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core::pack::task Namespace Reference

Namespaces

 operation
 
 residue_selector
 
 rna
 

Classes

class  ALLAA
 ALLAA is deprecated; allows repacking and designing to any canonical residue (default state of PackerTask) More...
 
class  ALLAAwc
 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  APOLA
 APOLA is a deprecated version of APOLAR allows nonpolar residues and packing. More...
 
class  APOLAR
 APOLAR allows nonpolar residues and packing. More...
 
class  AROMATIC
 AROMATIC allows designing only aromatic residues. JAB. More...
 
class  AUTO
 AUTO suggests that a packer can/should reconsider the design setting at a/each residue. More...
 
class  CHARGED
 CHARGED allows charged residues and packing JAB. More...
 
class  EMPTY
 EMPTY disallows all canonical and noncanonical residues. More...
 
class  EX
 EX handles the various extrachi options. More...
 
class  EX_CUTOFF
 EX_CUTOFF allows setting of the extrachi_cutoff (for determining burial for extra rotamers) 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  IGEdgeReweightContainer
 class that interfaces to containers holding IGedge weights between individual residues of the task More...
 
class  IGEdgeReweighter
 helper class for IGEdgeReweightContainer More...
 
class  NATAA
 NATAA allows repacking but no sequence changes (all rotamers are of the original residue) More...
 
class  NATRO
 NATRO disables packing and designing at a position, the residue will be totally unchanged. More...
 
class  NC
 NC handles explicit allowance of noncanonical residue types. More...
 
class  NO_ADDUCTS
 NO_ADDUCTS will disable adducts, assuming they exist. More...
 
class  NOTAA
 NOTAA disallows residues specified in a following string, and allows packing. More...
 
class  PackerTask
 Task class that gives instructions to the packer. More...
 
class  PackerTask_
 the PackerTask controls what rotameric (including sequence) changes the packer is allowed to make 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  POLAR
 POLAR allows polar residues and packing. More...
 
class  PROPERTY
 Allows designing on ANY residue type Property. (Only currently works with Cannonical AAs) JAB. More...
 
class  RESET
 RESET restores the list of allowd residue types to the CAAs. More...
 
class  ResfileCommand
 abstract/interface class for Resfile reader command objects More...
 
class  ResfileContents
 
class  ResfileReaderException
 
class  ResidueLevelTask
 
class  ResidueLevelTask_
 Residue-level task class. 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  TaskFactory
 Factory class for the creation and initialization of PackerTask objects. More...
 
class  USE_INPUT_SC
 USE_INPUT_SC turns on inclusion of the current rotamer for the packer. More...
 

Typedefs

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

Enumerations

enum  PackerTaskSymmetryStatus { NO_SYMMETRIZATION_REQUEST, REQUEST_SYMMETRIZE_BY_UNION, REQUEST_SYMMETRIZE_BY_INTERSECTION, ALREADY_SYMMETRIZED }
 
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")
 
static basic::Tracer T ("core.pack.task", basic::t_info)
 
std::ostream & operator<< (std::ostream &os, PackerTask const &task)
 output highlights of the internal data of PackerTask_: for each residue whether it is to be packed, designed and which amino acids are allowed. More...
 
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 More...
 
bool comment_begin (utility::vector1< std::string > const &tokens, Size which_token)
 utility function for resfile reader (checks for a leading # signaling a comment) More...
 
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. More...
 
void parse_resfile (pose::Pose const &pose, PackerTask &the_task, std::string const &filename)
 changes the state of the given PackerTask according to the commands in the resfile at filename More...
 
void parse_resfile_string (pose::Pose const &pose, PackerTask &the_task, std::string const &resfile_fname, std::string const &resfile_string)
 changes the state of the given PackerTask according to the commands in the resfile. More...
 
void parse_resfile_string (pose::Pose const &pose, PackerTask &the_task, std::string const &resfile_fname, std::string const &resfile_string, core::select::residue_selector::ResidueSubset const &mask)
 changes the state of the given PackerTask according to the commands in the resfile. More...
 
std::string get_token (const Size which_token, const utility::vector1< std::string > &tokens, const bool make_upper_case=true)
 utility function to increment next token to be parsed More...
 
utility::vector1< std::string > tokenize_line (std::istream &inputstream)
 Split the line into vector of strings. Each separated string is a 'token'. More...
 
utility::vector1< std::string > tokenize_line (std::string const &line)
 Split the line into vector of strings. Each separated string is a 'token'. More...
 
void onError (std::string message)
 
static basic::Tracer T ("core.pack.task", basic::t_info)
 
ExtraRotSample rot_sample_from_name (std::string const &name)
 
bool is_rot_sample_name (std::string const &name)
 
utility::vector1
< ResfileCommandOP
parse_res_agnostic_commands (std::string const &line, std::map< std::string, ResfileCommandOP > const &command_map)
 Parse a command line that is residue agnostic and has no residue information. IE "PIKAA ST" or [EMPTY NC xxx NC xxx]. More...
 
vector1< vector1
< ResfileCommandOP > > 
get_resfile_commands (std::string const &motif)
 Take a Design Sequence Motif (like a simple version of a resfile), and parse into a list of ResfileCommands. These commands can then be used to do whatever you want with, including non-cannonicals. More...
 
vector1< TaskOperationOPget_task_operations (TagCOP tag, DataMap const &data)
 
TaskFactoryOP parse_task_operations (TagCOP tag, DataMap const &data)
 
TaskFactoryOP parse_task_operations (string const &task_list, DataMap const &data)
 Construct a task factory from the task operations referenced in the given comma-separated list of names. More...
 
TaskFactoryOP parse_task_operations (TagCOP tag, DataMap &data, TaskFactoryOP &task_factory)
 
void attributes_for_parse_task_operations (AttributeList &attributes, string const &description)
 
void attributes_for_parse_task_operations_w_factory (AttributeList &attributes, string const &used_for_descr)
 
utility::vector1
< core::pack::task::operation::TaskOperationOP
get_task_operations (utility::tag::TagCOP tag, basic::datacache::DataMap const &data)
 Return a list of the task operations referenced in the given tag. More...
 
core::pack::task::TaskFactoryOP parse_task_operations (utility::tag::TagCOP tag, basic::datacache::DataMap const &data)
 Construct a TaskFactory from the task operations referenced in the given tag. More...
 
core::pack::task::TaskFactoryOP parse_task_operations (std::string const &task_list, basic::datacache::DataMap const &data)
 Construct a task factory from the task operations referenced in the given comma-separated list of names. More...
 
core::pack::task::TaskFactoryOP parse_task_operations (utility::tag::TagCOP tag, basic::datacache::DataMap &data, core::pack::task::TaskFactoryOP &task_factory)
 Construct a TaskFactory by adding the task operations referenced in the given tag to a task factory already present in the data map. More...
 
void attributes_for_parse_task_operations (utility::tag::AttributeList &attributes, std::string const &description="")
 Append the 'task_operation' attribute. More...
 
void attributes_for_parse_task_operations_w_factory (utility::tag::AttributeList &attributes, std::string const &used_for_descr="")
 Append the 'task_operation' and 'task_factory' attributes. More...
 

Variables

const int EXTRACHI_CUTOFF_LIMIT = 18
 
std::string const TASK_OPERATIONS_TAG = "task_operations"
 
std::string const TASK_FACTORY_TAG = "task_factory"
 

Typedef Documentation

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

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 
Enumerator
NO_SYMMETRIZATION_REQUEST 
REQUEST_SYMMETRIZE_BY_UNION 
REQUEST_SYMMETRIZE_BY_INTERSECTION 
ALREADY_SYMMETRIZED 

Function Documentation

void core::pack::task::attributes_for_parse_task_operations ( utility::tag::AttributeList &  attributes,
std::string const &  description = "" 
)

Append the 'task_operation' attribute.

"description" can be used to specify for what the TaskOperations are being used for.

void core::pack::task::attributes_for_parse_task_operations ( AttributeList &  attributes,
string const &  description 
)

References TASK_OPERATIONS_TAG.

Referenced by protocols::hbnet::HBNet::attributes_for_hbnet(), protocols::features::ReportToDB::attributes_for_report_to_db(), protocols::loop_modeling::utilities::attributes_for_set_task_factory_from_tag(), protocols::minimization_packing::PackRotamersMover::complex_type_generator_for_pack_rotamers_mover(), protocols::minimization_packing::RotamerTrialsMover::complex_type_generator_for_rotamer_trials_mover(), protocols::monte_carlo::GenericMonteCarloMover::define_composition_schema(), protocols::simple_ddg::ddG::define_ddG_schema(), protocols::simple_moves::WaterBoxMover::define_water_box_mover_schema(), protocols::calc_taskop_movers::DesignRepackMover::get_xsd_complex_type(), protocols::dna_dock::DNAClashCheckFilterCreator::provide_xml_schema(), protocols::dna_dock::PropagateClashCheckFilterCreator::provide_xml_schema(), protocols::protein_interface_design::movers::DockAndRetrieveSidechains::provide_xml_schema(), protocols::protein_interface_design::movers::BuildAlaPose::provide_xml_schema(), protocols::protein_interface_design::movers::TaskAwareCsts::provide_xml_schema(), protocols::simple_filters::TotalSasaFilter::provide_xml_schema(), protocols::protein_interface_design::movers::PrepackMover::provide_xml_schema(), protocols::task_operations::StoreTaskMover::provide_xml_schema(), protocols::protein_interface_design::movers::RandomMutation::provide_xml_schema(), protocols::matdes::SchemePlaceMotifsMover::provide_xml_schema(), protocols::simple_filters::ResidueBurialFilter::provide_xml_schema(), protocols::protein_interface_design::movers::BackrubDDMover::provide_xml_schema(), protocols::simple_filters::NetChargeFilter::provide_xml_schema(), protocols::splice::SpliceOutTail::provide_xml_schema(), protocols::simple_filters::MembAccesResidueLipophilicityFilter::provide_xml_schema(), protocols::splice::SpliceInTail::provide_xml_schema(), protocols::protein_interface_design::filters::AverageDegreeFilter::provide_xml_schema(), protocols::dna::DesignProteinBackboneAroundDNA::provide_xml_schema(), protocols::protein_interface_design::movers::ProteinInterfaceMultiStateDesignMover::provide_xml_schema(), protocols::protein_interface_design::filters::SpecificResiduesNearInterfaceFilter::provide_xml_schema(), protocols::protein_interface_design::filters::AtomicContactCountFilter::provide_xml_schema(), protocols::dna::DnaInterfaceMultiStateDesign::provide_xml_schema(), protocols::protein_interface_design::filters::BindingStrainFilter::provide_xml_schema(), protocols::protein_interface_design::filters::DesignableResiduesFilter::provide_xml_schema(), protocols::protein_interface_design::filters::Torsion::provide_xml_schema(), protocols::minimization_packing::symmetry::TaskAwareSymMinMover::provide_xml_schema(), protocols::simple_ddg::DdgFilter::provide_xml_schema(), protocols::splice::TailSegmentMover::provide_xml_schema(), protocols::splice::SpliceOutAntibody::provide_xml_schema(), protocols::frag_picker::FragmentScoreFilter::provide_xml_schema(), protocols::protein_interface_design::movers::LoopRemodel::provide_xml_schema(), protocols::simple_filters::BuriedUnsatHbondFilter::provide_xml_schema(), protocols::constraint_movers::AddConstraintsToCurrentConformationMover::provide_xml_schema(), protocols::protein_interface_design::filters::SequenceRecoveryFilter::provide_xml_schema(), protocols::simple_filters::MutationsFilter::provide_xml_schema(), protocols::hotspot_hashing::movers::PlaceSurfaceProbe::provide_xml_schema(), protocols::splice::SpliceOut::provide_xml_schema(), protocols::mean_field::GenMeanFieldMover::provide_xml_schema(), protocols::coupled_moves::CoupledMovesProtocol::provide_xml_schema(), protocols::splice::SpliceIn::provide_xml_schema(), protocols::minimization_packing::TaskAwareMinMover::provide_xml_schema(), protocols::task_operations::StoreCompoundTaskMover::provide_xml_schema(), protocols::splice::SpliceInAntibody::provide_xml_schema(), protocols::simple_filters::TaskAwareScoreTypeFilter::provide_xml_schema(), protocols::evolution::NucleotideMutation::provide_xml_schema(), protocols::relax::AtomCoordinateCstMover::provide_xml_schema(), protocols::simple_moves::ReportEffectivePKA::provide_xml_schema(), protocols::features::RotamerRecoveryFeatures::provide_xml_schema(), protocols::calc_taskop_filters::RotamerBoltzmannWeight::provide_xml_schema(), protocols::calc_taskop_movers::ConsensusDesignMover::provide_xml_schema(), protocols::pose_creation::MergePDBMover::provide_xml_schema(), protocols::hybridization::BackboneTorsionPerturbation::provide_xml_schema(), protocols::hybridization::BackboneTorsionSampler::provide_xml_schema(), protocols::protein_interface_design::movers::PlaceSimultaneouslyMover::provide_xml_schema(), protocols::protein_interface_design::filters::FilterScanFilter::provide_xml_schema(), protocols::minimization_packing::RotamerTrialsMinMover::provide_xml_schema(), protocols::simple_ddg::DdGScan::provide_xml_schema(), protocols::protein_interface_design::movers::PlaceStubMover::provide_xml_schema(), protocols::backrub::BackrubProtocol::provide_xml_schema(), protocols::dna::DnaInterfacePacker::provide_xml_schema(), protocols::loops::loop_mover::refine::LoopMover_Refine_CCD::provide_xml_schema(), protocols::minimization_packing::BoltzmannRotamerMover::provide_xml_schema(), protocols::minimization_packing::MinPackMover::provide_xml_schema(), protocols::matdes::ClashCheckFilter::provide_xml_schema(), protocols::simple_filters::TaskAwareSASAFilter::provide_xml_schema(), protocols::analysis::simple_metrics::SequenceRecoveryMetric::provide_xml_schema(), protocols::matdes::OligomericAverageDegreeFilter::provide_xml_schema(), protocols::simple_filters::SaveResfileToDiskFilter::provide_xml_schema(), protocols::hybridization::HybridizeProtocol::provide_xml_schema(), protocols::carbohydrates::GlycanTreeSampler::provide_xml_schema(), protocols::symmetric_docking::SymDockProtocol::provide_xml_schema(), protocols::simple_moves::sidechain_moves::SidechainMCMover::provide_xml_schema(), protocols::simple_filters::ResidueCountFilter::provide_xml_schema(), protocols::flxbb::FlxbbDesign::provide_xml_schema(), protocols::docking::DockingProtocol::provide_xml_schema(), protocols::splice::Splice::provide_xml_schema(), protocols::simple_moves::sidechain_moves::SidechainMover::provide_xml_schema(), core::pack::task::residue_selector::ClashBasedShellSelector::provide_xml_schema_attributes(), and protocols::design_opt::GreedyOptMutationMover::root_node_for_greedy_opt().

void core::pack::task::attributes_for_parse_task_operations_w_factory ( utility::tag::AttributeList &  attributes,
std::string const &  used_for_descr = "" 
)

Append the 'task_operation' and 'task_factory' attributes.

void core::pack::task::attributes_for_parse_task_operations_w_factory ( AttributeList &  attributes,
string const &  used_for_descr 
)
bool core::pack::task::comment_begin ( utility::vector1< std::string > const &  tokens,
Size  which_token 
)
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 core::pack::task::NATRO::name(), core::pack::task::NATAA::name(), core::pack::task::ALLAA::name(), core::pack::task::ALLAAxc::name(), core::pack::task::ALLAAwc::name(), core::pack::task::PIKAA::name(), core::pack::task::PIKNA::name(), core::pack::task::PIKRNA::name(), core::pack::task::NOTAA::name(), core::pack::task::EMPTY::name(), core::pack::task::RESET::name(), core::pack::task::PROPERTY::name(), core::pack::task::POLAR::name(), core::pack::task::APOLAR::name(), core::pack::task::APOLA::name(), core::pack::task::CHARGED::name(), core::pack::task::AROMATIC::name(), core::pack::task::EX::name(), core::pack::task::NC::name(), core::pack::task::EX_CUTOFF::name(), core::pack::task::USE_INPUT_SC::name(), core::pack::task::AUTO::name(), core::pack::task::SCAN::name(), core::pack::task::TARGET::name(), core::pack::task::NO_ADDUCTS::name(), and core::pack::task::FIX_HIS_TAUTOMER::name().

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

utility::vector1< utility::vector1< ResfileCommandOP > > core::pack::task::get_resfile_commands ( std::string const &  motif)

Take a Design Sequence Motif (like a simple version of a resfile), and parse into a list of ResfileCommands. These commands can then be used to do whatever you want with, including non-cannonicals.

This is used in the CreateSequenceMotifMover and the SequenceMotifTaskOperation interfaces.

This is slightly similar to a regex, but not quite. We are not matching a sequence, we are designing in a motif regardless of the current sequence, anywhere in a protein.

  • Each letter corresponds to a position. Using [ ] indicates a more complicated expression for that position.
  • An X indicates it can be anything, and that we are designing here.
  • An AA Letter, like V, indicates that that position will be designed to a V.
  • A - charactor indicates that that position stays with whatever it is currently. We essentially skip this position.
  • An expression like: [^PAV] indicates that we will design anything except Proline, Alanine, and Valine
  • An expression like: [NTS] indicates that that position can be Asparigine, Threonine, or Serine and only of these will be enabled during the design.
  • RESFILE commands are accepted as well. These require a % Charactor to start the whole line off. For example [POLAR] is totally cool, as is [PIKAA ST] or [EMPTY NC R2 NC T6 NC OP5] for Noncannonicals.

    (Non-cannonical, DNA, RNA, etc. should all work here!!)

EXAMPLE: Glycosylation N-Linked motif design: N[^P][ST]

References create_command_map(), parse_res_agnostic_commands(), core::sequence::split_sequence_motif(), core::id::to_string(), and TR().

Referenced by protocols::task_operations::SequenceMotifTaskOperation::setup_commands().

utility::vector1< core::pack::task::operation::TaskOperationOP > core::pack::task::get_task_operations ( utility::tag::TagCOP  tag,
basic::datacache::DataMap const &  data 
)

Return a list of the task operations referenced in the given tag.

vector1<TaskOperationOP> core::pack::task::get_task_operations ( TagCOP  tag,
DataMap const &  data 
)
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::NATRO::initialize_from_tokens(), core::pack::task::NATAA::initialize_from_tokens(), core::pack::task::ALLAA::initialize_from_tokens(), core::pack::task::ALLAAxc::initialize_from_tokens(), core::pack::task::ALLAAwc::initialize_from_tokens(), core::pack::task::PIKAA::initialize_from_tokens(), core::pack::task::PIKNA::initialize_from_tokens(), core::pack::task::NOTAA::initialize_from_tokens(), core::pack::task::EMPTY::initialize_from_tokens(), core::pack::task::RESET::initialize_from_tokens(), core::pack::task::PROPERTY::initialize_from_tokens(), core::pack::task::POLAR::initialize_from_tokens(), core::pack::task::APOLAR::initialize_from_tokens(), core::pack::task::APOLA::initialize_from_tokens(), core::pack::task::CHARGED::initialize_from_tokens(), core::pack::task::AROMATIC::initialize_from_tokens(), core::pack::task::EX::initialize_from_tokens(), core::pack::task::NC::initialize_from_tokens(), core::pack::task::EX_CUTOFF::initialize_from_tokens(), core::pack::task::USE_INPUT_SC::initialize_from_tokens(), core::pack::task::AUTO::initialize_from_tokens(), core::pack::task::SCAN::initialize_from_tokens(), core::pack::task::TARGET::initialize_from_tokens(), core::pack::task::NO_ADDUCTS::initialize_from_tokens(), core::pack::task::ResfileContents::locate_command(), core::pack::task::ResfileContents::parse_header_line(), parse_res_agnostic_commands(), protocols::forge::methods::parse_resfile_string_with_no_lockdown(), and core::pack::task::ResfileContents::parse_resid().

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 &  task 
)

output highlights of the internal data of PackerTask_: for each residue whether it is to be packed, designed and which amino acids are allowed.

output operator

References core::pack::task::PackerTask::show().

utility::vector1< ResfileCommandOP > core::pack::task::parse_res_agnostic_commands ( std::string const &  line,
std::map< std::string, ResfileCommandOP > const &  command_map 
)

Parse a command line that is residue agnostic and has no residue information. IE "PIKAA ST" or [EMPTY NC xxx NC xxx].

References get_token(), and tokenize_line().

Referenced by get_resfile_commands(), and protocols::task_operations::ResfileCommandOperation::set_command().

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::hotspot_hashing::HotspotStubSet::add_hotspot_constraints_to_wholepose(), protocols::abinitio::DomainAssembly::apply(), core::pack::task::operation::ReadResfile::apply(), protocols::ddG_main(), protocols::protein_interface_design::movers::SetupHotspotConstraintsLoopsMover::generate_csts(), protocols::hydrate::hydrate_hyfile(), protocols::ligand_docking::HighResDocker::make_packer_task_from_vector(), protocols::protein_interface_design::movers::PlaceSimultaneouslyMover::parse_my_tag(), protocols::protein_interface_design::movers::PlaceStubMover::parse_my_tag(), protocols::simple_moves::FindConsensusSequence::parse_resfiles(), protocols::simple_moves::MSDMover::parse_resfiles(), protocols::protein_interface_design::movers::parse_stub_sets(), protocols::hotspot_hashing::HotspotStubSet::prepare_hashing_packer_task_(), protocols::hydrate::set_task_and_movemap(), protocols::hydrate::set_task_with_de_novo_water_using_resfile(), and protocols::calc_taskop_movers::DesignRepackMover::setup_packer_and_movemap().

void core::pack::task::parse_resfile ( pose::Pose const &  pose,
PackerTask &  the_task,
std::string const &  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_string ( pose::Pose const &  pose,
PackerTask &  the_task,
std::string const &  resfile_fname,
std::string const &  resfile_string 
)

changes the state of the given PackerTask according to the commands in the resfile.

This version calls the overloaded parse_resfile_string and just passes it a ResidueSubset that's set to "true" for every residue of the pose.

References core::pose::Pose::size().

Referenced by protocols::task_operations::ReadResfileFromDB::apply(), core::pack::task::operation::ReadResfile::apply(), protocols::forge::remodel::RemodelWorkingSet::manualPackerTaskGen(), and parse_resfile().

void core::pack::task::parse_resfile_string ( pose::Pose const &  pose,
PackerTask &  the_task,
std::string const &  resfile_fname,
std::string const &  resfile_string,
core::select::residue_selector::ResidueSubset const &  mask 
)

changes the state of the given PackerTask according to the commands in the resfile.

This version accepts a ResidueSubset (a utility::vector1<bool>) that serves as a mask. Residues set to "false" don't have their packer behaviour altered by this TaskOperation.

References core::pack::task::ResfileContents::commands_for_residue(), core::pack::task::ResfileContents::default_commands(), core::pose::Pose::size(), and core::pack::task::ResfileContents::specialized_commands_exist_for_residue().

core::pack::task::TaskFactoryOP core::pack::task::parse_task_operations ( utility::tag::TagCOP  tag,
basic::datacache::DataMap const &  data 
)

Construct a TaskFactory from the task operations referenced in the given tag.

core::pack::task::TaskFactoryOP core::pack::task::parse_task_operations ( std::string const &  task_list,
basic::datacache::DataMap const &  data 
)

Construct a task factory from the task operations referenced in the given comma-separated list of names.

References TASK_OPERATIONS_TAG, and TR().

TaskFactoryOP core::pack::task::parse_task_operations ( TagCOP  tag,
DataMap const &  data 
)

References TASK_OPERATIONS_TAG, and TR().

Referenced by protocols::protein_interface_design::movers::TaskAwareCsts::parse_my_tag(), protocols::protein_interface_design::movers::DockAndRetrieveSidechains::parse_my_tag(), protocols::simple_moves::FindConsensusSequence::parse_my_tag(), protocols::simple_filters::ResidueBurialFilter::parse_my_tag(), protocols::protein_interface_design::movers::PrepackMover::parse_my_tag(), protocols::protein_interface_design::movers::BuildAlaPose::parse_my_tag(), protocols::protein_interface_design::movers::RandomMutation::parse_my_tag(), protocols::task_operations::StoreTaskMover::parse_my_tag(), protocols::matdes::SchemePlaceMotifsMover::parse_my_tag(), protocols::simple_filters::TotalSasaFilter::parse_my_tag(), protocols::protein_interface_design::filters::SpecificResiduesNearInterfaceFilter::parse_my_tag(), protocols::protein_interface_design::filters::Torsion::parse_my_tag(), protocols::protein_interface_design::filters::BindingStrainFilter::parse_my_tag(), protocols::protein_interface_design::movers::ProteinInterfaceMultiStateDesignMover::parse_my_tag(), protocols::simple_filters::TaskAwareScoreTypeFilter::parse_my_tag(), protocols::protein_interface_design::filters::AverageDegreeFilter::parse_my_tag(), protocols::fold_from_loops::movers::DisplayPoseLabelsMover::parse_my_tag(), protocols::calc_taskop_movers::DesignRepackMover::parse_my_tag(), protocols::protein_interface_design::filters::DesignableResiduesFilter::parse_my_tag(), protocols::calc_taskop_filters::RotamerBoltzmannWeight::parse_my_tag(), protocols::protein_interface_design::filters::AtomicContactCountFilter::parse_my_tag(), protocols::simple_filters::NetChargeFilter::parse_my_tag(), protocols::evolution::NucleotideMutation::parse_my_tag(), protocols::simple_filters::MembAccesResidueLipophilicityFilter::parse_my_tag(), protocols::relax::AtomCoordinateCstMover::parse_my_tag(), protocols::enzdes::PackRotamersMoverPartGreedy::parse_my_tag(), protocols::simple_ddg::DdgFilter::parse_my_tag(), protocols::minimization_packing::symmetry::TaskAwareSymMinMover::parse_my_tag(), protocols::enzdes::EnzRepackMinimize::parse_my_tag(), protocols::simple_ddg::ddG::parse_my_tag(), protocols::protein_interface_design::movers::LoopRemodel::parse_my_tag(), protocols::simple_filters::BuriedUnsatHbondFilter::parse_my_tag(), protocols::design_opt::GreedyOptMutationMover::parse_my_tag(), protocols::hotspot_hashing::movers::PlaceSurfaceProbe::parse_my_tag(), protocols::protein_interface_design::filters::SequenceRecoveryFilter::parse_my_tag(), protocols::protein_interface_design::filters::FilterScanFilter::parse_my_tag(), protocols::simple_filters::MutationsFilter::parse_my_tag(), protocols::protein_interface_design::movers::BackrubDDMover::parse_my_tag(), protocols::features::RotamerRecoveryFeatures::parse_my_tag(), protocols::splice::TailSegmentMover::parse_my_tag(), protocols::matdes::MatDesGreedyOptMutationMover::parse_my_tag(), protocols::mean_field::GenMeanFieldMover::parse_my_tag(), protocols::simple_filters::ResidueCountFilter::parse_my_tag(), protocols::loops::loop_mover::refine::LoopMover_Refine_CCD::parse_my_tag(), protocols::coupled_moves::CoupledMovesProtocol::parse_my_tag(), protocols::protein_interface_design::movers::PlaceSimultaneouslyMover::parse_my_tag(), protocols::simple_ddg::DdGScan::parse_my_tag(), protocols::fldsgn::filters::SecondaryStructureHasResidueFilter::parse_my_tag(), protocols::hybridization::BackboneTorsionPerturbation::parse_my_tag(), protocols::hybridization::BackboneTorsionSampler::parse_my_tag(), protocols::splice::Splice::parse_my_tag(), protocols::simple_moves::ReportEffectivePKA::parse_my_tag(), protocols::pose_creation::MergePDBMover::parse_my_tag(), protocols::minimization_packing::RotamerTrialsMinMover::parse_my_tag(), protocols::calc_taskop_movers::ConsensusDesignMover::parse_my_tag(), protocols::minimization_packing::RotamerTrialsMover::parse_my_tag(), protocols::matdes::ClashCheckFilter::parse_my_tag(), protocols::backrub::BackrubProtocol::parse_my_tag(), protocols::protein_interface_design::movers::PlaceStubMover::parse_my_tag(), protocols::simple_filters::TaskAwareSASAFilter::parse_my_tag(), protocols::minimization_packing::BoltzmannRotamerMover::parse_my_tag(), protocols::matdes::OligomericAverageDegreeFilter::parse_my_tag(), protocols::simple_filters::SaveResfileToDiskFilter::parse_my_tag(), protocols::hybridization::HybridizeProtocol::parse_my_tag(), protocols::relax::FastRelax::parse_my_tag(), protocols::analysis::simple_metrics::SequenceRecoveryMetric::parse_my_tag(), protocols::carbohydrates::GlycanTreeSampler::parse_my_tag(), protocols::symmetric_docking::SymDockProtocol::parse_my_tag(), core::pack::task::residue_selector::ClashBasedShellSelector::parse_my_tag(), protocols::enzdes::PredesignPerturbMover::parse_my_tag(), protocols::features::ReportToDB::parse_my_tag(), protocols::docking::DockingProtocol::parse_my_tag(), protocols::simple_moves::WaterBoxMover::parse_my_tag(), protocols::hbnet::HBNet::parse_my_tag(), protocols::splice::SpliceManager::parse_tags(), protocols::minimization_packing::TaskAwareMinMover::parse_task_operations(), protocols::constraint_movers::AddConstraintsToCurrentConformationMover::parse_task_operations(), protocols::minimization_packing::MinPackMover::parse_task_operations(), protocols::minimization_packing::PackRotamersMover::parse_task_operations(), protocols::monte_carlo::GenericMonteCarloMover::parse_task_operations(), and protocols::loop_modeling::utilities::set_task_factory_from_tag().

core::pack::task::TaskFactoryOP core::pack::task::parse_task_operations ( utility::tag::TagCOP  tag,
basic::datacache::DataMap &  data,
core::pack::task::TaskFactoryOP task_factory 
)

Construct a TaskFactory by adding the task operations referenced in the given tag to a task factory already present in the data map.

This allows the transfer of whole task factories on the data map. This way a "base" task factory can be created, transferred on the data map, and individual mover's specific task operations can be added on top.

TaskFactoryOP core::pack::task::parse_task_operations ( string const &  task_list,
DataMap const &  data 
)

Construct a task factory from the task operations referenced in the given comma-separated list of names.

References TASK_OPERATIONS_TAG, and TR().

TaskFactoryOP core::pack::task::parse_task_operations ( TagCOP  tag,
DataMap &  data,
TaskFactoryOP &  task_factory 
)
ExtraRotSample core::pack::task::rot_sample_from_name ( std::string const &  name)
static basic::Tracer core::pack::task::T ( "core.pack.task"  ,
basic::t_info   
)
static
static basic::Tracer core::pack::task::T ( "core.pack.task"  ,
basic::t_info   
)
static
utility::vector1< std::string > core::pack::task::tokenize_line ( std::istream &  inputstream)
utility::vector1< std::string > core::pack::task::tokenize_line ( std::string const &  input_line)

Split the line into vector of strings. Each separated string is a 'token'.

static basic::Tracer core::pack::task::tr ( "core.pack.task.IGEdgeReweightContainer"  )
static
static basic::Tracer core::pack::task::TR ( "core.pack.task.ResfileReader"  )
static

Variable Documentation

const int core::pack::task::EXTRACHI_CUTOFF_LIMIT = 18
std::string const core::pack::task::TASK_FACTORY_TAG = "task_factory"
std::string const core::pack::task::TASK_OPERATIONS_TAG = "task_operations"