disulfidBondProcessor.h

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#ifndef BALL_STRUCTURE_DISULFIDBONDPROCESSOR_H
#define BALL_STRUCTURE_DISULFIDBONDPROCESSOR_H

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

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

#include <set>

namespace BALL
{
  class BALL_EXPORT DisulfidBondProcessor
    : public UnaryProcessor<AtomContainer>
  {
    public:
    typedef std::pair<Residue*, Residue*>  DisulfidBond;
    typedef std::set<DisulfidBond>         DisulfidBonds;

    BALL_CREATE(DisulfidBondProcessor);



    DisulfidBondProcessor();

    virtual ~DisulfidBondProcessor();


    virtual bool start();

    void clear();

    virtual Processor::Result operator ()(AtomContainer& ac);

    virtual bool finish();



    Size getNumberOfDetectedDisulfidBonds() {return sulfur_bridges_.size();};

    DisulfidBonds& getDisulfidBonds() {return sulfur_bridges_;};

    const DisulfidBonds& getDisulfidBonds() const {return sulfur_bridges_;};


    bool connect(Atom* atom1, Atom* atom2, bool toggle = false);

    bool connect(Residue* residue1, Residue* residue2, bool toggle = false);

    bool connect(Composite* composite1, Composite* composite2, bool toggle = false);

    bool disconnect(Atom* atom1, Atom* atom2);

    bool disconnect(Residue* residue1, Residue* residue2);

    bool disconnect(Composite* composite1, Composite* composite2);


    protected:
      DisulfidBonds  sulfur_bridges_;
  };
}

#endif // BALL_STRUCTURE_DISULFIDBONDPROCESSOR_H