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protocols::constraint_generator::ResidueTypeConstraintGenerator Class Reference

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

#include <ResidueTypeConstraintGenerator.hh>

Inheritance diagram for protocols::constraint_generator::ResidueTypeConstraintGenerator:
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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

◆ ResidueTypeConstraintGenerator()

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

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

◆ ~ResidueTypeConstraintGenerator()

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

Member Function Documentation

◆ apply()

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

◆ class_name()

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

◆ clone()

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

◆ generate_residue_type_constraints() [1/2]

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

◆ generate_residue_type_constraints() [2/2]

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

◆ get_favor_native_bonus()

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

References favor_native_bonus_.

◆ get_reference_pose()

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

References ref_pose_.

◆ get_residue_selector()

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

References selector_.

◆ get_rsd_type_name3()

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

References rsd_type_name3_.

◆ parse_tag()

void protocols::constraint_generator::ResidueTypeConstraintGenerator::parse_tag ( utility::tag::TagCOP  tag,
basic::datacache::DataMap data 
)
overrideprotectedvirtual

◆ provide_citation_info()

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().

◆ provide_xml_schema()

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

◆ set_favor_native_bonus()

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

References favor_native_bonus_.

◆ set_reference_pose()

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

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

Referenced by parse_tag().

◆ set_residue_selector()

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

References selector_.

◆ set_rsd_type_name3()

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

References rsd_type_name3_.

Member Data Documentation

◆ favor_native_bonus_

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

◆ ref_pose_

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

◆ rsd_type_name3_

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

◆ selector_

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

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