#include <SheetConstraintGenerator.hh>

Inheritance diagram for protocols::fldsgn::SheetConstraintGenerator:

Public Types
typedef core::Size	Size

typedef core::Real	Real

typedef core::pose::Pose	Pose

typedef protocols::parser::BluePrintOP	BluePrintOP

Public Member Functions
	SheetConstraintGenerator ()

	~SheetConstraintGenerator () 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_secstruct (std::string const &ss)
	sets the secondary structure to be used for constraint generation More...

void	set_strand_pairs (std::string const &spairs)
	sets the strand pair string to be used for constraint generation (e.g. "2-3.P.1" ) means strands 2 and 3 are paired in a parallel orientation with register shift of 1 More...

void	set_use_dssp (bool const use_dssp)
	If true, and no secstruct is specified, DSSP will be used to determine the pose secondary structure. If false (and no secstruct is specified), the pose secondary structure will be directly used. More...

void	set_flat_bottom_constraints (bool const flat_csts)
	if set, a square-well, "flat bottom" function will be used for the constraints. Otherwise, harmonic constraints will be used. More...

void	set_weight (Real const coef)
	set the weight of the sheet constraints More...

void	set_distance (Real const dist)
	set the maximum Ca-Ca distance between paired residues More...

void	set_distance_tolerance (Real const dist_tol)
	sets the tolerance for the func to all atom pair constraints More...

void	set_angle_tolerance (Real const angle_tolerance)
	set the flat-bottom tolerance for the backbone angle between strands for each pair This is N1-C1-C2 and N2-C2-C1 for parallel sheets, and N1-C1-N2/N2-C2-N1 for antiparallel. More...

void	set_cacb_dihedral_tolerance (Real const dihedral_tolerance)
	set the flat-bottom tolerance for the Cb1-Ca1-Ca2-Cb2 dihedral angle (0 = optimal) More...

void	set_bb_dihedral_tolerance (Real const dihedral_tolerance)
	set the flat-bottom tolerance for the backbone dihedrals (0=optimal) Dihedral 1 = O1-N1-C1-C2, Dihedral 2 = O2-N2-C2-C1 More...

void	set_constrain_ca_ca_dist (bool const constrain_dist_only)
	sets whether we should constrain distance only, and not generate dihedral and angle constraints More...

void	set_constrain_bb_cacb_dihedral (bool const constrain_dihedral)
	sets whether we should constrain cb_ca_ca_cb dihedrals More...

void	set_constrain_bb_dihedral (bool const constrain_dihedral)
	sets whether we should constrain bb dihedrals More...

void	set_constrain_bb_angle (bool const constrain_angle)
	sets whether we should constrain bb angle More...

void	initialize_from_blueprint (std::string const &blueprint_file)
	initialize from a blueprint More...

void	initialize_from_blueprint (protocols::parser::BluePrintCOP bp)

ResiduePairs	compute_residue_pairs (topology::StrandPairings const &spairs) const
	computes and returns a vector of residues that are paired in the sheet More...

Public Member Functions inherited from protocols::constraint_generator::ConstraintGenerator
	ConstraintGenerator (std::string const &class_name)

	~ConstraintGenerator () override

virtual void	provide_citation_info (basic::citation_manager::CitationCollectionList &citations) const
	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	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)

static void	attributes_for_sheet_constraint_generator (utility::tag::AttributeList &)

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...

std::string	get_secstruct (core::pose::Pose const &pose) const
	returns secondary structure to be used in this constraint generator More...

utility::vector1< std::string >	get_abego (core::pose::Pose const &pose) const
	returns abego to be used in this constraint generator More...

std::string	get_strandpairings (core::pose::Pose const &pose) const
	return strand pairing string to be used in this constraint generator More...

Private Member Functions
core::scoring::func::FuncOP	weighted_func (core::scoring::func::FuncOP func) const

core::scoring::func::FuncOP	create_caca_atom_pair_func (core::Real const ideal_dist) const

core::scoring::func::FuncOP	create_bb_angle_func (core::Real const ideal_angle) const

core::scoring::func::FuncOP	create_bb_dihedral_func (core::Real const ideal_dihedral) const

core::scoring::func::FuncOP	create_cacb_dihedral_func (core::Real const ideal_dihedral) const

core::scoring::constraints::ConstraintOP	create_bb_dihedral_constraint (core::pose::Pose const &pose, core::Size const res1, core::Size const res2, core::scoring::func::FuncOP func1, core::scoring::func::FuncOP func2) const

core::scoring::constraints::ConstraintOP	create_ca_ca_atom_pair_constraint (core::id::AtomID const &atom1, core::id::AtomID const &atom2, core::scoring::func::FuncOP func) const

core::scoring::constraints::ConstraintOP	create_bb_angle_constraint (core::id::AtomID const &atom1, core::id::AtomID const &atom2, core::id::AtomID const &atom3, core::scoring::func::FuncOP func) const

core::scoring::constraints::ConstraintOP	create_bb_cacb_dihedral_constraint (core::id::AtomID const &atom1, core::id::AtomID const &atom2, core::id::AtomID const &atom3, core::id::AtomID const &atom4, core::scoring::func::FuncOP func) const

Private Attributes
Real	weight_

Real	dist_

Real	dist_tolerance_

Real	angle_tolerance_

Real	cacb_dihedral_tolerance_

Real	bb_dihedral_tolerance_

bool	constrain_ca_ca_dist_

bool	constrain_bb_cacb_dihedral_

bool	constrain_bb_dihedral_

bool	constrain_bb_angle_

bool	flat_bottom_constraints_

bool	use_dssp_

std::string	secstruct_

std::string	spairs_

std::string	sheet_name_

Member Typedef Documentation

typedef protocols::parser::BluePrintOP protocols::fldsgn::SheetConstraintGenerator::BluePrintOP

typedef core::pose::Pose protocols::fldsgn::SheetConstraintGenerator::Pose

typedef core::Real protocols::fldsgn::SheetConstraintGenerator::Real

typedef core::Size protocols::fldsgn::SheetConstraintGenerator::Size

Constructor & Destructor Documentation

protocols::fldsgn::SheetConstraintGenerator::SheetConstraintGenerator ( )

protocols::fldsgn::SheetConstraintGenerator::~SheetConstraintGenerator ( )

overridedefault

Member Function Documentation

core::scoring::constraints::ConstraintCOPs protocols::fldsgn::SheetConstraintGenerator::apply ( core::pose::Pose const & pose ) const

overridevirtual

generates constraints and adds them to the pose

Implements protocols::constraint_generator::ConstraintGenerator.

References core::scoring::abego, angle_tolerance_, core::chemical::ResidueType::atom_index(), bb_dihedral_tolerance_, cacb_dihedral_tolerance_, compute_residue_pairs(), constrain_bb_angle_, constrain_bb_cacb_dihedral_, constrain_bb_dihedral_, constrain_ca_ca_dist_, create_bb_angle_constraint(), create_bb_angle_func(), create_bb_cacb_dihedral_constraint(), create_bb_dihedral_constraint(), create_bb_dihedral_func(), create_ca_ca_atom_pair_constraint(), create_caca_atom_pair_func(), create_cacb_dihedral_func(), dist_, get_abego(), get_secstruct(), get_strandpairings(), core::chemical::ResidueType::has(), core::conformation::Residue::is_protein(), core::pose::Pose::residue(), core::pose::Pose::residue_type(), protocols::fldsgn::topology::StrandPairingSet::strand_pairings(), protocols::fldsgn::TR(), and weight_.

void protocols::fldsgn::SheetConstraintGenerator::attributes_for_sheet_constraint_generator ( utility::tag::AttributeList & attlist )

static

Referenced by protocols::fldsgn::SheetRemodelConstraintGenerator::provide_xml_schema(), and provide_xml_schema().

std::string protocols::fldsgn::SheetConstraintGenerator::class_name ( )

static

References protocols::fldsgn::SheetConstraintGeneratorCreator::constraint_generator_name().

Referenced by get_strandpairings(), and provide_xml_schema().

protocols::constraint_generator::ConstraintGeneratorOP protocols::fldsgn::SheetConstraintGenerator::clone ( ) const

overridevirtual

Implements protocols::constraint_generator::ConstraintGenerator.

ResiduePairs protocols::fldsgn::SheetConstraintGenerator::compute_residue_pairs ( topology::StrandPairings const & spairs ) const

computes and returns a vector of residues that are paired in the sheet

References protocols::fldsgn::TR().

Referenced by apply().

core::scoring::constraints::ConstraintOP protocols::fldsgn::SheetConstraintGenerator::create_bb_angle_constraint	(	core::id::AtomID const &	atom1,
		core::id::AtomID const &	atom2,
		core::id::AtomID const &	atom3,
		core::scoring::func::FuncOP	func
	)		const

private

Referenced by apply().

core::scoring::func::FuncOP protocols::fldsgn::SheetConstraintGenerator::create_bb_angle_func ( core::Real const ideal_angle ) const

private

References angle_tolerance_, flat_bottom_constraints_, and weighted_func().

Referenced by apply().

core::scoring::constraints::ConstraintOP protocols::fldsgn::SheetConstraintGenerator::create_bb_cacb_dihedral_constraint	(	core::id::AtomID const &	atom1,
		core::id::AtomID const &	atom2,
		core::id::AtomID const &	atom3,
		core::id::AtomID const &	atom4,
		core::scoring::func::FuncOP	func
	)		const

private

Referenced by apply().

core::scoring::constraints::ConstraintOP protocols::fldsgn::SheetConstraintGenerator::create_bb_dihedral_constraint	(	core::pose::Pose const &	pose,
		core::Size const	res1,
		core::Size const	res2,
		core::scoring::func::FuncOP	func1,
		core::scoring::func::FuncOP	func2
	)		const

private

References core::chemical::ResidueType::atom_index(), and core::pose::Pose::residue_type().

Referenced by apply().

core::scoring::func::FuncOP protocols::fldsgn::SheetConstraintGenerator::create_bb_dihedral_func ( core::Real const ideal_dihedral ) const

private

References bb_dihedral_tolerance_, flat_bottom_constraints_, and weighted_func().

Referenced by apply().

core::scoring::constraints::ConstraintOP protocols::fldsgn::SheetConstraintGenerator::create_ca_ca_atom_pair_constraint	(	core::id::AtomID const &	atom1,
		core::id::AtomID const &	atom2,
		core::scoring::func::FuncOP	func
	)		const

private

Referenced by apply().

core::scoring::func::FuncOP protocols::fldsgn::SheetConstraintGenerator::create_caca_atom_pair_func ( core::Real const ideal_dist ) const

private

References dist_tolerance_, flat_bottom_constraints_, and weighted_func().

Referenced by apply().

core::scoring::func::FuncOP protocols::fldsgn::SheetConstraintGenerator::create_cacb_dihedral_func ( core::Real const ideal_dihedral ) const

private

References cacb_dihedral_tolerance_, flat_bottom_constraints_, and weighted_func().

Referenced by apply().

utility::vector1< std::string > protocols::fldsgn::SheetConstraintGenerator::get_abego ( core::pose::Pose const & pose ) const

protected

returns abego to be used in this constraint generator

Parameters

[in] pose Input pose

Returns

ABEGO string of the pose according to the following rules:

StructureData abego if use_dssp_ is false AND StructureData is present
Computed abego of the input pose otherwise

References protocols::denovo_design::abego_str(), protocols::denovo_design::abego_vector(), core::sequence::get_abego(), protocols::denovo_design::components::StructureDataFactory::has_cached_data(), and use_dssp_.

Referenced by apply().

std::string protocols::fldsgn::SheetConstraintGenerator::get_secstruct ( core::pose::Pose const & pose ) const

protected

returns secondary structure to be used in this constraint generator

Parameters

[in] pose Input pose

Returns

Secondary stucture of the pose according to the following rules:

secstruct_ if it is non-empty
DSSP secondary structure of the input pose if use_dssp_ is true
Pose secondary structure if use_dssp_ is false

References protocols::simple_filters::dssp(), core::scoring::dssp::Dssp::get_dssp_secstruct(), core::pose::Pose::secstruct(), secstruct_, and use_dssp_.

Referenced by apply().

std::string protocols::fldsgn::SheetConstraintGenerator::get_strandpairings ( core::pose::Pose const & pose ) const

protected

return strand pairing string to be used in this constraint generator

Parameters

[in] pose Input pose

Returns

Strand pairing string for desired strand pairings, according to the following rules:

spairs_ if it is non-empty
Gets pairing string from StructureData if it is present
Throw error

References class_name(), and spairs_.

Referenced by apply().

void protocols::fldsgn::SheetConstraintGenerator::initialize_from_blueprint ( std::string const & blueprint_file )

initialize from a blueprint

sets the blueprint file used for determining proper sheet pairing This function will create the blueprint object for you from the file and use it

References protocols::fldsgn::TR().

Referenced by parse_tag().

void protocols::fldsgn::SheetConstraintGenerator::initialize_from_blueprint ( protocols::parser::BluePrintCOP bp )

References set_secstruct(), and set_strand_pairs().

void protocols::fldsgn::SheetConstraintGenerator::parse_tag	(	utility::tag::TagCOP	tag,
		basic::datacache::DataMap &	data
	)

overrideprotectedvirtual

void protocols::fldsgn::SheetConstraintGenerator::provide_xml_schema ( utility::tag::XMLSchemaDefinition & xsd )

static

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

Referenced by protocols::fldsgn::SheetConstraintGeneratorCreator::provide_xml_schema().

void protocols::fldsgn::SheetConstraintGenerator::set_angle_tolerance ( Real const angle_tolerance )

set the flat-bottom tolerance for the backbone angle between strands for each pair This is N1-C1-C2 and N2-C2-C1 for parallel sheets, and N1-C1-N2/N2-C2-N1 for antiparallel.

References angle_tolerance_.

Referenced by parse_tag().

void protocols::fldsgn::SheetConstraintGenerator::set_bb_dihedral_tolerance ( Real const dihedral_tolerance )

set the flat-bottom tolerance for the backbone dihedrals (0=optimal) Dihedral 1 = O1-N1-C1-C2, Dihedral 2 = O2-N2-C2-C1

References bb_dihedral_tolerance_.

Referenced by parse_tag().

void protocols::fldsgn::SheetConstraintGenerator::set_cacb_dihedral_tolerance ( Real const dihedral_tolerance )

set the flat-bottom tolerance for the Cb1-Ca1-Ca2-Cb2 dihedral angle (0 = optimal)

References cacb_dihedral_tolerance_.

Referenced by parse_tag().

void protocols::fldsgn::SheetConstraintGenerator::set_constrain_bb_angle ( bool const constrain_angle )

sets whether we should constrain bb angle

References constrain_bb_angle_.

Referenced by parse_tag().

void protocols::fldsgn::SheetConstraintGenerator::set_constrain_bb_cacb_dihedral ( bool const constrain_dihedral )

sets whether we should constrain cb_ca_ca_cb dihedrals

References constrain_bb_cacb_dihedral_.

Referenced by parse_tag().

void protocols::fldsgn::SheetConstraintGenerator::set_constrain_bb_dihedral ( bool const constrain_dihedral )

sets whether we should constrain bb dihedrals

References constrain_bb_dihedral_.

Referenced by parse_tag().

void protocols::fldsgn::SheetConstraintGenerator::set_constrain_ca_ca_dist ( bool const constrain_dist_only )

sets whether we should constrain distance only, and not generate dihedral and angle constraints

References constrain_ca_ca_dist_.

Referenced by parse_tag().

void protocols::fldsgn::SheetConstraintGenerator::set_distance ( Real const dist )

set the maximum Ca-Ca distance between paired residues

set distance of constraint

References dist_.

Referenced by parse_tag().

void protocols::fldsgn::SheetConstraintGenerator::set_distance_tolerance ( Real const dist_tol )

sets the tolerance for the func to all atom pair constraints

References dist_tolerance_.

Referenced by parse_tag().

void protocols::fldsgn::SheetConstraintGenerator::set_flat_bottom_constraints ( bool const flat_csts )

if set, a square-well, "flat bottom" function will be used for the constraints. Otherwise, harmonic constraints will be used.

References flat_bottom_constraints_.

Referenced by parse_tag().

void protocols::fldsgn::SheetConstraintGenerator::set_secstruct ( std::string const & ss )

sets the secondary structure to be used for constraint generation

References secstruct_.

Referenced by initialize_from_blueprint(), and parse_tag().

void protocols::fldsgn::SheetConstraintGenerator::set_strand_pairs ( std::string const & spairs )

sets the strand pair string to be used for constraint generation (e.g. "2-3.P.1" ) means strands 2 and 3 are paired in a parallel orientation with register shift of 1

References spairs_.

Referenced by initialize_from_blueprint(), and parse_tag().

void protocols::fldsgn::SheetConstraintGenerator::set_use_dssp ( bool const use_dssp )

If true, and no secstruct is specified, DSSP will be used to determine the pose secondary structure. If false (and no secstruct is specified), the pose secondary structure will be directly used.

Parameters

[in] use_dssp Desired value

References use_dssp_.

Referenced by parse_tag().

void protocols::fldsgn::SheetConstraintGenerator::set_weight ( Real const coef )

set the weight of the sheet constraints

set weight

References weight_.

Referenced by parse_tag().

core::scoring::func::FuncOP protocols::fldsgn::SheetConstraintGenerator::weighted_func ( core::scoring::func::FuncOP func ) const

private

References protocols::constraint_generator::scalar_weighted(), and weight_.