rGroupAssembler.h

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// ----------------------------------------------------
// $Maintainer: Marc Röttig $
// $Authors: Michael Betz, Marc Röttig $
// ----------------------------------------------------

#ifndef BALL_STRUCTURE_RGROUP_ASSEMBLER_H
#define BALL_STRUCTURE_RGROUP_ASSEMBLER_H

#include <map>
#include <vector>
#include <BALL/KERNEL/forEach.h>
#include <BALL/STRUCTURE/smilesParser.h>
#include <BALL/KERNEL/molecule.h>
#include <BALL/KERNEL/system.h>
#include <BALL/DATATYPE/string.h>
#include <BALL/KERNEL/atom.h>


namespace BALL
{
    class BALL_EXPORT RGroupAssembler
    {
      public:
        RGroupAssembler(String& scaffold, std::map<String, std::vector<String> > & rgroups);
        RGroupAssembler(std::vector<String>& scaffolds, std::map<String, std::vector<String> > & rgroups);
        ~RGroupAssembler();

        Molecule* generateNextMolecule();

      private:
        void initCounter_();
        bool incrementCounter_();
        void appendMoiety_(AtomContainer* molecule, AtomContainer* moiety, String pm_atom);
        bool isPlacemark_(const String& s);

        std::vector<System*> scaffolds_;
        std::map<String, std::vector<System*> > moieties_;

        unsigned int scaffold_counter_;
        std::map<String, unsigned int> moiety_counter_;
        std::vector<std::map<String, unsigned int> > maxcounter_;

        bool not_finished_;
    };
}

#endif /* BALL_STRUCTURE_RGROUP_ASSEMBLER_H */