Generally useful loop-sampling meta-algorithms. More...

Classes
class	AcceptanceCheck
	Apply an additional Monte Carlo acceptance check. More...

class	LoopFilter
	Apply any filter in the context of a loop modeling simulation. More...

class	LoopMoverGroup
	Manage a collection of loop-sampling algorithms. More...

class	PrepareForCentroid
	Convert a pose to centroid mode for low-resolution loop modeling. More...

class	PrepareForCentroidCreator

class	PrepareForFullatom
	Convert a pose to fullatom mode for high-resolution loop modeling. More...

class	PrepareForFullatomCreator

class	TrajectoryLogger
	Log a detailed account of everything that happens in a loop modeling simulation. More...

Typedefs
typedef utility::pointer::shared_ptr < AcceptanceCheck >	AcceptanceCheckOP

typedef utility::pointer::shared_ptr < AcceptanceCheck const >	AcceptanceCheckCOP

typedef utility::pointer::shared_ptr < LoopFilter >	LoopFilterOP

typedef utility::pointer::shared_ptr < LoopFilter const >	LoopFilterCOP

typedef utility::pointer::shared_ptr < LoopMoverGroup >	LoopMoverGroupOP

typedef utility::pointer::shared_ptr < LoopMoverGroup const >	LoopMoverGroupCOP

typedef utility::pointer::shared_ptr < PrepareForCentroid >	PrepareForCentroidOP

typedef utility::pointer::shared_ptr < PrepareForCentroid const >	PrepareForCentroidCOP

typedef utility::pointer::shared_ptr < PrepareForFullatom >	PrepareForFullatomOP

typedef utility::pointer::shared_ptr < PrepareForFullatom const >	PrepareForFullatomCOP

typedef utility::pointer::shared_ptr < TrajectoryLogger >	TrajectoryLoggerOP

typedef utility::pointer::shared_ptr < TrajectoryLogger const >	TrajectoryLoggerCOP

Functions
LoopMoverOP	loop_mover_from_tag (TagCOP tag, DataMap &data)

protocols::loops::LoopsOP	parse_loops_from_tag (utility::tag::TagCOP tag)
	return a Loops object from tags More...

std::string	loop_subelement_namer (std::string const &subelement_name)
	util function for append_subelement_and_attributes_for_parse_loops_from_tag More...

void	append_subelement_and_attributes_for_parse_loops_from_tag (utility::tag::XMLSchemaDefinition &xsd, utility::tag::XMLSchemaSimpleSubelementList &subelements, utility::tag::AttributeList &attributes)
	util function for append_subelement_and_attributes_for_parse_loops_from_tag More...

void	attributes_for_set_task_factory_from_tag (utility::tag::AttributeList &attributes)
	For XML schema: Appends the attributes read by set_task_factory_from_tag, which simply calls "parse_task_operations". More...

void	attributes_for_set_scorefxn_from_tag (utility::tag::AttributeList &attributes)
	For XML scheema: Appends the attributes read by set_scorefxn_from_tag, which simply calls "parse_score_function". More...

LoopMoverOP	loop_mover_from_tag (utility::tag::TagCOP tag, basic::datacache::DataMap &data)
	Instantiate a LoopMover from its rosetta-scripts tag. More...

template<class LoopMoverSubclass >
void	set_scorefxn_from_tag (LoopMoverSubclass &mover, utility::tag::TagCOP tag, basic::datacache::DataMap &data)
	Parse the "scorefxn" rosetta-scripts tag for the given mover. Has a compaion function: "attributes_for_set_scorefxn_from_tag" to generate the XSD. More...

template<class LoopMoverSubclass >
void	set_task_factory_from_tag (LoopMoverSubclass &mover, utility::tag::TagCOP tag, basic::datacache::DataMap &data)
	Parse the "task_operations" rosetta-scripts tag for the given mover. Has a compaion function: "attributes_for_set_task_factory_from_tag" to generate the XSD. More...

Detailed Description

Generally useful loop-sampling meta-algorithms.

This namespace contains generally useful LoopMover subclasses that don't directly perform loop sampling. For example, the AcceptanceCheck class makes it possible create protocols with additional acceptance checks. The LoopMoverGroup class makes it easy to work with a collection of loop movers.

Typedef Documentation

typedef utility::pointer::shared_ptr<AcceptanceCheck const> protocols::loop_modeling::utilities::AcceptanceCheckCOP

typedef utility::pointer::shared_ptr<AcceptanceCheck> protocols::loop_modeling::utilities::AcceptanceCheckOP

typedef utility::pointer::shared_ptr<LoopFilter const> protocols::loop_modeling::utilities::LoopFilterCOP

typedef utility::pointer::shared_ptr<LoopFilter> protocols::loop_modeling::utilities::LoopFilterOP

typedef utility::pointer::shared_ptr<LoopMoverGroup const> protocols::loop_modeling::utilities::LoopMoverGroupCOP

typedef utility::pointer::shared_ptr<LoopMoverGroup> protocols::loop_modeling::utilities::LoopMoverGroupOP

typedef utility::pointer::shared_ptr<PrepareForCentroid const> protocols::loop_modeling::utilities::PrepareForCentroidCOP

typedef utility::pointer::shared_ptr<PrepareForCentroid> protocols::loop_modeling::utilities::PrepareForCentroidOP

typedef utility::pointer::shared_ptr<PrepareForFullatom const> protocols::loop_modeling::utilities::PrepareForFullatomCOP

typedef utility::pointer::shared_ptr<PrepareForFullatom> protocols::loop_modeling::utilities::PrepareForFullatomOP

typedef utility::pointer::shared_ptr<TrajectoryLogger const> protocols::loop_modeling::utilities::TrajectoryLoggerCOP

typedef utility::pointer::shared_ptr<TrajectoryLogger> protocols::loop_modeling::utilities::TrajectoryLoggerOP

Function Documentation

void protocols::loop_modeling::utilities::append_subelement_and_attributes_for_parse_loops_from_tag	(	utility::tag::XMLSchemaDefinition &	xsd,
		utility::tag::XMLSchemaSimpleSubelementList &	subelements,
		utility::tag::AttributeList &	attributes
	)

util function for append_subelement_and_attributes_for_parse_loops_from_tag

use with XML schema if you use parse_loops_from_tag

appends the loopfile attribute to the AttributeList for the top level thing (the Mover itself), and appends the schema for Loops subtags to the provided (usually empty, but not necessarily) subelements list

References loop_subelement_namer().

Referenced by protocols::loop_modeling::LoopMover::define_composition_schema(), protocols::analysis::LoopAnalyzerMover::provide_xml_schema(), protocols::loops::filters::LoopAnalyzerFilter::provide_xml_schema(), and protocols::loops::loop_closure::jacobi::JacobiLoopClosureMover::provide_xml_schema().

void protocols::loop_modeling::utilities::attributes_for_set_scorefxn_from_tag ( utility::tag::AttributeList & attributes )

For XML scheema: Appends the attributes read by set_scorefxn_from_tag, which simply calls "parse_score_function".

Appends the attributes read by set_scorefxn_from_tag, which simply calls "parse_score_function".

References core::scoring::attributes_for_parse_score_function().

Referenced by protocols::loop_modeling::refiners::RotamerTrialsRefiner::provide_xml_schema(), protocols::loop_modeling::utilities::PrepareForFullatom::provide_xml_schema(), protocols::loop_modeling::refiners::MinimizationRefiner::provide_xml_schema(), and protocols::loop_modeling::refiners::RepackingRefiner::provide_xml_schema().

void protocols::loop_modeling::utilities::attributes_for_set_task_factory_from_tag ( utility::tag::AttributeList & attributes )

For XML schema: Appends the attributes read by set_task_factory_from_tag, which simply calls "parse_task_operations".

Appends the attributes read by set_task_factory_from_tag, which simply calls "parse_task_operations".

References core::pack::task::attributes_for_parse_task_operations().

Referenced by protocols::loop_modeling::refiners::RotamerTrialsRefiner::provide_xml_schema(), protocols::loop_modeling::refiners::RepackingRefiner::provide_xml_schema(), and protocols::loop_modeler::LoopModeler::provide_xml_schema().

LoopMoverOP protocols::loop_modeling::utilities::loop_mover_from_tag	(	utility::tag::TagCOP	tag,
		basic::datacache::DataMap &	data
	)

Instantiate a LoopMover from its rosetta-scripts tag.

If the given tag is not a LoopMover, a nice error message is thrown.

LoopMoverOP protocols::loop_modeling::utilities::loop_mover_from_tag	(	TagCOP	tag,
		DataMap &	data
	)

Referenced by protocols::loop_modeler::LoopModeler::parse_my_tag(), and protocols::loop_modeling::LoopProtocol::parse_my_tag().

std::string protocols::loop_modeling::utilities::loop_subelement_namer ( std::string const & subelement_name )

util function for append_subelement_and_attributes_for_parse_loops_from_tag

Referenced by append_subelement_and_attributes_for_parse_loops_from_tag().

protocols::loops::LoopsOP protocols::loop_modeling::utilities::parse_loops_from_tag ( utility::tag::TagCOP tag )

return a Loops object from tags

returns a LoopsOP object from tags "loops_file" or a Loop subtag. Moved from loop_modeling/LoopMover.cc.

References protocols::loops::skip_rate, protocols::loops::start, and protocols::loops::stop.

Referenced by protocols::analysis::LoopAnalyzerMover::parse_my_tag(), protocols::loops::filters::LoopAnalyzerFilter::parse_my_tag(), protocols::loop_modeling::LoopMover::parse_my_tag(), and protocols::loops::loop_closure::jacobi::JacobiLoopClosureMover::parse_my_tag().

template<class LoopMoverSubclass >

void protocols::loop_modeling::utilities::set_scorefxn_from_tag	(	LoopMoverSubclass &	mover,
		utility::tag::TagCOP	tag,
		basic::datacache::DataMap &	data
	)

Parse the "scorefxn" rosetta-scripts tag for the given mover. Has a compaion function: "attributes_for_set_scorefxn_from_tag" to generate the XSD.

The given mover must implement a set_score_function() method.

References core::scoring::parse_score_function().

Referenced by protocols::loop_modeling::refiners::RotamerTrialsRefiner::parse_my_tag(), protocols::loop_modeling::refiners::MinimizationRefiner::parse_my_tag(), protocols::loop_modeling::refiners::RepackingRefiner::parse_my_tag(), protocols::loop_modeling::utilities::PrepareForFullatom::parse_my_tag(), protocols::loop_modeling::LoopBuilder::parse_my_tag(), and protocols::loop_modeling::LoopProtocol::parse_my_tag().

template<class LoopMoverSubclass >

void protocols::loop_modeling::utilities::set_task_factory_from_tag	(	LoopMoverSubclass &	mover,
		utility::tag::TagCOP	tag,
		basic::datacache::DataMap &	data
	)

Parse the "task_operations" rosetta-scripts tag for the given mover. Has a compaion function: "attributes_for_set_task_factory_from_tag" to generate the XSD.

The given mover must implement a set_score_function() method.

References core::pack::task::parse_task_operations().

Referenced by protocols::loop_modeling::refiners::RotamerTrialsRefiner::parse_my_tag(), protocols::loop_modeling::refiners::RepackingRefiner::parse_my_tag(), and protocols::loop_modeler::LoopModeler::parse_my_tag().

Classes

Typedefs

Functions

Detailed Description

Typedef Documentation

Function Documentation