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

#include <HydrogenBondConstraintGenerator.hh>

Inheritance diagram for protocols::constraint_generator::HydrogenBondConstraintGenerator:

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

Additional Inherited Members

Detailed Description

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

Member Typedef Documentation

typedef std::set< std::string > protocols::constraint_generator::HydrogenBondConstraintGenerator::AtomNameSet

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

References protocols::constraint_generator::HydrogenBondInfo::add_atoms_from_string(), and protocols::constraint_generator::TR().

Referenced by parse_tag().

core::scoring::func::FuncOP protocols::constraint_generator::HydrogenBondConstraintGenerator::angle1_func ( HydrogenBondingAtom const & a1 ) const

private

References protocols::constraint_generator::HydrogenBondingAtom::angle(), angle1_func_, angle_sd_, and bounded_.

Referenced by create_residue_constraint().

core::scoring::func::FuncOP protocols::constraint_generator::HydrogenBondConstraintGenerator::angle2_func ( HydrogenBondingAtom const & a2 ) const

private

References protocols::constraint_generator::HydrogenBondingAtom::angle(), angle2_func_, angle_sd_, and bounded_.

Referenced by create_residue_constraint().

core::scoring::constraints::ConstraintCOPs protocols::constraint_generator::HydrogenBondConstraintGenerator::apply ( core::pose::Pose const & pose ) const

overridevirtual

generates constraints and adds them to the pose

Implements protocols::constraint_generator::ConstraintGenerator.

References create_residue_constraint(), core::pose::Pose::residue(), selector1_, selector2_, core::pose::Pose::size(), and protocols::constraint_generator::TR().

core::scoring::func::FuncOP protocols::constraint_generator::HydrogenBondConstraintGenerator::atom_pair_func	(	HydrogenBondingAtom const &	a1,
		HydrogenBondingAtom const &	a2
	)		const

private

References atom_pair_func_, atom_pair_sd_, bounded_, and protocols::constraint_generator::HydrogenBondingAtom::distance().

Referenced by create_residue_constraint().

HydrogenBondingAtoms protocols::constraint_generator::HydrogenBondConstraintGenerator::choose_atoms	(	core::conformation::Residue const &	rsd,
		AtomNameSet const &	allowed_atoms
	)		const

private

References compute_valid_atoms(), core::conformation::Residue::has(), core::conformation::Residue::name(), core::conformation::Residue::name3(), core::conformation::Residue::seqpos(), and protocols::constraint_generator::TR().

Referenced by create_residue_constraint().

static std::string protocols::constraint_generator::HydrogenBondConstraintGenerator::class_name ( )

inlinestatic

Referenced by protocols::constraint_generator::HydrogenBondConstraintGeneratorCreator::keyname(), provide_citation_info(), and provide_xml_schema().

protocols::constraint_generator::ConstraintGeneratorOP protocols::constraint_generator::HydrogenBondConstraintGenerator::clone ( ) const

overridevirtual

Implements protocols::constraint_generator::ConstraintGenerator.

void protocols::constraint_generator::HydrogenBondConstraintGenerator::compute_valid_atoms	(	HydrogenBondingAtoms &	valid_atoms,
		core::conformation::Residue const &	rsd
	)		const

private

References core::chemical::ResidueType::all_sc_atoms(), core::chemical::ResidueType::atom_type(), protocols::constraint_generator::can_hydrogen_bond(), core::chemical::AtomType::element(), and core::conformation::Residue::type().

Referenced by choose_atoms().

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

References protocols::constraint_generator::ambiguous_constraint_wrap(), core::chemical::ResidueType::atom_index(), create_residue_constraint(), core::conformation::Residue::seqpos(), protocols::constraint_generator::TR(), and core::conformation::Residue::type().

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

References protocols::constraint_generator::ambiguous_constraint_wrap(), angle1_func(), angle2_func(), atom_pair_func(), dihedral_func(), protocols::constraint_generator::HydrogenBondingAtom::dihedrals(), and protocols::constraint_generator::TR().

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

called by parse_my_tag – should not be used directly

Implements protocols::constraint_generator::ConstraintGenerator.

References add_atom_definitions(), bounded_, core::select::residue_selector::get_residue_selector(), set_angle1_func(), set_angle2_func(), set_atom_pair_func(), set_atoms1(), set_atoms2(), set_bounded(), set_residue_selector1(), and set_residue_selector2().

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

References class_name(), and protocols::constraint_generator::ConstraintGeneratorFactory::xsd_constraint_generator_type_definition_w_attributes().

Referenced by protocols::constraint_generator::HydrogenBondConstraintGeneratorCreator::provide_xml_schema().

void protocols::constraint_generator::HydrogenBondConstraintGenerator::set_angle1_func ( std::string const & func_def )

References angle1_func_, and protocols::constraint_generator::create_func().

Referenced by parse_tag().

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 )

References angle2_func_, and protocols::constraint_generator::create_func().

Referenced by parse_tag().

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 )

References atom_pair_func_, and protocols::constraint_generator::create_func().

Referenced by parse_tag().

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

Referenced by angle1_func(), angle2_func(), dihedral_func(), and set_angle_sd().

core::scoring::func::FuncOP protocols::constraint_generator::HydrogenBondConstraintGenerator::atom_pair_func_

private

Referenced by atom_pair_func(), and set_atom_pair_func().

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

Referenced by create_residue_constraint(), and set_atoms1().

AtomNameSet protocols::constraint_generator::HydrogenBondConstraintGenerator::atoms2_

private

Referenced by create_residue_constraint(), and set_atoms2().

bool protocols::constraint_generator::HydrogenBondConstraintGenerator::bounded_

private

Referenced by angle1_func(), angle2_func(), atom_pair_func(), dihedral_func(), parse_tag(), and set_bounded().

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:

src/protocols/constraint_generator/HydrogenBondConstraintGenerator.hh
src/protocols/constraint_generator/HydrogenBondConstraintGenerator.cc

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_

Public Types

Public Member Functions

Static Public Member Functions

Private Member Functions

Private Attributes

Additional Inherited Members

Detailed Description

Member Typedef Documentation

Constructor & Destructor Documentation

Member Function Documentation

Member Data Documentation