haintermol.h

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#ifndef HAINTERMOL_H
#define HAINTERMOL_H

class HaMolecule;
class CWinThread;

#include "hastl.h"
#include "command.h"
#include "haatgroup.h"
#include "hacompmod.h"
#include "hasurface.h"

class HaField3D;

const int NO_ELECTR=0;                 
const int CONTINUUM_ELECTR = 1;        
const int COULOMB_ELECTR = 2;          
const int CHARGES_IN_FIELD_ELECTR = 3; 

class HaInterMolMod : public HaCompMod
{
public:
        HaInterMolMod(HaMolSet* new_phost_mset);
        virtual ~HaInterMolMod();

        void SetStdParams(); 

        bool Initialize();            
        
        double CalculateMMEnergy();  

        double CalcElStaticInter(); 
                                  
    double CalcContElectrEne(vector<AtomList*> inter_groups); 

    bool CalcEffInterEne(); 

        int RunMCDock();          
        int PauseMCDock();        
        int ResumeMCDock();       
        int StopMCDock();         

        int RunMCDocThread(); 


        CWinThread* mc_dock_thread;

        int module_to_init_flag; 
        int build_nb_contact_list; 

        int BuildNonBondListInterMol(); 

        double cur_intermol_ene;  
        double electr_inter_ene;  
        double vdw_inter_ene;     
        double add_eff_ene;       
        double MC_temp;           
        double ang_ratio;         
        double tr_ratio;          
        int delay_time;           
        int stop_calc_flag;       
        int skip_pt_init;         
        int skip_pt_between;      
        
        int play_back_flag;       
    
        int dont_calc_ene_flag;   
        int save_image_seq_gif;   
        int save_image_seq_pict;  
        int trace_atoms_flag;     

        int output_rejected_points; 

        HaString MC_traj_file_name; 

        int electr_model;  


    int InitMolecularFields(); 
        double CalcChargesInFieldEne(); 

        int compute_pk;    

        void SetElectrModel(int new_elecr_model_idx); 

        int calc_et_rate; 

        int num_mc_steps; 

        vector<HaMolecule*> interact_mol; 

        HaField3D el_pot_field;   
        HaField3D vdw_pot_field;  

    AtomList traced_atoms;     
protected:

};

#endif // end if !defined(HAINTERMOL_H) 

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