molecularStructure.h

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// -*- Mode: C++; tab-width: 2; -*-
// vi: set ts=2:
//

#ifndef BALL_VIEW_WIDGETS_MOLECULARSTRUCTURE_H
#define BALL_VIEW_WIDGETS_MOLECULARSTRUCTURE_H

#ifndef BALL_VIEW_KERNEL_MODULARWIDGET_H
# include <BALL/VIEW/KERNEL/modularWidget.h>
#endif

#ifndef BALL_MATHS_VECTOR3_H
 #include <BALL/MATHS/vector3.h>
#endif

#ifndef BALL_VIEW_DIALOGS_AMBERCONFIGURATIONDIALOG_H
 #include <BALL/VIEW/DIALOGS/amberConfigurationDialog.h>
#endif

#ifndef BALL_VIEW_DIALOGS_MINIMIZATIONDIALOG_H
# include <BALL/VIEW/DIALOGS/minimizationDialog.h>
#endif

#ifndef BALL_VIEW_DIALOGS_MOLECULARDYNAMICSDIALOG_H
# include <BALL/VIEW/DIALOGS/molecularDynamicsDialog.h>
#endif

#ifndef BALL_VIEW_DIALOGS_CHARMMCONFIGURATIONDIALOG_H
# include <BALL/VIEW/DIALOGS/charmmConfigurationDialog.h>
#endif

#ifndef BALL_VIEW_DIALOGS_MMFF94CONFIGURATIONDIALOG_H
# include <BALL/VIEW/DIALOGS/MMFF94ConfigurationDialog.h>
#endif

#ifndef BALL_VIEW_DIALOGS_ASSIGNBONDORDERCONFIGURATIONDIALOG_H
# include <BALL/VIEW/DIALOGS/assignBondOrderConfigurationDialog.h>
#endif

#ifndef BALL_VIEW_DIALOGS_ASSIGNBONDORDERRESULTSDIALOG_H
# include <BALL/VIEW/DIALOGS/assignBondOrderResultsDialog.h>
#endif

#ifndef BALL_VIEW_DIALOGS_GENERaTECRYSTALDIALOG_H
# include <BALL/VIEW/DIALOGS/generateCrystalDialog.h>
#endif

#ifndef BALL_MOLMEC_AMBER_AMBER_H
# include <BALL/MOLMEC/AMBER/amber.h>
#endif

#ifndef BALL_MOLMEC_CHARMM_CHARMM_H
# include <BALL/MOLMEC/CHARMM/charmm.h>
#endif

#ifndef BALL_MOLMEC_MMFF94_MMFF94
# include <BALL/MOLMEC/MMFF94/MMFF94.h>
#endif


#include <QtGui/QWidget>

namespace BALL
{
  class Composite;

  namespace VIEW
  {
    class FDPBDialog;

    class BALL_VIEW_EXPORT MolecularStructure
      : public QWidget, 
        public ModularWidget
    {
      Q_OBJECT

      public:

      BALL_EMBEDDABLE(MolecularStructure, ModularWidget)

      
      enum
      {
        AMBER_FF = 0,

        CHARMM_FF,

        MMFF94_FF
      };
      

      MolecularStructure(QWidget* parent = 0, const char* name = 0);
      
      MolecularStructure(const MolecularStructure& m);
      


      virtual ~MolecularStructure();



      virtual void onNotify(Message *message);

      virtual void checkMenu(MainControl& main_control);

      virtual void initializeWidget(MainControl& main_control);
    
      ForceField& getForceField();

      Position getForceFieldID();

      AmberFF& getAmberFF();
      
      CharmmFF& getCharmmFF();

      MMFF94& getMMFF94();

      AmberConfigurationDialog& getAmberConfigurationDialog();
      
      CharmmConfigurationDialog& getCharmmConfigurationDialog();

      MMFF94ConfigurationDialog& getMMFF94ConfigurationDialog();

      virtual void fetchPreferences(INIFile &inifile);
          
      virtual void writePreferences(INIFile &inifile);

      MolecularDynamicsDialog& getMDSimulationDialog() { return md_dialog_;}

      MinimizationDialog& getMinimizationDialog() { return minimization_dialog_;}

      FDPBDialog* getFDPBDialog() { return fdpb_dialog_;}
      
      AssignBondOrderConfigurationDialog& getBondOrderDialog() { return bond_order_dialog_;}
      
      const AssignBondOrderConfigurationDialog& getBondOrderDialog() const { return bond_order_dialog_;}
  
      AssignBondOrderResultsDialog& getBondOrderResultsDialog() { return bond_order_results_dialog_;}
      
      const AssignBondOrderResultsDialog& getBondOrderResultsDialog() const { return bond_order_results_dialog_;}

          
      public slots:

      void centerCamera(Composite* composite = 0);

      void buildBonds();
      
      void buildEndcaps();

      void runBondOrderAssignment(bool show_dialog = true);
      

    void showBondOrderAssignmentResults(AssignBondOrderProcessor& bop);

      void addHydrogens();
      
      virtual bool checkResidue();

      virtual void createGridFromDistance();

      virtual void createGridFromCameraDistance();

      virtual void calculateSecondaryStructure();

      virtual void mapProteins();

      virtual void calculateRMSD();

      void buildPeptide();

      bool generateCrystal(bool show = true);
      
      void calculateHBonds();

      void calculateRamachandranPlot();

      // Calculate the charges for a Molecule
//      void assignCharges();

      void calculateForceFieldEnergy();

      void runMinimization(bool show_dialog_ = true);

      void MDSimulation(bool show_dialog_ = true);

      void showAmberForceFieldOptions();
      
      void showCharmmForceFieldOptions();

      void showMMFF94ForceFieldOptions();
      
      void chooseAmberFF();

      void chooseCharmmFF();
        
      void chooseMMFF94();

      void chooseForceField(Position nr);

      void setupForceField();

      bool calculateFDPB(bool show = true);
        
      
      private:

      virtual void addComposite_(Composite& composite, const String& name, bool normalize = true);

      void applyForceFieldSettings_();

      void selectUnassignedForceFieldAtoms_();

      bool setupForceField_(System* system, bool disable_selection = false);

      QAction* center_camera_id_;
      QAction* build_bonds_id_;
      QAction* build_endcaps_id_;
      QAction* assign_bond_orders_id_;
      QAction* add_hydrogens_id_;
      QAction* check_structure_id_;
      QAction* create_distance_grid_id_, *create_distance_grid_id2_;
      QAction* calculate_ss_id_;
      QAction* map_proteins_id_;
      QAction* calculate_RMSD_id_;
      QAction* assign_charges_id_;
      QAction* energy_id_;
      QAction* minimization_id_;
      QAction* mdsimulation_id_;
      QAction* build_peptide_id_;
      QAction* calculate_hbonds_id_;
      QAction* amber_ff_id_;
      QAction* charmm_ff_id_;
      QAction* mmff94_id_;
      QAction* setup_ff_;
      QAction* calculate_ramachandran_;
      QAction* menu_FPDB_;
      QAction* generate_crystal_;

      AmberFF                     amber_;
      CharmmFF                    charmm_;
      MMFF94                      mmff_;
      AmberConfigurationDialog    amber_dialog_;
      CharmmConfigurationDialog   charmm_dialog_;
      MMFF94ConfigurationDialog   mmff94_dialog_;
      MinimizationDialog          minimization_dialog_;
      MolecularDynamicsDialog     md_dialog_;
      FDPBDialog*                         fdpb_dialog_;
      AssignBondOrderConfigurationDialog  bond_order_dialog_;
      AssignBondOrderResultsDialog        bond_order_results_dialog_;
      Position                            force_field_id_;
      GenerateCrystalDialog*      crystal_dialog_;
    };

  } // namespace VIEW
} // namespace BALL

#endif // BALL_VIEW_WIDGETS_MOLECULARSTRUCTURE_H