haighMallionShiftProcessor.h

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// -*- Mode: C++; tab-width: 2; -*-
// vi: set ts=2:
//
// $Id: haighMallionShiftProcessor.h,v 1.16.10.6 2007-04-12 13:53:54 anne Exp $
//

#ifndef BALL_COMMON_H
# include <BALL/common.h>
#endif

#ifndef BALL_CONCEPT_PROCESSOR_H
# include <BALL/CONCEPT/processor.h>
#endif

#ifndef BALL_NMR_SHIFTMODULE_H
# include<BALL/NMR/shiftModule.h>
#endif

#ifndef BALL_DATATYPE_STRINGHASHMAP_H
# include <BALL/DATATYPE/stringHashMap.h>
#endif

#include <list>

namespace BALL 
{
  class BALL_EXPORT HaighMallionShiftProcessor
    : public ShiftModule
  {
    public:

    BALL_CREATE(HaighMallionShiftProcessor)
    
    

    static const char* PROPERTY__RING_CURRENT_SHIFT;
    


    HaighMallionShiftProcessor();
    
    HaighMallionShiftProcessor(const HaighMallionShiftProcessor& processor);

    virtual ~HaighMallionShiftProcessor();
    
    


    virtual void init();

    


    
    virtual bool start();
    
    
    virtual Processor::Result operator () (Composite& atom);
    
      
    virtual bool finish();

    
    

    protected:
    
    /*_ A flag indicating whether Hydrogens are effected by all effectors or 
        just by effectors of the same residue.
        Set this flag by specifying the option {\tt H_influenced_by_all_effectors = true} in 
        the HaighMallionRingCurrent section of the parameter file.
        Default is false.
    */
    bool                    H_influenced_by_all_effectors_;
  
    /*_ A flag indicating whether HA Hydrogens are effected by all effectors or 
        just by effectors of the same residue.
        Set this flag by specifying the option {\tt HA_influenced_by_all_effectors = true} in 
        the HaighMallionRingCurrent section of the parameter file.
        Default is false.
    */
    bool                    HA_influenced_by_all_effectors_;

    /*_ A flag indicating whether a cutoff for the ring current effect is used. 
        Set this flag by specifying the option {\tt   use_cut_off = true} in 
        the HaighMallionRingCurrent section of the parameter file.
        Default is false.
    */
    bool                    use_cut_off_;


    /*_ A cut off value for the ring current effect computation via Haigh Mallion.
        Set this flag by specifying the option {\tt   cut_off = 15.} in 
        the HaighMallionRingCurrent section of the parameter file.
        Default is 15.*15.
    */
    float                   cut_off2_;          
    
    /*_ A flag indicating whether all hydrogens are targets. 
        Set this flag by specifying the option {\tt all_hydrogen_are_targets = true} in 
        the HaighMallionRingCurrent section of the parameter file.
        Default is false.
    */
    bool                    all_hydrogen_are_targets_;

    bool                    correct_CA_shifts_;

    /*_ A flag indicating whether for the computation of the ring current effect
        the target has to be projected onto the effector ring plane or not.
        Set this flag by specifying the option {\tt project_target_to_ring_plane = true} in 
        the HaighMallionRingCurrent section of the parameter file.
        Default is false.
     */
    bool                    project_target_to_ring_plane_;

    /*_ The values of the target nucleus factors F.
     */
    StringHashMap<float>    target_nucleus_factors_;

    /*_ The default value of the target nucleus factors F for hydrogen atoms.
     */
    float                   default_hydrogen_target_nucleus_factor_;

    /*_ The default factor of negative ring current factors
     */
    float                   negative_ringcurrent_factor_ ;
    
    /*_ The effector residues stored as a vector of atoms the collected by {\tt operator ()}.
    */  
    std::vector< std::vector<Atom*> >     effectors_;
    
    /*_ The effector residue types stored as a vector of strings collected by {\tt operator ()}.
        This is necessary to allow, e.g., TRP1 and TRP2 as two different kinds of rings.
    */  
    std::vector<String>               effector_types_;

    /*_ The effector names collected from the ini-file by {\tt init ()}.
    */
    std::vector<BALL::String>         effector_names_;
    
    /*_ The intensities of the effecting residues collected from the ini-file by {\tt init ()}.
    */
    StringHashMap<float>              intensity_factors_;
    
    /*_ The ring atom names of the effecting residues collected from the ini-file by {\tt init ()}.
    */
    std::vector< std::vector<BALL::String> >    ring_atoms_;
    
    /*_ The targeted atom names collected by {\tt init ()}.
    */
    std::vector< BALL::String>              target_names_;
  
    /*_ The targeted atoms collected by {\tt operator ()}.
    */
    std::vector<Atom* >                   targets_;
  
    private:

    void      printParameters_();
    void      printEffectors_();
    void      printTargets_();
    void      postprocessing_();
    
  };
  
} // namespace BALL