Go to the documentation of this file.
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 <QtWidgets/QWidget>
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
virtual ~MolecularStructure()
bool calculateFDPB(bool show=true)
virtual void writePreferences(INIFile &inifile)
void buildPeptide()
Build a Peptide from a amino acid sequence.
MolecularStructure(QWidget *parent=0, const char *name=0)
void chooseMMFF94()
Slot for a menu entry to select the MMFF94 force field.
bool generateCrystal(bool show=true)
Build a crystal packing for a loaded system.
virtual void calculateRMSD()
Calculate the RMSD between two Molecules.
MinimizationDialog & getMinimizationDialog()
void chooseCharmmFF()
Slot for a menu entry to select the CHARMM force field.
virtual bool checkResidue()
#define BALL_EMBEDDABLE(TYPE, BASE)
Assignment of bond orders from topology information.
void chooseAmberFF()
Slot for a menu entry to select the AMBER force field.
void calculateHBonds()
Calculate the H-Bonds for a Protein.
virtual void checkMenu(MainControl &main_control)
const AssignBondOrderConfigurationDialog & getBondOrderDialog() const
void calculateForceFieldEnergy()
Calculate the energy for the currently selected force field.
void showMMFF94ForceFieldOptions()
void chooseForceField(Position nr)
Position getForceFieldID()
void runBondOrderAssignment(bool show_dialog=true)
virtual void createGridFromDistance()
Create a RegularData3D instance with the distance from the geometric center.
virtual void createGridFromCameraDistance()
AssignBondOrderResultsDialog & getBondOrderResultsDialog()
virtual void onNotify(Message *message)
virtual void fetchPreferences(INIFile &inifile)
AmberConfigurationDialog & getAmberConfigurationDialog()
Get an instance of an dialog to setup the AMBER forcefield.
MolecularStructure(const MolecularStructure &m)
only needed for Python Interface, dont call it!
const AssignBondOrderResultsDialog & getBondOrderResultsDialog() const
virtual void initializeWidget(MainControl &main_control)
virtual void mapProteins()
Map two Proteins and apply the resulting transformation matrix.
void calculateRamachandranPlot()
Calculate a Ramachandran Plot.
void setupForceField()
Show a dialog to setup the currently selected force field.
MMFF94ConfigurationDialog & getMMFF94ConfigurationDialog()
MolecularDynamicsDialog & getMDSimulationDialog()
void runMinimization(bool show_dialog_=true)
Run a energy minization with the currently selected force field.
void MDSimulation(bool show_dialog_=true)
Perfomr a molecular dynamics simulation with the currently selected force field.
AssignBondOrderConfigurationDialog & getBondOrderDialog()
void showBondOrderAssignmentResults(AssignBondOrderProcessor &bop)
void showCharmmForceFieldOptions()
Show the dialog to setup the CHARMM force field.
FDPBDialog * getFDPBDialog()
void showAmberForceFieldOptions()
Show the dialog to setup the AMBER force field.
ForceField & getForceField()
CharmmConfigurationDialog & getCharmmConfigurationDialog()
Get an instance of an dialog to setup the CHARMM forcefield.
virtual void calculateSecondaryStructure()
Calculate the secondary structure for a protein.
void centerCamera(Composite *composite=0)