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protocols::loop_modeling::utilities Namespace Reference

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< AcceptanceCheckAcceptanceCheckOP
 
typedef utility::pointer::shared_ptr< AcceptanceCheck const > AcceptanceCheckCOP
 
typedef utility::pointer::shared_ptr< LoopFilterLoopFilterOP
 
typedef utility::pointer::shared_ptr< LoopFilter const > LoopFilterCOP
 
typedef utility::pointer::shared_ptr< LoopMoverGroupLoopMoverGroupOP
 
typedef utility::pointer::shared_ptr< LoopMoverGroup const > LoopMoverGroupCOP
 
typedef utility::pointer::shared_ptr< PrepareForCentroidPrepareForCentroidOP
 
typedef utility::pointer::shared_ptr< PrepareForCentroid const > PrepareForCentroidCOP
 
typedef utility::pointer::shared_ptr< PrepareForFullatomPrepareForFullatomOP
 
typedef utility::pointer::shared_ptr< PrepareForFullatom const > PrepareForFullatomCOP
 
typedef utility::pointer::shared_ptr< TrajectoryLoggerTrajectoryLoggerOP
 
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

◆ AcceptanceCheckCOP

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

◆ AcceptanceCheckOP

◆ LoopFilterCOP

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

◆ LoopFilterOP

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

◆ LoopMoverGroupCOP

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

◆ LoopMoverGroupOP

◆ PrepareForCentroidCOP

◆ PrepareForCentroidOP

◆ PrepareForFullatomCOP

◆ PrepareForFullatomOP

◆ TrajectoryLoggerCOP

◆ TrajectoryLoggerOP

Function Documentation

◆ append_subelement_and_attributes_for_parse_loops_from_tag()

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

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

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::loops::filters::LoopAnalyzerFilter::provide_xml_schema(), protocols::analysis::LoopAnalyzerMover::provide_xml_schema(), and protocols::loops::loop_closure::jacobi::JacobiLoopClosureMover::provide_xml_schema().

◆ attributes_for_set_scorefxn_from_tag()

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

◆ attributes_for_set_task_factory_from_tag()

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_modeler::LoopModeler::provide_xml_schema(), protocols::loop_modeling::refiners::RepackingRefiner::provide_xml_schema(), and protocols::loop_modeling::refiners::RotamerTrialsRefiner::provide_xml_schema().

◆ loop_mover_from_tag() [1/2]

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

◆ loop_mover_from_tag() [2/2]

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.

◆ loop_subelement_namer()

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().

◆ parse_loops_from_tag()

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

◆ set_scorefxn_from_tag()

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

◆ set_task_factory_from_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_modeler::LoopModeler::parse_my_tag(), protocols::loop_modeling::refiners::RepackingRefiner::parse_my_tag(), and protocols::loop_modeling::refiners::RotamerTrialsRefiner::parse_my_tag().