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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:
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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::AtomIDcustom_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

◆ class_name()

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

◆ clone()

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

◆ 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

◆ parse_tag()

void protocols::constraint_generator::DihedralConstraintGenerator::parse_tag ( utility::tag::TagCOP  tag,
basic::datacache::DataMap data 
)
overrideprotectedvirtual

◆ 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

◆ 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)

Member Data Documentation

◆ custom_torsion_

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

◆ dihedral_angle_

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

◆ 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

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