| 
       
     | 
        ALLAA 
      ALLAA is deprecated; allows repacking and designing to any 
        canonical residue (default state of PackerTask)
     | 
  
    | 
       
     | 
        ALLAAAP
     | 
  
    | 
       
     | 
        ALLAACAP
     | 
  
    | 
       
     | 
        ALLAAwc 
      allows repacking and designing to any canonical residue (default 
        state of PackerTask)
     | 
  
    | 
       
     | 
        ALLAAwcAP
     | 
  
    | 
       
     | 
        ALLAAwcCAP
     | 
  
    | 
       
     | 
        ALLAAxc 
      ALLAAxc allows repacking and designing to any canonical noncysteine
        residue
     | 
  
    | 
       
     | 
        ALLAAxcAP
     | 
  
    | 
       
     | 
        ALLAAxcCAP
     | 
  
    | 
       
     | 
        APOLA 
      APOLA is deprecated, it calls APOLAR to allow nonpolar residues and
        packing
     | 
  
    | 
       
     | 
        APOLAAP
     | 
  
    | 
       
     | 
        APOLACAP
     | 
  
    | 
       
     | 
        APOLAR 
      APOLAR allows nonpolar residues and packing
     | 
  
    | 
       
     | 
        APOLARAP
     | 
  
    | 
       
     | 
        APOLARCAP
     | 
  
    | 
       
     | 
        AUTO 
      AUTO suggests that a packer can/should reconsider the design 
        setting at a/each residue This is a protocol-level flag to be used 
        in non-vanilla packers.
     | 
  
    | 
       
     | 
        AUTOAP
     | 
  
    | 
       
     | 
        AUTOCAP
     | 
  
    | 
       
     | 
        EMPTY 
      EMPTY disallows all canonical and noncanonical residues
     | 
  
    | 
       
     | 
        EMPTYAP
     | 
  
    | 
       
     | 
        EMPTYCAP
     | 
  
    | 
       
     | 
        EX 
      /////end of mode-style options////////////////////////...
     | 
  
    | 
       
     | 
        EXAP
     | 
  
    | 
       
     | 
        EXCAP
     | 
  
    | 
       
     | 
        EX_CUTOFF 
      EX_CUTOFF allows setting of the extrachi_cutoff (for determining 
        burial for extra rotamers)
     | 
  
    | 
       
     | 
        EX_CUTOFFAP
     | 
  
    | 
       
     | 
        EX_CUTOFFCAP
     | 
  
    | 
       
     | 
        ExtraRotSample 
      levels of extra rotamer sampling, i.e., step size and number of 
        steps.
     | 
  
    | 
       
     | 
        FIX_HIS_TAUTOMER 
      FIX_HIS_TAUTOMER: when a histidine is present when the PackerTask 
        is initialized, this flag will fix its tautomer (whether its 
        hydrogen is on ND1 or NE2.
     | 
  
    | 
       
     | 
        FIX_HIS_TAUTOMERAP
     | 
  
    | 
       
     | 
        FIX_HIS_TAUTOMERCAP
     | 
  
    | 
       
     | 
        IGEdgeReweightContainer 
      class that interfaces to containers holding IGedge weights between 
        individual residues of the task note: this class only knows about 
        the pose numbering, not about the numbers in the IG
     | 
  
    | 
       
     | 
        IGEdgeReweightContainerAP
     | 
  
    | 
       
     | 
        IGEdgeReweightContainerCAP
     | 
  
    | 
       
     | 
        IGEdgeReweighter 
      helper class for IGEdgeReweightContainer
     | 
  
    | 
       
     | 
        IGEdgeReweighterAP
     | 
  
    | 
       
     | 
        IGEdgeReweighterCAP
     | 
  
    | 
       
     | 
        NATAA 
      NATAA allows repacking but no sequence changes (all rotamers are of
        the original residue)
     | 
  
    | 
       
     | 
        NATAAAP
     | 
  
    | 
       
     | 
        NATAACAP
     | 
  
    | 
       
     | 
        NATRO 
      ////////////////////////////////////////////////////////////////////...
     | 
  
    | 
       
     | 
        NATROAP
     | 
  
    | 
       
     | 
        NATROCAP
     | 
  
    | 
       
     | 
        NC 
      NC handles explicit allowance of noncanonical residue types
     | 
  
    | 
       
     | 
        NCAP
     | 
  
    | 
       
     | 
        NCCAP
     | 
  
    | 
       
     | 
        NOTAA 
      NOTAA disallows residues specified in a following string, and 
        allows packing
     | 
  
    | 
       
     | 
        NOTAAAP
     | 
  
    | 
       
     | 
        NOTAACAP
     | 
  
    | 
       
     | 
        NO_ADDUCTS 
      NO_ADDUCTS will disable adducts, assuming they exist This command 
        exists because if adducts exist, then they are enabled by default 
        for all residues.
     | 
  
    | 
       
     | 
        NO_ADDUCTSAP
     | 
  
    | 
       
     | 
        NO_ADDUCTSCAP
     | 
  
    | 
       
     | 
        PIKAA 
      PIKAA allows residues specifed in a following string and packing
     | 
  
    | 
       
     | 
        PIKAAAP
     | 
  
    | 
       
     | 
        PIKAACAP
     | 
  
    | 
       
     | 
        PIKNA 
      PIKNA allows nucleic acid residues specifed in a following string
     | 
  
    | 
       
     | 
        PIKNAAP
     | 
  
    | 
       
     | 
        PIKNACAP
     | 
  
    | 
       
     | 
        PIKRNA 
      PIKRNA allows nucleic acid residues specifed in a following string
     | 
  
    | 
       
     | 
        PIKRNAAP
     | 
  
    | 
       
     | 
        PIKRNACAP
     | 
  
    | 
       
     | 
        POLAR 
      POLAR allows polar residues and packing
     | 
  
    | 
       
     | 
        POLARAP
     | 
  
    | 
       
     | 
        POLARCAP
     | 
  
    | 
       
     | 
        PackerTask 
      Task class that gives instructions to the packer
     | 
  
    | 
       
     | 
        PackerTaskAP
     | 
  
    | 
       
     | 
        PackerTaskCAP
     | 
  
    | 
       
     | 
        PackerTaskSymmetryStatus 
      core/pack/task/PackerTask_.hh:413
     | 
  
    | 
       
     | 
        PackerTask_ 
      //////////////////////////////////////////////////////////////////////////
        the PackerTask controls what rotameric (including sequence) changes
        the packer is allowed to make
     | 
  
    | 
       
     | 
        PackerTask_AP
     | 
  
    | 
       
     | 
        PackerTask_CAP
     | 
  
    | 
       
     | 
        RESET 
      RESET restores the list of allowd residue types to the CAAs
     | 
  
    | 
       
     | 
        RESETAP
     | 
  
    | 
       
     | 
        RESETCAP
     | 
  
    | 
       
     | 
        ResfileCommand 
      abstract/interface class for Resfile reader command objects
     | 
  
    | 
       
     | 
        ResfileCommandAP
     | 
  
    | 
       
     | 
        ResfileCommandCAP
     | 
  
    | 
       
     | 
        ResfileContents 
      core/pack/task/ResfileReader.hh:63
     | 
  
    | 
       
     | 
        ResfileContentsAP
     | 
  
    | 
       
     | 
        ResfileContentsCAP
     | 
  
    | 
       
     | 
        ResfileReaderException 
      core/pack/task/ResfileReader.hh:48
     | 
  
    | 
       
     | 
        ResfileReaderExceptionAP
     | 
  
    | 
       
     | 
        ResfileReaderExceptionCAP
     | 
  
    | 
       
     | 
        ResidueLevelTask 
      core/pack/task/PackerTask.hh:57
     | 
  
    | 
       
     | 
        ResidueLevelTaskAP
     | 
  
    | 
       
     | 
        ResidueLevelTaskCAP
     | 
  
    | 
       
     | 
        ResidueLevelTask_ 
      Residue-level task class; contained within PackerTask
     | 
  
    | 
       
     | 
        ResidueLevelTask_AP
     | 
  
    | 
       
     | 
        ResidueLevelTask_CAP
     | 
  
    | 
       
     | 
        SCAN 
      SCAN suggests to some packing routines that if there are multiple 
        type choices for this residue, then each of them should be 
        considered explicitly in one way or another This is a 
        protocol-level flag to be used in non-vanilla packers ashworth
     | 
  
    | 
       
     | 
        SCANAP
     | 
  
    | 
       
     | 
        SCANCAP
     | 
  
    | 
       
     | 
        SingletonBase_T_core_chemical_ChemicalManager_T 
      SingletonBase is meant to serve as a base class for singleton 
        classes in Rosetta handling the initialization of the singleton in 
        a thread-safe way.
     | 
  
    | 
       
     | 
        SingletonBase_T_core_chemical_ChemicalManager_TAP
     | 
  
    | 
       
     | 
        SingletonBase_T_core_chemical_ChemicalManager_TCAP
     | 
  
    | 
       
     | 
        TARGET 
      TARGET flags the position as "targeted", and can optionally specify a "targeted" type...
     | 
  
    | 
       
     | 
        TARGETAP
     | 
  
    | 
       
     | 
        TARGETCAP
     | 
  
    | 
       
     | 
        TaskFactory 
      Factory class for the creation and initialization of PackerTask 
        objects
     | 
  
    | 
       
     | 
        TaskFactoryAP
     | 
  
    | 
       
     | 
        TaskFactoryCAP
     | 
  
    | 
       
     | 
        USE_INPUT_SC 
      USE_INPUT_SC turns on inclusion of the current rotamer for the 
        packer
     | 
  
    | 
       
     | 
        USE_INPUT_SCAP
     | 
  
    | 
       
     | 
        USE_INPUT_SCCAP
     | 
  
    | 
       
     | 
        __CPP_ALLAA__
     | 
  
    | 
       
     | 
        __CPP_ALLAAwc__
     | 
  
    | 
       
     | 
        __CPP_ALLAAxc__
     | 
  
    | 
       
     | 
        __CPP_APOLAR__
     | 
  
    | 
       
     | 
        __CPP_APOLA__
     | 
  
    | 
       
     | 
        __CPP_AUTO__
     | 
  
    | 
       
     | 
        __CPP_EMPTY__
     | 
  
    | 
       
     | 
        __CPP_EX_CUTOFF__
     | 
  
    | 
       
     | 
        __CPP_EX__
     | 
  
    | 
       
     | 
        __CPP_FIX_HIS_TAUTOMER__
     | 
  
    | 
       
     | 
        __CPP_IGEdgeReweighter__
     | 
  
    | 
       
     | 
        __CPP_NATAA__
     | 
  
    | 
       
     | 
        __CPP_NATRO__
     | 
  
    | 
       
     | 
        __CPP_NC__
     | 
  
    | 
       
     | 
        __CPP_NOTAA__
     | 
  
    | 
       
     | 
        __CPP_NO_ADDUCTS__
     | 
  
    | 
       
     | 
        __CPP_PIKAA__
     | 
  
    | 
       
     | 
        __CPP_PIKNA__
     | 
  
    | 
       
     | 
        __CPP_PIKRNA__
     | 
  
    | 
       
     | 
        __CPP_POLAR__
     | 
  
    | 
       
     | 
        __CPP_RESET__
     | 
  
    | 
       
     | 
        __CPP_ResfileCommand__
     | 
  
    | 
       
     | 
        __CPP_ResidueLevelTask__
     | 
  
    | 
       
     | 
        __CPP_ResidueLevelTask___
     | 
  
    | 
       
     | 
        __CPP_SCAN__
     | 
  
    | 
       
     | 
        __CPP_TARGET__
     | 
  
    | 
       
     | 
        __CPP_TaskFactory__
     | 
  
    | 
       
     | 
        __CPP_USE_INPUT_SC__
     | 
  
    | 
       
     | 
      
        
          comment_begin(...) 
      comment_begin( (vector1_string)tokens, (int)which_token) -> bool :
    utility function for resfile reader (checks for a leading # signaling a comment) | 
          
            
            
           | 
         
       
      
     | 
  
    | 
      object :
     | 
      
        
          create_command_map() 
      utility for resfile reader, commands MUST be entered into this hard-coded map | 
          
            
            
           | 
         
       
      
     | 
  
    | 
       
     | 
      
        
          get_token(...) 
      get_token( (int)which_token, (vector1_string)tokens [, (bool)make_upper_case=True]) -> str :
    ////////end of other options//////////////////////////
    ////////utility functions for resfile reader//////////
     utility function to increment next token to be parsed | 
          
            
            
           | 
         
       
      
     | 
  
    | 
       
     | 
      
        
          is_rot_sample_name(...) 
      is_rot_sample_name( (str)name) -> bool :
    core/pack/task/RotamerSampleOptions.hh:40 | 
          
            
            
           | 
         
       
      
     | 
  
    | 
       
     | 
      
        
          onError(...) 
      onError( (str)message) -> None :
    core/pack/task/ResfileReader.hh:756 | 
          
            
            
           | 
         
       
      
     | 
  
    | 
       
     | 
      
        
          parse_resfile(...) 
      parse_resfile( (Pose)pose, (PackerTask)the_task, (str)filename) -> None :
    changes the state of the given PackerTask according to the commands in the resfile at filename | 
          
            
            
           | 
         
       
      
     | 
  
    | 
       
     | 
      
        
          parse_resfile_string(...) 
      parse_resfile_string( (Pose)pose, (PackerTask)the_task, (str)resfile_string) -> None :
    changes the state of the given PackerTask according to the commands in the resfile. | 
          
            
            
           | 
         
       
      
     | 
  
    | 
       
     | 
      
        
          rot_sample_from_name(...) 
      rot_sample_from_name( (str)name) -> ExtraRotSample :
    core/pack/task/RotamerSampleOptions.hh:37 | 
          
            
            
           | 
         
       
      
     | 
  
    | 
       
     | 
      
        
          tokenize_line(...) 
      tokenize_line( (std_istream)inputstream) -> vector1_string :
    utility function for resfile reader | 
          
            
            
           | 
         
       
      
     |