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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:
Inheritance graph
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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...
 
- 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
std::string protocols::constraint_generator::DihedralConstraintGenerator::class_name ( )
static
protocols::constraint_generator::ConstraintGeneratorOP protocols::constraint_generator::DihedralConstraintGenerator::clone ( ) const
overridevirtual
void protocols::constraint_generator::DihedralConstraintGenerator::parse_tag ( utility::tag::TagCOP  tag,
basic::datacache::DataMap &  data 
)
overrideprotectedvirtual
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
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
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: