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

#include <AtomPairConstraintGenerator.hh>

Inheritance diagram for protocols::constraint_generator::AtomPairConstraintGenerator:

Classes
struct	MappedAtom

Public Types
typedef utility::vector1 < MappedAtom >	MappedAtoms

Public Member Functions
	AtomPairConstraintGenerator ()

	~AtomPairConstraintGenerator () 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::ResidueSelector const &selector)

void	set_secondary_residue_selector (core::select::residue_selector::ResidueSelector const &selector)

void	set_sd (core::Real const sd)

void	set_ca_only (bool const ca_only)

void	set_use_harmonic_function (bool const use_harmonic)

void	set_unweighted_function (bool const unweighted)

void	set_max_distance (core::Real const max_dist)

void	set_min_seq_sep (core::Size const min_seq_sep)

void	set_weight (core::Real const weight)

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

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_constraints (core::pose::Pose const &pose, core::select::residue_selector::ResidueSubset const &subset) const

core::scoring::constraints::ConstraintCOPs	generate_atom_pair_constraints (core::pose::Pose const &pose, core::select::residue_selector::ResidueSubset const &subset, core::select::residue_selector::ResidueSubset const &subset2) const

core::scoring::constraints::ConstraintCOPs	generate_atom_pair_constraints (core::pose::Pose const &pose, core::pose::Pose const &ref_pose, core::select::residue_selector::ResidueSubset const &subset, core::select::residue_selector::ResidueSubset const &subset2) const

core::scoring::constraints::ConstraintCOPs	generate_atom_pair_constraints (core::pose::Pose const &pose, core::pose::Pose const &ref_pose, core::select::residue_selector::ResidueSubset const &subset, core::select::residue_selector::ResidueSubset const &subset2, core::id::SequenceMapping const &seqmap) const

core::scoring::constraints::ConstraintCOPs	generate_atom_pair_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

core::id::SequenceMapping	create_sequence_mapping (core::pose::Pose const &pose, core::pose::Pose const &ref_pose) const

MappedAtoms	atoms_to_constrain (core::conformation::Residue const &pose_rsd, core::conformation::Residue const &ref_rsd) const

void	add_constraints (core::scoring::constraints::ConstraintCOPs &csts, core::Size const pose_resid1, core::Size const pose_resid2, core::conformation::Residue const &ref_ires, core::conformation::Residue const &ref_jres, MappedAtoms const &iatoms, MappedAtoms const &jatoms) const

Detailed Description

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

Member Typedef Documentation

typedef utility::vector1< MappedAtom > protocols::constraint_generator::AtomPairConstraintGenerator::MappedAtoms

Constructor & Destructor Documentation

protocols::constraint_generator::AtomPairConstraintGenerator::AtomPairConstraintGenerator ( )

References set_secondary_residue_selector().

protocols::constraint_generator::AtomPairConstraintGenerator::~AtomPairConstraintGenerator ( )

overridedefault

Member Function Documentation

void protocols::constraint_generator::AtomPairConstraintGenerator::add_constraints	(	core::scoring::constraints::ConstraintCOPs &	csts,
		core::Size const	pose_resid1,
		core::Size const	pose_resid2,
		core::conformation::Residue const &	ref_ires,
		core::conformation::Residue const &	ref_jres,
		MappedAtoms const &	iatoms,
		MappedAtoms const &	jatoms
	)		const

private

References max_distance_, protocols::constraint_generator::scalar_weighted(), sd_, protocols::constraint_generator::TR(), unweighted_, use_harmonic_, weight_, and core::conformation::Residue::xyz().

Referenced by generate_atom_pair_constraints().

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

overridevirtual

generates constraints and adds them to the pose

Implements protocols::constraint_generator::ConstraintGenerator.

References generate_atom_pair_constraints(), secondary_selector_, and selector_.

AtomPairConstraintGenerator::MappedAtoms protocols::constraint_generator::AtomPairConstraintGenerator::atoms_to_constrain	(	core::conformation::Residue const &	pose_rsd,
		core::conformation::Residue const &	ref_rsd
	)		const

private

References core::chemical::ResidueType::atom_index(), ca_only_, core::conformation::Residue::has(), core::conformation::Residue::nbr_atom(), and core::conformation::Residue::type().

Referenced by generate_atom_pair_constraints().

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

inlinestatic

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

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

overridevirtual

Implements protocols::constraint_generator::ConstraintGenerator.

core::id::SequenceMapping protocols::constraint_generator::AtomPairConstraintGenerator::create_sequence_mapping	(	core::pose::Pose const &	pose,
		core::pose::Pose const &	ref_pose
	)		const

private

References core::id::SequenceMapping::identity(), core::pose::Pose::sequence(), core::pose::sequence_map_from_pdbinfo(), core::pose::Pose::size(), and protocols::constraint_generator::TR().

Referenced by generate_atom_pair_constraints().

core::scoring::constraints::ConstraintCOPs protocols::constraint_generator::AtomPairConstraintGenerator::generate_atom_pair_constraints	(	core::pose::Pose const &	pose,
		core::select::residue_selector::ResidueSubset const &	subset,
		core::select::residue_selector::ResidueSubset const &	subset2
	)		const

private

References reference_pose_.

Referenced by apply(), and generate_atom_pair_constraints().

core::scoring::constraints::ConstraintCOPs protocols::constraint_generator::AtomPairConstraintGenerator::generate_atom_pair_constraints	(	core::pose::Pose const &	pose,
		core::pose::Pose const &	ref_pose,
		core::select::residue_selector::ResidueSubset const &	subset,
		core::select::residue_selector::ResidueSubset const &	subset2
	)		const

private

References create_sequence_mapping(), generate_atom_pair_constraints(), and core::select::residue_selector::has_any_true_selection().

core::scoring::constraints::ConstraintCOPs protocols::constraint_generator::AtomPairConstraintGenerator::generate_atom_pair_constraints	(	core::pose::Pose const &	pose,
		core::pose::Pose const &	ref_pose,
		core::select::residue_selector::ResidueSubset const &	subset,
		core::select::residue_selector::ResidueSubset const &	subset2,
		core::id::SequenceMapping const &	seqmap
	)		const

private

References core::conformation::Residue::aa(), core::chemical::aa_vrt, add_constraints(), atoms_to_constrain(), protocols::constraint_generator::compute_nres_in_asymmetric_unit(), core::pose::Pose::residue(), core::pose::Pose::size(), and protocols::constraint_generator::TR().

core::scoring::constraints::ConstraintCOPs protocols::constraint_generator::AtomPairConstraintGenerator::generate_atom_pair_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, add_constraints(), atoms_to_constrain(), protocols::constraint_generator::compute_nres_in_asymmetric_unit(), min_seq_sep_, core::pose::Pose::residue(), core::pose::Pose::size(), and protocols::constraint_generator::TR().

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

private

void protocols::constraint_generator::AtomPairConstraintGenerator::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 ca_only_, protocols::constraint_generator::get_native_pose(), core::select::residue_selector::get_residue_selector(), max_distance_, min_seq_sep_, core::select::residue_selector::parse_residue_selector(), reference_pose_, sd_, secondary_selector_, selector_, set_ca_only(), set_max_distance(), set_min_seq_sep(), set_reference_pose(), set_residue_selector(), set_sd(), set_unweighted_function(), set_use_harmonic_function(), set_weight(), unweighted_, use_harmonic_, and weight_.

void protocols::constraint_generator::AtomPairConstraintGenerator::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().

void protocols::constraint_generator::AtomPairConstraintGenerator::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::AtomPairConstraintGeneratorCreator::provide_xml_schema().

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

References ca_only_.

Referenced by parse_tag().

void protocols::constraint_generator::AtomPairConstraintGenerator::set_max_distance ( core::Real const max_dist )

References max_distance_.

Referenced by parse_tag().

void protocols::constraint_generator::AtomPairConstraintGenerator::set_min_seq_sep ( core::Size const min_seq_sep )

References min_seq_sep_.

Referenced by parse_tag().

void protocols::constraint_generator::AtomPairConstraintGenerator::set_reference_pose ( core::pose::PoseCOP ref_pose )

References reference_pose_.

Referenced by protocols::fold_from_loops::constraint_generator::SegmentedAtomPairConstraintGenerator::apply(), and parse_tag().

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

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

Referenced by parse_tag().

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

References sd_.

Referenced by parse_tag().

void protocols::constraint_generator::AtomPairConstraintGenerator::set_secondary_residue_selector ( core::select::residue_selector::ResidueSelector const & selector )

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

Referenced by AtomPairConstraintGenerator().

void protocols::constraint_generator::AtomPairConstraintGenerator::set_unweighted_function ( bool const unweighted )

References unweighted_.

Referenced by parse_tag().

void protocols::constraint_generator::AtomPairConstraintGenerator::set_use_harmonic_function ( bool const use_harmonic )

References use_harmonic_.

Referenced by parse_tag().

void protocols::constraint_generator::AtomPairConstraintGenerator::set_weight ( core::Real const weight )

References weight_.

Referenced by parse_tag().

Member Data Documentation

bool protocols::constraint_generator::AtomPairConstraintGenerator::ca_only_

private

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

core::Real protocols::constraint_generator::AtomPairConstraintGenerator::max_distance_

private

Referenced by add_constraints(), parse_tag(), and set_max_distance().

core::Size protocols::constraint_generator::AtomPairConstraintGenerator::min_seq_sep_

private

Referenced by generate_atom_pair_constraints(), parse_tag(), and set_min_seq_sep().

core::pose::PoseCOP protocols::constraint_generator::AtomPairConstraintGenerator::reference_pose_

private

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

core::Real protocols::constraint_generator::AtomPairConstraintGenerator::sd_

private

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

core::select::residue_selector::ResidueSelectorCOP protocols::constraint_generator::AtomPairConstraintGenerator::secondary_selector_

private

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

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

private

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

bool protocols::constraint_generator::AtomPairConstraintGenerator::unweighted_

private

Referenced by add_constraints(), parse_tag(), and set_unweighted_function().

bool protocols::constraint_generator::AtomPairConstraintGenerator::use_harmonic_

private

Referenced by add_constraints(), parse_tag(), and set_use_harmonic_function().

core::Real protocols::constraint_generator::AtomPairConstraintGenerator::weight_

private

Referenced by add_constraints(), parse_tag(), and set_weight().

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

src/protocols/constraint_generator/AtomPairConstraintGenerator.hh
src/protocols/constraint_generator/AtomPairConstraintGenerator.cc

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

core::select::residue_selector::ResidueSelectorCOP	secondary_selector_

core::pose::PoseCOP	reference_pose_

core::Real	sd_

core::Real	weight_

bool	ca_only_

bool	use_harmonic_

bool	unweighted_

core::Real	max_distance_

core::Size	min_seq_sep_

Classes

Public Types

Public Member Functions

Static Public Member Functions

Protected Member Functions

Private Member Functions

Private Attributes

Detailed Description

Member Typedef Documentation

Constructor & Destructor Documentation

Member Function Documentation

Member Data Documentation