core::pack::task Namespace Reference

Namespaces
	operation
	residue_selector
	rna

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	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	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. More...
class	PIKNA
	PIKNA 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	PROPERTY
	Allows designing on ANY residue type Property. (Only currently works with Cannonical AAs) JAB. More...
class	POLAR
	POLAR allows polar residues and packing. More...
class	APOLAR
	APOLAR allows nonpolar residues and packing. More...
class	APOLA
	APOLA is a deprecated version of APOLAR allows nonpolar residues and packing. More...
class	CHARGED
	CHARGED allows charged residues and packing JAB. More...
class	AROMATIC
	AROMATIC allows designing only aromatic residues. JAB. 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	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. 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	ResidueLevelTask
class	ResidueLevelTask_
	Residue-level task class. More...
class	TaskFactory
	Factory class for the creation and initialization of PackerTask objects. 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-canonicals. More...
vector1< TaskOperationOP >	get_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)
TaskFactoryOP	parse_task_operations (TagCOP tag, DataMap &data, TaskFactoryOP &task_factory)
void	attributes_for_parse_task_operations (AttributeList &attributes, string const &description, string const &packerpalette_description)
void	attributes_for_parse_task_operations_w_factory (AttributeList &attributes, string const &used_for_descr)
void	set_up_packer_palette (utility::tag::TagCOP tag, basic::datacache::DataMap const &data, core::pack::task::TaskFactoryOP &task_factory)
	Parse a "packer_palette" tag from XML, and add a PackerPalette to a TaskFactory. More...
static const std::string	TASK_OPERATIONS_TAG ("task_operations")
static const std::string	PACKER_PALETTE_TAG ("packer_palette")
static const std::string	TASK_FACTORY_TAG ("task_factory")
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="", std::string const &packerpalette_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

Typedef Documentation

IGEdgeReweightContainerCOP

typedef utility::pointer::shared_ptr< IGEdgeReweightContainer const > core::pack::task::IGEdgeReweightContainerCOP

IGEdgeReweightContainerOP

typedef utility::pointer::shared_ptr< IGEdgeReweightContainer > core::pack::task::IGEdgeReweightContainerOP

IGEdgeReweighterCOP

typedef utility::pointer::shared_ptr< IGEdgeReweighter const > core::pack::task::IGEdgeReweighterCOP

IGEdgeReweighterOP

typedef utility::pointer::shared_ptr< IGEdgeReweighter > core::pack::task::IGEdgeReweighterOP

PackerTask_COP

typedef utility::pointer::shared_ptr< PackerTask_ const > core::pack::task::PackerTask_COP

PackerTask_OP

typedef utility::pointer::shared_ptr< PackerTask_ > core::pack::task::PackerTask_OP

PackerTaskCOP

typedef utility::pointer::shared_ptr< PackerTask const > core::pack::task::PackerTaskCOP

PackerTaskOP

typedef utility::pointer::shared_ptr< PackerTask > core::pack::task::PackerTaskOP

ResfileCommandCOP

typedef utility::pointer::shared_ptr< ResfileCommand const > core::pack::task::ResfileCommandCOP

ResfileCommandOP

typedef utility::pointer::shared_ptr< ResfileCommand > core::pack::task::ResfileCommandOP

ResfileContentsCOP

typedef utility::pointer::shared_ptr< ResfileContents const > core::pack::task::ResfileContentsCOP

ResfileContentsOP

typedef utility::pointer::shared_ptr< ResfileContents > core::pack::task::ResfileContentsOP

TaskFactoryCOP

typedef utility::pointer::shared_ptr< TaskFactory const > core::pack::task::TaskFactoryCOP

TaskFactoryOP

typedef utility::pointer::shared_ptr< TaskFactory > core::pack::task::TaskFactoryOP

Enumeration Type Documentation

ExtraRotSample

enum core::pack::task::ExtraRotSample

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

PackerTaskSymmetryStatus

enum core::pack::task::PackerTaskSymmetryStatus

Enumerator
NO_SYMMETRIZATION_REQUEST
REQUEST_SYMMETRIZE_BY_UNION
REQUEST_SYMMETRIZE_BY_INTERSECTION
ALREADY_SYMMETRIZED

Function Documentation

attributes_for_parse_task_operations() [1/2]

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

References PACKER_PALETTE_TAG(), and 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::ExplicitWaterMover::define_explicit_water_mover_schema(), protocols::calc_taskop_movers::DesignRepackMover::get_xsd_complex_type(), protocols::analysis::simple_metrics::SequenceRecoveryMetric::provide_xml_schema(), protocols::backrub::BackrubProtocol::provide_xml_schema(), protocols::buns::BuriedUnsatHbondFilter2::provide_xml_schema(), protocols::calc_taskop_filters::RotamerBoltzmannWeight::provide_xml_schema(), protocols::calc_taskop_movers::ConsensusDesignMover::provide_xml_schema(), protocols::carbohydrates::GlycanSampler::provide_xml_schema(), protocols::constraint_movers::AddConstraintsToCurrentConformationMover::provide_xml_schema(), protocols::coupled_moves::CoupledMovesProtocol::provide_xml_schema(), protocols::dna::DesignProteinBackboneAroundDNA::provide_xml_schema(), protocols::dna::DnaInterfaceMultiStateDesign::provide_xml_schema(), protocols::dna::DnaInterfacePacker::provide_xml_schema(), protocols::docking::DockingProtocol::provide_xml_schema(), protocols::evolution::NucleotideMutation::provide_xml_schema(), protocols::features::RotamerRecoveryFeatures::provide_xml_schema(), protocols::flxbb::FlxbbDesign::provide_xml_schema(), protocols::frag_picker::FragmentScoreFilter::provide_xml_schema(), protocols::hotspot_hashing::movers::PlaceSurfaceProbe::provide_xml_schema(), protocols::hybridization::BackboneTorsionPerturbation::provide_xml_schema(), protocols::hybridization::BackboneTorsionSampler::provide_xml_schema(), protocols::hybridization::HybridizeProtocol::provide_xml_schema(), protocols::loops::loop_mover::refine::LoopMover_Refine_CCD::provide_xml_schema(), protocols::matdes::ClashCheckFilter::provide_xml_schema(), protocols::matdes::OligomericAverageDegreeFilter::provide_xml_schema(), protocols::matdes::SchemePlaceMotifsMover::provide_xml_schema(), protocols::mean_field::GenMeanFieldMover::provide_xml_schema(), protocols::minimization_packing::BoltzmannRotamerMover::provide_xml_schema(), protocols::minimization_packing::MinPackMover::provide_xml_schema(), protocols::minimization_packing::RotamerTrialsMinMover::provide_xml_schema(), protocols::minimization_packing::symmetry::TaskAwareSymMinMover::provide_xml_schema(), protocols::minimization_packing::TaskAwareMinMover::provide_xml_schema(), protocols::pose_creation::MergePDBMover::provide_xml_schema(), protocols::protein_interface_design::filters::AtomicContactCountFilter::provide_xml_schema(), protocols::protein_interface_design::filters::AverageDegreeFilter::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::FilterScanFilter::provide_xml_schema(), protocols::protein_interface_design::filters::SequenceRecoveryFilter::provide_xml_schema(), protocols::protein_interface_design::filters::SpecificResiduesNearInterfaceFilter::provide_xml_schema(), protocols::protein_interface_design::filters::Torsion::provide_xml_schema(), protocols::protein_interface_design::movers::BackrubDDMover::provide_xml_schema(), protocols::protein_interface_design::movers::BuildAlaPose::provide_xml_schema(), protocols::protein_interface_design::movers::DockAndRetrieveSidechains::provide_xml_schema(), protocols::protein_interface_design::movers::LoopRemodel::provide_xml_schema(), protocols::protein_interface_design::movers::PlaceSimultaneouslyMover::provide_xml_schema(), protocols::protein_interface_design::movers::PlaceStubMover::provide_xml_schema(), protocols::protein_interface_design::movers::PrepackMover::provide_xml_schema(), protocols::protein_interface_design::movers::ProteinInterfaceMultiStateDesignMover::provide_xml_schema(), protocols::protein_interface_design::movers::RandomMutation::provide_xml_schema(), protocols::protein_interface_design::movers::SecretionOptimizationMover::provide_xml_schema(), protocols::protein_interface_design::movers::TaskAwareCsts::provide_xml_schema(), protocols::protein_mpnn::ProteinMPNNMover::provide_xml_schema(), protocols::quantum_annealing::InteractionGraphSummaryMetric::provide_xml_schema(), protocols::recon_design::FindConsensusSequence::provide_xml_schema(), protocols::relax::AtomCoordinateCstMover::provide_xml_schema(), protocols::simple_ddg::DdgFilter::provide_xml_schema(), protocols::simple_ddg::DdGScan::provide_xml_schema(), protocols::simple_filters::BuriedUnsatHbondFilter::provide_xml_schema(), protocols::simple_filters::MembAccesResidueLipophilicityFilter::provide_xml_schema(), protocols::simple_filters::MutationsFilter::provide_xml_schema(), protocols::simple_filters::NetChargeFilter::provide_xml_schema(), protocols::simple_filters::ResidueBurialFilter::provide_xml_schema(), protocols::simple_filters::ResidueCountFilter::provide_xml_schema(), protocols::simple_filters::SaveResfileToDiskFilter::provide_xml_schema(), protocols::simple_filters::TaskAwareSASAFilter::provide_xml_schema(), protocols::simple_filters::TaskAwareScoreTypeFilter::provide_xml_schema(), protocols::simple_filters::TotalSasaFilter::provide_xml_schema(), protocols::simple_moves::ReportEffectivePKA::provide_xml_schema(), protocols::simple_moves::sidechain_moves::SidechainMCMover::provide_xml_schema(), protocols::simple_moves::sidechain_moves::SidechainMover::provide_xml_schema(), protocols::simple_moves::SixDoFGridDockMover::provide_xml_schema(), protocols::splice::Splice::provide_xml_schema(), protocols::splice::SpliceIn::provide_xml_schema(), protocols::splice::SpliceInAntibody::provide_xml_schema(), protocols::splice::SpliceInTail::provide_xml_schema(), protocols::splice::SpliceOut::provide_xml_schema(), protocols::splice::SpliceOutAntibody::provide_xml_schema(), protocols::splice::SpliceOutTail::provide_xml_schema(), protocols::splice::TailSegmentMover::provide_xml_schema(), protocols::switches::GraftSwitchMover::provide_xml_schema(), protocols::symmetric_docking::SymDockProtocol::provide_xml_schema(), protocols::task_operations::StoreCompoundTaskMover::provide_xml_schema(), protocols::task_operations::StoreTaskMover::provide_xml_schema(), protocols::dna_dock::DNAClashCheckFilterCreator::provide_xml_schema(), protocols::dna_dock::PropagateClashCheckFilterCreator::provide_xml_schema(), core::pack::task::residue_selector::ClashBasedShellSelector::provide_xml_schema_attributes(), and protocols::design_opt::GreedyOptMutationMover::root_node_for_greedy_opt().

attributes_for_parse_task_operations() [2/2]

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

Append the 'task_operation' attribute.

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

attributes_for_parse_task_operations_w_factory() [1/2]

void core::pack::task::attributes_for_parse_task_operations_w_factory	(	AttributeList &	attributes,
		string const &	used_for_descr
	)

References PACKER_PALETTE_TAG(), TASK_FACTORY_TAG(), and TASK_OPERATIONS_TAG().

Referenced by protocols::relax::FastRelax::complex_type_generator_for_fast_relax(), protocols::backrub::BackrubSidechainMover::provide_xml_schema(), protocols::enzdes::PredesignPerturbMover::provide_xml_schema(), protocols::enzdes::EnzRepackMinimize::provide_xml_schema(), protocols::enzdes::PackRotamersMoverPartGreedy::provide_xml_schema(), and protocols::fold_from_loops::movers::DisplayPoseLabelsMover::provide_xml_schema().

attributes_for_parse_task_operations_w_factory() [2/2]

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.

comment_begin()

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 core::pack::task::ResfileContents::parse_body_line(), core::pack::task::ResfileContents::parse_header_line(), protocols::forge::methods::parse_resfile_string_with_no_lockdown(), and core::pack::task::ResfileContents::ResfileContents().

create_command_map()

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::NOTAA::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::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().

get_resfile_commands()

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-canonicals.

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].

  (Non-canonical, 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().

get_task_operations() [1/2]

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

References TASK_OPERATIONS_TAG().

Referenced by protocols::flxbb::FlxbbDesign::parse_my_tag().

get_task_operations() [2/2]

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.

get_token()

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::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::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().

is_rot_sample_name()

bool core::pack::task::is_rot_sample_name

(

std::string const &

name

)

References ExtraRotSampleCardinality.

Referenced by protocols::match::Matcher::initialize_from_file().

onError()

void core::pack::task::onError

(

std::string

message

)

References TR().

Referenced by get_token(), core::pack::task::PIKNA::initialize_from_tokens(), core::pack::task::EX::initialize_from_tokens(), core::pack::task::EX_CUTOFF::initialize_from_tokens(), core::pack::task::TARGET::initialize_from_tokens(), core::pack::task::ResfileContents::locate_command(), core::pack::task::ResfileContents::locate_resid(), core::pack::task::ResfileContents::parse_body_line(), protocols::forge::methods::parse_resfile_string_with_no_lockdown(), core::pack::task::ResfileContents::parse_resid(), core::pack::task::POLAR::residue_action(), core::pack::task::APOLAR::residue_action(), core::pack::task::CHARGED::residue_action(), core::pack::task::AROMATIC::residue_action(), and core::pack::task::TARGET::residue_action().

operator<<()

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

PACKER_PALETTE_TAG()

static const std::string core::pack::task::PACKER_PALETTE_TAG ( "packer_palette"  )

static

Referenced by attributes_for_parse_task_operations(), and attributes_for_parse_task_operations_w_factory().

parse_res_agnostic_commands()

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().

parse_resfile() [1/2]

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::finalize_stub_set(), protocols::protein_interface_design::movers::SetupHotspotConstraintsLoopsMover::generate_csts(), protocols::recon_design::get_designable_residues(), protocols::hydrate::hydrate_hyfile(), protocols::ligand_docking::HighResDocker::make_packer_task_from_vector(), 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().

parse_resfile() [2/2]

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 protocols::abinitio::filename(), parse_resfile_string(), and TR().

parse_resfile_string() [1/2]

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().

parse_resfile_string() [2/2]

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().

parse_task_operations() [1/6]

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.

parse_task_operations() [2/6]

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

References TASK_OPERATIONS_TAG(), and TR().

parse_task_operations() [3/6]

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

References set_up_packer_palette(), TASK_FACTORY_TAG(), TASK_OPERATIONS_TAG(), and TR().

parse_task_operations() [4/6]

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

References set_up_packer_palette(), TASK_OPERATIONS_TAG(), and TR().

Referenced by protocols::fldsgn::filters::SecondaryStructureHasResidueFilter::parse_my_tag(), protocols::matdes::ClashCheckFilter::parse_my_tag(), protocols::matdes::OligomericAverageDegreeFilter::parse_my_tag(), protocols::simple_filters::SaveResfileToDiskFilter::parse_my_tag(), protocols::simple_filters::TaskAwareSASAFilter::parse_my_tag(), protocols::backrub::BackrubProtocol::parse_my_tag(), protocols::minimization_packing::BoltzmannRotamerMover::parse_my_tag(), protocols::splice::TailSegmentMover::parse_my_tag(), protocols::task_operations::StoreTaskMover::parse_my_tag(), protocols::hybridization::BackboneTorsionPerturbation::parse_my_tag(), protocols::hybridization::BackboneTorsionSampler::parse_my_tag(), protocols::coupled_moves::CoupledMovesProtocol::parse_my_tag(), protocols::hybridization::HybridizeProtocol::parse_my_tag(), protocols::minimization_packing::RotamerTrialsMinMover::parse_my_tag(), protocols::protein_interface_design::movers::ProteinInterfaceMultiStateDesignMover::parse_my_tag(), protocols::recon_design::FindConsensusSequence::parse_my_tag(), protocols::simple_moves::ReportEffectivePKA::parse_my_tag(), protocols::buns::BuriedUnsatHbondFilter2::parse_my_tag(), protocols::calc_taskop_filters::RotamerBoltzmannWeight::parse_my_tag(), protocols::design_opt::GreedyOptMutationMover::parse_my_tag(), protocols::docking::DockingProtocol::parse_my_tag(), protocols::enzdes::EnzRepackMinimize::parse_my_tag(), protocols::enzdes::PackRotamersMoverPartGreedy::parse_my_tag(), protocols::evolution::NucleotideMutation::parse_my_tag(), protocols::hbnet::HBNet::parse_my_tag(), protocols::hotspot_hashing::movers::PlaceSurfaceProbe::parse_my_tag(), protocols::loops::loop_mover::refine::LoopMover_Refine_CCD::parse_my_tag(), protocols::matdes::MatDesGreedyOptMutationMover::parse_my_tag(), protocols::protein_interface_design::filters::AtomicContactCountFilter::parse_my_tag(), protocols::protein_interface_design::filters::AverageDegreeFilter::parse_my_tag(), protocols::protein_interface_design::filters::BindingStrainFilter::parse_my_tag(), protocols::protein_interface_design::filters::DesignableResiduesFilter::parse_my_tag(), protocols::protein_interface_design::filters::FilterScanFilter::parse_my_tag(), protocols::protein_interface_design::filters::SequenceRecoveryFilter::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::movers::BackrubDDMover::parse_my_tag(), protocols::protein_interface_design::movers::BuildAlaPose::parse_my_tag(), protocols::protein_interface_design::movers::DockAndRetrieveSidechains::parse_my_tag(), protocols::protein_interface_design::movers::PlaceSimultaneouslyMover::parse_my_tag(), protocols::protein_interface_design::movers::PlaceStubMover::parse_my_tag(), protocols::protein_interface_design::movers::PrepackMover::parse_my_tag(), protocols::protein_interface_design::movers::RandomMutation::parse_my_tag(), protocols::protein_interface_design::movers::TaskAwareCsts::parse_my_tag(), protocols::simple_ddg::DdgFilter::parse_my_tag(), protocols::simple_ddg::DdGScan::parse_my_tag(), protocols::simple_filters::BuriedUnsatHbondFilter::parse_my_tag(), protocols::simple_filters::MembAccesResidueLipophilicityFilter::parse_my_tag(), protocols::simple_filters::MutationsFilter::parse_my_tag(), protocols::simple_filters::NetChargeFilter::parse_my_tag(), protocols::simple_filters::ResidueBurialFilter::parse_my_tag(), protocols::simple_filters::ResidueCountFilter::parse_my_tag(), protocols::simple_filters::TaskAwareScoreTypeFilter::parse_my_tag(), protocols::simple_filters::TotalSasaFilter::parse_my_tag(), protocols::splice::Splice::parse_my_tag(), protocols::symmetric_docking::SymDockProtocol::parse_my_tag(), protocols::analysis::simple_metrics::SequenceRecoveryMetric::parse_my_tag(), protocols::carbohydrates::GlycanSampler::parse_my_tag(), protocols::features::ReportToDB::parse_my_tag(), protocols::features::RotamerRecoveryFeatures::parse_my_tag(), protocols::fold_from_loops::movers::DisplayPoseLabelsMover::parse_my_tag(), protocols::mean_field::GenMeanFieldMover::parse_my_tag(), protocols::minimization_packing::symmetry::TaskAwareSymMinMover::parse_my_tag(), protocols::pose_creation::MergePDBMover::parse_my_tag(), protocols::protein_interface_design::movers::LoopRemodel::parse_my_tag(), protocols::protein_mpnn::ProteinMPNNMover::parse_my_tag(), protocols::quantum_annealing::InteractionGraphSummaryMetric::parse_my_tag(), protocols::relax::AtomCoordinateCstMover::parse_my_tag(), protocols::relax::FastRelax::parse_my_tag(), protocols::simple_moves::ExplicitWaterMover::parse_my_tag(), protocols::calc_taskop_movers::ConsensusDesignMover::parse_my_tag(), core::pack::task::residue_selector::ClashBasedShellSelector::parse_my_tag(), protocols::enzdes::PredesignPerturbMover::parse_my_tag(), protocols::matdes::SchemePlaceMotifsMover::parse_my_tag(), protocols::calc_taskop_movers::DesignRepackMover::parse_my_tag(), protocols::protein_interface_design::movers::SecretionOptimizationMover::parse_my_tag(), protocols::simple_ddg::ddG::parse_my_tag(), protocols::splice::SpliceManager::parse_tags(), protocols::constraint_movers::AddConstraintsToCurrentConformationMover::parse_task_operations(), protocols::minimization_packing::MinPackMover::parse_task_operations(), protocols::minimization_packing::PackRotamersMover::parse_task_operations(), protocols::minimization_packing::TaskAwareMinMover::parse_task_operations(), protocols::monte_carlo::GenericMonteCarloMover::parse_task_operations(), protocols::switches::GraftSwitchMover::parse_task_operations(), and protocols::loop_modeling::utilities::set_task_factory_from_tag().

parse_task_operations() [5/6]

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.

parse_task_operations() [6/6]

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.

rot_sample_from_name()

ExtraRotSample core::pack::task::rot_sample_from_name

(

std::string const &

name

)

References ExtraRotSampleCardinality, and NO_EXTRA_CHI_SAMPLES.

Referenced by protocols::match::Matcher::initialize_from_file().

set_up_packer_palette()

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

Parse a "packer_palette" tag from XML, and add a PackerPalette to a TaskFactory.

Added as part of the 2016 Chemical XRW (eXtreme Rosetta Workshop), New Brunswick, NJ, 25 January 2016 to 1 February 2016.

Parameters

[in]	tag	Const owning pointer to an XML tag that may or may not contain a single "packer_palette=xxx" string.
[in]	data	Const reference to the data map, from which defined PackerPalettes will be sought.
[out]	task_factory	Non-const owning pointer to the task_factory that will have a PackerPalette added to it.

Author

Vikram K. Mulligan (vmull.nosp@m.ig@u.nosp@m.w.edu)

Note

Moved to core on 7 Nov. 2018 by VKM, vmull.nosp@m.igan.nosp@m.@flat.nosp@m.iron.nosp@m.insti.nosp@m.tute.nosp@m..org.

References TR().

Referenced by parse_task_operations().

T() [1/2]

static basic::Tracer core::pack::task::T ( "core.pack.task"  , basic::t_info    )

static

Referenced by core::pack::task::PackerTask_::initialize_from_options(), and core::pack::task::ResidueLevelTask_::target_type().

T() [2/2]

static basic::Tracer core::pack::task::T ( "core.pack.task"  , basic::t_info    )

static

TASK_FACTORY_TAG()

static const std::string core::pack::task::TASK_FACTORY_TAG ( "task_factory"  )

static

Referenced by attributes_for_parse_task_operations_w_factory(), and parse_task_operations().

TASK_OPERATIONS_TAG()

static const std::string core::pack::task::TASK_OPERATIONS_TAG ( "task_operations"  )

static

Referenced by attributes_for_parse_task_operations(), attributes_for_parse_task_operations_w_factory(), get_task_operations(), protocols::simple_moves::ExplicitWaterMover::parse_my_tag(), protocols::symmetry::SetupForSequenceSymmetryMover::parse_my_tag(), and parse_task_operations().

tokenize_line() [1/2]

utility::vector1< std::string > core::pack::task::tokenize_line

(

std::istream &

inputstream

)

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

Referenced by protocols::mean_field::AAMatrix::init(), protocols::optimize_weights::IterativeOptEDriver::initialize_free_and_fixed(), protocols::optimize_weights::load_component_weights(), parse_res_agnostic_commands(), protocols::forge::methods::parse_resfile_string_with_no_lockdown(), and core::pack::task::ResfileContents::ResfileContents().

tokenize_line() [2/2]

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'.

tr()

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

static

Referenced by core::pack::task::IGEdgeReweightContainer::res_res_weight().

TR()

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

static

Referenced by core::pack::task::TaskFactory::create_task_and_apply_taskoperations(), get_resfile_commands(), core::pack::task::PIKAA::initialize_from_tokens(), core::pack::task::PIKNA::initialize_from_tokens(), core::pack::task::NOTAA::initialize_from_tokens(), core::pack::task::APOLA::initialize_from_tokens(), onError(), parse_resfile(), parse_task_operations(), core::pack::task::ResfileContents::ResfileContents(), and set_up_packer_palette().

Variable Documentation

EXTRACHI_CUTOFF_LIMIT

const int core::pack::task::EXTRACHI_CUTOFF_LIMIT = 18

Referenced by core::pack::task::operation::parse_rotamer_sampling_data(), core::pack::task::operation::ExtraChiCutoffRLT::parse_tag(), core::pack::task::operation::ExtraChiCutoffRLT::provide_xml_schema(), and core::pack::task::operation::rotamer_sampling_data_xml_schema_attributes().