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ALLAA
ALLAA is deprecated; allows repacking and designing to any
canonical residue (default state of PackerTask)
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ALLAAAP
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ALLAACAP
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|
ALLAAwc
allows repacking and designing to any canonical residue (default
state of PackerTask)
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ALLAAwcAP
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ALLAAwcCAP
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ALLAAxc
ALLAAxc allows repacking and designing to any canonical noncysteine
residue
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ALLAAxcAP
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ALLAAxcCAP
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|
APOLA
APOLA is deprecated, it calls APOLAR to allow nonpolar residues and
packing
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|
APOLAAP
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APOLACAP
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|
APOLAR
APOLAR allows nonpolar residues and packing
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APOLARAP
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APOLARCAP
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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.
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|
AUTOAP
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AUTOCAP
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|
EMPTY
EMPTY disallows all canonical and noncanonical residues
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EMPTYAP
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EMPTYCAP
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|
EX
/////end of mode-style options////////////////////////...
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|
EXAP
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EXCAP
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EX_CUTOFF
EX_CUTOFF allows setting of the extrachi_cutoff (for determining
burial for extra rotamers)
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|
EX_CUTOFFAP
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EX_CUTOFFCAP
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|
ExtraRotSample
levels of extra rotamer sampling, i.e., step size and number of
steps.
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|
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.
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|
FIX_HIS_TAUTOMERAP
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FIX_HIS_TAUTOMERCAP
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|
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
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|
IGEdgeReweightContainerAP
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|
IGEdgeReweightContainerCAP
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|
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
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|
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 |
|
|