Package rosetta :: Package core :: Package pack :: Package task :: Module _core_pack_task_
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Module _core_pack_task_

Classes [hide private]
  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__
Functions [hide private]
 
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
Variables [hide private]
  ALREADY_SYMMETRIZED = rosetta.core.pack.task._core_pack_task_....
  EX_FOUR_HALF_STEP_STDDEVS = rosetta.core.pack.task._core_pack_...
  EX_ONE_HALF_STEP_STDDEV = rosetta.core.pack.task._core_pack_ta...
  EX_ONE_STDDEV = rosetta.core.pack.task._core_pack_task_.ExtraR...
  EX_SIX_QUARTER_STEP_STDDEVS = rosetta.core.pack.task._core_pac...
  EX_THREE_THIRD_STEP_STDDEVS = rosetta.core.pack.task._core_pac...
  EX_TWO_FULL_STEP_STDDEVS = rosetta.core.pack.task._core_pack_t...
  EX_TWO_HALF_STEP_STDDEVS = rosetta.core.pack.task._core_pack_t...
  ExtraRotSampleCardinality = rosetta.core.pack.task._core_pack_...
  NO_EXTRA_CHI_SAMPLES = rosetta.core.pack.task._core_pack_task_...
  NO_SYMMETRIZATION_REQUEST = rosetta.core.pack.task._core_pack_...
  REQUEST_SYMMETRIZE_BY_INTERSECTION = rosetta.core.pack.task._c...
  REQUEST_SYMMETRIZE_BY_UNION = rosetta.core.pack.task._core_pac...
  __package__ = None
Function Details [hide private]

comment_begin(...)

 

comment_begin( (vector1_string)tokens, (int)which_token) -> bool :
    utility function for resfile reader (checks for a leading # signaling a comment)
    

    C++ signature :
        bool comment_begin(utility::vector1<std::string, std::allocator<std::string> >,unsigned long)

create_command_map()

 
    utility for resfile reader, commands MUST be entered into this hard-coded map
    

    C++ signature :
        std::map<std::string, boost::shared_ptr<core::pack::task::ResfileCommand>, std::less<std::string>, std::allocator<std::pair<std::string const, boost::shared_ptr<core::pack::task::ResfileCommand> > > > create_command_map()

Returns: object :

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
    

    C++ signature :
        std::string get_token(unsigned long,utility::vector1<std::string, std::allocator<std::string> > [,bool=True])

is_rot_sample_name(...)

 

is_rot_sample_name( (str)name) -> bool :
    core/pack/task/RotamerSampleOptions.hh:40

    C++ signature :
        bool is_rot_sample_name(std::string)

onError(...)

 

onError( (str)message) -> None :
    core/pack/task/ResfileReader.hh:756

    C++ signature :
        void onError(std::string)

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
    

    C++ signature :
        void parse_resfile(core::pose::Pose,core::pack::task::PackerTask {lvalue},std::string)

parse_resfile( (Pose)pose, (PackerTask)the_task) -> None :
    changes the state of the given PackerTask according to the commands in the resfile at read in from the -pack:resfile option system.
    

    C++ signature :
        void parse_resfile(core::pose::Pose,core::pack::task::PackerTask {lvalue})

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.
    

    C++ signature :
        void parse_resfile_string(core::pose::Pose,core::pack::task::PackerTask {lvalue},std::string)

rot_sample_from_name(...)

 

rot_sample_from_name( (str)name) -> ExtraRotSample :
    core/pack/task/RotamerSampleOptions.hh:37

    C++ signature :
        core::pack::task::ExtraRotSample rot_sample_from_name(std::string)

tokenize_line(...)

 

tokenize_line( (std_istream)inputstream) -> vector1_string :
    utility function for resfile reader
    

    C++ signature :
        utility::vector1<std::string, std::allocator<std::string> > tokenize_line(std::istream {lvalue})


Variables Details [hide private]

ALREADY_SYMMETRIZED

Value:
rosetta.core.pack.task._core_pack_task_.PackerTaskSymmetryStatus.ALREA\
DY_SYMMETRIZED

EX_FOUR_HALF_STEP_STDDEVS

Value:
rosetta.core.pack.task._core_pack_task_.ExtraRotSample.EX_FOUR_HALF_ST\
EP_STDDEVS

EX_ONE_HALF_STEP_STDDEV

Value:
rosetta.core.pack.task._core_pack_task_.ExtraRotSample.EX_ONE_HALF_STE\
P_STDDEV

EX_ONE_STDDEV

Value:
rosetta.core.pack.task._core_pack_task_.ExtraRotSample.EX_ONE_STDDEV

EX_SIX_QUARTER_STEP_STDDEVS

Value:
rosetta.core.pack.task._core_pack_task_.ExtraRotSample.EX_SIX_QUARTER_\
STEP_STDDEVS

EX_THREE_THIRD_STEP_STDDEVS

Value:
rosetta.core.pack.task._core_pack_task_.ExtraRotSample.EX_THREE_THIRD_\
STEP_STDDEVS

EX_TWO_FULL_STEP_STDDEVS

Value:
rosetta.core.pack.task._core_pack_task_.ExtraRotSample.EX_TWO_FULL_STE\
P_STDDEVS

EX_TWO_HALF_STEP_STDDEVS

Value:
rosetta.core.pack.task._core_pack_task_.ExtraRotSample.EX_TWO_HALF_STE\
P_STDDEVS

ExtraRotSampleCardinality

Value:
rosetta.core.pack.task._core_pack_task_.ExtraRotSample.ExtraRotSampleC\
ardinality

NO_EXTRA_CHI_SAMPLES

Value:
rosetta.core.pack.task._core_pack_task_.ExtraRotSample.NO_EXTRA_CHI_SA\
MPLES

NO_SYMMETRIZATION_REQUEST

Value:
rosetta.core.pack.task._core_pack_task_.PackerTaskSymmetryStatus.NO_SY\
MMETRIZATION_REQUEST

REQUEST_SYMMETRIZE_BY_INTERSECTION

Value:
rosetta.core.pack.task._core_pack_task_.PackerTaskSymmetryStatus.REQUE\
ST_SYMMETRIZE_BY_INTERSECTION

REQUEST_SYMMETRIZE_BY_UNION

Value:
rosetta.core.pack.task._core_pack_task_.PackerTaskSymmetryStatus.REQUE\
ST_SYMMETRIZE_BY_UNION