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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 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::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_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::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: