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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 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_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: