support.h

Go to the documentation of this file.

// -*- Mode: C++; tab-width: 2; -*-
// vi: set ts=2:
//
// $Id: support.h,v 1.28 2005/12/23 17:01:52 amoll Exp $
//


#ifndef BALL_MOLMEC_COMMON_SUPPORT_H
#define BALL_MOLMEC_COMMON_SUPPORT_H

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

#ifndef BALL_MATHS_SIMPLEBOX3_H
# include <BALL/MATHS/simpleBox3.h>
#endif

#ifndef BALL_MOLMEC_COMMON_FORCEFIELD_H
# include <BALL/MOLMEC/COMMON/forceField.h>
#endif

#ifndef BALL_MOLMEC_COMMON_ATOMVECTOR_H
# include <BALL/MOLMEC/COMMON/atomVector.h>
#endif

#ifndef BALL_DATATYPE_HASHGRID_H
# include <BALL/DATATYPE/hashGrid.h>
#endif

#ifndef BALL_KERNEL_BOND_H
#     include <BALL/KERNEL/bond.h>
#endif

#include <vector>

namespace BALL 
{
  class Atom;
  class System;

  namespace MolmecSupport 
  {
    
    using std::pair;
      


    enum PairListAlgorithmType
    {
      HASH_GRID,

      BRUTE_FORCE
    };
      
    BALL_EXPORT BALL::Size calculateNonBondedAtomPairs
      (ForceField::PairVector& pair_vector, 
       const AtomVector& atom_vector, const SimpleBox3& box, 
       double distance, bool periodic_boundary_enabled, 
       PairListAlgorithmType type)
      throw(Exception::OutOfMemory);

    BALL_EXPORT Size sortNonBondedAtomPairsAfterSelection(ForceField::PairVector& pair_vector);

    BALL_EXPORT BALL::Size addNonOverlappingMolecules
      (System& system, const HashGrid3<const Atom*>& solute_grid,
       const System& solvent, const SimpleBox3& box, double distance);

    BALL_EXPORT void adaptWaterBox(System& system, const SimpleBox3& box);

    // ?????
    BALL_EXPORT void calculateMinimumImage
      (Vector3& distance, const Vector3& period);

    template <typename TorsionType, typename AtomIteratorType>
    Size computeTorsions
      (const AtomIteratorType& start, const AtomIteratorType& end,
       std::vector<TorsionType>& torsions, bool use_selection = false);


    // 
    template <typename TorsionType, typename AtomIteratorType>
    Size computeTorsions
      (const AtomIteratorType& start, const AtomIteratorType& end, 
       std::vector<TorsionType>& torsions, bool use_selection)
    {
      // pointers to the four atoms
      Atom* a1;
      Atom* a2;
      Atom* a3;
      Atom* a4;

      Size number_of_added_torsions = 0;

      // Iterate over all atoms...
      // 
      AtomIteratorType atom_it = start;
      for (; atom_it != end; ++atom_it) 
      {
        // ...and check each bond whether it is part of 
        // a torsion.
        Atom::BondIterator it1 = (*atom_it)->beginBond();
        for (; +it1 ; ++ it1) 
        {
          // Consider each bond just once by making sure that
          // our start atom is the *first* atom of the bond.
          if (*atom_it == it1->getFirstAtom()) 
          {
            // We know have the two central atoms of a potential
            // torsion and store them in a2 and a3.
            a2 = *atom_it;
            a3 = const_cast<Atom*>(it1->getSecondAtom());

            // Now, find all other atoms (atoms 1 and 4)
            Atom::BondIterator it2;
            Atom::BondIterator it3;
            for (it2 = (*atom_it)->beginBond(); +it2 ; ++it2) 
            {
              if (it2->getSecondAtom() != it1->getSecondAtom()) 
              {
                // determine the first atom
                if (it2->getFirstAtom() == *atom_it) 
                {
                  a1 = const_cast<Atom*>(it2->getSecondAtom());
                } 
                else 
                {
                  a1 = const_cast<Atom*>(it2->getFirstAtom());
                }
   
                for (it3 = const_cast<Atom*>(it1->getSecondAtom())->beginBond(); +it3 ; ++it3) 
                {
                  if (it3->getFirstAtom() != a2 ) 
                  {
                    // determine the fourth atom a4
                    if (it3->getFirstAtom() == a3)
                    {
                      a4 = const_cast<Atom*>(it3->getSecondAtom());
                    } 
                    else 
                    {
                      a4 = const_cast<Atom*>(it3->getFirstAtom());
                    }

                    if (use_selection == false 
                        || (use_selection == true 
                            && (a1->isSelected() || a2->isSelected() || a3->isSelected() || a4->isSelected())))
                    {
                      // Push the torsion onto the torsion vector.
                      TorsionType tmp;
                      tmp.atom1 = a1;
                      tmp.atom2 = a2;
                      tmp.atom3 = a3;
                      tmp.atom4 = a4;

                      torsions.push_back(tmp);
                      number_of_added_torsions++;
                    }
                  } 
                }
              }
            }
          }
        }
      }

      // return the number of torsions computed
      return number_of_added_torsions;
    }

  } // namespace MolmecSupport
} // namespace BALL

#endif // BALL_MOLMEC_COMMON_SUPPORT_H

---