templates.h

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

// Molecular Mechanics Parameter: class describing the atom type section of a parameter file

#ifndef BALL_MOLMEC_PARAMETER_TEMPLATES_H
#define BALL_MOLMEC_PARAMETER_TEMPLATES_H

#ifndef BALL_FORMAT_PARAMETERSECTION_H
# include <BALL/FORMAT/parameterSection.h>
#endif

#ifndef BALL_KERNEL_SYSTEM_H
# include <BALL/KERNEL/system.h>
#endif

#ifndef BALL_DATATYPE_HASHSET_H
# include <BALL/DATATYPE/hashset.h>
#endif

#include <BALL/KERNEL/atom.h>

namespace BALL 
{
  class Atom;

  class BALL_EXPORT Templates 
    : public ParameterSection
  {
    public:

    
    Templates();

    Templates(const Templates& templates, bool deep = true);

    virtual ~Templates() ;

    virtual void clear() ;



    virtual bool extractSection(Parameters& parameters, const String& section_name);

    float getCharge(const String& name) const;

    String getTypeName(const String& name) const;

    bool has(const String& name) const;

    void assign(System& system, bool overwrite_existing_typenames = true, 
                bool overwrite_non_zero_charges = true) const;

    void assignCharges(System& system, bool overwrite_non_zero_charges = true) const;

    void assignTypeNames(System& system, bool overwrite_existing_typenames = true) const;



    Templates& operator = (const Templates& templates);

    void setMaximumUnassignedAtoms(Size nr);

    Size getMaximumUnassignedAtoms() const;

    Size getNumberOfUnassignedAtoms() const;

    HashSet<const Atom*>& getUnassignedAtoms();


    protected:
    
    /*_ Contains the charge for each residue/atom combination
    */
    StringHashMap<float>  charges_;

    /*_ Contains the atom type names for each residue/atom combination
    */
    StringHashMap<String> type_names_;

    //_ Atoms, for which the assignment fails
    HashSet<const Atom*> unassigned_atoms_;

    //_ max number of unassigned atoms
    Size max_number_unassigned_atoms_;
  };
} // namespace BALL

#endif // BALL_MOLMEC_PARAMETER_TEMPLATES_H