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protocols::constraint_generator::HydrogenBondConstraintGenerator Class Reference

This constraint generator generates constraints for favoring formation of hydrogen bonds. More...

#include <HydrogenBondConstraintGenerator.hh>

Inheritance diagram for protocols::constraint_generator::HydrogenBondConstraintGenerator:
Inheritance graph
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Public Types

typedef std::set< std::string > AtomNameSet
 

Public Member Functions

 HydrogenBondConstraintGenerator ()
 
 ~HydrogenBondConstraintGenerator () override
 
protocols::constraint_generator::ConstraintGeneratorOP clone () const override
 
void parse_tag (utility::tag::TagCOP tag, basic::datacache::DataMap &data) override
 called by parse_my_tag – should not be used directly More...
 
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_selector1 (core::select::residue_selector::ResidueSelectorCOP selector)
 
void set_residue_selector2 (core::select::residue_selector::ResidueSelectorCOP selector)
 
void set_atoms1 (std::string const &atoms_str)
 
void set_atoms1 (AtomNameSet const &atoms)
 
void set_atoms2 (std::string const &atoms_str)
 
void set_atoms2 (AtomNameSet const &atoms)
 
void set_atom_pair_func (std::string const &func_def)
 
void set_atom_pair_func (core::scoring::func::FuncOP atompairfunc)
 
void set_angle1_func (std::string const &func_def)
 
void set_angle1_func (core::scoring::func::FuncOP angle_func)
 
void set_angle2_func (std::string const &func_def)
 
void set_angle2_func (core::scoring::func::FuncOP angle_func)
 
void set_bounded (bool const bounded)
 
void set_atom_pair_sd (core::Real const sd)
 
void set_angle_sd (core::Real const sd)
 
- 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)
 

Private Member Functions

void add_atom_definitions (std::string const &definition_str)
 
core::scoring::constraints::ConstraintOP create_residue_constraint (core::conformation::Residue const &rsd1, core::conformation::Residue const &rsd2) const
 
core::scoring::constraints::ConstraintOP create_residue_constraint (core::conformation::Residue const &rsd1, core::conformation::Residue const &rsd2, HydrogenBondingAtoms const &atoms1, HydrogenBondingAtoms const &atoms2) const
 
core::scoring::constraints::ConstraintOP create_residue_constraint (core::id::AtomID const &atomid1, core::id::AtomID const &parent_atomid1, core::id::AtomID const &parent2_atomid1, core::id::AtomID const &atomid2, core::id::AtomID const &parent_atomid2, core::id::AtomID const &parent2_atomid2, HydrogenBondingAtom const &a1, HydrogenBondingAtom const &a2) const
 
HydrogenBondingAtoms choose_atoms (core::conformation::Residue const &rsd, AtomNameSet const &allowed_atoms) const
 
void compute_valid_atoms (HydrogenBondingAtoms &valid_atoms, core::conformation::Residue const &rsd) const
 
core::scoring::func::FuncOP atom_pair_func (HydrogenBondingAtom const &a1, HydrogenBondingAtom const &a2) const
 
core::scoring::func::FuncOP angle1_func (HydrogenBondingAtom const &a1) const
 
core::scoring::func::FuncOP angle2_func (HydrogenBondingAtom const &a2) const
 
core::scoring::func::FuncOP dihedral_func (core::Real const dihedral_value) const
 

Private Attributes

core::select::residue_selector::ResidueSelectorCOP selector1_
 
core::select::residue_selector::ResidueSelectorCOP selector2_
 
AtomNameSet atoms1_
 
AtomNameSet atoms2_
 
core::scoring::func::FuncOP atom_pair_func_
 
core::scoring::func::FuncOP angle1_func_
 
core::scoring::func::FuncOP angle2_func_
 
bool bounded_
 
core::Real atom_pair_sd_
 
core::Real angle_sd_
 

Additional Inherited Members

Detailed Description

This constraint generator generates constraints for favoring formation of hydrogen bonds.

Member Typedef Documentation

Constructor & Destructor Documentation

protocols::constraint_generator::HydrogenBondConstraintGenerator::HydrogenBondConstraintGenerator ( )
protocols::constraint_generator::HydrogenBondConstraintGenerator::~HydrogenBondConstraintGenerator ( )
overridedefault

Member Function Documentation

void protocols::constraint_generator::HydrogenBondConstraintGenerator::add_atom_definitions ( std::string const &  definition_str)
private
core::scoring::func::FuncOP protocols::constraint_generator::HydrogenBondConstraintGenerator::angle1_func ( HydrogenBondingAtom const &  a1) const
private
core::scoring::func::FuncOP protocols::constraint_generator::HydrogenBondConstraintGenerator::angle2_func ( HydrogenBondingAtom const &  a2) const
private
core::scoring::constraints::ConstraintCOPs protocols::constraint_generator::HydrogenBondConstraintGenerator::apply ( core::pose::Pose const &  pose) const
overridevirtual
core::scoring::func::FuncOP protocols::constraint_generator::HydrogenBondConstraintGenerator::atom_pair_func ( HydrogenBondingAtom const &  a1,
HydrogenBondingAtom const &  a2 
) const
private
HydrogenBondingAtoms protocols::constraint_generator::HydrogenBondConstraintGenerator::choose_atoms ( core::conformation::Residue const &  rsd,
AtomNameSet const &  allowed_atoms 
) const
private
static std::string protocols::constraint_generator::HydrogenBondConstraintGenerator::class_name ( )
inlinestatic
protocols::constraint_generator::ConstraintGeneratorOP protocols::constraint_generator::HydrogenBondConstraintGenerator::clone ( ) const
overridevirtual
void protocols::constraint_generator::HydrogenBondConstraintGenerator::compute_valid_atoms ( HydrogenBondingAtoms valid_atoms,
core::conformation::Residue const &  rsd 
) const
private
core::scoring::constraints::ConstraintOP protocols::constraint_generator::HydrogenBondConstraintGenerator::create_residue_constraint ( core::conformation::Residue const &  rsd1,
core::conformation::Residue const &  rsd2 
) const
private

References atoms1_, atoms2_, and choose_atoms().

Referenced by apply(), and create_residue_constraint().

core::scoring::constraints::ConstraintOP protocols::constraint_generator::HydrogenBondConstraintGenerator::create_residue_constraint ( core::conformation::Residue const &  rsd1,
core::conformation::Residue const &  rsd2,
HydrogenBondingAtoms const &  atoms1,
HydrogenBondingAtoms const &  atoms2 
) const
private
core::scoring::constraints::ConstraintOP protocols::constraint_generator::HydrogenBondConstraintGenerator::create_residue_constraint ( core::id::AtomID const &  atomid1,
core::id::AtomID const &  parent_atomid1,
core::id::AtomID const &  parent2_atomid1,
core::id::AtomID const &  atomid2,
core::id::AtomID const &  parent_atomid2,
core::id::AtomID const &  parent2_atomid2,
HydrogenBondingAtom const &  a1,
HydrogenBondingAtom const &  a2 
) const
private
core::scoring::func::FuncOP protocols::constraint_generator::HydrogenBondConstraintGenerator::dihedral_func ( core::Real const  dihedral_value) const
private

References angle_sd_, and bounded_.

Referenced by create_residue_constraint().

void protocols::constraint_generator::HydrogenBondConstraintGenerator::parse_tag ( utility::tag::TagCOP  tag,
basic::datacache::DataMap &  data 
)
overridevirtual
void protocols::constraint_generator::HydrogenBondConstraintGenerator::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::HydrogenBondConstraintGenerator::provide_xml_schema ( utility::tag::XMLSchemaDefinition &  xsd)
static
void protocols::constraint_generator::HydrogenBondConstraintGenerator::set_angle1_func ( std::string const &  func_def)
void protocols::constraint_generator::HydrogenBondConstraintGenerator::set_angle1_func ( core::scoring::func::FuncOP  angle_func)

References angle1_func_.

void protocols::constraint_generator::HydrogenBondConstraintGenerator::set_angle2_func ( std::string const &  func_def)
void protocols::constraint_generator::HydrogenBondConstraintGenerator::set_angle2_func ( core::scoring::func::FuncOP  angle_func)

References angle2_func_.

void protocols::constraint_generator::HydrogenBondConstraintGenerator::set_angle_sd ( core::Real const  sd)

References angle_sd_.

void protocols::constraint_generator::HydrogenBondConstraintGenerator::set_atom_pair_func ( std::string const &  func_def)
void protocols::constraint_generator::HydrogenBondConstraintGenerator::set_atom_pair_func ( core::scoring::func::FuncOP  atompairfunc)

References atom_pair_func_.

void protocols::constraint_generator::HydrogenBondConstraintGenerator::set_atom_pair_sd ( core::Real const  sd)

References atom_pair_sd_.

void protocols::constraint_generator::HydrogenBondConstraintGenerator::set_atoms1 ( std::string const &  atoms_str)

References set_atoms2().

Referenced by parse_tag().

void protocols::constraint_generator::HydrogenBondConstraintGenerator::set_atoms1 ( AtomNameSet const &  atoms)

References atoms1_.

void protocols::constraint_generator::HydrogenBondConstraintGenerator::set_atoms2 ( std::string const &  atoms_str)

Referenced by parse_tag(), and set_atoms1().

void protocols::constraint_generator::HydrogenBondConstraintGenerator::set_atoms2 ( AtomNameSet const &  atoms)

References atoms2_.

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

References bounded_.

Referenced by parse_tag().

void protocols::constraint_generator::HydrogenBondConstraintGenerator::set_residue_selector1 ( core::select::residue_selector::ResidueSelectorCOP  selector)

References selector1_.

Referenced by parse_tag().

void protocols::constraint_generator::HydrogenBondConstraintGenerator::set_residue_selector2 ( core::select::residue_selector::ResidueSelectorCOP  selector)

References selector2_.

Referenced by parse_tag().

Member Data Documentation

core::scoring::func::FuncOP protocols::constraint_generator::HydrogenBondConstraintGenerator::angle1_func_
private

Referenced by angle1_func(), and set_angle1_func().

core::scoring::func::FuncOP protocols::constraint_generator::HydrogenBondConstraintGenerator::angle2_func_
private

Referenced by angle2_func(), and set_angle2_func().

core::Real protocols::constraint_generator::HydrogenBondConstraintGenerator::angle_sd_
private
core::scoring::func::FuncOP protocols::constraint_generator::HydrogenBondConstraintGenerator::atom_pair_func_
private
core::Real protocols::constraint_generator::HydrogenBondConstraintGenerator::atom_pair_sd_
private

Referenced by atom_pair_func(), and set_atom_pair_sd().

AtomNameSet protocols::constraint_generator::HydrogenBondConstraintGenerator::atoms1_
private
AtomNameSet protocols::constraint_generator::HydrogenBondConstraintGenerator::atoms2_
private
bool protocols::constraint_generator::HydrogenBondConstraintGenerator::bounded_
private
core::select::residue_selector::ResidueSelectorCOP protocols::constraint_generator::HydrogenBondConstraintGenerator::selector1_
private

Referenced by apply(), and set_residue_selector1().

core::select::residue_selector::ResidueSelectorCOP protocols::constraint_generator::HydrogenBondConstraintGenerator::selector2_
private

Referenced by apply(), and set_residue_selector2().


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