Classes
class	ParsedProtocol

class	ParsedProtocolCreator

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 core::Real	Real

typedef core::pose::Pose	Pose

typedef utility::pointer::owning_ptr < ParsedProtocol >	ParsedProtocolOP

typedef utility::pointer::owning_ptr < ParsedProtocol const >	ParsedProtocolCOP

typedef utility::pointer::owning_ptr < SavePoseMover >	SavePoseMoverOP

typedef utility::pointer::owning_ptr < SavePoseMover const >	SavePoseMoverCOP

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

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

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

static numeric::random::RandomGenerator	RG (48569)

core::pack::task::TaskFactoryOP	parse_task_operations (utility::tag::TagPtr const tag, protocols::moves::DataMap const &data)

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

core::pack::task::TaskFactoryOP	parse_task_operations (utility::tag::TagPtr const tag, protocols::moves::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::TagPtr const tag, protocols::moves::DataMap const &data)

core::scoring::ScoreFunctionOP	parse_score_function (utility::tag::TagPtr const tag, protocols::moves::DataMap const &data, std::string const dflt_key)

core::pose::PoseOP	saved_reference_pose (utility::tag::TagPtr const in_tag, protocols::moves::DataMap &data_map)
	convenience function to access pointers to poses that will be stored in the data map at an arbitrary point during an RS protocol More...

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

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::TagPtr 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...

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...

static basic::Tracer	TR ("protocols.rosetta_scripts.util.hh")

Typedef Documentation

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

Definition at line 26 of file ParsedProtocol.fwd.hh.

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

Definition at line 23 of file ParsedProtocol.fwd.hh.

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

Definition at line 74 of file ParsedProtocol.cc.

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

Definition at line 73 of file ParsedProtocol.cc.

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

Definition at line 24 of file SavePoseMover.fwd.hh.

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

Definition at line 22 of file SavePoseMover.fwd.hh.

Function Documentation

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

Definition at line 362 of file util.cc.

References core::conformation::Residue::chain(), 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::toolbox::task_operations::RestrictIdentitiesAtAlignedPositionsOperation::apply(), protocols::toolbox::task_operations::RestrictToAlignedSegmentsOperation::apply(), protocols::protein_interface_design::movers::Splice::apply(), protocols::protein_interface_design::movers::copy_stretch(), and protocols::protein_interface_design::movers::Splice::find_dbase_entry().

void protocols::rosetta_scripts::foreach_movemap_tag	(	utility::tag::TagPtr 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

Definition at line 202 of file util.cc.

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

Referenced by parse_movemap().

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

Definition at line 145 of file util.cc.

References core::sequence::end, protocols::moves::DataMap::get(), and protocols::moves::DataMap::has().

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

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

Definition at line 327 of file util.cc.

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

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

Definition at line 262 of file util.cc.

References protocols::moves::DataMap::add(), foreach_movemap_tag(), protocols::moves::DataMap::get(), protocols::moves::DataMap::has(), and TR().

Referenced by protocols::relax::FastRelax::apply(), protocols::protein_interface_design::movers::PrepackMover::parse_my_tag(), protocols::seeded_abinitio::SeedSetupMover::parse_my_tag(), protocols::loops::loop_mover::refine::LoopMover_Refine_CCD::parse_my_tag(), protocols::simple_moves::MinMover::parse_my_tag(), protocols::nonlocal::SingleFragmentMover::parse_my_tag(), protocols::relax::FastRelax::parse_my_tag(), protocols::simple_moves::BackboneMover::parse_my_tag(), and protocols::flxbb::FlxbbDesign::parse_my_tag().

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

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

Definition at line 299 of file util.cc.

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
	)

Definition at line 335 of file util.cc.

Referenced by 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::features::RotamerRecoveryFeatures::parse_my_tag(), protocols::rotamer_recovery::RotamerRecoveryMover::parse_my_tag(), and protocols::docking::DockSetupMover::parse_my_tag().

core::scoring::ScoreFunctionOP protocols::rosetta_scripts::parse_score_function	(	utility::tag::TagPtr const	tag,
		protocols::moves::DataMap const &	data,
		std::string const	dflt_key
	)

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

Definition at line 172 of file util.cc.

References protocols::moves::DataMap::get(), and protocols::moves::DataMap::has().

core::pack::task::TaskFactoryOP protocols::rosetta_scripts::parse_task_operations	(	utility::tag::TagPtr const	tag,
		protocols::moves::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)

Definition at line 63 of file util.cc.

References TR().

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

Definition at line 75 of file util.cc.

References core::sequence::end, protocols::moves::DataMap::get(), protocols::moves::DataMap::has(), and TR().

core::pack::task::TaskFactoryOP protocols::rosetta_scripts::parse_task_operations	(	utility::tag::TagPtr const	tag,
		protocols::moves::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

Definition at line 100 of file util.cc.

References protocols::moves::DataMap::add(), core::sequence::end, protocols::moves::DataMap::get(), protocols::moves::DataMap::has(), and TR().

numeric::xyzVector< core::Real > protocols::rosetta_scripts::parse_xyz_vector ( utility::tag::TagPtr const xyz_vector_tag)

utility function for parsing xyzVector

Definition at line 344 of file util.cc.

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

Definition at line 378 of file util.cc.

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::protein_interface_design::movers::PlaceStubMover::apply(), protocols::protein_interface_design::movers::Splice::apply(), protocols::simple_filters::BuriedUnsatHbondFilter::compute(), and protocols::protein_interface_design::movers::find_residues_on_chain1_outside_interface().

static numeric::random::RandomGenerator protocols::rosetta_scripts::RG ( 48569 )

static

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

core::pose::PoseOP protocols::rosetta_scripts::saved_reference_pose	(	utility::tag::TagPtr const	in_tag,
		protocols::moves::DataMap &	data_map
	)

convenience function to access pointers to poses that will be stored in the data map at an arbitrary point during an RS protocol

Definition at line 182 of file util.cc.

References protocols::moves::DataMap::add(), protocols::moves::DataMap::get(), and protocols::moves::DataMap::has().

Referenced by protocols::simple_filters::SidechainRmsdFilter::parse_my_tag(), protocols::simple_filters::DeltaFilter::parse_my_tag(), protocols::rosetta_scripts::SavePoseMover::parse_my_tag(), protocols::protein_interface_design::filters::RmsdFilter::parse_my_tag(), protocols::features::RotamerRecoveryFeatures::parse_my_tag(), and protocols::features::ProteinRMSDFeatures::parse_my_tag().

static basic::Tracer protocols::rosetta_scripts::TR ( "protocols.rosetta_scripts.util.hh" )

static

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

static

Referenced by parse_movemap(), protocols::rosetta_scripts::SavePoseMover::parse_my_tag(), and parse_task_operations().

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

static

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

static

Classes

Typedefs

Functions

Typedef Documentation

Function Documentation