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protocols::constraint_generator::AtomPairConstraintGenerator Class Reference

Generates atom pair constraints for a set of residues from the current or reference pose. More...

#include <AtomPairConstraintGenerator.hh>

Inheritance diagram for protocols::constraint_generator::AtomPairConstraintGenerator:
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Classes

struct  MappedAtom
 

Public Types

typedef utility::vector1
< MappedAtom
MappedAtoms
 

Public Member Functions

 AtomPairConstraintGenerator ()
 
 ~AtomPairConstraintGenerator () 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 set_residue_selector (core::select::residue_selector::ResidueSelector const &selector)
 
void set_secondary_residue_selector (core::select::residue_selector::ResidueSelector const &selector)
 
void set_sd (core::Real const sd)
 
void set_ca_only (bool const ca_only)
 
void set_use_harmonic_function (bool const use_harmonic)
 
void set_unweighted_function (bool const unweighted)
 
void set_max_distance (core::Real const max_dist)
 
void set_min_seq_sep (core::Size const min_seq_sep)
 
void set_weight (core::Real const weight)
 
void set_reference_pose (core::pose::PoseCOP ref_pose)
 
- 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::scoring::constraints::ConstraintCOPs generate_constraints (core::pose::Pose const &pose, core::select::residue_selector::ResidueSubset const &subset) const
 
core::scoring::constraints::ConstraintCOPs generate_atom_pair_constraints (core::pose::Pose const &pose, core::select::residue_selector::ResidueSubset const &subset, core::select::residue_selector::ResidueSubset const &subset2) const
 
core::scoring::constraints::ConstraintCOPs generate_atom_pair_constraints (core::pose::Pose const &pose, core::pose::Pose const &ref_pose, core::select::residue_selector::ResidueSubset const &subset, core::select::residue_selector::ResidueSubset const &subset2) const
 
core::scoring::constraints::ConstraintCOPs generate_atom_pair_constraints (core::pose::Pose const &pose, core::pose::Pose const &ref_pose, core::select::residue_selector::ResidueSubset const &subset, core::select::residue_selector::ResidueSubset const &subset2, core::id::SequenceMapping const &seqmap) const
 
core::scoring::constraints::ConstraintCOPs generate_atom_pair_constraints (core::pose::Pose const &pose, core::pose::Pose const &ref_pose, core::select::residue_selector::ResidueSubset const &subset, core::id::SequenceMapping const &seqmap) const
 
core::id::SequenceMapping create_sequence_mapping (core::pose::Pose const &pose, core::pose::Pose const &ref_pose) const
 
MappedAtoms atoms_to_constrain (core::conformation::Residue const &pose_rsd, core::conformation::Residue const &ref_rsd) const
 
void add_constraints (core::scoring::constraints::ConstraintCOPs &csts, core::Size const pose_resid1, core::Size const pose_resid2, core::conformation::Residue const &ref_ires, core::conformation::Residue const &ref_jres, MappedAtoms const &iatoms, MappedAtoms const &jatoms) const
 

Private Attributes

core::select::residue_selector::ResidueSelectorCOP selector_
 
core::select::residue_selector::ResidueSelectorCOP secondary_selector_
 
core::pose::PoseCOP reference_pose_
 
core::Real sd_
 
core::Real weight_
 
bool ca_only_
 
bool use_harmonic_
 
bool unweighted_
 
core::Real max_distance_
 
core::Size min_seq_sep_
 

Detailed Description

Generates atom pair constraints for a set of residues from the current or reference pose.

Member Typedef Documentation

Constructor & Destructor Documentation

protocols::constraint_generator::AtomPairConstraintGenerator::AtomPairConstraintGenerator ( )
protocols::constraint_generator::AtomPairConstraintGenerator::~AtomPairConstraintGenerator ( )
overridedefault

Member Function Documentation

void protocols::constraint_generator::AtomPairConstraintGenerator::add_constraints ( core::scoring::constraints::ConstraintCOPs csts,
core::Size const  pose_resid1,
core::Size const  pose_resid2,
core::conformation::Residue const &  ref_ires,
core::conformation::Residue const &  ref_jres,
MappedAtoms const &  iatoms,
MappedAtoms const &  jatoms 
) const
private
core::scoring::constraints::ConstraintCOPs protocols::constraint_generator::AtomPairConstraintGenerator::apply ( core::pose::Pose const &  pose) const
overridevirtual

generates constraints and adds them to the pose

Implements protocols::constraint_generator::ConstraintGenerator.

References generate_atom_pair_constraints(), secondary_selector_, and selector_.

AtomPairConstraintGenerator::MappedAtoms protocols::constraint_generator::AtomPairConstraintGenerator::atoms_to_constrain ( core::conformation::Residue const &  pose_rsd,
core::conformation::Residue const &  ref_rsd 
) const
private
static std::string protocols::constraint_generator::AtomPairConstraintGenerator::class_name ( )
inlinestatic
protocols::constraint_generator::ConstraintGeneratorOP protocols::constraint_generator::AtomPairConstraintGenerator::clone ( ) const
overridevirtual
core::id::SequenceMapping protocols::constraint_generator::AtomPairConstraintGenerator::create_sequence_mapping ( core::pose::Pose const &  pose,
core::pose::Pose const &  ref_pose 
) const
private
core::scoring::constraints::ConstraintCOPs protocols::constraint_generator::AtomPairConstraintGenerator::generate_atom_pair_constraints ( core::pose::Pose const &  pose,
core::select::residue_selector::ResidueSubset const &  subset,
core::select::residue_selector::ResidueSubset const &  subset2 
) const
private

References reference_pose_.

Referenced by apply(), and generate_atom_pair_constraints().

core::scoring::constraints::ConstraintCOPs protocols::constraint_generator::AtomPairConstraintGenerator::generate_atom_pair_constraints ( core::pose::Pose const &  pose,
core::pose::Pose const &  ref_pose,
core::select::residue_selector::ResidueSubset const &  subset,
core::select::residue_selector::ResidueSubset const &  subset2 
) const
private
core::scoring::constraints::ConstraintCOPs protocols::constraint_generator::AtomPairConstraintGenerator::generate_atom_pair_constraints ( core::pose::Pose const &  pose,
core::pose::Pose const &  ref_pose,
core::select::residue_selector::ResidueSubset const &  subset,
core::select::residue_selector::ResidueSubset const &  subset2,
core::id::SequenceMapping const &  seqmap 
) const
private
core::scoring::constraints::ConstraintCOPs protocols::constraint_generator::AtomPairConstraintGenerator::generate_atom_pair_constraints ( core::pose::Pose const &  pose,
core::pose::Pose const &  ref_pose,
core::select::residue_selector::ResidueSubset const &  subset,
core::id::SequenceMapping const &  seqmap 
) const
private
core::scoring::constraints::ConstraintCOPs protocols::constraint_generator::AtomPairConstraintGenerator::generate_constraints ( core::pose::Pose const &  pose,
core::select::residue_selector::ResidueSubset const &  subset 
) const
private
void protocols::constraint_generator::AtomPairConstraintGenerator::parse_tag ( utility::tag::TagCOP  tag,
basic::datacache::DataMap &  data 
)
overrideprotectedvirtual
void protocols::constraint_generator::AtomPairConstraintGenerator::provide_xml_schema ( utility::tag::XMLSchemaDefinition &  xsd)
static
void protocols::constraint_generator::AtomPairConstraintGenerator::set_ca_only ( bool const  ca_only)

References ca_only_.

Referenced by parse_tag().

void protocols::constraint_generator::AtomPairConstraintGenerator::set_max_distance ( core::Real const  max_dist)

References max_distance_.

Referenced by parse_tag().

void protocols::constraint_generator::AtomPairConstraintGenerator::set_min_seq_sep ( core::Size const  min_seq_sep)

References min_seq_sep_.

Referenced by parse_tag().

void protocols::constraint_generator::AtomPairConstraintGenerator::set_reference_pose ( core::pose::PoseCOP  ref_pose)
void protocols::constraint_generator::AtomPairConstraintGenerator::set_residue_selector ( core::select::residue_selector::ResidueSelector const &  selector)
void protocols::constraint_generator::AtomPairConstraintGenerator::set_sd ( core::Real const  sd)

References sd_.

Referenced by parse_tag().

void protocols::constraint_generator::AtomPairConstraintGenerator::set_secondary_residue_selector ( core::select::residue_selector::ResidueSelector const &  selector)
void protocols::constraint_generator::AtomPairConstraintGenerator::set_unweighted_function ( bool const  unweighted)

References unweighted_.

Referenced by parse_tag().

void protocols::constraint_generator::AtomPairConstraintGenerator::set_use_harmonic_function ( bool const  use_harmonic)

References use_harmonic_.

Referenced by parse_tag().

void protocols::constraint_generator::AtomPairConstraintGenerator::set_weight ( core::Real const  weight)

References weight_.

Referenced by parse_tag().

Member Data Documentation

bool protocols::constraint_generator::AtomPairConstraintGenerator::ca_only_
private
core::Real protocols::constraint_generator::AtomPairConstraintGenerator::max_distance_
private
core::Size protocols::constraint_generator::AtomPairConstraintGenerator::min_seq_sep_
private
core::pose::PoseCOP protocols::constraint_generator::AtomPairConstraintGenerator::reference_pose_
private
core::Real protocols::constraint_generator::AtomPairConstraintGenerator::sd_
private

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

core::select::residue_selector::ResidueSelectorCOP protocols::constraint_generator::AtomPairConstraintGenerator::secondary_selector_
private
core::select::residue_selector::ResidueSelectorCOP protocols::constraint_generator::AtomPairConstraintGenerator::selector_
private
bool protocols::constraint_generator::AtomPairConstraintGenerator::unweighted_
private
bool protocols::constraint_generator::AtomPairConstraintGenerator::use_harmonic_
private
core::Real protocols::constraint_generator::AtomPairConstraintGenerator::weight_
private

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