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protocols::constraint_generator::CoordinateConstraintGenerator Class Reference

Generates coodinate constraints. More...

#include <CoordinateConstraintGenerator.hh>

Inheritance diagram for protocols::constraint_generator::CoordinateConstraintGenerator:
Inheritance graph
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Public Member Functions

 CoordinateConstraintGenerator ()
 
 ~CoordinateConstraintGenerator () override
 
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 set_residue_selector (core::select::residue_selector::ResidueSelectorCOP selector)
 
void set_sidechain (bool const sidechain)
 
void set_ca_only (bool const ca_only)
 
void set_ambiguous_hnq (bool const ambiguous_hnq)
 
void set_sd (core::Real const sd)
 
void set_bounded (bool const bounded)
 
void set_bounded_width (core::Real const bounded_width)
 
void set_reference_pose (core::pose::PoseCOP refpose)
 
- 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::pose::Pose const & select_constraint_target_pose (core::pose::Pose const &pose) const
 
core::id::SequenceMapping generate_seqmap (core::pose::Pose const &pose) const
 
core::pose::PoseOP prepare_constraint_target_pose (core::pose::Pose const &input, core::id::SequenceMapping const &seq_map) const
 
void create_residue_constraints (core::scoring::constraints::ConstraintCOPs &csts, core::id::AtomID const &root_atomid, core::conformation::Residue const &pose_rsd, core::conformation::Residue const &ref_rsd) const
 
core::scoring::func::FuncOP create_function () const
 
core::scoring::constraints::ConstraintOP create_coordinate_constraint (core::id::AtomID const &pose_atomid, core::id::AtomID const &ref_atom, core::id::AtomID const &root_atom, core::conformation::Residue const &ref_rsd) const
 
core::scoring::constraints::ConstraintOP create_ambiguous_constraint (core::id::AtomID const &pose_atomid, core::conformation::Residue const &ref_rsd, core::id::AtomID const &root_atomid, std::pair< std::string, std::string > const &hnq_atoms) const
 
void align_reference_pose (core::pose::Pose &reference, core::pose::Pose const &input_pose, core::id::SequenceMapping const &seq_map) const
 

Private Attributes

core::select::residue_selector::ResidueSelectorCOP selector_
 
core::pose::PoseCOP refpose_
 
bool bounded_
 
core::Real bounded_width_
 
core::Real sd_
 
bool ca_only_
 
bool sidechain_
 
bool ambiguous_hnq_
 
bool align_reference_
 

Detailed Description

Generates coodinate constraints.

Constructor & Destructor Documentation

protocols::constraint_generator::CoordinateConstraintGenerator::CoordinateConstraintGenerator ( )
protocols::constraint_generator::CoordinateConstraintGenerator::~CoordinateConstraintGenerator ( )
overridedefault

Member Function Documentation

void protocols::constraint_generator::CoordinateConstraintGenerator::align_reference_pose ( core::pose::Pose reference,
core::pose::Pose const &  input_pose,
core::id::SequenceMapping const &  seq_map 
) const
private
core::scoring::constraints::ConstraintCOPs protocols::constraint_generator::CoordinateConstraintGenerator::apply ( core::pose::Pose const &  pose) const
overridevirtual
static std::string protocols::constraint_generator::CoordinateConstraintGenerator::class_name ( )
inlinestatic
ConstraintGeneratorOP protocols::constraint_generator::CoordinateConstraintGenerator::clone ( ) const
overridevirtual
core::scoring::constraints::ConstraintOP protocols::constraint_generator::CoordinateConstraintGenerator::create_ambiguous_constraint ( core::id::AtomID const &  pose_atomid,
core::conformation::Residue const &  ref_rsd,
core::id::AtomID const &  root_atomid,
std::pair< std::string, std::string > const &  hnq_atoms 
) const
private
core::scoring::constraints::ConstraintOP protocols::constraint_generator::CoordinateConstraintGenerator::create_coordinate_constraint ( core::id::AtomID const &  pose_atomid,
core::id::AtomID const &  ref_atom,
core::id::AtomID const &  root_atom,
core::conformation::Residue const &  ref_rsd 
) const
private
core::scoring::func::FuncOP protocols::constraint_generator::CoordinateConstraintGenerator::create_function ( ) const
private

References bounded_, bounded_width_, and sd_.

Referenced by create_coordinate_constraint().

void protocols::constraint_generator::CoordinateConstraintGenerator::create_residue_constraints ( core::scoring::constraints::ConstraintCOPs csts,
core::id::AtomID const &  root_atomid,
core::conformation::Residue const &  pose_rsd,
core::conformation::Residue const &  ref_rsd 
) const
private
core::id::SequenceMapping protocols::constraint_generator::CoordinateConstraintGenerator::generate_seqmap ( core::pose::Pose const &  pose) const
private
void protocols::constraint_generator::CoordinateConstraintGenerator::parse_tag ( utility::tag::TagCOP  tag,
basic::datacache::DataMap &  data 
)
overrideprotectedvirtual
core::pose::PoseOP protocols::constraint_generator::CoordinateConstraintGenerator::prepare_constraint_target_pose ( core::pose::Pose const &  input,
core::id::SequenceMapping const &  seq_map 
) const
private
void protocols::constraint_generator::CoordinateConstraintGenerator::provide_xml_schema ( utility::tag::XMLSchemaDefinition &  xsd)
static
core::pose::Pose const & protocols::constraint_generator::CoordinateConstraintGenerator::select_constraint_target_pose ( core::pose::Pose const &  pose) const
private
void protocols::constraint_generator::CoordinateConstraintGenerator::set_ambiguous_hnq ( bool const  ambiguous_hnq)

References ambiguous_hnq_.

Referenced by parse_tag().

void protocols::constraint_generator::CoordinateConstraintGenerator::set_bounded ( bool const  bounded)

References bounded_.

Referenced by parse_tag().

void protocols::constraint_generator::CoordinateConstraintGenerator::set_bounded_width ( core::Real const  bounded_width)

References bounded_width_.

Referenced by parse_tag().

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

References ca_only_.

Referenced by parse_tag().

void protocols::constraint_generator::CoordinateConstraintGenerator::set_reference_pose ( core::pose::PoseCOP  refpose)

References refpose_.

Referenced by parse_tag().

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

References selector_.

Referenced by parse_tag().

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

References sd_.

Referenced by parse_tag().

void protocols::constraint_generator::CoordinateConstraintGenerator::set_sidechain ( bool const  sidechain)

References sidechain_.

Referenced by parse_tag().

Member Data Documentation

bool protocols::constraint_generator::CoordinateConstraintGenerator::align_reference_
private
bool protocols::constraint_generator::CoordinateConstraintGenerator::ambiguous_hnq_
private
bool protocols::constraint_generator::CoordinateConstraintGenerator::bounded_
private
core::Real protocols::constraint_generator::CoordinateConstraintGenerator::bounded_width_
private
bool protocols::constraint_generator::CoordinateConstraintGenerator::ca_only_
private
core::pose::PoseCOP protocols::constraint_generator::CoordinateConstraintGenerator::refpose_
private
core::Real protocols::constraint_generator::CoordinateConstraintGenerator::sd_
private

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

core::select::residue_selector::ResidueSelectorCOP protocols::constraint_generator::CoordinateConstraintGenerator::selector_
private
bool protocols::constraint_generator::CoordinateConstraintGenerator::sidechain_
private

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