A cst generator that creates Dihedral constraints for specified residues using a residue selector. More...

#include <DihedralConstraintGenerator.hh>

Inheritance diagram for protocols::constraint_generator::DihedralConstraintGenerator:

Public Member Functions
	DihedralConstraintGenerator ()

	~DihedralConstraintGenerator () 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_torsion_type (core::id::MainchainTorsionType torsion)
	Set the torsion type we will be working with. More...

void	set_custom_dihedral (utility::vector1< core::id::AtomID > const &ids)
	MANUALLY set the dihedrals we will work with. IGNORES Residue selector, but allows setting dihedrals for ANY torsion. More...

void	set_sd_degree (core::Real sd_degree)
	Set the standard deviation for the dihedral constraint. Default is 16.0. This which was found by taking the mean SD of all dihedral angles of either PHI or PSI for each North CDR Cluster. This is a fairly tight constraint and allows a bit of movement while not changing overall struture much. More...

void	set_use_custom_dihedral_angle (bool use_custom_dihedral_angle)

bool	get_use_custom_dihedral_angle () const

void	set_dihedral_angle (core::Real dihedral_angle)
	Set the desired dihedral angle in degrees. This is not compatible if you use_custom_dihedral_angle set_custom_dihedral. If you do call this function in addition to setting a custom dihedral, no constraints will be applied and an error will be returned. More...

core::Real	get_dihedral_angle () 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 Attributes
core::id::MainchainTorsionType	torsion_

core::Real	sd_ = 16.0

core::Real	dihedral_angle_ = 0.0

core::select::residue_selector::ResidueSelectorCOP	selector_ = nullptr

std::string	parsed_resnums_ = ""

std::string	parsed_atoms_ = ""

bool	parsed_custom_torsion_ = false

bool	use_custom_dihedral_angle_ = false

utility::vector1< core::id::AtomID >	custom_torsion_

Detailed Description

A cst generator that creates Dihedral constraints for specified residues using a residue selector.

Uses CircularHarmonic constraints, since CircularGaussian func does not exist. By default, works on Protein and carbohydrate BB dihedrals. You must set either the set of atom names or phi/psi/omega. Will only work on ONE type of dihedral angle.

Constructor & Destructor Documentation

◆ DihedralConstraintGenerator()

protocols::constraint_generator::DihedralConstraintGenerator::DihedralConstraintGenerator ( )

◆ ~DihedralConstraintGenerator()

protocols::constraint_generator::DihedralConstraintGenerator::~DihedralConstraintGenerator ( )

override

Member Function Documentation

◆ apply()

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

overridevirtual

generates constraints and adds them to the pose

Implements protocols::constraint_generator::ConstraintGenerator.

References core::id::BB, core::pose::Pose::conformation(), custom_torsion_, dihedral_angle_, core::conformation::carbohydrates::get_glycosidic_torsion(), core::conformation::carbohydrates::get_reference_atoms(), core::conformation::Conformation::get_torsion_angle_atom_ids(), core::chemical::ResidueType::is_carbohydrate(), protocols::constraint_generator::parse_custom_torsion(), parsed_atoms_, parsed_custom_torsion_, parsed_resnums_, core::pose::Pose::residue(), core::pose::Pose::residue_type(), sd_, core::select::residue_selector::selection_positions(), selector_, torsion_, core::conformation::Conformation::torsion_angle(), protocols::constraint_generator::TR(), use_custom_dihedral_angle_, and core::conformation::Residue::xyz().

◆ class_name()

std::string protocols::constraint_generator::DihedralConstraintGenerator::class_name ( )

static

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

◆ clone()

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

overridevirtual

Implements protocols::constraint_generator::ConstraintGenerator.

◆ get_dihedral_angle()

core::Real protocols::constraint_generator::DihedralConstraintGenerator::get_dihedral_angle ( ) const

References dihedral_angle_.

◆ get_use_custom_dihedral_angle()

bool protocols::constraint_generator::DihedralConstraintGenerator::get_use_custom_dihedral_angle ( ) const

References use_custom_dihedral_angle_.

◆ parse_tag()

void protocols::constraint_generator::DihedralConstraintGenerator::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 core::select::residue_selector::parse_residue_selector(), protocols::constraint_generator::parse_torsion_type(), parsed_atoms_, parsed_custom_torsion_, parsed_resnums_, sd_, set_dihedral_angle(), set_residue_selector(), set_sd_degree(), and set_torsion_type().

◆ provide_citation_info()

void protocols::constraint_generator::DihedralConstraintGenerator::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 Jared Adolf-Bryfogle.

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

static

References protocols::rosetta_scripts::attributes_for_parse_residue_selector(), class_name(), and protocols::constraint_generator::ConstraintGeneratorFactory::xsd_constraint_generator_type_definition_w_attributes().

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

◆ set_custom_dihedral()

void protocols::constraint_generator::DihedralConstraintGenerator::set_custom_dihedral ( utility::vector1< core::id::AtomID > const & ids )

MANUALLY set the dihedrals we will work with. IGNORES Residue selector, but allows setting dihedrals for ANY torsion.

References custom_torsion_.

◆ set_dihedral_angle()

void protocols::constraint_generator::DihedralConstraintGenerator::set_dihedral_angle ( core::Real dihedral_angle )

Set the desired dihedral angle in degrees. This is not compatible if you use_custom_dihedral_angle set_custom_dihedral. If you do call this function in addition to setting a custom dihedral, no constraints will be applied and an error will be returned.

References dihedral_angle_, and use_custom_dihedral_angle_.

Referenced by parse_tag().

◆ set_residue_selector()

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

References selector_.

Referenced by parse_tag().

◆ set_sd_degree()

void protocols::constraint_generator::DihedralConstraintGenerator::set_sd_degree ( core::Real sd_degree )

Set the standard deviation for the dihedral constraint. Default is 16.0. This which was found by taking the mean SD of all dihedral angles of either PHI or PSI for each North CDR Cluster. This is a fairly tight constraint and allows a bit of movement while not changing overall struture much.

Set this in Degrees.

References sd_.

Referenced by parse_tag().

◆ set_torsion_type()

void protocols::constraint_generator::DihedralConstraintGenerator::set_torsion_type ( core::id::MainchainTorsionType torsion )

Set the torsion type we will be working with.

References custom_torsion_, and torsion_.

Referenced by parse_tag().

◆ set_use_custom_dihedral_angle()

void protocols::constraint_generator::DihedralConstraintGenerator::set_use_custom_dihedral_angle ( bool use_custom_dihedral_angle )

References use_custom_dihedral_angle_.

Member Data Documentation

◆ custom_torsion_

utility::vector1< core::id::AtomID > protocols::constraint_generator::DihedralConstraintGenerator::custom_torsion_

private

Referenced by apply(), set_custom_dihedral(), and set_torsion_type().

◆ dihedral_angle_

core::Real protocols::constraint_generator::DihedralConstraintGenerator::dihedral_angle_ = 0.0

private

Referenced by apply(), get_dihedral_angle(), and set_dihedral_angle().

◆ parsed_atoms_

std::string protocols::constraint_generator::DihedralConstraintGenerator::parsed_atoms_ = ""

private

Referenced by apply(), and parse_tag().

◆ parsed_custom_torsion_

bool protocols::constraint_generator::DihedralConstraintGenerator::parsed_custom_torsion_ = false

private

Referenced by apply(), and parse_tag().

◆ parsed_resnums_

std::string protocols::constraint_generator::DihedralConstraintGenerator::parsed_resnums_ = ""

private

Referenced by apply(), and parse_tag().

◆ sd_

core::Real protocols::constraint_generator::DihedralConstraintGenerator::sd_ = 16.0

private

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

◆ selector_

core::select::residue_selector::ResidueSelectorCOP protocols::constraint_generator::DihedralConstraintGenerator::selector_ = nullptr

private

Referenced by apply(), and set_residue_selector().

◆ torsion_

core::id::MainchainTorsionType protocols::constraint_generator::DihedralConstraintGenerator::torsion_

private

Referenced by apply(), and set_torsion_type().

◆ use_custom_dihedral_angle_

bool protocols::constraint_generator::DihedralConstraintGenerator::use_custom_dihedral_angle_ = false

private

Referenced by apply(), get_use_custom_dihedral_angle(), set_dihedral_angle(), and set_use_custom_dihedral_angle().

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

src/protocols/constraint_generator/DihedralConstraintGenerator.hh
src/protocols/constraint_generator/DihedralConstraintGenerator.cc

Public Member Functions

Static Public Member Functions

Protected Member Functions

Private Attributes

Detailed Description

Constructor & Destructor Documentation

◆ DihedralConstraintGenerator()

◆ ~DihedralConstraintGenerator()

Member Function Documentation

◆ apply()

◆ class_name()

◆ clone()

◆ get_dihedral_angle()

◆ get_use_custom_dihedral_angle()

◆ parse_tag()

◆ provide_citation_info()

◆ provide_xml_schema()

◆ set_custom_dihedral()

◆ set_dihedral_angle()

◆ set_residue_selector()

◆ set_sd_degree()

◆ set_torsion_type()

◆ set_use_custom_dihedral_angle()

Member Data Documentation

◆ custom_torsion_

◆ dihedral_angle_

◆ parsed_atoms_

◆ parsed_custom_torsion_

◆ parsed_resnums_

◆ sd_

◆ selector_

◆ torsion_

◆ use_custom_dihedral_angle_