Generates coodinate constraints. More...

#include <CoordinateConstraintGenerator.hh>

Inheritance diagram for protocols::constraint_generator::CoordinateConstraintGenerator:

Public Member Functions
	CoordinateConstraintGenerator ()

	~CoordinateConstraintGenerator () override

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_sidechain (bool const sidechain)

void	set_ca_only (bool const ca_only)

void	set_ambiguous_hnq (bool const ambiguous_hnq)

void	set_sd (core::Real const sd)

void	set_bounded (bool const bounded)

void	set_bounded_width (core::Real const bounded_width)

void	set_reference_pose (core::pose::PoseCOP refpose)

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::pose::Pose const &	select_constraint_target_pose (core::pose::Pose const &pose) const

core::id::SequenceMapping	generate_seqmap (core::pose::Pose const &pose) const

core::pose::PoseOP	prepare_constraint_target_pose (core::pose::Pose const &input, core::id::SequenceMapping const &seq_map) const

void	create_residue_constraints (core::scoring::constraints::ConstraintCOPs &csts, core::id::AtomID const &root_atomid, core::conformation::Residue const &pose_rsd, core::conformation::Residue const &ref_rsd) const

core::scoring::func::FuncOP	create_function () const

core::scoring::constraints::ConstraintOP	create_coordinate_constraint (core::id::AtomID const &pose_atomid, core::id::AtomID const &ref_atom, core::id::AtomID const &root_atom, core::conformation::Residue const &ref_rsd) const

core::scoring::constraints::ConstraintOP	create_ambiguous_constraint (core::id::AtomID const &pose_atomid, core::conformation::Residue const &ref_rsd, core::id::AtomID const &root_atomid, std::pair< std::string, std::string > const &hnq_atoms) const

void	align_reference_pose (core::pose::Pose &reference, core::pose::Pose const &input_pose, core::id::SequenceMapping const &seq_map) const

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

core::pose::PoseCOP	refpose_

bool	bounded_

core::Real	bounded_width_

core::Real	sd_

bool	ca_only_

bool	sidechain_

bool	ambiguous_hnq_

bool	align_reference_

Detailed Description

Generates coodinate constraints.

Constructor & Destructor Documentation

◆ CoordinateConstraintGenerator()

protocols::constraint_generator::CoordinateConstraintGenerator::CoordinateConstraintGenerator ( )

◆ ~CoordinateConstraintGenerator()

protocols::constraint_generator::CoordinateConstraintGenerator::~CoordinateConstraintGenerator ( )

overridedefault

Member Function Documentation

◆ align_reference_pose()

void protocols::constraint_generator::CoordinateConstraintGenerator::align_reference_pose	(	core::pose::Pose &	reference,
		core::pose::Pose const &	input_pose,
		core::id::SequenceMapping const &	seq_map
	)		const

private

References core::sequence::calpha_superimpose_with_mapping(), and core::id::SequenceMapping::reverse().

Referenced by prepare_constraint_target_pose().

◆ apply()

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

overridevirtual

generates constraints and adds them to the pose

Implements protocols::constraint_generator::ConstraintGenerator.

References core::conformation::Residue::aa(), core::chemical::aa_vrt, create_residue_constraints(), core::pose::Pose::fold_tree(), generate_seqmap(), prepare_constraint_target_pose(), core::pose::Pose::residue(), core::kinematics::FoldTree::root(), core::id::AtomID::rsd(), selector_, core::pose::Pose::size(), and protocols::constraint_generator::TR().

◆ class_name()

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

inlinestatic

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

◆ clone()

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

overridevirtual

Implements protocols::constraint_generator::ConstraintGenerator.

◆ create_ambiguous_constraint()

core::scoring::constraints::ConstraintOP protocols::constraint_generator::CoordinateConstraintGenerator::create_ambiguous_constraint	(	core::id::AtomID const &	pose_atomid,
		core::conformation::Residue const &	ref_rsd,
		core::id::AtomID const &	root_atomid,
		std::pair< std::string, std::string > const &	hnq_atoms
	)		const

private

References core::conformation::Residue::atom_index(), create_coordinate_constraint(), and core::conformation::Residue::seqpos().

Referenced by create_residue_constraints().

◆ create_coordinate_constraint()

core::scoring::constraints::ConstraintOP protocols::constraint_generator::CoordinateConstraintGenerator::create_coordinate_constraint	(	core::id::AtomID const &	pose_atomid,
		core::id::AtomID const &	ref_atom,
		core::id::AtomID const &	root_atom,
		core::conformation::Residue const &	ref_rsd
	)		const

private

References core::id::AtomID::atomno(), create_function(), and core::conformation::Residue::xyz().

Referenced by create_ambiguous_constraint(), and create_residue_constraints().

◆ create_function()

core::scoring::func::FuncOP protocols::constraint_generator::CoordinateConstraintGenerator::create_function ( ) const

private

References bounded_, bounded_width_, and sd_.

Referenced by create_coordinate_constraint().

◆ create_residue_constraints()

void protocols::constraint_generator::CoordinateConstraintGenerator::create_residue_constraints	(	core::scoring::constraints::ConstraintCOPs &	csts,
		core::id::AtomID const &	root_atomid,
		core::conformation::Residue const &	pose_rsd,
		core::conformation::Residue const &	ref_rsd
	)		const

private

References core::conformation::Residue::aa(), core::chemical::aa_asn, core::chemical::aa_gln, core::chemical::aa_his, ambiguous_hnq_, core::conformation::Residue::atom_name(), ca_only_, protocols::constraint_generator::compute_hnq_atoms(), protocols::constraint_generator::compute_ref_atom(), create_ambiguous_constraint(), create_coordinate_constraint(), core::conformation::Residue::last_backbone_atom(), core::conformation::Residue::nheavyatoms(), core::conformation::Residue::seqpos(), sidechain_, and protocols::constraint_generator::TR().

Referenced by apply().

◆ generate_seqmap()

core::id::SequenceMapping protocols::constraint_generator::CoordinateConstraintGenerator::generate_seqmap ( core::pose::Pose const & pose ) const

private

References protocols::constraint_generator::generate_seqmap_from_poses(), and select_constraint_target_pose().

Referenced by apply().

◆ parse_tag()

void protocols::constraint_generator::CoordinateConstraintGenerator::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 align_reference_, ambiguous_hnq_, bounded_, bounded_width_, ca_only_, protocols::constraint_generator::get_native_pose(), core::select::residue_selector::parse_residue_selector(), refpose_, sd_, selector_, set_ambiguous_hnq(), set_bounded(), set_bounded_width(), set_ca_only(), set_reference_pose(), set_residue_selector(), set_sd(), set_sidechain(), and sidechain_.

◆ prepare_constraint_target_pose()

core::pose::PoseOP protocols::constraint_generator::CoordinateConstraintGenerator::prepare_constraint_target_pose	(	core::pose::Pose const &	input,
		core::id::SequenceMapping const &	seq_map
	)		const

private

References core::conformation::Residue::aa(), core::chemical::aa_vrt, align_reference_, align_reference_pose(), core::pose::Pose::clone(), core::pose::Pose::fold_tree(), refpose_, core::pose::Pose::residue(), core::kinematics::FoldTree::root(), select_constraint_target_pose(), and protocols::constraint_generator::TR().

Referenced by apply().

◆ provide_citation_info()

void protocols::constraint_generator::CoordinateConstraintGenerator::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 Tom Linsky, who created the constraint generator framework.

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::CoordinateConstraintGenerator::provide_xml_schema ( utility::tag::XMLSchemaDefinition & xsd )

static

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

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

◆ select_constraint_target_pose()

core::pose::Pose const & protocols::constraint_generator::CoordinateConstraintGenerator::select_constraint_target_pose ( core::pose::Pose const & pose ) const

private

References refpose_.

Referenced by generate_seqmap(), and prepare_constraint_target_pose().

◆ set_ambiguous_hnq()

void protocols::constraint_generator::CoordinateConstraintGenerator::set_ambiguous_hnq ( bool const ambiguous_hnq )

References ambiguous_hnq_.

Referenced by parse_tag().

◆ set_bounded()

void protocols::constraint_generator::CoordinateConstraintGenerator::set_bounded ( bool const bounded )

References bounded_.

Referenced by parse_tag().

◆ set_bounded_width()

void protocols::constraint_generator::CoordinateConstraintGenerator::set_bounded_width ( core::Real const bounded_width )

References bounded_width_.

Referenced by parse_tag().

◆ set_ca_only()

void protocols::constraint_generator::CoordinateConstraintGenerator::set_ca_only ( bool const ca_only )

References ca_only_.

Referenced by parse_tag().

◆ set_reference_pose()

void protocols::constraint_generator::CoordinateConstraintGenerator::set_reference_pose ( core::pose::PoseCOP refpose )

References refpose_.

Referenced by parse_tag().

◆ set_residue_selector()

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

References selector_.

Referenced by parse_tag().

◆ set_sd()

void protocols::constraint_generator::CoordinateConstraintGenerator::set_sd ( core::Real const sd )

References sd_.

Referenced by parse_tag().

◆ set_sidechain()

void protocols::constraint_generator::CoordinateConstraintGenerator::set_sidechain ( bool const sidechain )

References sidechain_.

Referenced by parse_tag().

Member Data Documentation

◆ align_reference_

bool protocols::constraint_generator::CoordinateConstraintGenerator::align_reference_

private

Referenced by parse_tag(), and prepare_constraint_target_pose().

◆ ambiguous_hnq_

bool protocols::constraint_generator::CoordinateConstraintGenerator::ambiguous_hnq_

private

Referenced by create_residue_constraints(), parse_tag(), and set_ambiguous_hnq().

◆ bounded_

bool protocols::constraint_generator::CoordinateConstraintGenerator::bounded_

private

Referenced by create_function(), parse_tag(), and set_bounded().

◆ bounded_width_

core::Real protocols::constraint_generator::CoordinateConstraintGenerator::bounded_width_

private

Referenced by create_function(), parse_tag(), and set_bounded_width().

◆ ca_only_

bool protocols::constraint_generator::CoordinateConstraintGenerator::ca_only_

private

Referenced by create_residue_constraints(), parse_tag(), and set_ca_only().

◆ refpose_

core::pose::PoseCOP protocols::constraint_generator::CoordinateConstraintGenerator::refpose_

private

Referenced by parse_tag(), prepare_constraint_target_pose(), select_constraint_target_pose(), and set_reference_pose().

◆ sd_

core::Real protocols::constraint_generator::CoordinateConstraintGenerator::sd_

private

Referenced by create_function(), parse_tag(), and set_sd().

◆ selector_

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

private

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

◆ sidechain_

bool protocols::constraint_generator::CoordinateConstraintGenerator::sidechain_

private

Referenced by create_residue_constraints(), parse_tag(), and set_sidechain().

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

src/protocols/constraint_generator/CoordinateConstraintGenerator.hh
src/protocols/constraint_generator/CoordinateConstraintGenerator.cc

Public Member Functions

Static Public Member Functions

Protected Member Functions

Private Member Functions

Private Attributes

Detailed Description

Constructor & Destructor Documentation

◆ CoordinateConstraintGenerator()

◆ ~CoordinateConstraintGenerator()

Member Function Documentation

◆ align_reference_pose()

◆ apply()

◆ class_name()

◆ clone()

◆ create_ambiguous_constraint()

◆ create_coordinate_constraint()

◆ create_function()

◆ create_residue_constraints()

◆ generate_seqmap()

◆ parse_tag()

◆ prepare_constraint_target_pose()

◆ provide_citation_info()

◆ provide_xml_schema()

◆ select_constraint_target_pose()

◆ set_ambiguous_hnq()

◆ set_bounded()

◆ set_bounded_width()

◆ set_ca_only()

◆ set_reference_pose()

◆ set_residue_selector()

◆ set_sd()

◆ set_sidechain()

Member Data Documentation

◆ align_reference_

◆ ambiguous_hnq_

◆ bounded_

◆ bounded_width_

◆ ca_only_

◆ refpose_

◆ sd_

◆ selector_

◆ sidechain_