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	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	PosePropertyReporterFactory
class	PoseSelector
class	PoseSelectorCreator
	Abstract base class for a PoseSelector factory; the Creator class is responsible for creating a particular PoseSelector class. More...
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	PoseSelectorFactory
class	RosettaScriptsJobQueen
class	RosettaScriptsParser
	Reading the xml file and generating the mover. More...
class	RosettaScriptsSchemaValidator
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
class	XmlObjects

Typedefs
typedef utility::pointer::shared_ptr< MultiplePoseMover >	MultiplePoseMoverOP
typedef utility::pointer::shared_ptr< MultiplePoseMover const >	MultiplePoseMoverCOP
using	Real = core::Real
using	Pose = core::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
using	TagCOPs = utility::vector0< TagCOP >
typedef utility::pointer::shared_ptr< RosettaScriptsParser >	RosettaScriptsParserOP
typedef utility::pointer::shared_ptr< RosettaScriptsParser const >	RosettaScriptsParserCOP
typedef utility::pointer::shared_ptr< SavePoseMover >	SavePoseMoverOP
typedef utility::pointer::shared_ptr< SavePoseMover const >	SavePoseMoverCOP
typedef utility::pointer::shared_ptr< XmlObjects >	XmlObjectsOP
typedef utility::pointer::shared_ptr< XmlObjects const >	XmlObjectsCOP
typedef utility::pointer::weak_ptr< XmlObjects >	XmlObjectsAP
typedef utility::pointer::weak_ptr< XmlObjects const >	XmlObjectsCAP

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

Functions
static basic::Tracer	TR ("protocols.rosetta_scripts.AdditionalOutputWrapper")
static basic::Tracer	TR ("protocols.rosetta_scripts.MultipleOutputWrapper")
static basic::Tracer	TR ("protocols.rosetta_scripts.MultiplePoseMover")
void	recursively_access_all_attributes (utility::tag::TagCOP tag)
	Recurse through the tree of Tags and for each one, read each option, so that every option is set as "read". More...
std::string	mpm_mangler (std::string const &element_name)
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")
std::pair< moves::MoverOP, std::string >	parse_mover_subtag (utility::tag::TagCOP const tag_ptr, basic::datacache::DataMap &data)
std::string	complex_type_name_for_parsed_protocol_subelement (std::string const &foo)
static basic::Tracer	TR ("protocols.rosetta_scripts.PosePropertyReporterFactory")
static basic::Tracer	TR ("protocols.rosetta_scripts.PoseSelectorFactory")
static basic::Tracer	TR ("protocols.rosetta_scripts.RosettaScriptsJobQueen")
static basic::Tracer	TR ("protocols.rosetta_scripts.RosettaScriptsParser")
static basic::Tracer	TR ("protocols.rosetta_scripts.RosettaScriptsSchemaValidator")
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	attributes_for_parse_residue_selector (utility::tag::AttributeList &attributes, std::string const &description)
	Appends the attributes read by parse_residue_selector. More...
void	attributes_for_saved_reference_pose (utility::tag::AttributeList &attributes, std::string const &attribute_name="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	attributes_for_saved_reference_pose_w_description (utility::tag::AttributeList &attributes, std::string const &description, std::string const &attribute_name="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...
core::pose::PoseOP	saved_reference_pose (utility::tag::TagCOP const in_tag, basic::datacache::DataMap &data_map, std::string const &tag_name)
core::pose::PoseCOP	legacy_saved_pose_or_input (utility::tag::TagCOP tag, basic::datacache::DataMap &data, std::string const &class_name, bool use_native=true, std::string const &refname="reference_name")
	Retrieve the reference pose. If not given, fall back to the native pose (if asked for), or the input pose as a last resort. Will print a warning message if the input pose is used. More...
void	foreach_movemap_tag (utility::tag::TagCOP const in_tag, basic::datacache::DataMap &data, core::select::movemap::MoveMapFactoryOP mmf)
	utility function for parse_movemap which goes over each of the tags in a movemap section More...
void	parse_movemap_tag (utility::tag::TagCOP const in_tag, core::select::movemap::MoveMapFactoryOP mmf)
core::select::movemap::MoveMapFactoryOP	parse_movemap_factory_legacy (utility::tag::TagCOP in_tag, basic::datacache::DataMap &data, bool const reset_movemap=true, core::select::movemap::MoveMapFactoryOP mmf_to_modify=nullptr)
	Parse a MoveMap factory from tags using the old MoveMap specification syntax. More...
core::select::movemap::MoveMapFactoryOP	parse_named_movemap_factory_legacy (utility::tag::TagCOP in_tag, std::string const &name, basic::datacache::DataMap &data, bool const reset_movemap=true, core::select::movemap::MoveMapFactoryOP mmf_to_modify=nullptr)
	Parse a MoveMap factory from tags using the old MoveMap specification syntax. Will look for a MoveMap entry with a particular name entry. More...
std::string	move_map_tag_namer (std::string const &subelement_name)
std::string	optionally_named_move_map_ct_namer (std::string const &)
void	common_movemap_complex_type_def (utility::tag::XMLSchemaComplexTypeGenerator &ct_gen)
void	append_subelement_for_parse_movemap_factory_legacy (utility::tag::XMLSchemaDefinition &xsd, utility::tag::XMLSchemaSimpleSubelementList &subelements, std::string const &description="")
	Adds a subelement to an input subelement list describing a MoveMap subtag that will be used by the parse_movemap_legacy function. More...
protocols::filters::FilterOP	parse_filter (std::string const &filter_name, basic::datacache::DataMap const &d)
	Return the Filter with the given name. Raise a RosettaScriptsOptionError if not present. More...
protocols::filters::FilterOP	parse_filter_or_null (std::string const &filter_name, basic::datacache::DataMap const &d)
	Return the Filter with the given name. Return nullptr if not present. More...
protocols::moves::MoverOP	parse_mover (std::string const &mover_name, basic::datacache::DataMap const &d)
	Return the Mover with the given name. Raise a RosettaScriptsOptionError if not present. More...
protocols::moves::MoverOP	parse_mover_or_null (std::string const &mover_name, basic::datacache::DataMap const &d)
	Return the Mover with the given name. Return nullptr if not present. More...
void	attributes_for_parse_xyz_vector (utility::tag::AttributeList &attlist)
numeric::xyzVector< core::Real >	parse_xyz_vector (utility::tag::TagCOP const xyz_vector_tag)
	utility function for parsing xyzVector More...
utility::sql_database::sessionOP	parse_database_session (utility::tag::TagCOP tag, basic::datacache::DataMap const &datamap)
	This is kind of a strange place for this, but for library-level reasons it needs to be more accessible than a more logical home with ReportToDB, and cannot live in basic because it needs other functions in this file. (There is also value in not creating a new file b/c it breaks the fast-compile system XML XSD XRW is using, and it's 6pm on Friday!) More...
void	attributes_for_parse_database_session (utility::tag::XMLSchemaDefinition &xsd, utility::tag::AttributeList &attlist)
void	print_template_script ()
	Prints out an empty template RosettaScript to the tracer. More...
bool	print_information (std::string const &component_name, std::stringstream &outstream)
	Prints out XSD information about the XML-accessible options for a given RosettaScipts-accessible mover, filter, task operation, residue selector, simple_metric, or packer palette. More...
void	print_information (utility::vector1< std::string > const &component_names)
	Prints out XSD information about the XML-accessible options for a given set of RosettaScipts-accessible movers, filters, task operations, residue selectors, simple metric, constraint generators, or packer palette. More...
void	save_schema (std::string const &filename)
	Saves the XSD to the given file. More...
std::ostream &	operator<< (std::ostream &output, XmlObjects const &object_to_output)
	Insertion operator (overloaded so that XmlObjects can be "printed" in PyRosetta). More...

Typedef Documentation

MultiplePoseMoverCOP

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

MultiplePoseMoverOP

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

ParsedProtocolAP

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

ParsedProtocolCAP

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

ParsedProtocolCOP

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

ParsedProtocolOP

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

Pose

using protocols::rosetta_scripts::Pose = typedef core::pose::Pose

PosePropertyReporterCOP

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

PosePropertyReporterCreatorCOP

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

PosePropertyReporterCreatorOP

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

PosePropertyReporterFactoryCOP

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

PosePropertyReporterFactoryOP

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

PosePropertyReporterOP

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

PoseSelectorCOP

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

PoseSelectorCreatorCOP

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

PoseSelectorCreatorOP

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

PoseSelectorFactoryCOP

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

PoseSelectorFactoryOP

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

PoseSelectorOP

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

Real

using protocols::rosetta_scripts::Real = typedef core::Real

RosettaScriptsParserCOP

typedef utility::pointer::shared_ptr< RosettaScriptsParser const > protocols::rosetta_scripts::RosettaScriptsParserCOP

RosettaScriptsParserOP

typedef utility::pointer::shared_ptr< RosettaScriptsParser > protocols::rosetta_scripts::RosettaScriptsParserOP

SavePoseMoverCOP

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

SavePoseMoverOP

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

TagCOPs

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

XmlObjectsAP

typedef utility::pointer::weak_ptr< XmlObjects > protocols::rosetta_scripts::XmlObjectsAP

XmlObjectsCAP

typedef utility::pointer::weak_ptr< XmlObjects const > protocols::rosetta_scripts::XmlObjectsCAP

XmlObjectsCOP

typedef utility::pointer::shared_ptr< XmlObjects const > protocols::rosetta_scripts::XmlObjectsCOP

XmlObjectsOP

typedef utility::pointer::shared_ptr< XmlObjects > protocols::rosetta_scripts::XmlObjectsOP

Enumeration Type Documentation

PoseSelectorFlags

enum protocols::rosetta_scripts::PoseSelectorFlags

Enumerator
PSF_NONE
PSF_NEED_FULL_POSE_SET

Function Documentation

append_subelement_for_parse_movemap_factory_legacy()

void protocols::rosetta_scripts::append_subelement_for_parse_movemap_factory_legacy	(	utility::tag::XMLSchemaDefinition &	xsd,
		utility::tag::XMLSchemaSimpleSubelementList &	subelements,
		std::string const &	description
	)

Adds a subelement to an input subelement list describing a MoveMap subtag that will be used by the parse_movemap_legacy function.

References common_movemap_complex_type_def(), and optionally_named_move_map_ct_namer().

Referenced by protocols::grafting::AnchoredGraftMover::complex_type_generator_for_anchored_graft_mover(), protocols::simple_moves::BackboneMover::complex_type_generator_for_backbone_mover(), protocols::backrub::BackrubMover::complex_type_generator_for_backrub_mover(), protocols::kinematic_closure::BalancedKicMover::complex_type_generator_for_balancedKIC_mover(), protocols::relax::FastRelax::complex_type_generator_for_fast_relax(), protocols::minimization_packing::MinMover::complex_type_generator_for_min_mover(), protocols::carbohydrates::RingPlaneFlipMover::provide_xml_schema(), protocols::cryst::SetCrystWeightMover::provide_xml_schema(), protocols::flxbb::FlxbbDesign::provide_xml_schema(), protocols::loops::loop_mover::refine::LoopMover_Refine_CCD::provide_xml_schema(), protocols::minimization_packing::PertMinMover::provide_xml_schema(), protocols::nonlocal::SingleFragmentMover::provide_xml_schema(), protocols::normalmode::NormalModeMinimizer::provide_xml_schema(), protocols::normalmode::NormalModeRelaxMover::provide_xml_schema(), protocols::protein_interface_design::movers::PrepackMover::provide_xml_schema(), protocols::simple_moves::DisulfideInsertionMover::provide_xml_schema(), protocols::simple_moves::RandomOmegaFlipMover::provide_xml_schema(), protocols::simple_moves::RandomTorsionMover::provide_xml_schema(), and protocols::simple_moves::RingConformationMover::provide_xml_schema().

attributes_for_parse_database_session()

void protocols::rosetta_scripts::attributes_for_parse_database_session	(	utility::tag::XMLSchemaDefinition &	xsd,
		utility::tag::AttributeList &	attlist
	)

Referenced by protocols::features::ReportToDB::attributes_for_report_to_db(), protocols::loops::loops_definers::LoopsDatabaseDefiner::provide_xml_schema(), and protocols::task_operations::ReadResfileFromDB::provide_xml_schema().

attributes_for_parse_residue_selector()

void protocols::rosetta_scripts::attributes_for_parse_residue_selector	(	utility::tag::AttributeList &	attributes,
		std::string const &	description
	)

Appends the attributes read by parse_residue_selector.

References core::select::residue_selector::attributes_for_parse_residue_selector_default_option_name().

Referenced by protocols::carbohydrates::GlycanSampler::provide_xml_schema(), protocols::carbohydrates::GlycanTreeMinMover::provide_xml_schema(), protocols::carbohydrates::GlycanTreeModeler::provide_xml_schema(), protocols::carbohydrates::IdealizeAnomericHydrogens::provide_xml_schema(), protocols::carbohydrates::LinkageConformerMover::provide_xml_schema(), protocols::carbohydrates::RingPlaneFlipMover::provide_xml_schema(), protocols::carbohydrates::SimpleGlycosylateMover::provide_xml_schema(), protocols::carbohydrates::TautomerizeAnomerMover::provide_xml_schema(), protocols::constraint_generator::DihedralConstraintGenerator::provide_xml_schema(), protocols::cyclic_peptide::CycpepRigidBodyPermutationMover::provide_xml_schema(), protocols::minimization_packing::PertMinMover::provide_xml_schema(), protocols::simple_filters::LongestContinuousApolarSegmentFilter::provide_xml_schema(), protocols::simple_filters::LongestContinuousPolarSegmentFilter::provide_xml_schema(), protocols::simple_moves::ConvertRealToVirtualMover::provide_xml_schema(), and protocols::simple_moves::ConvertVirtualToRealMover::provide_xml_schema().

attributes_for_parse_xyz_vector()

void protocols::rosetta_scripts::attributes_for_parse_xyz_vector

(

utility::tag::AttributeList &

attlist

)

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

attributes_for_saved_reference_pose()

void protocols::rosetta_scripts::attributes_for_saved_reference_pose	(	utility::tag::AttributeList &	attributes,
		std::string const &	attribute_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 attributes_for_saved_reference_pose_w_description().

Referenced by protocols::grafting::AnchoredGraftMover::complex_type_generator_for_anchored_graft_mover(), protocols::antibody::AntibodyCDRGrafter::provide_xml_schema(), protocols::features::ProteinRMSDFeatures::provide_xml_schema(), protocols::features::ProteinRMSDNoSuperpositionFeatures::provide_xml_schema(), protocols::fold_from_loops::filters::RmsdFromResidueSelectorFilter::provide_xml_schema(), protocols::fold_from_loops::movers::AlignByResidueSelectorMover::provide_xml_schema(), protocols::grafting::simple_movers::InsertPoseIntoPoseMover::provide_xml_schema(), protocols::grafting::simple_movers::ReplaceRegionMover::provide_xml_schema(), protocols::matdes::MatDesGreedyOptMutationMover::provide_xml_schema(), protocols::matdes::SymUnsatHbondFilter::provide_xml_schema(), protocols::protein_interface_design::filters::FNatFilter::provide_xml_schema(), protocols::protein_interface_design::filters::IRmsdFilter::provide_xml_schema(), protocols::protein_interface_design::filters::LRmsdFilter::provide_xml_schema(), protocols::protein_interface_design::filters::RmsdFilter::provide_xml_schema(), protocols::protein_interface_design::filters::RmsdSimpleFilter::provide_xml_schema(), protocols::protein_interface_design::filters::SSamountFilter::provide_xml_schema(), protocols::rosetta_scripts::SavePoseMover::provide_xml_schema(), protocols::simple_filters::DeltaFilter::provide_xml_schema(), protocols::simple_filters::SidechainRmsdFilter::provide_xml_schema(), and protocols::simple_moves::SuperimposeMover::provide_xml_schema().

attributes_for_saved_reference_pose_w_description()

void protocols::rosetta_scripts::attributes_for_saved_reference_pose_w_description	(	utility::tag::AttributeList &	attributes,
		std::string const &	description,
		std::string const &	attribute_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 core::pose::attributes_for_saved_reference_pose_w_description().

Referenced by attributes_for_saved_reference_pose(), and protocols::fold_from_loops::utils::Nub::provide_xml_definition().

common_movemap_complex_type_def()

void protocols::rosetta_scripts::common_movemap_complex_type_def

(

utility::tag::XMLSchemaComplexTypeGenerator &

ct_gen

)

References move_map_tag_namer().

Referenced by append_subelement_for_parse_movemap_factory_legacy().

complex_type_name_for_parsed_protocol_subelement()

std::string protocols::rosetta_scripts::complex_type_name_for_parsed_protocol_subelement

(

std::string const &

foo

)

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

find_nearest_disulfide()

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::chemical::DISULFIDE, core::conformation::Residue::has_variant_type(), core::pose::Pose::pdb_info(), core::pose::Pose::residue(), and core::pose::Pose::size().

Referenced by protocols::splice::Splice::apply(), protocols::splice::min_seg(), protocols::splice::Splice::parse_my_tag(), protocols::splice::Splice::remove_hairpin(), protocols::splice::SpliceOut::remove_hairpin(), protocols::splice::Splice::set_fold_tree(), and protocols::splice::Splice::superimpose_source_on_pose().

find_nearest_res() [1/2]

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(), core::conformation::Residue::is_ligand(), core::pose::Pose::residue(), core::pose::Pose::size(), and core::conformation::Residue::xyz().

find_nearest_res() [2/2]

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(), core::conformation::Residue::is_ligand(), core::pose::Pose::residue(), core::pose::Pose::size(), and core::conformation::Residue::xyz().

Referenced by protocols::splice::Splice::add_coordinate_constraints(), protocols::splice::SpliceManager::add_coordinate_constraints(), protocols::splice::Splice::add_dihedral_constraints(), protocols::splice::SpliceManager::add_dihedral_constraints(), protocols::splice::SpliceOutAntibody::adjust_n_ter_tail_length(), protocols::splice::SpliceManager::adjust_stem_positions_by_template(), protocols::splice::SampleRotamersFromPDB_RotamerSetOperation::alter_rotamer_set_from_pdb(), protocols::legacy_sewing::LegacyAddStartnodeFragments::apply(), protocols::task_operations::DatabaseThread::apply(), protocols::task_operations::RestrictIdentitiesAtAlignedPositionsOperation::apply(), protocols::task_operations::RestrictToAlignedSegmentsOperation::apply(), protocols::protein_interface_design::filters::RelativeSegmentFilter::apply(), protocols::simple_filters::StemFinder::apply(), protocols::splice::Splice::apply(), protocols::splice::SpliceOutAntibody::apply(), protocols::splice::SpliceIn::assign_from_res_to_res(), protocols::splice::SpliceInTail::assign_from_res_to_res(), protocols::splice::Splice::copy_stretch(), protocols::splice::Splice::find_dbase_entry(), protocols::task_operations::DatabaseThread::find_length(), protocols::splice::RotLibOut::find_matching_res(), protocols::task_operations::DatabaseThread::mark_designable(), protocols::task_operations::DatabaseThread::mark_leave_as_is(), protocols::splice::nearest_to_entry_stop_on_pose(), protocols::relax::AtomCoordinateCstMover::set_constraints_on_func_groups(), protocols::splice::Splice::set_fold_tree(), protocols::splice::SpliceOut::set_source_from_to_res(), protocols::splice::SpliceOutTail::set_source_from_to_res(), and protocols::splice::SpliceOutTail::superimpose_source_on_pose().

foreach_movemap_tag()

void protocols::rosetta_scripts::foreach_movemap_tag	(	utility::tag::TagCOP const	in_tag,
		basic::datacache::DataMap &	data,
		core::select::movemap::MoveMapFactoryOP	mmf
	)

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

References core::sequence::end, core::select::movemap::mm_disable, core::select::movemap::mm_enable, and core::select::residue_selector::parse_residue_selector().

Referenced by parse_movemap_factory_legacy().

legacy_saved_pose_or_input()

core::pose::PoseCOP protocols::rosetta_scripts::legacy_saved_pose_or_input	(	utility::tag::TagCOP	tag,
		basic::datacache::DataMap &	data,
		std::string const &	class_name,
		bool	use_native = true,
		std::string const &	refname = "reference_name"
	)

Retrieve the reference pose. If not given, fall back to the native pose (if asked for), or the input pose as a last resort. Will print a warning message if the input pose is used.

The XSD is the same as for saved_reference_pose.

References protocols::jd2::get_current_jobs_starting_pose(), protocols::jd2::jd2_used(), core::pose::saved_native_pose(), core::pose::saved_reference_pose(), and TR().

Referenced by protocols::contact_map::ContactMap::parse_my_tag(), protocols::protein_interface_design::filters::SequenceRecoveryFilter::parse_my_tag(), protocols::protein_interface_design::filters::StubScoreFilter::parse_my_tag(), protocols::protein_interface_design::movers::PlacementAuctionMover::parse_my_tag(), protocols::protein_interface_design::movers::PlacementMinimizationMover::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::SaveAndRetrieveSidechains::parse_my_tag(), protocols::seeded_abinitio::GrowPeptides::parse_my_tag(), protocols::simple_filters::DeltaFilter::parse_my_tag(), protocols::simple_filters::MutationsFilter::parse_my_tag(), protocols::simple_filters::SidechainRmsdFilter::parse_my_tag(), protocols::simple_moves::FavorSequenceProfile::parse_my_tag(), protocols::splice::Splice::parse_my_tag(), protocols::features::ProteinRMSDFeatures::parse_my_tag(), protocols::features::ProteinRMSDNoSuperpositionFeatures::parse_my_tag(), protocols::fold_from_loops::movers::AlignByResidueSelectorMover::parse_my_tag(), protocols::rbsegment_relax::MakeStarTopologyMover::parse_my_tag(), protocols::fold_from_loops::filters::RmsdFromResidueSelectorFilter::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::LRmsdFilter::parse_my_tag(), protocols::protein_interface_design::filters::RmsdFilter::parse_my_tag(), and protocols::protein_interface_design::movers::InterfaceRecapitulationMover::parse_my_tag().

move_map_tag_namer()

std::string protocols::rosetta_scripts::move_map_tag_namer

(

std::string const &

subelement_name

)

Referenced by common_movemap_complex_type_def().

mpm_mangler()

std::string protocols::rosetta_scripts::mpm_mangler

(

std::string const &

element_name

)

Referenced by protocols::rosetta_scripts::MultiplePoseMover::provide_xml_schema().

operator<<()

std::ostream& protocols::rosetta_scripts::operator<<	(	std::ostream &	output,
		XmlObjects const &	object_to_output
	)

Insertion operator (overloaded so that XmlObjects can be "printed" in PyRosetta).

optionally_named_move_map_ct_namer()

std::string protocols::rosetta_scripts::optionally_named_move_map_ct_namer

(

std::string const &

)

Referenced by append_subelement_for_parse_movemap_factory_legacy().

parse_database_session()

utility::sql_database::sessionOP protocols::rosetta_scripts::parse_database_session	(	utility::tag::TagCOP	tag,
		basic::datacache::DataMap const &	datamap
	)

This is kind of a strange place for this, but for library-level reasons it needs to be more accessible than a more logical home with ReportToDB, and cannot live in basic because it needs other functions in this file. (There is also value in not creating a new file b/c it breaks the fast-compile system XML XSD XRW is using, and it's 6pm on Friday!)

References TR().

Referenced by protocols::features::ReportToDB::parse_my_tag(), protocols::loops::loops_definers::LoopsDatabaseDefiner::parse_my_tag(), and protocols::task_operations::ReadResfileFromDB::parse_tag().

parse_filter()

protocols::filters::FilterOP protocols::rosetta_scripts::parse_filter	(	std::string const &	filter_name,
		basic::datacache::DataMap const &	data
	)

Return the Filter with the given name. Raise a RosettaScriptsOptionError if not present.

References protocols::filters::parse_filter_with_logic().

Referenced by protocols::simple_filters::RangeFilter::parse_my_tag(), protocols::monte_carlo::GenericMonteCarloMover::parse_my_tag(), protocols::moves::IteratedConvergenceMover::parse_my_tag(), protocols::calc_taskop_filters::Operator::parse_my_tag(), protocols::calc_taskop_filters::RelativePoseFilter::parse_my_tag(), protocols::calc_taskop_filters::Sigmoid::parse_my_tag(), protocols::design_opt::GreedyOptMutationMover::parse_my_tag(), protocols::enzdes::RemoveLigandFilter::parse_my_tag(), protocols::filters::CalculatorFilter::parse_my_tag(), protocols::filters::ReplicateFilter::parse_my_tag(), protocols::loophash::LoopHashDiversifier::parse_my_tag(), protocols::loophash::LoopHashMoverWrapper::parse_my_tag(), protocols::matdes::MatDesGreedyOptMutationMover::parse_my_tag(), protocols::motif_grafting::movers::MotifGraftMover::parse_my_tag(), protocols::protein_interface_design::filters::BoltzmannFilter::parse_my_tag(), protocols::protein_interface_design::filters::FilterScanFilter::parse_my_tag(), protocols::protein_interface_design::movers::LoopOver::parse_my_tag(), protocols::protein_interface_design::movers::MapHotspot::parse_my_tag(), protocols::protein_interface_design::movers::PlaceSimultaneouslyMover::parse_my_tag(), protocols::protein_interface_design::movers::SetTemperatureFactor::parse_my_tag(), protocols::simple_ddg::DdgFilter::parse_my_tag(), protocols::simple_filters::DeltaFilter::parse_my_tag(), protocols::simple_filters::ReportFilter::parse_my_tag(), protocols::splice::Splice::parse_my_tag(), protocols::features::DdGFeatures::parse_my_tag(), protocols::filters::FilterValueMetric::parse_my_tag(), protocols::generalized_kinematic_closure::GeneralizedKIC::parse_my_tag(), protocols::helical_bundle::BackboneGridSampler::parse_my_tag(), protocols::helical_bundle::BundleGridSampler::parse_my_tag(), protocols::monte_carlo::ResetBaselineMover::parse_my_tag(), protocols::moves::FilterReportAsPoseExtraScoresMover::parse_my_tag(), protocols::pose_sewing::movers::PickRandomSegmentMover::parse_my_tag(), protocols::pose_sewing::movers::SewAnythingAddMover::parse_my_tag(), protocols::simple_moves::ContingentAcceptMover::parse_my_tag(), protocols::filters::IfThenFilter::parse_my_tag(), protocols::simple_ddg::ddG::parse_my_tag(), and protocols::splice::SpliceOut::parse_SpliceOut_tags().

parse_filter_or_null()

protocols::filters::FilterOP protocols::rosetta_scripts::parse_filter_or_null	(	std::string const &	filter_name,
		basic::datacache::DataMap const &	data
	)

Return the Filter with the given name. Return nullptr if not present.

References protocols::filters::parse_filter_with_logic(), and TR().

Referenced by protocols::denovo_design::movers::FoldArchitectMover::parse_filters(), protocols::monte_carlo::GenericMonteCarloMover::parse_my_tag(), protocols::loophash::LoopHashDiversifier::parse_my_tag(), protocols::loophash::LoopHashMoverWrapper::parse_my_tag(), protocols::protein_interface_design::filters::FilterScanFilter::parse_my_tag(), protocols::protein_interface_design::movers::HotspotHasherMover::parse_my_tag(), protocols::protein_interface_design::movers::PlaceStubMover::parse_my_tag(), protocols::protein_interface_design::movers::TryRotamers::parse_my_tag(), protocols::simple_ddg::InterfaceBindingEnergyDensityFilter::parse_my_tag(), protocols::fold_from_loops::NubInitioMover::parse_my_tag(), protocols::filters::CompoundFilter::parse_my_tag(), protocols::filters::CombinedFilter::parse_my_tag(), protocols::filters::MoveBeforeFilter::parse_my_tag(), and protocols::rosetta_scripts::ParsedProtocol::parse_my_tag().

parse_movemap_factory_legacy()

core::select::movemap::MoveMapFactoryOP protocols::rosetta_scripts::parse_movemap_factory_legacy	(	utility::tag::TagCOP	in_tag,
		basic::datacache::DataMap &	data,
		bool const	reset_movemap = true,
		core::select::movemap::MoveMapFactoryOP	mmf_to_modify = nullptr
	)

Parse a MoveMap factory from tags using the old MoveMap specification syntax.

Will return nullptr if the tag doesn't contain a MoveMap specification.

References foreach_movemap_tag(), core::select::movemap::get_movemap_factory(), core::select::movemap::movemap_factory_category(), parse_movemap_tag(), and TR().

Referenced by protocols::md::CartesianMD::parse_movemap(), protocols::minimization_packing::MinMover::parse_movemap_factory(), protocols::carbohydrates::RingPlaneFlipMover::parse_my_tag(), protocols::flxbb::FlxbbDesign::parse_my_tag(), protocols::normalmode::NormalModeRelaxMover::parse_my_tag(), protocols::simple_moves::RingConformationMover::parse_my_tag(), protocols::normalmode::NormalModeMinimizer::parse_my_tag(), protocols::simple_moves::BBGaussianMover::parse_my_tag(), protocols::loops::loop_mover::refine::LoopMover_Refine_CCD::parse_my_tag(), protocols::protein_interface_design::movers::PrepackMover::parse_my_tag(), protocols::seeded_abinitio::SeedSetupMover::parse_my_tag(), protocols::simple_moves::RandomOmegaFlipMover::parse_my_tag(), protocols::simple_moves::RandomTorsionMover::parse_my_tag(), protocols::cryst::SetCrystWeightMover::parse_my_tag(), protocols::minimization_packing::PertMinMover::parse_my_tag(), protocols::nonlocal::SingleFragmentMover::parse_my_tag(), protocols::relax::FastRelax::parse_my_tag(), protocols::simple_moves::BackboneMover::parse_my_tag(), protocols::simple_moves::DisulfideInsertionMover::parse_my_tag(), and parse_named_movemap_factory_legacy().

parse_movemap_tag()

void protocols::rosetta_scripts::parse_movemap_tag	(	utility::tag::TagCOP const	in_tag,
		core::select::movemap::MoveMapFactoryOP	mmf
	)

Referenced by parse_movemap_factory_legacy().

parse_mover()

protocols::moves::MoverOP protocols::rosetta_scripts::parse_mover	(	std::string const &	mover_name,
		basic::datacache::DataMap const &	data
	)

Return the Mover with the given name. Raise a RosettaScriptsOptionError if not present.

Referenced by protocols::backrub::BackrubProtocol::parse_my_tag(), protocols::fldsgn::BluePrintBDR::parse_my_tag(), protocols::forge::constraints::RemoveRemodelCsts::parse_my_tag(), protocols::monte_carlo::GenericSimulatedAnnealer::parse_my_tag(), protocols::simple_ddg::SSElementBisectddGFilter::parse_my_tag(), protocols::moves::IteratedConvergenceMover::parse_my_tag(), protocols::recon_design::MSDMover::parse_my_tag(), protocols::rotamer_recovery::RotamerRecoveryMover::parse_my_tag(), protocols::calc_taskop_filters::RelativePoseFilter::parse_my_tag(), protocols::design_opt::GreedyOptMutationMover::parse_my_tag(), protocols::docking::DockSetupMover::parse_my_tag(), protocols::enzdes::RemoveLigandFilter::parse_my_tag(), protocols::protein_interface_design::filters::BindingStrainFilter::parse_my_tag(), protocols::protein_interface_design::movers::LoopOver::parse_my_tag(), protocols::protein_interface_design::movers::MapHotspot::parse_my_tag(), protocols::simple_ddg::DdgFilter::parse_my_tag(), protocols::simple_ddg::DdGScan::parse_my_tag(), protocols::simple_filters::DeltaFilter::parse_my_tag(), protocols::canonical_sampling::MetropolisHastingsMover::parse_my_tag(), protocols::evolution::AlignmentAAFinder::parse_my_tag(), protocols::features::InterfaceDdGMover::parse_my_tag(), protocols::features::RotamerRecoveryFeatures::parse_my_tag(), protocols::generalized_kinematic_closure::GeneralizedKIC::parse_my_tag(), protocols::helical_bundle::BackboneGridSampler::parse_my_tag(), protocols::helical_bundle::BundleGridSampler::parse_my_tag(), protocols::pose_creation::SliceToMiniProteinMover::parse_my_tag(), protocols::simple_moves::ContingentAcceptMover::parse_my_tag(), protocols::moves::RampingMover::parse_my_tag(), and protocols::simple_ddg::ddG::parse_my_tag().

parse_mover_or_null()

protocols::moves::MoverOP protocols::rosetta_scripts::parse_mover_or_null	(	std::string const &	mover_name,
		basic::datacache::DataMap const &	data
	)

Return the Mover with the given name. Return nullptr if not present.

Referenced by protocols::environment::find_mover(), protocols::protein_interface_design::movers::generate_taskfactory_and_add_task_awareness(), protocols::splice::SpliceOut::handle_mover_tag(), protocols::splice::SpliceOutAntibody::handle_tail_mover_tag(), parse_mover_subtag(), protocols::denovo_design::movers::FoldArchitectMover::parse_movers(), protocols::monte_carlo::GenericMonteCarloMover::parse_my_tag(), protocols::monte_carlo::MonteCarloRecover::parse_my_tag(), protocols::monte_carlo::MonteCarloReset::parse_my_tag(), protocols::monte_carlo::MonteCarloTest::parse_my_tag(), protocols::moves::TrialMover::parse_my_tag(), protocols::loophash::LoopHashMoverWrapper::parse_my_tag(), protocols::matdes::MatDesGreedyOptMutationMover::parse_my_tag(), protocols::protein_interface_design::filters::FilterScanFilter::parse_my_tag(), protocols::protein_interface_design::movers::PlaceSimultaneouslyMover::parse_my_tag(), protocols::protein_interface_design::movers::PlaceStubMover::parse_my_tag(), protocols::abinitio::abscript::AbscriptMover::parse_my_tag(), protocols::abinitio::abscript::RigidChunkCM::parse_my_tag(), protocols::environment::ScriptCM::parse_my_tag(), protocols::filters::MoveBeforeFilter::parse_my_tag(), and protocols::protein_interface_design::movers::InterfaceRecapitulationMover::parse_my_tag().

parse_mover_subtag()

std::pair< moves::MoverOP, std::string > protocols::rosetta_scripts::parse_mover_subtag	(	utility::tag::TagCOP const	tag_ptr,
		basic::datacache::DataMap &	data
	)

May return nullptr for the Mover if one isn't present in the tag.

References protocols::rosetta_scripts::ParsedProtocol::mover_name(), parse_mover_or_null(), and TR().

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

parse_named_movemap_factory_legacy()

core::select::movemap::MoveMapFactoryOP protocols::rosetta_scripts::parse_named_movemap_factory_legacy	(	utility::tag::TagCOP	in_tag,
		std::string const &	name,
		basic::datacache::DataMap &	data,
		bool const	reset_movemap = true,
		core::select::movemap::MoveMapFactoryOP	mmf_to_modify = nullptr
	)

Parse a MoveMap factory from tags using the old MoveMap specification syntax. Will look for a MoveMap entry with a particular name entry.

Will return nullptr if the tag doesn't contain a MoveMap specification.

References parse_movemap_factory_legacy().

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

parse_xyz_vector()

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().

print_information() [1/2]

bool protocols::rosetta_scripts::print_information	(	std::string const &	component_name,
		std::stringstream &	outstream
	)

Prints out XSD information about the XML-accessible options for a given RosettaScipts-accessible mover, filter, task operation, residue selector, simple_metric, or packer palette.

Returns true for FAILURE to find the given component, false otherwise.

Author

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

References protocols::filters::FilterFactory::filter_exists(), protocols::constraint_generator::ConstraintGeneratorFactory::get_citation_humanreadable(), protocols::filters::FilterFactory::get_citation_humanreadable(), core::simple_metrics::SimpleMetricFactory::get_citation_humanreadable(), protocols::moves::MoverFactory::get_citation_humanreadable(), core::pack::palette::PackerPaletteFactory::get_citation_humanreadable(), core::select::residue_selector::ResidueSelectorFactory::get_citation_humanreadable(), core::pack::task::operation::ResLvlTaskOperationFactory::get_citation_humanreadable(), core::pack::task::operation::TaskOperationFactory::get_citation_humanreadable(), core::pack::palette::PackerPaletteFactory::has_type(), core::pack::task::operation::ResLvlTaskOperationFactory::has_type(), core::pack::task::operation::TaskOperationFactory::has_type(), core::select::residue_selector::ResidueSelectorFactory::has_type(), protocols::constraint_generator::ConstraintGeneratorFactory::has_type(), core::simple_metrics::SimpleMetricFactory::has_type(), protocols::moves::MoverFactory::mover_exists(), protocols::constraint_generator::ConstraintGeneratorFactory::provide_xml_schema(), protocols::filters::FilterFactory::provide_xml_schema(), protocols::moves::MoverFactory::provide_xml_schema(), core::pack::palette::PackerPaletteFactory::provide_xml_schema(), core::select::residue_selector::ResidueSelectorFactory::provide_xml_schema(), core::simple_metrics::SimpleMetricFactory::provide_xml_schema(), core::pack::task::operation::ResLvlTaskOperationFactory::provide_xml_schema(), and core::pack::task::operation::TaskOperationFactory::provide_xml_schema().

Referenced by print_information().

print_information() [2/2]

void protocols::rosetta_scripts::print_information

(

utility::vector1< std::string > const &

component_names

)

Prints out XSD information about the XML-accessible options for a given set of RosettaScipts-accessible movers, filters, task operations, residue selectors, simple metric, constraint generators, or packer palette.

Prints out XSD information about the XML-accessible options for a given set of RosettaScipts-accessible movers, filters, task operations, residue selectors, simple metrics, or packer palettes.

Calls the single string version.

Author

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

References print_information(), and TR().

print_template_script()

void protocols::rosetta_scripts::print_template_script

(

)

Prints out an empty template RosettaScript to the tracer.

This is kind of a strange place for this, but for library-level reasons it needs to be more accessible than a more logical home with ReportToDB, and cannot live in basic because it needs other functions in this file. (There is also value in not creating a new file b/c it breaks the fast-compile system XML XSD XRW is using, and it's 6pm on Friday!)

Author

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

Prints out an empty template RosettaScript to the tracer.

Author

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

References TR().

recursively_access_all_attributes()

void protocols::rosetta_scripts::recursively_access_all_attributes

(

utility::tag::TagCOP

tag

)

Recurse through the tree of Tags and for each one, read each option, so that every option is set as "read".

As a safety check to make sure that no options are misspelled, at the conclusion of parsing, all options contained in all tags are examined to determine if they have been accessed or not. If an option has not been accessed, then an error message is written to the screen, and the program exits. However, it is not possible to parse all movers in the absence of the Pose that is going to be used, and that Pose isn't available to the MPM until execution. So we work around this issue by accessing each of the options in the input tag and all of its children

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

residue_packer_states()

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::size().

Referenced by protocols::protein_interface_design::movers::PlaceStubMover::apply(), protocols::splice::TailSegmentMover::apply(), protocols::splice::DesignInterfacesOperation::apply(), protocols::task_operations::RestrictToAlignedSegmentsOperation::apply(), protocols::protein_interface_design::filters::Torsion::apply(), protocols::simple_filters::ResidueBurialFilter::apply(), protocols::protein_interface_design::movers::TaskAwareCsts::apply(), protocols::splice::Splice::apply(), protocols::splice::SpliceInTail::apply(), protocols::splice::SpliceOut::apply(), protocols::task_operations::SeqprofConsensusOperation::apply(), protocols::buns::BuriedUnsatHbondFilter2::compute(), protocols::simple_filters::BuriedUnsatHbondFilter::compute(), protocols::simple_filters::NetChargeFilter::compute(), protocols::simple_filters::ResidueCountFilter::compute(), protocols::splice::find_residues_on_chain1_inside_interface(), protocols::splice::report_des_pack_res(), protocols::splice::report_designable_packable_residues(), and protocols::splice::SpliceIn::rtmin().

save_schema()

void protocols::rosetta_scripts::save_schema

(

std::string const &

filename

)

Saves the XSD to the given file.

References protocols::abinitio::filename(), TR(), and protocols::rosetta_scripts::RosettaScriptsParser::xsd_for_rosetta_scripts().

saved_reference_pose()

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
	)

References core::pose::saved_reference_pose().

Referenced by protocols::matdes::SymUnsatHbondFilter::parse_my_tag(), protocols::grafting::simple_movers::InsertPoseIntoPoseMover::parse_my_tag(), protocols::grafting::simple_movers::ReplaceRegionMover::parse_my_tag(), protocols::rosetta_scripts::SavePoseMover::parse_my_tag(), protocols::matdes::MatDesGreedyOptMutationMover::parse_my_tag(), protocols::antibody::AntibodyCDRGrafter::parse_my_tag(), protocols::grafting::AnchoredGraftMover::parse_my_tag(), protocols::simple_moves::AddChainMover::parse_my_tag(), protocols::protein_interface_design::filters::SSamountFilter::parse_my_tag(), protocols::simple_moves::SuperimposeMover::parse_my_tag(), protocols::task_operations::SelectByDeltaScoreOperation::parse_tag(), and protocols::fold_from_loops::utils::Nub::parse_tag().

TR() [1/9]

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

static

Referenced by protocols::rosetta_scripts::MultiplePoseMover::apply(), protocols::rosetta_scripts::ParsedProtocol::apply(), protocols::rosetta_scripts::ParsedProtocol::apply_filter(), protocols::rosetta_scripts::ParsedProtocol::apply_metrics(), protocols::rosetta_scripts::ParsedProtocol::apply_mover(), protocols::rosetta_scripts::RosettaScriptsJobQueen::complete_larval_job_maturation(), protocols::rosetta_scripts::XmlObjects::create_from_file(), protocols::rosetta_scripts::XmlObjects::create_from_string(), protocols::rosetta_scripts::RosettaScriptsJobQueen::derived_process_deallocation_message(), protocols::rosetta_scripts::MultiplePoseMover::fill_input_cache(), protocols::rosetta_scripts::RosettaScriptsParser::finish_creating_tag(), protocols::rosetta_scripts::ParsedProtocol::finish_protocol(), protocols::rosetta_scripts::RosettaScriptsParser::generate_mover(), protocols::rosetta_scripts::RosettaScriptsParser::generate_mover_for_protocol(), protocols::rosetta_scripts::MultipleOutputWrapper::generate_pose(), protocols::rosetta_scripts::ParsedProtocol::get_additional_output(), protocols::rosetta_scripts::RosettaScriptsParser::import_tags(), protocols::rosetta_scripts::RosettaScriptsParser::initialize_data_map(), protocols::rosetta_scripts::RosettaScriptsParser::instantiate_filter(), protocols::rosetta_scripts::RosettaScriptsParser::instantiate_mover(), protocols::rosetta_scripts::RosettaScriptsParser::instantiate_packer_palette(), protocols::rosetta_scripts::RosettaScriptsParser::instantiate_taskoperation(), legacy_saved_pose_or_input(), protocols::rosetta_scripts::RosettaScriptsParser::load_native(), protocols::rosetta_scripts::PosePropertyReporterFactory::newPosePropertyReporter(), protocols::rosetta_scripts::PoseSelectorFactory::newPoseSelector(), protocols::rosetta_scripts::RosettaScriptsParser::parse_apply_to_pose_tag(), parse_database_session(), parse_filter_or_null(), parse_movemap_factory_legacy(), parse_mover_subtag(), protocols::rosetta_scripts::SavePoseMover::parse_my_tag(), protocols::rosetta_scripts::MultiplePoseMover::parse_my_tag(), protocols::rosetta_scripts::PosePropertyReporter::parse_my_tag(), protocols::rosetta_scripts::PoseSelector::parse_my_tag(), protocols::rosetta_scripts::ParsedProtocol::parse_my_tag(), protocols::rosetta_scripts::RosettaScriptsParser::parse_resources_tag(), print_information(), print_template_script(), protocols::rosetta_scripts::MultiplePoseMover::process_pose(), protocols::rosetta_scripts::MultiplePoseMover::process_poses(), protocols::rosetta_scripts::RosettaScriptsParser::read_in_and_recursively_replace_includes(), protocols::rosetta_scripts::ParsedProtocol::report_filters_to_pose(), protocols::rosetta_scripts::RosettaScriptsJobQueen::RosettaScriptsJobQueen(), protocols::rosetta_scripts::RosettaScriptsSchemaValidator::RosettaScriptsSchemaValidator(), save_schema(), protocols::rosetta_scripts::MultiplePoseMover::select_poses(), protocols::rosetta_scripts::XmlObjects::static_get_filter(), protocols::rosetta_scripts::XmlObjects::static_get_mover(), protocols::rosetta_scripts::XmlObjects::static_get_residue_selector(), protocols::rosetta_scripts::XmlObjects::static_get_score_function(), protocols::rosetta_scripts::XmlObjects::static_get_simple_metric(), protocols::rosetta_scripts::XmlObjects::static_get_task_operation(), protocols::rosetta_scripts::RosettaScriptsParser::substitute_variables_in_stream(), protocols::rosetta_scripts::RosettaScriptsParser::validate_input_script_against_xsd(), and protocols::rosetta_scripts::RosettaScriptsSchemaValidator::xsd_for_rosetta_scripts().

TR() [2/9]

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

static

TR() [3/9]

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

static

TR() [4/9]

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

static

TR() [5/9]

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

static

TR() [6/9]

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

static

TR() [7/9]

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

static

TR() [8/9]

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

static

TR() [9/9]

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

static

TR_call_order()

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

static

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

TR_report()

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

static

Referenced by protocols::rosetta_scripts::ParsedProtocol::apply_filter(), protocols::rosetta_scripts::ParsedProtocol::finish_protocol(), protocols::rosetta_scripts::ParsedProtocol::get_additional_output(), and protocols::rosetta_scripts::ParsedProtocol::report_all().