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protocols::fold_from_loops::constraint_generator::SegmentedAtomPairConstraintGenerator Class Reference

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

#include <SegmentedAtomPairConstraintGenerator.hh>

Inheritance diagram for protocols::fold_from_loops::constraint_generator::SegmentedAtomPairConstraintGenerator:
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Public Member Functions

 SegmentedAtomPairConstraintGenerator ()
 
 ~SegmentedAtomPairConstraintGenerator () 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 set_residue_selector (core::select::residue_selector::ResidueSelector const &selector)
 
void set_inner_sd (core::Real const sd)
 
void set_inner_ca_only (bool const ca_only)
 
void set_inner_use_harmonic_function (bool const use_harmonic)
 
void set_inner_unweighted_function (bool const unweighted)
 
void set_inner_min_seq_sep (core::Size const min_seq_sep)
 
void set_inner_weight (core::Real const weight)
 
void set_outer_sd (core::Real const sd)
 
void set_outer_ca_only (bool const ca_only)
 
void set_outer_use_harmonic_function (bool const use_harmonic)
 
void set_outer_unweighted_function (bool const unweighted)
 
void set_outer_max_distance (core::Real const max_dist)
 
void set_outer_weight (core::Real const weight)
 
void set_reference_pose (core::pose::PoseCOP ref_pose)
 
void set_do_inner (bool pick)
 
void set_do_outer (bool pick)
 
- Public Member Functions inherited from protocols::constraint_generator::ConstraintGenerator
 ConstraintGenerator (std::string const &class_name)
 
 ~ConstraintGenerator () override
 
virtual void provide_citation_info (basic::citation_manager::CitationCollectionList &citations) const
 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 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...
 

Static Private Member Functions

static std::string add_sub_ct_name (std::string tag_name)
 
static ConstraintConditions default_inner ()
 
static ConstraintConditions default_outer ()
 
static bool default_do_inner ()
 
static bool default_do_outer ()
 

Private Attributes

core::select::residue_selector::ResidueSelectorCOP selector_
 
core::pose::PoseOP reference_pose_
 
ConstraintConditions inner_
 
ConstraintConditions outer_
 
bool do_inner_
 
bool do_outer_
 

Detailed Description

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

Constructor & Destructor Documentation

◆ SegmentedAtomPairConstraintGenerator()

protocols::fold_from_loops::constraint_generator::SegmentedAtomPairConstraintGenerator::SegmentedAtomPairConstraintGenerator ( )

◆ ~SegmentedAtomPairConstraintGenerator()

protocols::fold_from_loops::constraint_generator::SegmentedAtomPairConstraintGenerator::~SegmentedAtomPairConstraintGenerator ( )
overridedefault

Member Function Documentation

◆ add_sub_ct_name()

static std::string protocols::fold_from_loops::constraint_generator::SegmentedAtomPairConstraintGenerator::add_sub_ct_name ( std::string  tag_name)
inlinestaticprivate

Referenced by provide_xml_schema().

◆ apply()

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

generates constraints and adds them to the pose

Implements protocols::constraint_generator::ConstraintGenerator.

References protocols::constraint_generator::AtomPairConstraintGenerator::apply(), protocols::fold_from_loops::constraint_generator::ConstraintConditions::ca_only, do_inner_, do_outer_, core::select::residue_selector::ResidueRanges::from_subset(), inner_, protocols::fold_from_loops::constraint_generator::ConstraintConditions::max_distance, protocols::fold_from_loops::constraint_generator::ConstraintConditions::min_seq_sep, outer_, reference_pose_, protocols::fold_from_loops::constraint_generator::ConstraintConditions::sd, selector_, protocols::constraint_generator::AtomPairConstraintGenerator::set_ca_only(), protocols::constraint_generator::ConstraintGenerator::set_id(), protocols::constraint_generator::AtomPairConstraintGenerator::set_max_distance(), protocols::constraint_generator::AtomPairConstraintGenerator::set_min_seq_sep(), protocols::constraint_generator::AtomPairConstraintGenerator::set_reference_pose(), protocols::constraint_generator::AtomPairConstraintGenerator::set_residue_selector(), protocols::constraint_generator::AtomPairConstraintGenerator::set_sd(), protocols::constraint_generator::AtomPairConstraintGenerator::set_secondary_residue_selector(), protocols::constraint_generator::AtomPairConstraintGenerator::set_unweighted_function(), protocols::constraint_generator::AtomPairConstraintGenerator::set_use_harmonic_function(), protocols::constraint_generator::AtomPairConstraintGenerator::set_weight(), core::id::to_string(), protocols::fold_from_loops::constraint_generator::ConstraintConditions::unweighted, protocols::fold_from_loops::constraint_generator::ConstraintConditions::use_harmonic, and protocols::fold_from_loops::constraint_generator::ConstraintConditions::weight.

◆ class_name()

static std::string protocols::fold_from_loops::constraint_generator::SegmentedAtomPairConstraintGenerator::class_name ( )
inlinestatic

◆ clone()

protocols::constraint_generator::ConstraintGeneratorOP protocols::fold_from_loops::constraint_generator::SegmentedAtomPairConstraintGenerator::clone ( ) const
overridevirtual

◆ default_do_inner()

static bool protocols::fold_from_loops::constraint_generator::SegmentedAtomPairConstraintGenerator::default_do_inner ( )
inlinestaticprivate

◆ default_do_outer()

static bool protocols::fold_from_loops::constraint_generator::SegmentedAtomPairConstraintGenerator::default_do_outer ( )
inlinestaticprivate

◆ default_inner()

static ConstraintConditions protocols::fold_from_loops::constraint_generator::SegmentedAtomPairConstraintGenerator::default_inner ( )
inlinestaticprivate

Referenced by parse_tag(), and provide_xml_schema().

◆ default_outer()

static ConstraintConditions protocols::fold_from_loops::constraint_generator::SegmentedAtomPairConstraintGenerator::default_outer ( )
inlinestaticprivate

Referenced by parse_tag(), and provide_xml_schema().

◆ parse_tag()

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

◆ provide_xml_schema()

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

◆ set_do_inner()

void protocols::fold_from_loops::constraint_generator::SegmentedAtomPairConstraintGenerator::set_do_inner ( bool  pick)

References do_inner_.

◆ set_do_outer()

void protocols::fold_from_loops::constraint_generator::SegmentedAtomPairConstraintGenerator::set_do_outer ( bool  pick)

References do_outer_.

◆ set_inner_ca_only()

void protocols::fold_from_loops::constraint_generator::SegmentedAtomPairConstraintGenerator::set_inner_ca_only ( bool const  ca_only)

◆ set_inner_min_seq_sep()

void protocols::fold_from_loops::constraint_generator::SegmentedAtomPairConstraintGenerator::set_inner_min_seq_sep ( core::Size const  min_seq_sep)

◆ set_inner_sd()

void protocols::fold_from_loops::constraint_generator::SegmentedAtomPairConstraintGenerator::set_inner_sd ( core::Real const  sd)

◆ set_inner_unweighted_function()

void protocols::fold_from_loops::constraint_generator::SegmentedAtomPairConstraintGenerator::set_inner_unweighted_function ( bool const  unweighted)

◆ set_inner_use_harmonic_function()

void protocols::fold_from_loops::constraint_generator::SegmentedAtomPairConstraintGenerator::set_inner_use_harmonic_function ( bool const  use_harmonic)

◆ set_inner_weight()

void protocols::fold_from_loops::constraint_generator::SegmentedAtomPairConstraintGenerator::set_inner_weight ( core::Real const  weight)

◆ set_outer_ca_only()

void protocols::fold_from_loops::constraint_generator::SegmentedAtomPairConstraintGenerator::set_outer_ca_only ( bool const  ca_only)

◆ set_outer_max_distance()

void protocols::fold_from_loops::constraint_generator::SegmentedAtomPairConstraintGenerator::set_outer_max_distance ( core::Real const  max_dist)

◆ set_outer_sd()

void protocols::fold_from_loops::constraint_generator::SegmentedAtomPairConstraintGenerator::set_outer_sd ( core::Real const  sd)

◆ set_outer_unweighted_function()

void protocols::fold_from_loops::constraint_generator::SegmentedAtomPairConstraintGenerator::set_outer_unweighted_function ( bool const  unweighted)

◆ set_outer_use_harmonic_function()

void protocols::fold_from_loops::constraint_generator::SegmentedAtomPairConstraintGenerator::set_outer_use_harmonic_function ( bool const  use_harmonic)

◆ set_outer_weight()

void protocols::fold_from_loops::constraint_generator::SegmentedAtomPairConstraintGenerator::set_outer_weight ( core::Real const  weight)

◆ set_reference_pose()

void protocols::fold_from_loops::constraint_generator::SegmentedAtomPairConstraintGenerator::set_reference_pose ( core::pose::PoseCOP  ref_pose)

References reference_pose_.

Referenced by parse_tag().

◆ set_residue_selector()

void protocols::fold_from_loops::constraint_generator::SegmentedAtomPairConstraintGenerator::set_residue_selector ( core::select::residue_selector::ResidueSelector const &  selector)

Member Data Documentation

◆ do_inner_

bool protocols::fold_from_loops::constraint_generator::SegmentedAtomPairConstraintGenerator::do_inner_
private

Referenced by apply(), parse_tag(), and set_do_inner().

◆ do_outer_

bool protocols::fold_from_loops::constraint_generator::SegmentedAtomPairConstraintGenerator::do_outer_
private

Referenced by apply(), parse_tag(), and set_do_outer().

◆ inner_

ConstraintConditions protocols::fold_from_loops::constraint_generator::SegmentedAtomPairConstraintGenerator::inner_
private

◆ outer_

ConstraintConditions protocols::fold_from_loops::constraint_generator::SegmentedAtomPairConstraintGenerator::outer_
private

◆ reference_pose_

core::pose::PoseOP protocols::fold_from_loops::constraint_generator::SegmentedAtomPairConstraintGenerator::reference_pose_
private

◆ selector_

core::select::residue_selector::ResidueSelectorCOP protocols::fold_from_loops::constraint_generator::SegmentedAtomPairConstraintGenerator::selector_
private

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