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:

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

protocols::fold_from_loops::constraint_generator::SegmentedAtomPairConstraintGenerator::SegmentedAtomPairConstraintGenerator

(

)

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

overridedefault

Member Function Documentation

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

inlinestaticprivate

Referenced by provide_xml_schema().

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::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_reference_pose(), 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.

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

inlinestatic

Referenced by protocols::fold_from_loops::constraint_generator::SegmentedAtomPairConstraintGeneratorCreator::keyname(), and provide_xml_schema().

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

overridevirtual

Implements protocols::constraint_generator::ConstraintGenerator.

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

inlinestaticprivate

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

inlinestaticprivate

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

inlinestaticprivate

Referenced by parse_tag(), and provide_xml_schema().

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

inlinestaticprivate

Referenced by parse_tag(), and provide_xml_schema().

void protocols::fold_from_loops::constraint_generator::SegmentedAtomPairConstraintGenerator::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 protocols::fold_from_loops::constraint_generator::ConstraintConditions::ca_only, default_inner(), default_outer(), do_inner_, do_outer_, protocols::constraint_generator::get_native_pose(), protocols::fold_from_loops::constraint_generator::ConstraintConditions::max_distance, protocols::fold_from_loops::constraint_generator::ConstraintConditions::min_seq_sep, core::select::residue_selector::parse_residue_selector(), reference_pose_, protocols::fold_from_loops::constraint_generator::ConstraintConditions::sd, selector_, set_inner_ca_only(), set_inner_min_seq_sep(), set_inner_sd(), set_inner_unweighted_function(), set_inner_use_harmonic_function(), set_inner_weight(), set_outer_ca_only(), set_outer_max_distance(), set_outer_sd(), set_outer_unweighted_function(), set_outer_use_harmonic_function(), set_outer_weight(), set_reference_pose(), set_residue_selector(), 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.

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

static

References add_sub_ct_name(), core::select::residue_selector::attributes_for_parse_residue_selector_when_required(), class_name(), protocols::constraint_generator::ConstraintGeneratorFactory::complex_type_name_for_constraint_generator(), default_inner(), default_outer(), and core::id::to_string().

Referenced by protocols::fold_from_loops::constraint_generator::SegmentedAtomPairConstraintGeneratorCreator::provide_xml_schema().

void protocols::fold_from_loops::constraint_generator::SegmentedAtomPairConstraintGenerator::set_do_inner

(

bool

pick

)

References do_inner_.

void protocols::fold_from_loops::constraint_generator::SegmentedAtomPairConstraintGenerator::set_do_outer

(

bool

pick

)

References do_outer_.

void protocols::fold_from_loops::constraint_generator::SegmentedAtomPairConstraintGenerator::set_inner_ca_only

(

bool const

ca_only

)

References protocols::fold_from_loops::constraint_generator::ConstraintConditions::ca_only, and inner_.

Referenced by parse_tag().

void protocols::fold_from_loops::constraint_generator::SegmentedAtomPairConstraintGenerator::set_inner_min_seq_sep

(

core::Size const

min_seq_sep

)

References inner_, and protocols::fold_from_loops::constraint_generator::ConstraintConditions::min_seq_sep.

Referenced by parse_tag().

void protocols::fold_from_loops::constraint_generator::SegmentedAtomPairConstraintGenerator::set_inner_sd

(

core::Real const

sd

)

References inner_, and protocols::fold_from_loops::constraint_generator::ConstraintConditions::sd.

Referenced by parse_tag().

void protocols::fold_from_loops::constraint_generator::SegmentedAtomPairConstraintGenerator::set_inner_unweighted_function

(

bool const

unweighted

)

References inner_, and protocols::fold_from_loops::constraint_generator::ConstraintConditions::unweighted.

Referenced by parse_tag().

void protocols::fold_from_loops::constraint_generator::SegmentedAtomPairConstraintGenerator::set_inner_use_harmonic_function

(

bool const

use_harmonic

)

References inner_, and protocols::fold_from_loops::constraint_generator::ConstraintConditions::use_harmonic.

Referenced by parse_tag().

void protocols::fold_from_loops::constraint_generator::SegmentedAtomPairConstraintGenerator::set_inner_weight

(

core::Real const

weight

)

References inner_, and protocols::fold_from_loops::constraint_generator::ConstraintConditions::weight.

Referenced by parse_tag().

void protocols::fold_from_loops::constraint_generator::SegmentedAtomPairConstraintGenerator::set_outer_ca_only

(

bool const

ca_only

)

References protocols::fold_from_loops::constraint_generator::ConstraintConditions::ca_only, and outer_.

Referenced by parse_tag().

void protocols::fold_from_loops::constraint_generator::SegmentedAtomPairConstraintGenerator::set_outer_max_distance

(

core::Real const

max_dist

)

References protocols::fold_from_loops::constraint_generator::ConstraintConditions::max_distance, and outer_.

Referenced by parse_tag().

void protocols::fold_from_loops::constraint_generator::SegmentedAtomPairConstraintGenerator::set_outer_sd

(

core::Real const

sd

)

References outer_, and protocols::fold_from_loops::constraint_generator::ConstraintConditions::sd.

Referenced by parse_tag().

void protocols::fold_from_loops::constraint_generator::SegmentedAtomPairConstraintGenerator::set_outer_unweighted_function

(

bool const

unweighted

)

References outer_, and protocols::fold_from_loops::constraint_generator::ConstraintConditions::unweighted.

Referenced by parse_tag().

void protocols::fold_from_loops::constraint_generator::SegmentedAtomPairConstraintGenerator::set_outer_use_harmonic_function

(

bool const

use_harmonic

)

References outer_, and protocols::fold_from_loops::constraint_generator::ConstraintConditions::use_harmonic.

Referenced by parse_tag().

void protocols::fold_from_loops::constraint_generator::SegmentedAtomPairConstraintGenerator::set_outer_weight

(

core::Real const

weight

)

References outer_, and protocols::fold_from_loops::constraint_generator::ConstraintConditions::weight.

Referenced by parse_tag().

void protocols::fold_from_loops::constraint_generator::SegmentedAtomPairConstraintGenerator::set_reference_pose

(

core::pose::PoseCOP

ref_pose

)

References reference_pose_.

Referenced by parse_tag().

void protocols::fold_from_loops::constraint_generator::SegmentedAtomPairConstraintGenerator::set_residue_selector

(

core::select::residue_selector::ResidueSelector const &

selector

)

References core::select::residue_selector::ResidueSelector::clone(), and selector_.

Referenced by parse_tag().

Member Data Documentation

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

private

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

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

private

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

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

private

Referenced by apply(), set_inner_ca_only(), set_inner_min_seq_sep(), set_inner_sd(), set_inner_unweighted_function(), set_inner_use_harmonic_function(), and set_inner_weight().

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

private

Referenced by apply(), set_outer_ca_only(), set_outer_max_distance(), set_outer_sd(), set_outer_unweighted_function(), set_outer_use_harmonic_function(), and set_outer_weight().

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

private

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

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

private

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

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

• src/protocols/fold_from_loops/constraint_generator/SegmentedAtomPairConstraintGenerator.hh
• src/protocols/fold_from_loops/constraint_generator/SegmentedAtomPairConstraintGenerator.cc