Generates atom pair constraints for a set of residues in the current pose. More...

#include <ResidueTypeConstraintGenerator.hh>

Inheritance diagram for protocols::constraint_generator::ResidueTypeConstraintGenerator:

Public Member Functions
	ResidueTypeConstraintGenerator ()
	Generates atom pair constraints for a set of residues from the current or reference pose. More...

	~ResidueTypeConstraintGenerator () override

protocols::constraint_generator::ConstraintGeneratorOP	clone () const override

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...

void	set_residue_selector (core::select::residue_selector::ResidueSelectorCOP selector)

void	set_favor_native_bonus (core::Real bonus)

void	set_rsd_type_name3 (std::string name3)

void	set_reference_pose (core::pose::PoseCOP)

core::select::residue_selector::ResidueSelectorCOP	get_residue_selector () const

core::Real	get_favor_native_bonus () const

std::string	get_rsd_type_name3 () const

core::pose::PoseCOP	get_reference_pose () const

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)

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...

Private Member Functions
core::scoring::constraints::ConstraintCOPs	generate_residue_type_constraints (core::pose::Pose const &pose, core::select::residue_selector::ResidueSubset const &subset) const

core::scoring::constraints::ConstraintCOPs	generate_residue_type_constraints (core::pose::Pose const &pose, core::pose::Pose const &ref_pose, core::select::residue_selector::ResidueSubset const &subset, core::id::SequenceMapping const &seqmap) const

Private Attributes
core::select::residue_selector::ResidueSelectorCOP	selector_

core::Real	favor_native_bonus_ = 1.0

std::string	rsd_type_name3_ = ""

core::pose::PoseCOP	ref_pose_

Detailed Description

Generates atom pair constraints for a set of residues in the current pose.

Constructor & Destructor Documentation

protocols::constraint_generator::ResidueTypeConstraintGenerator::ResidueTypeConstraintGenerator ( )

Generates atom pair constraints for a set of residues from the current or reference pose.

protocols::constraint_generator::ResidueTypeConstraintGenerator::~ResidueTypeConstraintGenerator ( )

overridedefault

Member Function Documentation

core::scoring::constraints::ConstraintCOPs protocols::constraint_generator::ResidueTypeConstraintGenerator::apply ( core::pose::Pose const & pose ) const

overridevirtual

generates constraints and adds them to the pose

Implements protocols::constraint_generator::ConstraintGenerator.

References generate_residue_type_constraints(), protocols::constraint_generator::generate_seqmap_from_poses(), ref_pose_, selector_, and protocols::constraint_generator::TR().

static std::string protocols::constraint_generator::ResidueTypeConstraintGenerator::class_name ( )

inlinestatic

Referenced by protocols::constraint_generator::ResidueTypeConstraintGeneratorCreator::keyname(), provide_citation_info(), and provide_xml_schema().

ConstraintGeneratorOP protocols::constraint_generator::ResidueTypeConstraintGenerator::clone ( ) const

overridevirtual

Implements protocols::constraint_generator::ConstraintGenerator.

core::scoring::constraints::ConstraintCOPs protocols::constraint_generator::ResidueTypeConstraintGenerator::generate_residue_type_constraints	(	core::pose::Pose const &	pose,
		core::select::residue_selector::ResidueSubset const &	subset
	)		const

private

References core::conformation::Residue::aa(), core::chemical::aa_vrt, protocols::constraint_generator::compute_nres_in_asymmetric_unit(), favor_native_bonus_, core::pose::Pose::residue(), and rsd_type_name3_.

Referenced by apply().

core::scoring::constraints::ConstraintCOPs protocols::constraint_generator::ResidueTypeConstraintGenerator::generate_residue_type_constraints	(	core::pose::Pose const &	pose,
		core::pose::Pose const &	ref_pose,
		core::select::residue_selector::ResidueSubset const &	subset,
		core::id::SequenceMapping const &	seqmap
	)		const

private

References core::conformation::Residue::aa(), core::chemical::aa_vrt, protocols::constraint_generator::compute_nres_in_asymmetric_unit(), favor_native_bonus_, core::id::SequenceMapping::get_corresponding_residue_in_current(), core::chemical::ResidueTypeBase::name3(), core::pose::Pose::residue(), core::pose::Pose::residue_type(), rsd_type_name3_, and protocols::constraint_generator::TR().

core::Real protocols::constraint_generator::ResidueTypeConstraintGenerator::get_favor_native_bonus ( ) const

References favor_native_bonus_.

core::pose::PoseCOP protocols::constraint_generator::ResidueTypeConstraintGenerator::get_reference_pose ( ) const

References ref_pose_.

core::select::residue_selector::ResidueSelectorCOP protocols::constraint_generator::ResidueTypeConstraintGenerator::get_residue_selector ( ) const

References selector_.

std::string protocols::constraint_generator::ResidueTypeConstraintGenerator::get_rsd_type_name3 ( ) const

References rsd_type_name3_.

void protocols::constraint_generator::ResidueTypeConstraintGenerator::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.

References favor_native_bonus_, protocols::constraint_generator::get_native_pose(), core::select::residue_selector::parse_residue_selector(), ref_pose_, rsd_type_name3_, selector_, and set_reference_pose().

void protocols::constraint_generator::ResidueTypeConstraintGenerator::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.

Cites Sharon Guffy.

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 class_name().

void protocols::constraint_generator::ResidueTypeConstraintGenerator::provide_xml_schema ( utility::tag::XMLSchemaDefinition & xsd )

static

References core::select::residue_selector::attributes_for_parse_residue_selector_default_option_name(), class_name(), and protocols::constraint_generator::ConstraintGeneratorFactory::xsd_constraint_generator_type_definition_w_attributes().

Referenced by protocols::constraint_generator::ResidueTypeConstraintGeneratorCreator::provide_xml_schema().

void protocols::constraint_generator::ResidueTypeConstraintGenerator::set_favor_native_bonus ( core::Real bonus )

References favor_native_bonus_.

void protocols::constraint_generator::ResidueTypeConstraintGenerator::set_reference_pose ( core::pose::PoseCOP ref )

References core::scoring::ref, and ref_pose_.

Referenced by parse_tag().

void protocols::constraint_generator::ResidueTypeConstraintGenerator::set_residue_selector ( core::select::residue_selector::ResidueSelectorCOP selector )

References selector_.

void protocols::constraint_generator::ResidueTypeConstraintGenerator::set_rsd_type_name3 ( std::string name3 )

References rsd_type_name3_.

Member Data Documentation

core::Real protocols::constraint_generator::ResidueTypeConstraintGenerator::favor_native_bonus_ = 1.0

private

Referenced by generate_residue_type_constraints(), get_favor_native_bonus(), parse_tag(), and set_favor_native_bonus().

core::pose::PoseCOP protocols::constraint_generator::ResidueTypeConstraintGenerator::ref_pose_

private

Referenced by apply(), get_reference_pose(), parse_tag(), and set_reference_pose().

std::string protocols::constraint_generator::ResidueTypeConstraintGenerator::rsd_type_name3_ = ""

private

Referenced by generate_residue_type_constraints(), get_rsd_type_name3(), parse_tag(), and set_rsd_type_name3().

core::select::residue_selector::ResidueSelectorCOP protocols::constraint_generator::ResidueTypeConstraintGenerator::selector_

private

Referenced by apply(), get_residue_selector(), parse_tag(), and set_residue_selector().

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

src/protocols/constraint_generator/ResidueTypeConstraintGenerator.hh
src/protocols/constraint_generator/ResidueTypeConstraintGenerator.cc

Public Member Functions

Static Public Member Functions

Protected Member Functions

Private Member Functions

Private Attributes

Detailed Description

Constructor & Destructor Documentation

Member Function Documentation

Member Data Documentation