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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 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_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_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 Tom Linsky, who created the constraint generator framework.

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::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: