sideChainPlacementProcessor.h

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#ifndef BALL_STRUCTURE_SIDECHAINPLACEMENTPROCESSOR_H
#define BALL_STRUCTURE_SIDECHAINPLACEMENTPROCESSOR_H

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

#ifndef BALL_KERNEL_ATOMCONTAINER_H
  #include <BALL/KERNEL/atomContainer.h>
#endif

#ifndef BALL_DATATYPE_OPTIONS_H
# include <BALL/DATATYPE/options.h>
#endif

namespace BALL 
{
  class BALL_EXPORT SideChainPlacementProcessor 
    : public UnaryProcessor<AtomContainer> 
  {
    public:


      struct BALL_EXPORT Option
      { 
        static const char* METHOD; 
        
        static const char* SCWRL_BINARY_PATH; 

        static const char* SCWRL_INPUT_FILE;

        static const char* SCWRL_SEQUENCE_FILE;

        static const char* SCWRL_OUTPUT_FILE;

        static const char* MUTATE_SELECTED_SIDE_CHAINS;
        
      };

      struct BALL_EXPORT Default
      {
        static const String METHOD;
        static const String SCWRL_BINARY_PATH;
        static const bool   MUTATE_SELECTED_SIDE_CHAINS;
        static const String SCWRL_INPUT_FILE;
        static const String SCWRL_SEQUENCE_FILE;
        static const String SCWRL_OUTPUT_FILE;
      };

      struct BALL_EXPORT Method
      {
        static const String SCWRL_4_0;
        //static const String SCWRL_SERVER; 
        //static const String ILP;
      };
      
    
      BALL_CREATE(SideChainPlacementProcessor);

          
      SideChainPlacementProcessor();
    
      SideChainPlacementProcessor(const SideChainPlacementProcessor& scpp);
    
      virtual ~SideChainPlacementProcessor();


      virtual bool start();
  
      void clear();

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

      virtual bool finish();

    
      
      void setDefaultOptions();
      
      void setMutations(String mutated_seq) {mutated_sequence_ = mutated_seq;} 
      
      const String& getMutations() const {return mutated_sequence_;}
      
      String getMutations() {return mutated_sequence_;}



      SideChainPlacementProcessor& operator = (const SideChainPlacementProcessor& scpp);
      
      


      Options options;

    
    protected:
      bool readOptions_(); 
    
      String mutated_sequence_; 

      // The processor state. 
      bool valid_;

  };

} // namespace BALL 


#endif // BALL_STRUCTURE_SIDECHAINPLACEMENTPROCESSOR_H

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