367 QAction* assign_bond_orders_id_;
368 QAction* add_hydrogens_id_;
369 QAction* check_structure_id_;
370 QAction* create_distance_grid_id_, *create_distance_grid_id2_;
371 QAction* calculate_ss_id_;
372 QAction* map_proteins_id_;
373 QAction* calculate_RMSD_id_;
374 QAction* assign_charges_id_;
376 QAction* minimization_id_;
377 QAction* mdsimulation_id_;
378 QAction* build_peptide_id_;
379 QAction* calculate_hbonds_id_;
380 QAction* amber_ff_id_;
381 QAction* charmm_ff_id_;
384 QAction* calculate_ramachandran_;
386 QAction* generate_crystal_;
406 #endif // BALL_VIEW_WIDGETS_MOLECULARSTRUCTURE_H
Assignment of bond orders from topology information.
AssignBondOrderResultsDialog & getBondOrderResultsDialog()
FDPBDialog * getFDPBDialog()
#define BALL_EMBEDDABLE(TYPE, BASE)
const AssignBondOrderResultsDialog & getBondOrderResultsDialog() const
MolecularDynamicsDialog & getMDSimulationDialog()
AssignBondOrderConfigurationDialog & getBondOrderDialog()
MinimizationDialog & getMinimizationDialog()
-*- Mode: C++; tab-width: 2; -*-
const AssignBondOrderConfigurationDialog & getBondOrderDialog() const