Rosetta 3.4
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core::pack::task Namespace Reference

Namespaces

namespace  operation

Classes

class  IGEdgeReweighter
 helper class for IGEdgeReweightContainer More...
class  IGEdgeReweightContainer
 class that interfaces to containers holding IGedge weights between individual residues of the task More...
class  ResidueLevelTask
class  PackerTask
 Task class that gives instructions to the packer. More...
class  ResidueLevelTask_
 Residue-level task class; contained within PackerTask. More...
class  PackerTask_
 the PackerTask controls what rotameric (including sequence) changes the packer is allowed to make More...
class  ResfileReaderException
class  ResfileContents
class  ResfileCommand
 abstract/interface class for Resfile reader command objects More...
class  NATRO
 NATRO disables packing and designing at a position, the residue will be totally unchanged. More...
class  NATAA
 NATAA allows repacking but no sequence changes (all rotamers are of the original residue) More...
class  ALLAA
 ALLAA is deprecated; allows repacking and designing to any canonical residue (default state of PackerTask) More...
class  ALLAAxc
 ALLAAxc allows repacking and designing to any canonical noncysteine residue. More...
class  ALLAAwc
 allows repacking and designing to any canonical residue (default state of PackerTask) More...
class  PIKAA
 PIKAA allows residues specifed in a following string and packing. More...
class  PIKNA
 PIKNA allows nucleic acid residues specifed in a following string. More...
class  PIKRNA
 PIKRNA allows nucleic acid residues specifed in a following string. More...
class  NOTAA
 NOTAA disallows residues specified in a following string, and allows packing. More...
class  EMPTY
 EMPTY disallows all canonical residues but leaves packing and designing unchanged (for noncanonicals) More...
class  POLAR
 POLAR allows polar residues and packing. More...
class  APOLAR
 APOLAR allows nonpolar residues and packing. More...
class  APOLA
 APOLA is deprecated, it calls APOLAR to allow nonpolar residues and packing. More...
class  EX
 EX handles the various extrachi options. More...
class  NC
 NC handles explicit allowance of noncanonical residue types. More...
class  EX_CUTOFF
 EX_CUTOFF allows setting of the extrachi_cutoff (for determining burial for extra rotamers) More...
class  USE_INPUT_SC
 USE_INPUT_SC turns on inclusion of the current rotamer for the packer. More...
class  AUTO
 AUTO suggests that a packer can/should reconsider the design setting at a/each residue. More...
class  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. More...
class  TARGET
 TARGET flags the position as "targeted", and can optionally specify a "targeted" type. More...
class  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. More...
class  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. Does nothing if not histidine at initialization (meaning if it mutates to histidine later this flag will have no effect). More...
class  TaskFactory
 Factory class for the creation and initialization of PackerTask objects. More...

Typedefs

typedef
utility::pointer::owning_ptr
< IGEdgeReweighter
IGEdgeReweighterOP
typedef
utility::pointer::owning_ptr
< IGEdgeReweighter const > 
IGEdgeReweighterCOP
typedef
utility::pointer::owning_ptr
< IGEdgeReweightContainer
IGEdgeReweightContainerOP
typedef
utility::pointer::owning_ptr
< IGEdgeReweightContainer
const > 
IGEdgeReweightContainerCOP
typedef
utility::pointer::owning_ptr
< PackerTask
PackerTaskOP
typedef
utility::pointer::owning_ptr
< PackerTask const > 
PackerTaskCOP
typedef
utility::pointer::owning_ptr
< PackerTask_
PackerTask_OP
typedef
utility::pointer::owning_ptr
< PackerTask_ const > 
PackerTask_COP
typedef
utility::pointer::owning_ptr
< ResfileCommand
ResfileCommandOP
typedef
utility::pointer::owning_ptr
< ResfileCommand const > 
ResfileCommandCOP
typedef
utility::pointer::owning_ptr
< ResfileContents
ResfileContentsOP
typedef
utility::pointer::owning_ptr
< ResfileContents const > 
ResfileContentsCOP
typedef
utility::pointer::owning_ptr
< TaskFactory
TaskFactoryOP
typedef
utility::pointer::owning_ptr
< TaskFactory const > 
TaskFactoryCOP

Enumerations

enum  ExtraRotSample {
  NO_EXTRA_CHI_SAMPLES = 0, EX_ONE_STDDEV, EX_ONE_HALF_STEP_STDDEV, EX_TWO_FULL_STEP_STDDEVS,
  EX_TWO_HALF_STEP_STDDEVS, EX_FOUR_HALF_STEP_STDDEVS, EX_THREE_THIRD_STEP_STDDEVS, EX_SIX_QUARTER_STEP_STDDEVS,
  ExtraRotSampleCardinality
}
 levels of extra rotamer sampling, i.e., step size and number of steps. More...

Functions

static basic::Tracer tr ("core.pack.task.IGEdgeReweightContainer")
basic::Tracer T ("core.pack.task", basic::t_info)
std::ostream & operator<< (std::ostream &os, PackerTask const &t)
 output highlights of the internal data of PackerTask_: for each residue whether it is to be packed, designed and which amino acids are allowed.
static basic::Tracer TR ("core.pack.task.ResfileReader")
std::map< std::string,
ResfileCommandOP
create_command_map ()
 utility for resfile reader, commands MUST be entered into this hard-coded map
bool comment_begin (utility::vector1< std::string > const &tokens, Size which_token)
 utility function for resfile reader (checks for a leading # signaling a comment)
void parse_resfile (pose::Pose const &pose, PackerTask &the_task)
 changes the state of the given PackerTask according to the commands in the resfile at read in from the -pack:resfile option system.
void parse_resfile (pose::Pose const &pose, PackerTask &the_task, std::string filename)
 changes the state of the given PackerTask according to the commands in the resfile at filename
void parse_resfile_string (pose::Pose const &pose, PackerTask &the_task, std::string const &resfile_string) throw (ResfileReaderException)
 changes the state of the given PackerTask according to the commands in the resfile.
std::string get_token (const Size which_token, const utility::vector1< std::string > &tokens, const bool make_uper_case=true)
 utility function to increment next token to be parsed
utility::vector1< std::string > tokenize_line (std::istream &inputstream)
 utility function for resfile reader
void onError (std::string message)
ExtraRotSample rot_sample_from_name (std::string const &name)
bool is_rot_sample_name (std::string const &name)

Variables

const int EXTRACHI_CUTOFF_LIMIT = 18

Typedef Documentation


Enumeration Type Documentation

levels of extra rotamer sampling, i.e., step size and number of steps.

Enumerator:
NO_EXTRA_CHI_SAMPLES 
EX_ONE_STDDEV 
EX_ONE_HALF_STEP_STDDEV 
EX_TWO_FULL_STEP_STDDEVS 
EX_TWO_HALF_STEP_STDDEVS 
EX_FOUR_HALF_STEP_STDDEVS 
EX_THREE_THIRD_STEP_STDDEVS 
EX_SIX_QUARTER_STEP_STDDEVS 
ExtraRotSampleCardinality 

Function Documentation

bool core::pack::task::comment_begin ( utility::vector1< std::string > const &  tokens,
Size  which_token 
)

utility function for resfile reader (checks for a leading # signaling a comment)

References get_token().

Referenced by protocols::forge::methods::parse_resfile_string_with_no_lockdown(), and core::pack::task::ResfileContents::ResfileContents().

std::map< std::string, ResfileCommandOP > core::pack::task::create_command_map ( )

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

this creates a map linking the parsed strings from the resfile to the command objects. NEW COMMANDS MUST BE ADDED HERE, HARD CODED note that it uses the command object name() method, not hard coded strings (of course, the name() method has hard coded strings...)

References make_table_of_pilot_apps::name.

Referenced by protocols::enzdes::SetCatalyticResPackBehavior::apply(), protocols::forge::remodel::RemodelData::getLoopsToBuildFromFile(), protocols::forge::methods::parse_resfile_string_with_no_lockdown(), and core::pack::task::ResfileContents::ResfileContents().

std::string core::pack::task::get_token ( const Size  which_token,
const utility::vector1< std::string > &  tokens,
bool  make_upper_case 
)

utility function to increment next token to be parsed

utility function to increment next token to be parsed

The PDB specification is case insensitive everywhere except for the chain identifiers. By default get_tokens makes everything upper case. To handle this special case, get_tokens optionally allows it to not convert it to upper case.

References onError().

Referenced by comment_begin(), core::pack::task::TARGET::initialize_from_tokens(), core::pack::task::EX_CUTOFF::initialize_from_tokens(), core::pack::task::NC::initialize_from_tokens(), core::pack::task::EX::initialize_from_tokens(), core::pack::task::APOLA::initialize_from_tokens(), core::pack::task::NOTAA::initialize_from_tokens(), core::pack::task::PIKNA::initialize_from_tokens(), core::pack::task::PIKAA::initialize_from_tokens(), core::pack::task::ALLAA::initialize_from_tokens(), core::pack::task::FIX_HIS_TAUTOMER::initialize_from_tokens(), and protocols::forge::methods::parse_resfile_string_with_no_lockdown().

bool core::pack::task::is_rot_sample_name ( std::string const &  name)
void core::pack::task::onError ( std::string  message)
std::ostream& core::pack::task::operator<< ( std::ostream &  os,
PackerTask const &  t 
)
void core::pack::task::parse_resfile ( pose::Pose const &  pose,
PackerTask &  the_task,
std::string  filename 
)

changes the state of the given PackerTask according to the commands in the resfile at filename

References parse_resfile_string(), and TR().

void core::pack::task::parse_resfile ( pose::Pose const &  pose,
PackerTask &  the_task 
)

changes the state of the given PackerTask according to the commands in the resfile at read in from the -pack:resfile option system.

resfile parser applies a resfile filename to a PackerTask each line of the resfile is broken into whitespace-delimited tokens whenever it reads a comment token, it ignores the rest of the line commands read before a "start" token are stored for application later as defaults lines after the start token alter specific ResidueLevelTasks in the PackerTask currently the reader assumes residue ID = PDB ID at the end, any residues not explicitly specified have the default actions performed on them

Referenced by protocols::hotspot_hashing::HotspotStubSet::add_hotspot_constraints_to_pose(), protocols::abinitio::DomainAssembly::apply(), core::pack::task::operation::ReadResfile::apply(), protocols::ddG_main(), protocols::protein_interface_design::movers::PlaceStubMover::parse_my_tag(), protocols::protein_interface_design::movers::PlaceSimultaneouslyMover::parse_my_tag(), protocols::protein_interface_design::movers::parse_stub_sets(), protocols::hotspot_hashing::HotspotStubSet::prepare_hashing_packer_task_(), and protocols::simple_moves::DesignRepackMover::setup_packer_and_movemap().

void core::pack::task::parse_resfile_string ( pose::Pose const &  pose,
PackerTask &  the_task,
std::string const &  resfile_string 
) throw (ResfileReaderException)
ExtraRotSample core::pack::task::rot_sample_from_name ( std::string const &  name)
basic::Tracer core::pack::task::T ( "core.pack.task"  ,
basic::t_info   
)
utility::vector1< std::string > core::pack::task::tokenize_line ( std::istream &  inputstream)
static basic::Tracer core::pack::task::TR ( "core.pack.task.ResfileReader"  ) [static]
static basic::Tracer core::pack::task::tr ( "core.pack.task.IGEdgeReweightContainer"  ) [static]

Variable Documentation

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