protocols::rosetta_scripts Namespace Reference

Classes
class	AdditionalOutputWrapper
class	AdditionalOutputWrapperCreator
class	MultipleOutputWrapper
class	MultipleOutputWrapperCreator
class	MultiplePoseMover
class	MultiplePoseMoverCreator
class	ParsedProtocol
class	ParsedProtocolCreator
class	PosePropertyReporter
class	PosePropertyReporterCreator
	Abstract base class for a PosePropertyReporter factory; the Creator class is responsible for creating a particular PosePropertyReporter class. More...
class	PosePropertyReporterFactory
class	PosePropertyReporterRegistrator
	This templated class will register an instance of an PosePropertyReporterCreator (class T) with the PosePropertyReporterFactory. It will ensure that no PosePropertyReporterCreator is registered twice, and, centralizes this registration logic so that thread safety issues can be handled in one place. More...
class	PoseSelector
class	PoseSelectorCreator
	Abstract base class for a PoseSelector factory; the Creator class is responsible for creating a particular PoseSelector class. More...
class	PoseSelectorFactory
class	PoseSelectorRegistrator
	This templated class will register an instance of an PoseSelectorCreator (class T) with the PoseSelectorFactory. It will ensure that no PoseSelectorCreator is registered twice, and, centralizes this registration logic so that thread safety issues can be handled in one place. More...
class	RosettaScriptsParser
	Reading the xml file and generating the mover. More...
class	SavePoseMover
	mover that can be used to save or restore a pose at an arbitrary point during a rosetta scripts protocol. other movers or filters can be set up to access poses saved by this mover during their apply calls. More...
class	SavePoseMoverCreator

Typedefs
typedef utility::pointer::shared_ptr < MultiplePoseMover >	MultiplePoseMoverOP
typedef utility::pointer::shared_ptr < MultiplePoseMover const >	MultiplePoseMoverCOP
typedef core::Real	Real
typedef core::pose::Pose	Pose
typedef utility::pointer::shared_ptr < ParsedProtocol >	ParsedProtocolOP
typedef utility::pointer::shared_ptr < ParsedProtocol const >	ParsedProtocolCOP
typedef utility::pointer::weak_ptr < ParsedProtocol >	ParsedProtocolAP
typedef utility::pointer::weak_ptr < ParsedProtocol const >	ParsedProtocolCAP
typedef utility::pointer::shared_ptr < PosePropertyReporter >	PosePropertyReporterOP
typedef utility::pointer::shared_ptr < PosePropertyReporter const >	PosePropertyReporterCOP
typedef utility::pointer::shared_ptr < PosePropertyReporterCreator >	PosePropertyReporterCreatorOP
typedef utility::pointer::shared_ptr < PosePropertyReporterCreator const >	PosePropertyReporterCreatorCOP
typedef utility::pointer::shared_ptr < PosePropertyReporterFactory >	PosePropertyReporterFactoryOP
typedef utility::pointer::shared_ptr < PosePropertyReporterFactory const >	PosePropertyReporterFactoryCOP
typedef utility::pointer::shared_ptr < PoseSelector >	PoseSelectorOP
typedef utility::pointer::shared_ptr < PoseSelector const >	PoseSelectorCOP
typedef utility::pointer::shared_ptr < PoseSelectorCreator >	PoseSelectorCreatorOP
typedef utility::pointer::shared_ptr < PoseSelectorCreator const >	PoseSelectorCreatorCOP
typedef utility::pointer::shared_ptr < PoseSelectorFactory >	PoseSelectorFactoryOP
typedef utility::pointer::shared_ptr < PoseSelectorFactory const >	PoseSelectorFactoryCOP
typedef utility::vector0< TagCOP >	TagCOPs
typedef utility::pointer::shared_ptr < SavePoseMover >	SavePoseMoverOP
typedef utility::pointer::shared_ptr < SavePoseMover const >	SavePoseMoverCOP

Enumerations
enum	PoseSelectorFlags { PSF_NONE = 0, PSF_NEED_FULL_POSE_SET = (1 << 0) }

Functions
static thread_local basic::Tracer	TR ("protocols.rosetta_scripts.AdditionalOutputWrapper")
static thread_local basic::Tracer	TR ("protocols.rosetta_scripts.MultipleOutputWrapper")
static thread_local basic::Tracer	TR ("protocols.rosetta_scripts.MultiplePoseMover")
static thread_local basic::Tracer	TR ("protocols.rosetta_scripts.ParsedProtocol")
static thread_local basic::Tracer	TR_call_order ("protocols.rosetta_scripts.ParsedProtocol_call_order")
static thread_local basic::Tracer	TR_report ("protocols.rosetta_scripts.ParsedProtocol.REPORT")
std::pair< moves::MoverOP, std::string >	parse_mover_subtag (utility::tag::TagCOP const tag_ptr, basic::datacache::DataMap &data, protocols::filters::Filters_map const &filters, protocols::moves::Movers_map const &movers, core::pose::Pose const &pose)
static thread_local basic::Tracer	TR ("protocols.rosetta_scripts.PosePropertyReporterFactory")
static thread_local basic::Tracer	TR ("protocols.rosetta_scripts.PoseSelectorFactory")
static thread_local basic::Tracer	TR ("protocols.rosetta_scripts.RosettaScriptsParser")
core::pack::task::TaskFactoryOP	parse_task_operations (utility::tag::TagCOP tag, basic::datacache::DataMap const &data)
core::pack::task::TaskFactoryOP	parse_task_operations (std::string const task_list, basic::datacache::DataMap const &data)
core::pack::task::TaskFactoryOP	parse_task_operations (utility::tag::TagCOP tag, basic::datacache::DataMap &data, core::pack::task::TaskFactoryOP &task_factory)
	option to add or refer to a Taskfactory through the datamap, similar to how to add/refer to movemap OPs (EMS) More...
utility::vector1 < core::pack::task::operation::TaskOperationOP >	get_task_operations (utility::tag::TagCOP tag, basic::datacache::DataMap const &data)
core::scoring::ScoreFunctionOP	parse_score_function (utility::tag::TagCOP tag, std::string const &option_name, basic::datacache::DataMap const &data, std::string const dflt_key="talaris2013")
	Look up the score function defined in the <SCOREFXNS> through the given option. Default to 'talaris2013' by default. More...
core::scoring::ScoreFunctionOP	parse_score_function (utility::tag::TagCOP tag, basic::datacache::DataMap const &data, std::string const dflt_key="talaris2013")
	Look up the score function defined in the <SCOREFXNS> through the option 'scorefxn='. Default to 'talaris2013' by default. More...
std::string	get_score_function_name (utility::tag::TagCOP tag, std::string const &option_name)
	Look up the name of assigned score function to the given option. Use this to prevent hard coding default score functions into protocols. More...
std::string	get_score_function_name (utility::tag::TagCOP tag)
	Look up the name of assigned score function to the 'scorefxn=' option. Use this to prevent hard coding default score functions into protocols. More...
core::pose::PoseOP	saved_reference_pose (utility::tag::TagCOP in_tag, basic::datacache::DataMap &data_map, std::string const tag_str="reference_name")
	convenience function to access pointers to poses that will be stored in the data map at an arbitrary point during an RS protocol Will look for tag in in_tag variable More...
void	foreach_movemap_tag (utility::tag::TagCOP const in_tag, core::pose::Pose const &pose, core::kinematics::MoveMapOP mm)
	utility function for parse_movemap which goes over each of the tags in a movemap section More...
void	parse_movemap (utility::tag::TagCOP const in_tag, core::pose::Pose const &pose, core::kinematics::MoveMapOP &mm, basic::datacache::DataMap &data, bool const reset_map)
	variant of parse_movemap that takes in a datamap and searches it for already existing movemaps More...
void	parse_movemap (utility::tag::TagCOP const in_tag, core::pose::Pose const &pose, core::kinematics::MoveMapOP mm, bool const reset_movemap)
void	add_movemaps_to_datamap (utility::tag::TagCOP in_tag, core::pose::Pose const &pose, basic::datacache::DataMap &data, bool initialize_mm_as_true=false)
	Parses in_tag, adding any MoveMaps specified in branches with names to the datamap for use after. Skips any mm names that are already loaded. This should allow multiple MoveMaps to be specified and loaded in a mover. More...
bool	has_branch (utility::tag::TagCOP in_tag, std::string const branch_name)
	Does the tag have a branch of the given name. More...
protocols::filters::FilterOP	parse_filter (std::string const filter_name, protocols::filters::Filters_map const &filters)
protocols::moves::MoverOP	parse_mover (std::string const mover_name, protocols::moves::Movers_map const &movers)
numeric::xyzVector< core::Real >	parse_xyz_vector (utility::tag::TagCOP const xyz_vector_tag)
	utility function for parsing xyzVector More...
core::Size	find_nearest_res (core::pose::Pose const &source, core::pose::Pose const &target, core::Size const res, core::Size const chain)
	Return the number of the residue on source that is nearest to res on target. If the distance is greater than 2.0 returns 0 to indicate error. More...
void	find_nearest_res (core::pose::Pose const &source, core::pose::Pose const &target, core::Size const res, core::Size &target_res, core::Real &dist, core::Size const chain=0)
	find nearest residue and also return the distance More...
utility::vector1< core::Size >	residue_packer_states (core::pose::Pose const &pose, core::pack::task::TaskFactoryCOP tf, bool const designable, bool const packable)
	returns a vector containing all the residues with a given packer state according to the TF More...
core::Size	find_nearest_disulfide (core::pose::Pose const &pose, core::Size const res)
	finds the nearest disulife to given residue on pose by searching both up and down stream to the given postion More...
void	parse_bogus_res_tag (utility::tag::TagCOP tag, std::string const prefix)
	Access res_num/pdb_num tag with prefix. This is to allow parsing at apply time (pdb_num) instead of at parse_my_tag. This allows one to use SavePoseMovers within a protocol with the correct residue from pdb_num. This function is to prevent unused variable crash. More...

Typedef Documentation

typedef utility::pointer::shared_ptr< MultiplePoseMover const > protocols::rosetta_scripts::MultiplePoseMoverCOP

typedef utility::pointer::shared_ptr< MultiplePoseMover > protocols::rosetta_scripts::MultiplePoseMoverOP

typedef utility::pointer::weak_ptr< ParsedProtocol > protocols::rosetta_scripts::ParsedProtocolAP

typedef utility::pointer::weak_ptr< ParsedProtocol const > protocols::rosetta_scripts::ParsedProtocolCAP

typedef utility::pointer::shared_ptr< ParsedProtocol const > protocols::rosetta_scripts::ParsedProtocolCOP

typedef utility::pointer::shared_ptr< ParsedProtocol > protocols::rosetta_scripts::ParsedProtocolOP

typedef core::pose::Pose protocols::rosetta_scripts::Pose

typedef utility::pointer::shared_ptr< PosePropertyReporter const > protocols::rosetta_scripts::PosePropertyReporterCOP

typedef utility::pointer::shared_ptr< PosePropertyReporterCreator const > protocols::rosetta_scripts::PosePropertyReporterCreatorCOP

typedef utility::pointer::shared_ptr< PosePropertyReporterCreator > protocols::rosetta_scripts::PosePropertyReporterCreatorOP

typedef utility::pointer::shared_ptr< PosePropertyReporterFactory const > protocols::rosetta_scripts::PosePropertyReporterFactoryCOP

typedef utility::pointer::shared_ptr< PosePropertyReporterFactory > protocols::rosetta_scripts::PosePropertyReporterFactoryOP

typedef utility::pointer::shared_ptr< PosePropertyReporter > protocols::rosetta_scripts::PosePropertyReporterOP

typedef utility::pointer::shared_ptr< PoseSelector const > protocols::rosetta_scripts::PoseSelectorCOP

typedef utility::pointer::shared_ptr< PoseSelectorCreator const > protocols::rosetta_scripts::PoseSelectorCreatorCOP

typedef utility::pointer::shared_ptr< PoseSelectorCreator > protocols::rosetta_scripts::PoseSelectorCreatorOP

typedef utility::pointer::shared_ptr< PoseSelectorFactory const > protocols::rosetta_scripts::PoseSelectorFactoryCOP

typedef utility::pointer::shared_ptr< PoseSelectorFactory > protocols::rosetta_scripts::PoseSelectorFactoryOP

typedef utility::pointer::shared_ptr< PoseSelector > protocols::rosetta_scripts::PoseSelectorOP

typedef core::Real protocols::rosetta_scripts::Real

typedef utility::pointer::shared_ptr< SavePoseMover const > protocols::rosetta_scripts::SavePoseMoverCOP

typedef utility::pointer::shared_ptr< SavePoseMover > protocols::rosetta_scripts::SavePoseMoverOP

typedef utility::vector0< TagCOP > protocols::rosetta_scripts::TagCOPs

Enumeration Type Documentation

enum protocols::rosetta_scripts::PoseSelectorFlags

Enumerator
PSF_NONE
PSF_NEED_FULL_POSE_SET

Function Documentation

void protocols::rosetta_scripts::add_movemaps_to_datamap	(	utility::tag::TagCOP	in_tag,
		core::pose::Pose const &	pose,
		basic::datacache::DataMap &	data,
		bool	initialize_mm_as_true
	)

Parses in_tag, adding any MoveMaps specified in branches with names to the datamap for use after. Skips any mm names that are already loaded. This should allow multiple MoveMaps to be specified and loaded in a mover.

References basic::datacache::DataMap::add(), foreach_movemap_tag(), and basic::datacache::DataMap::has().

Referenced by protocols::grafting::AnchoredGraftMover::parse_my_tag().

core::Size protocols::rosetta_scripts::find_nearest_disulfide	(	core::pose::Pose const &	pose,
		core::Size const	res
	)

finds the nearest disulife to given residue on pose by searching both up and down stream to the given postion

References core::conformation::Residue::has_variant_type(), core::pose::Pose::pdb_info(), core::pose::Pose::residue(), core::pose::Pose::total_residue(), and utility_exit_with_message.

Referenced by protocols::protein_interface_design::movers::SetAtomTree::set_ab_fold_tree().

core::Size protocols::rosetta_scripts::find_nearest_res	(	core::pose::Pose const &	source,
		core::pose::Pose const &	target,
		core::Size const	res,
		core::Size const	chain
	)

Return the number of the residue on source that is nearest to res on target. If the distance is greater than 2.0 returns 0 to indicate error.

find source residue that is nearest to res on source. If distance is greater than 2.0A, return 0. chain=0, search all chains, chain=1,2,3 etc. search only that chain

References core::conformation::Residue::chain(), numeric::xyzVector< class >::distance(), core::conformation::Residue::is_ligand(), core::pose::Pose::residue(), core::pose::Pose::total_residue(), and core::conformation::Residue::xyz().

Referenced by protocols::protein_interface_design::filters::RelativeSegmentFilter::apply(), protocols::simple_filters::StemFinder::apply(), protocols::toolbox::task_operations::DatabaseThread::apply(), protocols::toolbox::task_operations::RestrictIdentitiesAtAlignedPositionsOperation::apply(), protocols::toolbox::task_operations::RestrictToAlignedSegmentsOperation::apply(), protocols::toolbox::task_operations::DatabaseThread::find_length(), protocols::toolbox::task_operations::DatabaseThread::mark_designable(), and protocols::toolbox::task_operations::DatabaseThread::mark_leave_as_is().

void protocols::rosetta_scripts::find_nearest_res	(	core::pose::Pose const &	source,
		core::pose::Pose const &	target,
		core::Size const	res,
		core::Size &	target_res,
		core::Real &	target_dist,
		core::Size const	chain
	)

find nearest residue and also return the distance

References core::conformation::Residue::chain(), numeric::xyzVector< class >::distance(), core::conformation::Residue::is_ligand(), core::pose::Pose::residue(), core::pose::Pose::total_residue(), and core::conformation::Residue::xyz().

void protocols::rosetta_scripts::foreach_movemap_tag	(	utility::tag::TagCOP const	in_tag,
		core::pose::Pose const &	pose,
		core::kinematics::MoveMapOP	mm
	)

utility function for parse_movemap which goes over each of the tags in a movemap section

References begin, bondangle(), core::conformation::Conformation::chain_begin(), core::conformation::Conformation::chain_end(), core::pose::Pose::conformation(), core::id::D, end, core::chemical::ResidueType::natoms(), core::pose::Pose::residue_type(), runtime_assert, and core::id::THETA.

Referenced by add_movemaps_to_datamap(), and parse_movemap().

std::string protocols::rosetta_scripts::get_score_function_name	(	utility::tag::TagCOP	tag,
		std::string const &	option_name
	)

Look up the name of assigned score function to the given option. Use this to prevent hard coding default score functions into protocols.

Referenced by get_score_function_name(), protocols::protein_interface_design::movers::DockAndRetrieveSidechains::parse_my_tag(), protocols::protein_interface_design::movers::PrepackMover::parse_my_tag(), protocols::simple_filters::BuriedUnsatHbondFilter::parse_my_tag(), protocols::simple_filters::EnergyPerResidueFilter::parse_my_tag(), protocols::protein_interface_design::movers::MapHotspot::parse_my_tag(), protocols::simple_moves::DesignRepackMover::parse_my_tag(), protocols::protein_interface_design::filters::FNatFilter::parse_my_tag(), protocols::protein_interface_design::filters::IRmsdFilter::parse_my_tag(), protocols::simple_filters::DdgFilter::parse_my_tag(), protocols::enzdes::EnzRepackMinimize::parse_my_tag(), protocols::protein_interface_design::movers::LoopRemodel::parse_my_tag(), protocols::protein_interface_design::movers::TryRotamers::parse_my_tag(), protocols::simple_moves::sidechain_moves::SidechainMCMover::parse_my_tag(), and protocols::enzdes::EnzScoreFilter::parse_my_tag().

std::string protocols::rosetta_scripts::get_score_function_name

(

utility::tag::TagCOP

tag

)

Look up the name of assigned score function to the 'scorefxn=' option. Use this to prevent hard coding default score functions into protocols.

References get_score_function_name().

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

References end, basic::datacache::DataMap::get_ptr(), basic::datacache::DataMap::has(), and utility::string_split().

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

bool protocols::rosetta_scripts::has_branch	(	utility::tag::TagCOP	in_tag,
		std::string const	branch_name
	)

Does the tag have a branch of the given name.

Referenced by protocols::grafting::AnchoredGraftMover::parse_my_tag().

void protocols::rosetta_scripts::parse_bogus_res_tag	(	utility::tag::TagCOP	tag,
		std::string const	prefix
	)

Access res_num/pdb_num tag with prefix. This is to allow parsing at apply time (pdb_num) instead of at parse_my_tag. This allows one to use SavePoseMovers within a protocol with the correct residue from pdb_num. This function is to prevent unused variable crash.

Referenced by protocols::grafting::simple_movers::InsertPoseIntoPoseMover::parse_my_tag(), protocols::grafting::simple_movers::ReplaceRegionMover::parse_my_tag(), protocols::grafting::simple_movers::DeleteRegionMover::parse_my_tag(), protocols::grafting::simple_movers::KeepRegionMover::parse_my_tag(), and protocols::grafting::AnchoredGraftMover::parse_my_tag().

protocols::filters::FilterOP protocols::rosetta_scripts::parse_filter	(	std::string const	filter_name,
		protocols::filters::Filters_map const &	filters
	)

Referenced by protocols::simple_moves::ResetBaselineMover::parse_my_tag(), protocols::simple_moves::ContingentAcceptMover::parse_my_tag(), protocols::simple_filters::Operator::parse_my_tag(), protocols::simple_filters::Sigmoid::parse_my_tag(), protocols::simple_filters::DeltaFilter::parse_my_tag(), protocols::loophash::LoopHashMoverWrapper::parse_my_tag(), protocols::filters::ReplicateFilter::parse_my_tag(), protocols::protein_interface_design::filters::BoltzmannFilter::parse_my_tag(), protocols::simple_filters::RelativePoseFilter::parse_my_tag(), protocols::simple_filters::ReportFilter::parse_my_tag(), protocols::filters::CalculatorFilter::parse_my_tag(), protocols::simple_filters::DdgFilter::parse_my_tag(), protocols::design_opt::ParetoOptMutationMover::parse_my_tag(), protocols::simple_moves::ddG::parse_my_tag(), protocols::generalized_kinematic_closure::GeneralizedKIC::parse_my_tag(), protocols::design_opt::GreedyOptMutationMover::parse_my_tag(), protocols::protein_interface_design::filters::FilterScanFilter::parse_my_tag(), protocols::loophash::LoopHashDiversifier::parse_my_tag(), protocols::matdes::MatDesGreedyOptMutationMover::parse_my_tag(), protocols::features::DdGFeatures::parse_my_tag(), protocols::helical_bundle::BundleGridSampler::parse_my_tag(), protocols::filters::IfThenFilter::parse_my_tag(), and protocols::simple_moves::GenericMonteCarloMover::parse_my_tag().

void protocols::rosetta_scripts::parse_movemap	(	utility::tag::TagCOP const	in_tag,
		core::pose::Pose const &	pose,
		core::kinematics::MoveMapOP &	mm,
		basic::datacache::DataMap &	data,
		bool const	reset_map
	)

variant of parse_movemap that takes in a datamap and searches it for already existing movemaps

variant of parse_movemap that takes in a datamap and searches it for already existing movemaps Still resets movemap if MoveMap branch not found!

References basic::datacache::DataMap::add(), foreach_movemap_tag(), basic::datacache::DataMap::get_ptr(), basic::datacache::DataMap::has(), and TR().

Referenced by protocols::relax::FastRelax::apply(), protocols::md::CartesianMD::parse_movemap(), protocols::cryst::SetCrystWeightMover::parse_my_tag(), protocols::protein_interface_design::movers::PrepackMover::parse_my_tag(), protocols::seeded_abinitio::SeedSetupMover::parse_my_tag(), protocols::simple_moves::RandomTorsionMover::parse_my_tag(), protocols::simple_moves::RandomOmegaFlipMover::parse_my_tag(), protocols::normalmode::NormalModeMinimizer::parse_my_tag(), protocols::loops::loop_mover::refine::LoopMover_Refine_CCD::parse_my_tag(), protocols::md::CartesianMD::parse_my_tag(), protocols::nonlocal::SingleFragmentMover::parse_my_tag(), protocols::simple_moves::MinMover::parse_my_tag(), protocols::relax::FastRelax::parse_my_tag(), protocols::simple_moves::BackboneMover::parse_my_tag(), protocols::simple_moves::BBGaussianMover::parse_my_tag(), and protocols::flxbb::FlxbbDesign::parse_my_tag().

void protocols::rosetta_scripts::parse_movemap	(	utility::tag::TagCOP const	in_tag,
		core::pose::Pose const &	pose,
		core::kinematics::MoveMapOP	mm,
		bool const	reset_movemap
	)

modifies an existing movemap according to tag the movemap defaults to move all bb, chi, and jumps.

modifies an existing movemap according to tag the movemap defaults to move all bb, chi, and jumps. Still resets movemap if MoveMap branch not found!

References foreach_movemap_tag(), and TR().

protocols::moves::MoverOP protocols::rosetta_scripts::parse_mover	(	std::string const	mover_name,
		protocols::moves::Movers_map const &	movers
	)

Referenced by protocols::simple_moves::ContingentAcceptMover::parse_my_tag(), protocols::simple_filters::DeltaFilter::parse_my_tag(), protocols::simple_filters::RelativePoseFilter::parse_my_tag(), protocols::protein_interface_design::filters::BindingStrainFilter::parse_my_tag(), protocols::forge::constraints::RemoveCsts::parse_my_tag(), protocols::simple_filters::DdgFilter::parse_my_tag(), protocols::simple_moves::ddG::parse_my_tag(), protocols::generalized_kinematic_closure::GeneralizedKIC::parse_my_tag(), protocols::features::RotamerRecoveryFeatures::parse_my_tag(), protocols::simple_filters::DdGScan::parse_my_tag(), protocols::rotamer_recovery::RotamerRecoveryMover::parse_my_tag(), protocols::docking::DockSetupMover::parse_my_tag(), protocols::helical_bundle::BundleGridSampler::parse_my_tag(), and protocols::fldsgn::BluePrintBDR::parse_my_tag().

std::pair< moves::MoverOP, std::string > protocols::rosetta_scripts::parse_mover_subtag	(	utility::tag::TagCOP const	tag_ptr,
		basic::datacache::DataMap &	data,
		protocols::filters::Filters_map const &	filters,
		protocols::moves::Movers_map const &	movers,
		core::pose::Pose const &	pose
	)

References basic::datacache::DataMap::add(), protocols::environment::find_mover(), protocols::moves::MoverFactory::get_instance(), basic::datacache::DataMap::get_ptr(), basic::datacache::DataMap::has(), and runtime_assert.

Referenced by protocols::rosetta_scripts::ParsedProtocol::parse_my_tag().

core::scoring::ScoreFunctionOP protocols::rosetta_scripts::parse_score_function	(	utility::tag::TagCOP	tag,
		std::string const &	option_name,
		basic::datacache::DataMap const &	data,
		std::string const	dflt_key
	)

Look up the score function defined in the <SCOREFXNS> through the given option. Default to 'talaris2013' by default.

Utility function to find a scorefunction from parser-provided data. This is essentially a shameless copy of Justin's PackRotamersMover::parse_score_function.

References core::init::check_score_function_sanity(), basic::datacache::DataMap::get_ptr(), and basic::datacache::DataMap::has().

Referenced by protocols::rosetta_scripts::RosettaScriptsParser::generate_mover_for_protocol(), protocols::jd2::parser::MonteCarloLoader::load_data(), protocols::simple_moves::AddChainMover::parse_my_tag(), protocols::simple_moves::ForceDisulfidesMover::parse_my_tag(), protocols::cryst::SetCrystWeightMover::parse_my_tag(), protocols::protein_interface_design::movers::HotspotDisjointedFoldTreeMover::parse_my_tag(), protocols::seeded_abinitio::SwapSegment::parse_my_tag(), protocols::seeded_abinitio::GrowPeptides::parse_my_tag(), protocols::protein_interface_design::movers::PrepackMover::parse_my_tag(), protocols::protein_interface_design::movers::RandomMutation::parse_my_tag(), protocols::seeded_abinitio::SeedSetupMover::parse_my_tag(), protocols::simple_filters::DeltaFilter::parse_my_tag(), protocols::simple_moves::DumpPdb::parse_my_tag(), protocols::seeded_abinitio::CloseFold::parse_my_tag(), protocols::protein_interface_design::movers::HotspotHasherMover::parse_my_tag(), protocols::simple_moves::SwitchChainOrderMover::parse_my_tag(), protocols::seeded_abinitio::SegmentHybridizer::parse_my_tag(), protocols::protein_interface_design::movers::PlaceOnLoop::parse_my_tag(), protocols::simple_filters::RelativePoseFilter::parse_my_tag(), protocols::simple_filters::EnergyPerResidueFilter::parse_my_tag(), protocols::protein_interface_design::filters::BindingStrainFilter::parse_my_tag(), protocols::simple_moves::DesignRepackMover::parse_my_tag(), protocols::protein_interface_design::movers::MapHotspot::parse_my_tag(), protocols::simple_filters::TaskAwareScoreTypeFilter::parse_my_tag(), protocols::protein_interface_design::movers::ProteinInterfaceMultiStateDesignMover::parse_my_tag(), protocols::simple_filters::ResidueIEFilter::parse_my_tag(), protocols::simple_filters::ScoreTypeFilter::parse_my_tag(), protocols::simple_filters::RotamerBoltzmannWeight::parse_my_tag(), protocols::simple_moves::symmetry::TaskAwareSymMinMover::parse_my_tag(), protocols::seeded_abinitio::SeedFoldTree::parse_my_tag(), protocols::protein_interface_design::filters::FNatFilter::parse_my_tag(), protocols::protein_interface_design::filters::IRmsdFilter::parse_my_tag(), protocols::protein_interface_design::movers::BackrubDDMover::parse_my_tag(), protocols::simple_filters::ResidueSetChainEnergyFilter::parse_my_tag(), protocols::simple_moves::TaskAwareMinMover::parse_my_tag(), protocols::enzdes::PackRotamersMoverPartGreedy::parse_my_tag(), protocols::simple_filters::DdgFilter::parse_my_tag(), protocols::design_opt::ParetoOptMutationMover::parse_my_tag(), protocols::enzdes::BackboneSampler::parse_my_tag(), protocols::simple_moves::ddG::parse_my_tag(), protocols::generalized_kinematic_closure::GeneralizedKIC::parse_my_tag(), protocols::simple_filters::AlaScan::parse_my_tag(), protocols::enzdes::EnzRepackMinimize::parse_my_tag(), protocols::design_opt::GreedyOptMutationMover::parse_my_tag(), protocols::loop_modeling::LoopModeler::parse_my_tag(), protocols::abinitio::abscript::AbscriptLoopCloserCM::parse_my_tag(), protocols::protein_interface_design::movers::LoopMoverFromCommandLine::parse_my_tag(), protocols::protein_interface_design::filters::FilterScanFilter::parse_my_tag(), protocols::protein_interface_design::movers::DisulfideMover::parse_my_tag(), protocols::features::RotamerRecoveryFeatures::parse_my_tag(), protocols::flexpep_docking::FlexPepDockingProtocol::parse_my_tag(), protocols::protein_interface_design::movers::LoopRemodel::parse_my_tag(), protocols::matdes::MatDesGreedyOptMutationMover::parse_my_tag(), protocols::protein_interface_design::movers::TryRotamers::parse_my_tag(), protocols::rotamer_recovery::RotamerRecoveryMover::parse_my_tag(), protocols::simple_filters::DdGScan::parse_my_tag(), protocols::simple_moves::sidechain_moves::SidechainMCMover::parse_my_tag(), protocols::simple_moves::ReportEffectivePKA::parse_my_tag(), protocols::simple_moves::ConsensusDesignMover::parse_my_tag(), protocols::simple_moves::RotamerTrialsMinMover::parse_my_tag(), protocols::helical_bundle::BundleGridSampler::parse_my_tag(), protocols::simple_moves::RotamerTrialsMover::parse_my_tag(), protocols::canonical_sampling::MetropolisHastingsMover::parse_my_tag(), protocols::simple_moves::BoltzmannRotamerMover::parse_my_tag(), protocols::relax::FastRelax::parse_my_tag(), protocols::enzdes::LigInterfaceEnergyFilter::parse_my_tag(), protocols::symmetric_docking::SymDockProtocol::parse_my_tag(), protocols::moves::RampingMover::parse_my_tag(), protocols::enzdes::EnzScoreFilter::parse_my_tag(), protocols::comparative_modeling::LoopRelaxMover::parse_my_tag(), protocols::flxbb::FlxbbDesign::parse_my_tag(), protocols::analysis::InterfaceAnalyzerMover::parse_my_tag(), protocols::enzdes::RepackWithoutLigandFilter::parse_my_tag(), protocols::analysis::PeptideDeriverFilter::parse_my_tag(), protocols::simple_moves::MinMover::parse_opts(), protocols::hotspot_hashing::movers::PlaceProbeMover::parse_place_probe_tag(), protocols::simple_moves::RepackSidechainsMover::parse_score_function(), protocols::simple_moves::MinPackMover::parse_score_function(), protocols::simple_moves::PackRotamersMover::parse_score_function(), parse_score_function(), protocols::toolbox::task_operations::SelectByDeltaScoreOperation::parse_tag(), and protocols::loop_modeling::utilities::set_scorefxn_from_tag().

core::scoring::ScoreFunctionOP protocols::rosetta_scripts::parse_score_function	(	utility::tag::TagCOP	tag,
		basic::datacache::DataMap const &	data,
		std::string const	dflt_key
	)

Look up the score function defined in the <SCOREFXNS> through the option 'scorefxn='. Default to 'talaris2013' by default.

Utility function to find a scorefunction from parser-provided data for the option 'scorefxn'.

References parse_score_function().

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

This is essentially a shameless copy of Justin's PackRotamersMover::parse_task_operations. In truth DesignRepackMover should disappear into Justin's better organized class, but this will wait... (SJF)

References 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::RandomMutation::parse_my_tag(), protocols::simple_moves::AddConstraintsToCurrentConformationMover::parse_my_tag(), protocols::simple_filters::BuriedUnsatHbondFilter::parse_my_tag(), protocols::toolbox::task_operations::StoreTaskMover::parse_my_tag(), protocols::protein_interface_design::movers::BuildAlaPose::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::relax::AtomCoordinateCstMover::parse_my_tag(), protocols::protein_interface_design::filters::BindingStrainFilter::parse_my_tag(), protocols::protein_interface_design::filters::AverageDegreeFilter::parse_my_tag(), protocols::simple_filters::TaskAwareScoreTypeFilter::parse_my_tag(), protocols::simple_moves::DesignRepackMover::parse_my_tag(), protocols::protein_interface_design::movers::ProteinInterfaceMultiStateDesignMover::parse_my_tag(), protocols::protein_interface_design::filters::DesignableResiduesFilter::parse_my_tag(), protocols::simple_filters::RotamerBoltzmannWeight::parse_my_tag(), protocols::simple_moves::symmetry::TaskAwareSymMinMover::parse_my_tag(), protocols::protein_interface_design::filters::AtomicContactCountFilter::parse_my_tag(), protocols::simple_filters::NetChargeFilter::parse_my_tag(), protocols::protein_interface_design::movers::BackrubDDMover::parse_my_tag(), protocols::simple_moves::ModifyVariantTypeMover::parse_my_tag(), protocols::simple_filters::DdgFilter::parse_my_tag(), protocols::enzdes::PackRotamersMoverPartGreedy::parse_my_tag(), protocols::design_opt::ParetoOptMutationMover::parse_my_tag(), protocols::simple_moves::ddG::parse_my_tag(), protocols::enzdes::EnzRepackMinimize::parse_my_tag(), protocols::hotspot_hashing::movers::PlaceSurfaceProbe::parse_my_tag(), protocols::protein_interface_design::filters::SequenceRecoveryFilter::parse_my_tag(), protocols::design_opt::GreedyOptMutationMover::parse_my_tag(), protocols::simple_filters::MutationsFilter::parse_my_tag(), protocols::protein_interface_design::filters::FilterScanFilter::parse_my_tag(), protocols::features::RotamerRecoveryFeatures::parse_my_tag(), protocols::protein_interface_design::movers::LoopRemodel::parse_my_tag(), protocols::matdes::MatDesGreedyOptMutationMover::parse_my_tag(), protocols::simple_filters::ResidueCountFilter::parse_my_tag(), protocols::loops::loop_mover::refine::LoopMover_Refine_CCD::parse_my_tag(), protocols::simple_filters::DdGScan::parse_my_tag(), protocols::protein_interface_design::movers::PlaceStubMover::parse_my_tag(), protocols::hybridization::BackboneTorsionSampler::parse_my_tag(), protocols::protein_interface_design::movers::PlaceSimultaneouslyMover::parse_my_tag(), protocols::fldsgn::filters::SecondaryStructureHasResidueFilter::parse_my_tag(), protocols::hybridization::BackboneTorsionPerturbation::parse_my_tag(), protocols::simple_moves::ReportEffectivePKA::parse_my_tag(), protocols::hybridization::CartesianHybridize::parse_my_tag(), protocols::simple_moves::RotamerTrialsMinMover::parse_my_tag(), protocols::simple_moves::ConsensusDesignMover::parse_my_tag(), protocols::simple_moves::RotamerTrialsMover::parse_my_tag(), protocols::matdes::ClashCheckFilter::parse_my_tag(), protocols::hybridization::HybridizeProtocol::parse_my_tag(), protocols::simple_filters::TaskAwareSASAFilter::parse_my_tag(), protocols::simple_moves::BoltzmannRotamerMover::parse_my_tag(), protocols::matdes::OligomericAverageDegreeFilter::parse_my_tag(), protocols::relax::FastRelax::parse_my_tag(), protocols::simple_filters::SaveResfileToDiskFilter::parse_my_tag(), protocols::symmetric_docking::SymDockProtocol::parse_my_tag(), protocols::hybridization::FoldTreeHybridize::parse_my_tag(), protocols::features::ReportToDB::parse_my_tag(), protocols::enzdes::PredesignPerturbMover::parse_my_tag(), protocols::docking::DockingProtocol::parse_my_tag(), protocols::simple_moves::AddConstraintsToCurrentConformationMover::parse_task_operations(), protocols::simple_moves::TaskAwareMinMover::parse_task_operations(), protocols::simple_moves::MinPackMover::parse_task_operations(), protocols::simple_moves::PackRotamersMover::parse_task_operations(), protocols::simple_moves::GenericMonteCarloMover::parse_task_operations(), and protocols::loop_modeling::utilities::set_task_factory_from_tag().

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

References end, basic::datacache::DataMap::get_ptr(), basic::datacache::DataMap::has(), utility::string_split(), and TR().

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

option to add or refer to a Taskfactory through the datamap, similar to how to add/refer to movemap OPs (EMS)

allows the transfer of whole taskfactories on the datamap. This way a "base" taskfactory can be created, transferred on the datamap, and individual mover's specific taskoperations can be added on top

References basic::datacache::DataMap::add(), end, basic::datacache::DataMap::get_ptr(), basic::datacache::DataMap::has(), utility::string_split(), and TR().

numeric::xyzVector< core::Real > protocols::rosetta_scripts::parse_xyz_vector

(

utility::tag::TagCOP const

xyz_vector_tag

)

utility function for parsing xyzVector

Referenced by protocols::rigid::RollMover::parse_my_tag().

utility::vector1< core::Size > protocols::rosetta_scripts::residue_packer_states	(	core::pose::Pose const &	pose,
		core::pack::task::TaskFactoryCOP	tf,
		bool const	designable,
		bool const	packable
	)

returns a vector containing all the residues with a given packer state according to the TF

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

Referenced by protocols::simple_filters::ResidueBurialFilter::apply(), protocols::protein_interface_design::movers::TaskAwareCsts::apply(), protocols::protein_interface_design::filters::Torsion::apply(), protocols::toolbox::task_operations::RestrictToAlignedSegmentsOperation::apply(), protocols::toolbox::task_operations::SeqprofConsensusOperation::apply(), protocols::protein_interface_design::movers::PlaceStubMover::apply(), protocols::simple_filters::BuriedUnsatHbondFilter::compute(), protocols::simple_filters::NetChargeFilter::compute(), and protocols::simple_filters::ResidueCountFilter::compute().

core::pose::PoseOP protocols::rosetta_scripts::saved_reference_pose	(	utility::tag::TagCOP const	in_tag,
		basic::datacache::DataMap &	data_map,
		std::string const	tag_name
	)

convenience function to access pointers to poses that will be stored in the data map at an arbitrary point during an RS protocol Will look for tag in in_tag variable

References basic::datacache::DataMap::add(), basic::datacache::DataMap::get_ptr(), basic::datacache::DataMap::has(), and TR().

Referenced by protocols::simple_filters::SidechainRmsdFilter::parse_my_tag(), protocols::simple_filters::DeltaFilter::parse_my_tag(), protocols::rosetta_scripts::SavePoseMover::parse_my_tag(), protocols::simple_moves::SuperimposeMover::parse_my_tag(), protocols::protein_interface_design::filters::LRmsdFilter::parse_my_tag(), protocols::protein_interface_design::filters::RmsdFilter::parse_my_tag(), protocols::protein_interface_design::filters::FNatFilter::parse_my_tag(), protocols::protein_interface_design::filters::IRmsdFilter::parse_my_tag(), protocols::protein_interface_design::filters::SSamountFilter::parse_my_tag(), protocols::protein_interface_design::filters::RmsdSimpleFilter::parse_my_tag(), protocols::grafting::simple_movers::InsertPoseIntoPoseMover::parse_my_tag(), protocols::grafting::simple_movers::ReplaceRegionMover::parse_my_tag(), protocols::features::RotamerRecoveryFeatures::parse_my_tag(), protocols::matdes::MatDesGreedyOptMutationMover::parse_my_tag(), protocols::features::ProteinRMSDFeatures::parse_my_tag(), protocols::features::ProteinRMSDNoSuperpositionFeatures::parse_my_tag(), protocols::matdes::SymUnsatHbondFilter::parse_my_tag(), protocols::grafting::AnchoredGraftMover::parse_my_tag(), and protocols::toolbox::task_operations::SelectByDeltaScoreOperation::parse_tag().

static thread_local basic::Tracer protocols::rosetta_scripts::TR ( "protocols.rosetta_scripts.PosePropertyReporterFactory"  )

static

static thread_local basic::Tracer protocols::rosetta_scripts::TR ( "protocols.rosetta_scripts.PoseSelectorFactory"  )

static

static thread_local basic::Tracer protocols::rosetta_scripts::TR ( "protocols.rosetta_scripts.MultiplePoseMover"  )

static

static thread_local basic::Tracer protocols::rosetta_scripts::TR ( "protocols.rosetta_scripts.MultipleOutputWrapper"  )

static

static thread_local basic::Tracer protocols::rosetta_scripts::TR ( "protocols.rosetta_scripts.AdditionalOutputWrapper"  )

static

Referenced by protocols::rosetta_scripts::MultiplePoseMover::apply(), protocols::rosetta_scripts::MultiplePoseMover::fill_input_cache(), protocols::rosetta_scripts::RosettaScriptsParser::generate_mover_for_protocol(), protocols::rosetta_scripts::RosettaScriptsParser::generate_mover_from_pose(), protocols::rosetta_scripts::MultipleOutputWrapper::generate_pose(), protocols::rosetta_scripts::RosettaScriptsParser::import_tags(), protocols::rosetta_scripts::RosettaScriptsParser::instantiate_filter(), protocols::rosetta_scripts::RosettaScriptsParser::instantiate_mover(), protocols::rosetta_scripts::RosettaScriptsParser::instantiate_taskoperation(), protocols::rosetta_scripts::PosePropertyReporterFactory::newPosePropertyReporter(), protocols::rosetta_scripts::PoseSelectorFactory::newPoseSelector(), parse_movemap(), protocols::rosetta_scripts::SavePoseMover::parse_my_tag(), protocols::rosetta_scripts::PosePropertyReporter::parse_my_tag(), protocols::rosetta_scripts::PoseSelector::parse_my_tag(), protocols::rosetta_scripts::MultiplePoseMover::parse_my_tag(), parse_task_operations(), protocols::rosetta_scripts::RosettaScriptsParser::process_include_xml(), protocols::rosetta_scripts::MultiplePoseMover::process_pose(), protocols::rosetta_scripts::MultiplePoseMover::process_poses(), saved_reference_pose(), protocols::rosetta_scripts::MultiplePoseMover::select_poses(), and protocols::rosetta_scripts::RosettaScriptsParser::substitute_variables_in_stream().

static thread_local basic::Tracer protocols::rosetta_scripts::TR ( "protocols.rosetta_scripts.ParsedProtocol"  )

static

static thread_local basic::Tracer protocols::rosetta_scripts::TR ( "protocols.rosetta_scripts.RosettaScriptsParser"  )

static

static thread_local basic::Tracer protocols::rosetta_scripts::TR_call_order ( "protocols.rosetta_scripts.ParsedProtocol_call_order"  )

static

static thread_local basic::Tracer protocols::rosetta_scripts::TR_report ( "protocols.rosetta_scripts.ParsedProtocol.REPORT"  )

static