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 deprecated, it calls APOLAR to allow nonpolar residues and packing. More...

class	APOLAR
	APOLAR allows nonpolar residues and packing. More...

class	AUTO
	AUTO suggests that a packer can/should reconsider the design setting at a/each residue. 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	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 THREAD_LOCAL basic::Tracer	tr ("core.pack.task.IGEdgeReweightContainer")

static THREAD_LOCAL 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 THREAD_LOCAL 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 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) throw (ResfileReaderException)
	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) throw (ResfileReaderException)
	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)
	utility function for resfile reader More...

void	onError (std::string message)

static THREAD_LOCAL 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)

Variables
const int	EXTRACHI_CUTOFF_LIMIT = 18

Typedef Documentation

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

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

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

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

enum core::pack::task::PackerTaskSymmetryStatus

Enumerator
NO_SYMMETRIZATION_REQUEST
REQUEST_SYMMETRIZE_BY_UNION
REQUEST_SYMMETRIZE_BY_INTERSECTION
ALREADY_SYMMETRIZED

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 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().

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...)

Referenced by protocols::enzdes::SetCatalyticResPackBehavior::apply(), protocols::forge::remodel::RemodelData::getLoopsToBuildFromBlueprint(), 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

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().

bool core::pack::task::is_rot_sample_name ( std::string const & name )

References ExtraRotSampleCardinality.

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

void core::pack::task::onError ( std::string message )

References TR().

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().

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::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_(), and protocols::simple_moves::DesignRepackMover::setup_packer_and_movemap().

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_string	(	pose::Pose const &	pose,
		PackerTask &	the_task,
		std::string const &	resfile_fname,
		std::string const &	resfile_string
	)
throw	(	ResfileReaderException
	)

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.

Referenced by protocols::toolbox::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
	)
throw	(	ResfileReaderException
	)

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(), and core::pack::task::ResfileContents::specialized_commands_exist_for_residue().

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().

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

static

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

static THREAD_LOCAL 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 function for resfile reader

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

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

static

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

static

Referenced by core::pack::task::PIKAA::initialize_from_tokens(), core::pack::task::PIKNA::initialize_from_tokens(), core::pack::task::PIKRNA::initialize_from_tokens(), core::pack::task::NOTAA::initialize_from_tokens(), core::pack::task::APOLA::initialize_from_tokens(), onError(), parse_resfile(), and core::pack::task::ResfileContents::ResfileContents().

Variable Documentation

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

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

Namespaces

Classes

Typedefs

Enumerations

Functions

Variables

Typedef Documentation

Enumeration Type Documentation

Function Documentation

Variable Documentation