HBondShiftProcessor.h

Go to the documentation of this file.

// -*- Mode: C++; tab-width: 2; -*-
// vi: set ts=2:
//
// $Id: HBondShiftProcessor.h,v 1.14.10.5 2007-04-12 13:53:53 anne Exp $
//
 
#ifndef BALL_NMR_HBONDSHIFTPROCESSOR_H
#define BALL_NMR_HBONDSHIFTPROCESSOR_H
 
#ifndef BALL_KERNEL_PTE_H
# include <BALL/KERNEL/PTE.h>
#endif
 
#ifndef BALL_KERNEL_BOND_H
# include <BALL/KERNEL/bond.h>
#endif
 
#ifndef BALL_KERNEL_ATOM_H
# include <BALL/KERNEL/atom.h>
#endif
 
#ifndef BALL_NMR_SHIFT_MODULE_H
# include <BALL/NMR/shiftModule.h>
#endif
 
#ifndef BALL_FORMAT_PARAMETERSECTION_H
# include <BALL/FORMAT/parameterSection.h>
#endif
 
#include <map>
 
namespace BALL
{
  class BALL_EXPORT HBondShiftProcessor
  : public ShiftModule
  {
    public:
    BALL_CREATE(HBondShiftProcessor)
 
    
 
    static const char* PROPERTY__HBOND_SHIFT;



    HBondShiftProcessor()
      ;

    HBondShiftProcessor(const HBondShiftProcessor& processor)
      ;

    virtual ~HBondShiftProcessor()
      ;



    virtual void init();



    virtual bool start();

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

 
    protected:
    
    /*_ Vector of hydrogen bond acceptor types collected from the <tt>ShiftX.ini-file</tt> by <tt>init ()</tt>.
     */
    std::vector<String>         acceptor_types_;
    
    /*_ Vector of hydrogen bond donors collected by <tt>operator ()</tt>.
     */
    std::vector<Atom*>            donors_;
 
    /*_ Vector of hydrogen bond acceptors collected by <tt>operator ()</tt> as defined in <tt>acceptor_types_</tt>. 
     */
    std::vector<Atom*>            acceptors_;
 
    /*_  A flag indicating whether the HBond effect affects amide protons too.
     */
    bool                        amide_protons_are_targets_;
    
    /*_  The default factor for computing the amide protons shift.
     */
    float                       amide_proton_factor_ ; 
    
    /*_  The default subtrahend for computing the amide protons shift.
     */
    float                       amide_proton_subtrahend_;
 
    /*_  The default distance between oxygen and hydrogen for amide hydrogens.
     */
    float                       amide_proton_oxygen_hydrogen_separation_distance_;
    
    /*_  The default distance between oxygen and hydrogen for alpha hydrogens.
     */
    float                       alpha_proton_oxygen_hydrogen_separation_distance_;
    
    /*_  A flag indicating whether the HBond-donar and acceptor must be on different residues.
     *   The default value is true. 
     */
    bool                        exclude_selfinteraction_;
 
    /*_  A flag indicating whether the HBonds should be computed ShiftX-wise. 
     *   NOTE: This will just compute __temporarily__  hydrogen bonds 
     *          found with the ShiftX - algorithm, whose definition of a 
     *          hydrogen bond differ substantially from a BALL definition.
     *         The ShiftX definition of hydrogen bonds is: 
     *          Donors are: H and HA
     *          Acceptors are: O, OD_n, OE_n, OG_n, OH_n or water in the solvent! ...
     *          By now, we do not consider water!  
     *   The default value is false! 
     */
    bool                        ShiftXwise_hydrogen_bonds_computation_;
 
    private:
    void      printParameters_();
    void      printEffectors_();
    void      printTargets_();
    Atom*     getDonor_(Atom* a);
    void      postprocessing_();
 
 
    /* Distance, donor, acceptor for the ShiftXwise hydrogenbond determination.*/
    std::multimap<float, std::pair<Atom*, Atom*> >  hbonds_;
    std::map<Atom*, bool> donor_occupied_;
    std::map<Atom*, bool> acceptor_occupied_;
};
} // namespace BALL
 
#endif