protocols::trRosetta_protocols::constraint_generators::trRosettaConstraintGenerator Class Reference

A module that runs a trRosetta neural network on an input multiple sequence alignment and uses the output to apply distance and/or angle constraints to a pose for subsequent structure prediction or refinement. More...

#include <trRosettaConstraintGenerator.hh>

Inheritance diagram for protocols::trRosetta_protocols::constraint_generators::trRosettaConstraintGenerator:

Public Member Functions
	trRosettaConstraintGenerator ()
	Default constructor. More...
	trRosettaConstraintGenerator (basic::options::OptionCollection const &opts)
	OptionsCollection constructor. More...
	~trRosettaConstraintGenerator () override
	Destructor. More...
protocols::constraint_generator::ConstraintGeneratorOP	clone () const override
	Copy this object and return owning pointer to copy. More...
core::scoring::constraints::ConstraintCOPs	apply (core::pose::Pose const &pose) const override
	generates constraints and adds them to the pose More...
void	provide_citation_info (basic::citation_manager::CitationCollectionList &citations) const override
	Provide citations to the passed CitationCollectionList. This allows the constraint generator to provide citations for itself and for any modules that it invokes. More...
Public Member Functions inherited from protocols::constraint_generator::ConstraintGenerator
	ConstraintGenerator (std::string const &class_name)
	~ConstraintGenerator () override
void	parse_my_tag (utility::tag::TagCOP tag, basic::datacache::DataMap &data)
	parses XML tag – calls protected parse_tag() function More...
std::string const &	id () const
void	set_id (std::string const &id)
std::string const &	class_name () const

Static Public Member Functions
static std::string	class_name ()
static void	provide_xml_schema (utility::tag::XMLSchemaDefinition &xsd)
static void	provide_citation_info_static (basic::citation_manager::CitationCollectionList &citations)
	Provide citations for hte trRosettaConstraintGenerator, without needing an instance. More...

Protected Member Functions
void	parse_tag (utility::tag::TagCOP tag, basic::datacache::DataMap &data) override
	called by parse_my_tag – should not be used directly More...

Detailed Description

A module that runs a trRosetta neural network on an input multiple sequence alignment and uses the output to apply distance and/or angle constraints to a pose for subsequent structure prediction or refinement.

Constructor & Destructor Documentation

protocols::trRosetta_protocols::constraint_generators::trRosettaConstraintGenerator::trRosettaConstraintGenerator

(

)

Default constructor.

protocols::trRosetta_protocols::constraint_generators::trRosettaConstraintGenerator::trRosettaConstraintGenerator

(

basic::options::OptionCollection const &

opts

)

OptionsCollection constructor.

protocols::trRosetta_protocols::constraint_generators::trRosettaConstraintGenerator::~trRosettaConstraintGenerator ( )

overridedefault

Destructor.

Member Function Documentation

core::scoring::constraints::ConstraintCOPs protocols::trRosetta_protocols::constraint_generators::trRosettaConstraintGenerator::apply ( core::pose::Pose const &  pose ) const

overridevirtual

generates constraints and adds them to the pose

Implements protocols::constraint_generator::ConstraintGenerator.

std::string protocols::trRosetta_protocols::constraint_generators::trRosettaConstraintGenerator::class_name ( )

static

Referenced by protocols::trRosetta_protocols::constraint_generators::trRosettaConstraintGeneratorCreator::keyname(), provide_citation_info_static(), and provide_xml_schema().

protocols::constraint_generator::ConstraintGeneratorOP protocols::trRosetta_protocols::constraint_generators::trRosettaConstraintGenerator::clone ( ) const

overridevirtual

Copy this object and return owning pointer to copy.

Implements protocols::constraint_generator::ConstraintGenerator.

void protocols::trRosetta_protocols::constraint_generators::trRosettaConstraintGenerator::parse_tag ( utility::tag::TagCOP  tag, basic::datacache::DataMap &  data  )

overrideprotectedvirtual

called by parse_my_tag – should not be used directly

Implements protocols::constraint_generator::ConstraintGenerator.

void protocols::trRosetta_protocols::constraint_generators::trRosettaConstraintGenerator::provide_citation_info ( basic::citation_manager::CitationCollectionList &  citations ) const

overridevirtual

Provide citations to the passed CitationCollectionList. This allows the constraint generator to provide citations for itself and for any modules that it invokes.

Calls the static version of this function, to allow citation info to be obtained without an instance.

Author

Vikram K. Mulligan (vmull.nosp@m.igan.nosp@m.@flat.nosp@m.iron.nosp@m.insti.nosp@m.tute.nosp@m..org).

The default implementation of this does nothing. Should be overridden by derived classes.

Author

Vikram K. Mulligan (vmull.nosp@m.igan.nosp@m.@flat.nosp@m.iron.nosp@m.insti.nosp@m.tute.nosp@m..org).

Reimplemented from protocols::constraint_generator::ConstraintGenerator.

References provide_citation_info_static().

void protocols::trRosetta_protocols::constraint_generators::trRosettaConstraintGenerator::provide_citation_info_static ( basic::citation_manager::CitationCollectionList &  citations )

static

Provide citations for hte trRosettaConstraintGenerator, without needing an instance.

Author

Vikram K. Mulligan (vmull.nosp@m.igan.nosp@m.@flat.nosp@m.iron.nosp@m.insti.nosp@m.tute.nosp@m..org).

References class_name(), and protocols::trRosetta::trRosettaProtocol_v1::get_trRosetta_neural_net_citation().

Referenced by provide_citation_info(), and protocols::abinitio::AbrelaxApplication::provide_citation_info().

void protocols::trRosetta_protocols::constraint_generators::trRosettaConstraintGenerator::provide_xml_schema ( utility::tag::XMLSchemaDefinition &  xsd )

static

References class_name(), and protocols::constraint_generator::ConstraintGeneratorFactory::xsd_constraint_generator_type_definition_w_attributes().

Referenced by protocols::trRosetta_protocols::constraint_generators::trRosettaConstraintGeneratorCreator::provide_xml_schema().

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The documentation for this class was generated from the following files:

• src/protocols/trRosetta_protocols/constraint_generators/trRosettaConstraintGenerator.hh
• src/protocols/trRosetta_protocols/constraint_generators/trRosettaConstraintGenerator.cc