protocols::constraint_generator::DihedralConstraintGenerator Class Reference

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...
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::select::residue_selector::ResidueSelectorCOP	selector_ = nullptr
std::string	parsed_resnums_ = ""
std::string	parsed_atoms_ = ""
bool	parsed_custom_torsion_ = 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

protocols::constraint_generator::DihedralConstraintGenerator::DihedralConstraintGenerator

(

)

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

override

Member Function Documentation

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_, 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(), and core::conformation::Residue::xyz().

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

static

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

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

overridevirtual

Implements protocols::constraint_generator::ConstraintGenerator.

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_residue_selector(), set_sd_degree(), and set_torsion_type().

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().

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().

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_.

void protocols::constraint_generator::DihedralConstraintGenerator::set_residue_selector

(

core::select::residue_selector::ResidueSelectorCOP

selector

)

References selector_.

Referenced by parse_tag().

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().

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().

Member Data Documentation

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

private

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

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

private

Referenced by apply(), and parse_tag().

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

private

Referenced by apply(), and parse_tag().

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

private

Referenced by apply(), and parse_tag().

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

private

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

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

private

Referenced by apply(), and set_residue_selector().

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

private

Referenced by apply(), and set_torsion_type().

---

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

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