#include <GeneralizedKICfilter.hh>

Inheritance diagram for protocols::generalized_kinematic_closure::filter::GeneralizedKICfilter:

Public Member Functions
	GeneralizedKICfilter ()
	Constructor for GeneralizedKICfilter. More...

	GeneralizedKICfilter (GeneralizedKICfilter const &src)
	Copy constructor for GeneralizedKICfilter. More...

	~GeneralizedKICfilter () override
	Destructor for GeneralizedKICfilter mover. More...

GeneralizedKICfilterOP	clone () const
	Clone operator to create a pointer to a fresh GeneralizedKICfilter object that copies this one. More...

std::string	get_name () const
	Returns the name of this class. More...

std::string	get_filter_type_name (core::Size const filter_type) const
	Given a filter type, return its name. Returns "unknown_filter" if not recognized. More...

filter_type	get_filter_type_by_name (std::string const &filtername) const
	Given the name of a filter type, return the filter type enum. Returns unknown_filter if not recognized. More...

void	set_filter_type (filter_type const &ftype)
	Sets the filter type for this filter. More...

void	set_filter_type (std::string const &ftypename)
	Sets the filter type for this filter by name. More...

std::string	get_this_filter_type_name () const
	Gets the filter type name for THIS filter. More...

void	add_filter_param (std::string const &param_name, core::Real const &value)
	Add a real-valued filter parameter. More...

void	add_filter_param (std::string const &param_name, core::Size const value)
	Add a integer-valued filter parameter. More...

void	add_filter_param (std::string const &param_name, bool const value)
	Add a Boolean-valued filter parameter. More...

void	add_filter_param (std::string const &param_name, std::string const &value)
	Add a string-valued filter parameter. More...

bool	get_filter_param (std::string const &param_name, core::Real &outvalue) const
	Get a real-valued filter parameter. More...

bool	get_filter_param (std::string const &param_name, core::Size &outvalue) const
	Get a integer-valued filter parameter. More...

bool	get_filter_param (std::string const &param_name, bool &outvalue) const
	Get a Boolean-valued filter parameter. More...

bool	get_filter_param (std::string const &param_name, std::string &outvalue) const
	Get a string-valued filter parameter. More...

void	set_resnum (core::Size const val)
	Set the residue number that this filter acts on. More...

core::Size	resnum () const
	Get the residue number that this filter acts on. More...

void	set_binname (std::string const &name_in)
	Set the bin name for this filter. More...

void	set_rama_cutoff_energy (core::Real const &val)
	Set the alpha_aa_rama_check or rama_prepro_check filter's rama term cutoff energy. More...

core::Real	rama_cutoff_energy () const
	Get the alpha_aa_rama_check or rama_prepro_check filter's rama term cutoff energy. More...

std::string	binname () const
	Get the bin name for this filter. More...

void	load_bin_params (std::string const &bin_params_file)
	Initializes the BinTransitionCalculator object and loads a bin_params file. More...

bool	apply (core::pose::Pose const &original_pose, core::pose::Pose const &loop_pose, utility::vector1< std::pair< core::Size, core::Size > > const &residue_map, utility::vector1< std::pair< core::Size, core::Size > > const &tail_residue_map, utility::vector1< std::pair< core::id::AtomID, numeric::xyzVector< core::Real > > > const &atomlist, utility::vector1< core::Real > const &torsions, utility::vector1< core::Real > const &bondangles, utility::vector1< core::Real > const &bondlengths) const
	Apply this filter to ONE of the kinematic closure solutions produced by the bridgeObjects function, and return pass or fail. More...

void	set_attach_boinc_ghost_observer (bool const setting)
	Sets whether we are attaching a BOINC "ghost" pose observer. More...

bool	attach_boinc_ghost_observer () const
	Gets whether we are attaching a BOINC "ghost" pose observer. More...

Static Public Member Functions
static void	define_valid_filter_name_enumeration (utility::tag::XMLSchemaDefinition &xsd)

Private Member Functions
core::Size	get_loop_index (core::Size const original_pose_index, utility::vector1< std::pair< core::Size, core::Size > > const &residue_map) const
	Given an index in the original pose and a mapping from loop to pose, return the index in the loop. More...

bool	apply_loop_bump_check (core::pose::Pose const &original_pose, core::pose::Pose const &loop_pose, utility::vector1< std::pair< core::Size, core::Size > > const &residue_map, utility::vector1< std::pair< core::Size, core::Size > > const &tail_residue_map, utility::vector1< std::pair< core::id::AtomID, numeric::xyzVector< core::Real > > > const &atomlist, utility::vector1< core::Real > const &torsions, utility::vector1< core::Real > const &bondangles, utility::vector1< core::Real > const &bondlengths) const
	Applies the loop_bump_check filter, which checks for clashes between the atoms in the chain to be closed and the rest of the structure (or for clashes within these atoms). More...

bool	apply_atom_pair_distance (core::pose::Pose const &original_pose, core::pose::Pose const &loop_pose, utility::vector1< std::pair< core::Size, core::Size > > const &residue_map, utility::vector1< std::pair< core::Size, core::Size > > const &tail_residue_map, utility::vector1< std::pair< core::id::AtomID, numeric::xyzVector< core::Real > > > const &atomlist, utility::vector1< core::Real > const &torsions, utility::vector1< core::Real > const &bondangles, utility::vector1< core::Real > const &bondlengths) const
	Applies the atom_pair_distance filter, checking that the distance between two atoms is less than a given threshold (or greater than a given threshold if the user so specifies with the "greater_than" option). More...

bool	apply_backbone_bin (core::pose::Pose const &original_pose, core::pose::Pose const &loop_pose, utility::vector1< std::pair< core::Size, core::Size > > const &residue_map, utility::vector1< std::pair< core::Size, core::Size > > const &tail_residue_map, utility::vector1< std::pair< core::id::AtomID, numeric::xyzVector< core::Real > > > const &atomlist, utility::vector1< core::Real > const &torsions, utility::vector1< core::Real > const &bondangles, utility::vector1< core::Real > const &bondlengths) const
	Applies the backbone_bin filter, checking that a given residue lies within a defined mainchain torsion bin and failing if it does not. More...

bool	apply_alpha_aa_rama_check (core::pose::Pose const &original_pose, core::pose::Pose const &loop_pose, utility::vector1< std::pair< core::Size, core::Size > > const &residue_map, utility::vector1< std::pair< core::Size, core::Size > > const &tail_residue_map, utility::vector1< std::pair< core::id::AtomID, numeric::xyzVector< core::Real > > > const &atomlist, utility::vector1< core::Real > const &torsions, utility::vector1< core::Real > const &bondangles, utility::vector1< core::Real > const &bondlengths) const
	Calculates Ramachandran energy for an alpha-amino acid based on its phi/psi values. More...

bool	apply_rama_prepro_check (core::pose::Pose const &original_pose, core::pose::Pose const &loop_pose, utility::vector1< std::pair< core::Size, core::Size > > const &residue_map, utility::vector1< std::pair< core::Size, core::Size > > const &tail_residue_map, utility::vector1< std::pair< core::id::AtomID, numeric::xyzVector< core::Real > > > const &atomlist, utility::vector1< core::Real > const &torsions, utility::vector1< core::Real > const &bondangles, utility::vector1< core::Real > const &bondlengths) const
	Calculates RamaPrePro energy for a residue based on its mainchain torsion values. More...

Private Attributes
filter_type	filtertype_
	The filter type for this filter (see the filter_type enum for all types). More...

utility::vector1< std::pair< std::string, core::Real > >	filter_params_real_
	Real-valued filter parameters. More...

utility::vector1< std::pair< std::string, core::Size > >	filter_params_size_
	Integer-valued filter parameters. More...

utility::vector1< std::pair< std::string, bool > >	filter_params_bool_
	Boolean-valued filter parameters. More...

utility::vector1< std::pair< std::string, std::string > >	filter_params_string_
	String-valued filter parameters. More...

core::scoring::bin_transitions::BinTransitionCalculatorCOP	bin_transition_calculator_
	A BinTransitionCalculatorOP. This will be null by default, and will only point to a BinTransitionCalculator object in the case of those filters that use torsion bin transition probabilities. More...

std::string	bin_
	A parameter specifically for the backbone_bin filter. The bin that the residue must lie within. More...

core::Size	resnum_
	A parameter specifically for the backbone_bin filter. The residue that must lie within the mainchain torsion bin specified. More...

core::Real	rama_threshold_
	A parameter specifically for the alpha_aa_rama_check and rama_prepro_check filters. Rama energy above which the solution is rejected. Set to 0.3 by default. More...

bool	attach_boinc_ghost_observer_
	Should poses generated by this filter during processing be used for the BOINC "ghost" display? More...

Constructor & Destructor Documentation

◆ GeneralizedKICfilter() [1/2]

protocols::generalized_kinematic_closure::filter::GeneralizedKICfilter::GeneralizedKICfilter ( )

Constructor for GeneralizedKICfilter.

◆ GeneralizedKICfilter() [2/2]

protocols::generalized_kinematic_closure::filter::GeneralizedKICfilter::GeneralizedKICfilter ( GeneralizedKICfilter const & src )

Copy constructor for GeneralizedKICfilter.

References bin_transition_calculator_.

◆ ~GeneralizedKICfilter()

protocols::generalized_kinematic_closure::filter::GeneralizedKICfilter::~GeneralizedKICfilter ( )

overridedefault

Destructor for GeneralizedKICfilter mover.

Member Function Documentation

◆ add_filter_param() [1/4]

void protocols::generalized_kinematic_closure::filter::GeneralizedKICfilter::add_filter_param	(	std::string const &	param_name,
		bool const	value
	)

Add a Boolean-valued filter parameter.

References filter_params_bool_.

◆ add_filter_param() [2/4]

void protocols::generalized_kinematic_closure::filter::GeneralizedKICfilter::add_filter_param	(	std::string const &	param_name,
		core::Real const &	value
	)

Add a real-valued filter parameter.

References filter_params_real_.

◆ add_filter_param() [3/4]

void protocols::generalized_kinematic_closure::filter::GeneralizedKICfilter::add_filter_param	(	std::string const &	param_name,
		core::Size const	value
	)

Add a integer-valued filter parameter.

References filter_params_size_.

◆ add_filter_param() [4/4]

void protocols::generalized_kinematic_closure::filter::GeneralizedKICfilter::add_filter_param	(	std::string const &	param_name,
		std::string const &	value
	)

Add a string-valued filter parameter.

References filter_params_string_.

◆ apply()

bool protocols::generalized_kinematic_closure::filter::GeneralizedKICfilter::apply	(	core::pose::Pose const &	original_pose,
		core::pose::Pose const &	loop_pose,
		utility::vector1< std::pair< core::Size, core::Size > > const &	residue_map,
		utility::vector1< std::pair< core::Size, core::Size > > const &	tail_residue_map,
		utility::vector1< std::pair< core::id::AtomID, numeric::xyzVector< core::Real > > > const &	atomlist,
		utility::vector1< core::Real > const &	torsions,
		utility::vector1< core::Real > const &	bondangles,
		utility::vector1< core::Real > const &	bondlengths
	)		const

Apply this filter to ONE of the kinematic closure solutions produced by the bridgeObjects function, and return pass or fail.

Parameters

[in]	original_pose	– The full, initial pose.
[in]	loop_pose	– A pose consisting of just the loop to be closed.
[in]	residue_map	– The mapping of (residue index in loop_pose, residue index in original_pose).
[in]	tail_residue_map	– The mapping of (tail residue index in loop_pose, tail residue index in original_pose).
[in]	atomlist	– A list of atoms making the chain that was closed by bridgeObjects, with residue indices corresponding to loop_pose.
[in]	torsions	– A vector of dihedral angles that the bridgeObjects function spat out.
[in]	bondangles	– A vector of bond angles that the bridgeObjects function spat out.
[in]	bondlengths	– A vector of bond lengths that the bridgeObjects function spat out.

References protocols::generalized_kinematic_closure::filter::alpha_aa_rama_check, apply_alpha_aa_rama_check(), apply_atom_pair_distance(), apply_backbone_bin(), apply_loop_bump_check(), apply_rama_prepro_check(), protocols::generalized_kinematic_closure::filter::atom_pair_distance, protocols::generalized_kinematic_closure::filter::backbone_bin, filtertype_, protocols::generalized_kinematic_closure::filter::loop_bump_check, and protocols::generalized_kinematic_closure::filter::rama_prepro_check.

◆ apply_alpha_aa_rama_check()

bool protocols::generalized_kinematic_closure::filter::GeneralizedKICfilter::apply_alpha_aa_rama_check	(	core::pose::Pose const &	original_pose,
		core::pose::Pose const &	loop_pose,
		utility::vector1< std::pair< core::Size, core::Size > > const &	residue_map,
		utility::vector1< std::pair< core::Size, core::Size > > const &	tail_residue_map,
		utility::vector1< std::pair< core::id::AtomID, numeric::xyzVector< core::Real > > > const &	atomlist,
		utility::vector1< core::Real > const &	torsions,
		utility::vector1< core::Real > const &	bondangles,
		utility::vector1< core::Real > const &	bondlengths
	)		const

private

Calculates Ramachandran energy for an alpha-amino acid based on its phi/psi values.

Returns "true" for pass (below threshold) and "false" for fail.

Parameters

[in]	original_pose	– The full, initial pose.
[in]	loop_pose	– A pose consisting of just the loop to be closed.
[in]	residue_map	– The mapping of (residue index in loop_pose, residue index in original_pose).
[in]	tail_residue_map	– The mapping of (tail residue index in loop_pose, tail residue index in original_pose).
[in]	atomlist	– A list of atoms making the chain that was closed by bridgeObjects, with residue indices corresponding to loop_pose.
[in]	torsions	– A vector of dihedral angles that the bridgeObjects function spat out.
[in]	bondangles	– A vector of bond angles that the bridgeObjects function spat out.
[in]	bondlengths	– A vector of bond lengths that the bridgeObjects function spat out.

References attach_boinc_ghost_observer(), get_loop_index(), core::conformation::Residue::name3(), protocols::generalized_kinematic_closure::original_pose_residue_is_in_residue_map(), core::scoring::rama, rama_cutoff_energy(), core::pose::Pose::residue(), resnum(), protocols::generalized_kinematic_closure::set_loop_pose(), core::pose::Pose::size(), and protocols::generalized_kinematic_closure::filter::TR().

Referenced by apply().

◆ apply_atom_pair_distance()

bool protocols::generalized_kinematic_closure::filter::GeneralizedKICfilter::apply_atom_pair_distance	(	core::pose::Pose const &	original_pose,
		core::pose::Pose const &	loop_pose,
		utility::vector1< std::pair< core::Size, core::Size > > const &	residue_map,
		utility::vector1< std::pair< core::Size, core::Size > > const &	tail_residue_map,
		utility::vector1< std::pair< core::id::AtomID, numeric::xyzVector< core::Real > > > const &	atomlist,
		utility::vector1< core::Real > const &	torsions,
		utility::vector1< core::Real > const &	bondangles,
		utility::vector1< core::Real > const &	bondlengths
	)		const

private

Applies the atom_pair_distance filter, checking that the distance between two atoms is less than a given threshold (or greater than a given threshold if the user so specifies with the "greater_than" option).

Returns "true" for pass and "false" for fail. The user can set the following options: "distance" (real-valued, mandatory) "atom1" (string-valued, mandatory) "atom2" (string-valued, mandatory) "res1" (integer-valued, mandatory, based on original pose numbering) "res2" (integer-valued, mandatory, based on original pose numbering) "greater_than" (boolean, optional, false by default)

Parameters

[in]	original_pose	– The full, initial pose.
[in]	loop_pose	– A pose consisting of just the loop to be closed.
[in]	residue_map	– The mapping of (residue index in loop_pose, residue index in original_pose).
[in]	tail_residue_map	– The mapping of (tail residue index in loop_pose, tail residue index in original_pose).
[in]	atomlist	– A list of atoms making the chain that was closed by bridgeObjects, with residue indices corresponding to loop_pose.
[in]	torsions	– A vector of dihedral angles that the bridgeObjects function spat out.
[in]	bondangles	– A vector of bond angles that the bridgeObjects function spat out.
[in]	bondlengths	– A vector of bond lengths that the bridgeObjects function spat out.

References attach_boinc_ghost_observer(), protocols::generalized_kinematic_closure::copy_loop_pose_to_original(), get_filter_param(), core::conformation::Residue::has(), protocols::generalized_kinematic_closure::original_pose_residue_is_in_residue_map(), core::pose::Pose::residue(), protocols::generalized_kinematic_closure::set_loop_pose(), protocols::generalized_kinematic_closure::filter::TR(), and core::conformation::Residue::xyz().

Referenced by apply().

◆ apply_backbone_bin()

bool protocols::generalized_kinematic_closure::filter::GeneralizedKICfilter::apply_backbone_bin	(	core::pose::Pose const &	original_pose,
		core::pose::Pose const &	loop_pose,
		utility::vector1< std::pair< core::Size, core::Size > > const &	residue_map,
		utility::vector1< std::pair< core::Size, core::Size > > const &	tail_residue_map,
		utility::vector1< std::pair< core::id::AtomID, numeric::xyzVector< core::Real > > > const &	atomlist,
		utility::vector1< core::Real > const &	torsions,
		utility::vector1< core::Real > const &	bondangles,
		utility::vector1< core::Real > const &	bondlengths
	)		const

private

Applies the backbone_bin filter, checking that a given residue lies within a defined mainchain torsion bin and failing if it does not.

Returns "true" for pass and "false" for fail. The user needs to have set a bin transition probabilities file, a bin, and a residue.

Parameters

[in]	original_pose	– The full, initial pose.
[in]	loop_pose	– A pose consisting of just the loop to be closed.
[in]	residue_map	– The mapping of (residue index in loop_pose, residue index in original_pose).
[in]	tail_residue_map	– The mapping of (tail residue index in loop_pose, tail residue index in original_pose).
[in]	atomlist	– A list of atoms making the chain that was closed by bridgeObjects, with residue indices corresponding to loop_pose.
[in]	torsions	– A vector of dihedral angles that the bridgeObjects function spat out.
[in]	bondangles	– A vector of bond angles that the bridgeObjects function spat out.
[in]	bondlengths	– A vector of bond lengths that the bridgeObjects function spat out.

References attach_boinc_ghost_observer(), bin_, bin_transition_calculator_, get_loop_index(), core::conformation::Residue::mainchain_torsion(), core::conformation::Residue::mainchain_torsions(), protocols::generalized_kinematic_closure::original_pose_residue_is_in_residue_map(), core::pose::Pose::residue(), resnum(), protocols::generalized_kinematic_closure::set_loop_pose(), core::pose::Pose::size(), and protocols::generalized_kinematic_closure::filter::TR().

Referenced by apply().

◆ apply_loop_bump_check()

bool protocols::generalized_kinematic_closure::filter::GeneralizedKICfilter::apply_loop_bump_check	(	core::pose::Pose const &	original_pose,
		core::pose::Pose const &	loop_pose,
		utility::vector1< std::pair< core::Size, core::Size > > const &	residue_map,
		utility::vector1< std::pair< core::Size, core::Size > > const &	tail_residue_map,
		utility::vector1< std::pair< core::id::AtomID, numeric::xyzVector< core::Real > > > const &	atomlist,
		utility::vector1< core::Real > const &	torsions,
		utility::vector1< core::Real > const &	bondangles,
		utility::vector1< core::Real > const &	bondlengths
	)		const

private

Applies the loop_bump_check filter, which checks for clashes between the atoms in the chain to be closed and the rest of the structure (or for clashes within these atoms).

Returns "true" for pass and "false" for fail. Does NOT check for clashes with tail residues.

Parameters

[in]	original_pose	– The full, initial pose.
[in]	loop_pose	– A pose consisting of just the loop to be closed.
[in]	residue_map	– The mapping of (residue index in loop_pose, residue index in original_pose).
[in]	tail_residue_map	– The mapping of (tail residue index in loop_pose, tail residue index in original_pose).
[in]	atomlist	– A list of atoms making the chain that was closed by bridgeObjects, with residue indices corresponding to loop_pose.
[in]	torsions	– A vector of dihedral angles that the bridgeObjects function spat out.
[in]	bondangles	– A vector of bond angles that the bridgeObjects function spat out.
[in]	bondlengths	– A vector of bond lengths that the bridgeObjects function spat out.

References core::conformation::Residue::atom_index(), core::conformation::Residue::atom_name(), core::chemical::ResidueType::atom_type(), attach_boinc_ghost_observer(), core::conformation::Residue::connected_residue_at_resconn(), protocols::generalized_kinematic_closure::get_original_pose_rsd(), core::conformation::Residue::has(), core::chemical::ResidueType::is_alpha_aa(), core::chemical::ResidueType::is_beta_aa(), core::chemical::ResidueType::is_oligourea(), core::chemical::ResidueTypeBase::is_peptoid(), core::chemical::AtomType::lj_radius(), core::conformation::Residue::mainchain_atoms(), core::conformation::Residue::n_possible_residue_connections(), protocols::generalized_kinematic_closure::original_pose_residue_is_in_residue_map(), core::scoring::pair, core::pose::Pose::residue(), core::pose::Pose::residue_type(), protocols::generalized_kinematic_closure::set_loop_pose(), core::pose::Pose::size(), protocols::generalized_kinematic_closure::filter::TR(), core::conformation::Residue::type(), and core::conformation::Residue::xyz().

Referenced by apply().

◆ apply_rama_prepro_check()

bool protocols::generalized_kinematic_closure::filter::GeneralizedKICfilter::apply_rama_prepro_check	(	core::pose::Pose const &	original_pose,
		core::pose::Pose const &	loop_pose,
		utility::vector1< std::pair< core::Size, core::Size > > const &	residue_map,
		utility::vector1< std::pair< core::Size, core::Size > > const &	tail_residue_map,
		utility::vector1< std::pair< core::id::AtomID, numeric::xyzVector< core::Real > > > const &	atomlist,
		utility::vector1< core::Real > const &	torsions,
		utility::vector1< core::Real > const &	bondangles,
		utility::vector1< core::Real > const &	bondlengths
	)		const

private

Calculates RamaPrePro energy for a residue based on its mainchain torsion values.

Returns "true" for pass (below threshold) and "false" for fail.

Parameters

[in]	original_pose	– The full, initial pose.
[in]	loop_pose	– A pose consisting of just the loop to be closed.
[in]	residue_map	– The mapping of (residue index in loop_pose, residue index in original_pose).
[in]	tail_residue_map	– The mapping of (tail residue index in loop_pose, tail residue index in original_pose).
[in]	atomlist	– A list of atoms making the chain that was closed by bridgeObjects, with residue indices corresponding to loop_pose.
[in]	torsions	– A vector of dihedral angles that the bridgeObjects function spat out.
[in]	bondangles	– A vector of bond angles that the bridgeObjects function spat out.
[in]	bondlengths	– A vector of bond lengths that the bridgeObjects function spat out.

References attach_boinc_ghost_observer(), core::pose::Pose::conformation(), get_loop_index(), core::conformation::Residue::has_upper_connect(), core::chemical::ResidueConnection::index(), core::conformation::Residue::mainchain_torsions(), core::conformation::Residue::name3(), protocols::generalized_kinematic_closure::original_pose_residue_is_in_residue_map(), core::scoring::rama, rama_cutoff_energy(), core::pose::Pose::residue(), core::conformation::Residue::residue_connection_partner(), core::pose::Pose::residue_type_ptr(), resnum(), protocols::generalized_kinematic_closure::set_loop_pose(), core::pose::Pose::size(), protocols::generalized_kinematic_closure::filter::TR(), core::conformation::Residue::type_ptr(), and core::conformation::Residue::upper_connect().

Referenced by apply().

◆ attach_boinc_ghost_observer()

bool protocols::generalized_kinematic_closure::filter::GeneralizedKICfilter::attach_boinc_ghost_observer ( ) const

inline

Gets whether we are attaching a BOINC "ghost" pose observer.

Only does anything in the BOINC graphics build.

References attach_boinc_ghost_observer_.

Referenced by apply_alpha_aa_rama_check(), apply_atom_pair_distance(), apply_backbone_bin(), apply_loop_bump_check(), and apply_rama_prepro_check().

◆ binname()

std::string protocols::generalized_kinematic_closure::filter::GeneralizedKICfilter::binname ( ) const

inline

Get the bin name for this filter.

Only used by some filters.

References bin_.

◆ clone()

GeneralizedKICfilterOP protocols::generalized_kinematic_closure::filter::GeneralizedKICfilter::clone ( ) const

Clone operator to create a pointer to a fresh GeneralizedKICfilter object that copies this one.

◆ define_valid_filter_name_enumeration()

void protocols::generalized_kinematic_closure::filter::GeneralizedKICfilter::define_valid_filter_name_enumeration ( utility::tag::XMLSchemaDefinition & xsd )

static

Referenced by protocols::generalized_kinematic_closure::GeneralizedKIC::provide_xml_schema().

◆ get_filter_param() [1/4]

bool protocols::generalized_kinematic_closure::filter::GeneralizedKICfilter::get_filter_param	(	std::string const &	param_name,
		bool &	outvalue
	)		const

Get a Boolean-valued filter parameter.

Returns false if the parameter couldn't be found.

References filter_params_bool_.

◆ get_filter_param() [2/4]

bool protocols::generalized_kinematic_closure::filter::GeneralizedKICfilter::get_filter_param	(	std::string const &	param_name,
		core::Real &	outvalue
	)		const

Get a real-valued filter parameter.

Returns false if the parameter couldn't be found.

References filter_params_real_.

Referenced by apply_atom_pair_distance().

◆ get_filter_param() [3/4]

bool protocols::generalized_kinematic_closure::filter::GeneralizedKICfilter::get_filter_param	(	std::string const &	param_name,
		core::Size &	outvalue
	)		const

Get a integer-valued filter parameter.

Returns false if the parameter couldn't be found.

References filter_params_size_.

◆ get_filter_param() [4/4]

bool protocols::generalized_kinematic_closure::filter::GeneralizedKICfilter::get_filter_param	(	std::string const &	param_name,
		std::string &	outvalue
	)		const

Get a string-valued filter parameter.

Returns false if the parameter couldn't be found.

References filter_params_string_.

◆ get_filter_type_by_name()

filter_type protocols::generalized_kinematic_closure::filter::GeneralizedKICfilter::get_filter_type_by_name ( std::string const & filtername ) const

Given the name of a filter type, return the filter type enum. Returns unknown_filter if not recognized.

References protocols::generalized_kinematic_closure::filter::end_of_filter_list, get_filter_type_name(), and protocols::generalized_kinematic_closure::filter::unknown_filter.

Referenced by set_filter_type().

◆ get_filter_type_name()

std::string protocols::generalized_kinematic_closure::filter::GeneralizedKICfilter::get_filter_type_name ( core::Size const filter_type ) const

Given a filter type, return its name. Returns "unknown_filter" if not recognized.

References protocols::generalized_kinematic_closure::filter::alpha_aa_rama_check, protocols::generalized_kinematic_closure::filter::atom_pair_distance, protocols::generalized_kinematic_closure::filter::backbone_bin, protocols::generalized_kinematic_closure::filter::loop_bump_check, protocols::generalized_kinematic_closure::filter::no_filter, and protocols::generalized_kinematic_closure::filter::rama_prepro_check.

Referenced by get_filter_type_by_name(), and get_this_filter_type_name().

◆ get_loop_index()

core::Size protocols::generalized_kinematic_closure::filter::GeneralizedKICfilter::get_loop_index	(	core::Size const	original_pose_index,
		utility::vector1< std::pair< core::Size, core::Size > > const &	residue_map
	)		const

private

Given an index in the original pose and a mapping from loop to pose, return the index in the loop.

Referenced by apply_alpha_aa_rama_check(), apply_backbone_bin(), and apply_rama_prepro_check().

◆ get_name()

std::string protocols::generalized_kinematic_closure::filter::GeneralizedKICfilter::get_name ( ) const

Returns the name of this class.

Returns the name of this class ("GeneralizedKICfilter").

◆ get_this_filter_type_name()

std::string protocols::generalized_kinematic_closure::filter::GeneralizedKICfilter::get_this_filter_type_name ( ) const

Gets the filter type name for THIS filter.

References filtertype_, and get_filter_type_name().

◆ load_bin_params()

void protocols::generalized_kinematic_closure::filter::GeneralizedKICfilter::load_bin_params ( std::string const & bin_params_file )

Initializes the BinTransitionCalculator object and loads a bin_params file.

References bin_transition_calculator_, and protocols::generalized_kinematic_closure::filter::TR().

◆ rama_cutoff_energy()

core::Real protocols::generalized_kinematic_closure::filter::GeneralizedKICfilter::rama_cutoff_energy ( ) const

inline

Get the alpha_aa_rama_check or rama_prepro_check filter's rama term cutoff energy.

Only used by alpha_aa_rama_check and rama_prepro_check filters.

References rama_threshold_.

Referenced by apply_alpha_aa_rama_check(), and apply_rama_prepro_check().

◆ resnum()

core::Size protocols::generalized_kinematic_closure::filter::GeneralizedKICfilter::resnum ( ) const

inline

Get the residue number that this filter acts on.

Only used by some filters.

References resnum_.

Referenced by apply_alpha_aa_rama_check(), apply_backbone_bin(), and apply_rama_prepro_check().

◆ set_attach_boinc_ghost_observer()

void protocols::generalized_kinematic_closure::filter::GeneralizedKICfilter::set_attach_boinc_ghost_observer ( bool const setting )

inline

Sets whether we are attaching a BOINC "ghost" pose observer.

Only does anything in the BOINC graphics build.

References attach_boinc_ghost_observer_.

◆ set_binname()

void protocols::generalized_kinematic_closure::filter::GeneralizedKICfilter::set_binname ( std::string const & name_in )

inline

Set the bin name for this filter.

Only used by some filters.

References bin_.

◆ set_filter_type() [1/2]

void protocols::generalized_kinematic_closure::filter::GeneralizedKICfilter::set_filter_type ( filter_type const & ftype )

Sets the filter type for this filter.

References protocols::generalized_kinematic_closure::filter::end_of_filter_list, filter_params_bool_, filter_params_real_, filter_params_size_, and filtertype_.

◆ set_filter_type() [2/2]

void protocols::generalized_kinematic_closure::filter::GeneralizedKICfilter::set_filter_type ( std::string const & ftypename )

Sets the filter type for this filter by name.

References protocols::generalized_kinematic_closure::filter::end_of_filter_list, filter_params_bool_, filter_params_real_, filter_params_size_, filtertype_, and get_filter_type_by_name().

◆ set_rama_cutoff_energy()

void protocols::generalized_kinematic_closure::filter::GeneralizedKICfilter::set_rama_cutoff_energy ( core::Real const & val )

inline

Set the alpha_aa_rama_check or rama_prepro_check filter's rama term cutoff energy.

Only used by alpha_aa_rama_check and rama_prepro_check filters.

References rama_threshold_, and protocols::hybridization::val.

◆ set_resnum()

void protocols::generalized_kinematic_closure::filter::GeneralizedKICfilter::set_resnum ( core::Size const val )

inline

Set the residue number that this filter acts on.

Only used by some filters.

References resnum_, and protocols::hybridization::val.

Member Data Documentation

◆ attach_boinc_ghost_observer_

bool protocols::generalized_kinematic_closure::filter::GeneralizedKICfilter::attach_boinc_ghost_observer_

private

Should poses generated by this filter during processing be used for the BOINC "ghost" display?

Only does anytihng in the BOINC build.

Referenced by attach_boinc_ghost_observer(), and set_attach_boinc_ghost_observer().

◆ bin_

std::string protocols::generalized_kinematic_closure::filter::GeneralizedKICfilter::bin_

private

A parameter specifically for the backbone_bin filter. The bin that the residue must lie within.

Referenced by apply_backbone_bin(), binname(), and set_binname().

◆ bin_transition_calculator_

core::scoring::bin_transitions::BinTransitionCalculatorCOP protocols::generalized_kinematic_closure::filter::GeneralizedKICfilter::bin_transition_calculator_

private

A BinTransitionCalculatorOP. This will be null by default, and will only point to a BinTransitionCalculator object in the case of those filters that use torsion bin transition probabilities.

Referenced by apply_backbone_bin(), GeneralizedKICfilter(), and load_bin_params().

◆ filter_params_bool_

utility::vector1< std::pair<std::string, bool > > protocols::generalized_kinematic_closure::filter::GeneralizedKICfilter::filter_params_bool_

private

Boolean-valued filter parameters.

Referenced by add_filter_param(), get_filter_param(), and set_filter_type().

◆ filter_params_real_

utility::vector1< std::pair<std::string, core::Real > > protocols::generalized_kinematic_closure::filter::GeneralizedKICfilter::filter_params_real_

private

Real-valued filter parameters.

Referenced by add_filter_param(), get_filter_param(), and set_filter_type().

◆ filter_params_size_

utility::vector1< std::pair<std::string, core::Size > > protocols::generalized_kinematic_closure::filter::GeneralizedKICfilter::filter_params_size_

private

Integer-valued filter parameters.

Referenced by add_filter_param(), get_filter_param(), and set_filter_type().

◆ filter_params_string_

utility::vector1< std::pair<std::string, std::string > > protocols::generalized_kinematic_closure::filter::GeneralizedKICfilter::filter_params_string_

private

String-valued filter parameters.

Referenced by add_filter_param(), and get_filter_param().

◆ filtertype_

filter_type protocols::generalized_kinematic_closure::filter::GeneralizedKICfilter::filtertype_

private

The filter type for this filter (see the filter_type enum for all types).

Referenced by apply(), get_this_filter_type_name(), and set_filter_type().

◆ rama_threshold_

core::Real protocols::generalized_kinematic_closure::filter::GeneralizedKICfilter::rama_threshold_

private

A parameter specifically for the alpha_aa_rama_check and rama_prepro_check filters. Rama energy above which the solution is rejected. Set to 0.3 by default.

Referenced by rama_cutoff_energy(), and set_rama_cutoff_energy().

◆ resnum_

core::Size protocols::generalized_kinematic_closure::filter::GeneralizedKICfilter::resnum_

private

A parameter specifically for the backbone_bin filter. The residue that must lie within the mainchain torsion bin specified.

Referenced by resnum(), and set_resnum().

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

src/protocols/generalized_kinematic_closure/filter/GeneralizedKICfilter.hh
src/protocols/generalized_kinematic_closure/filter/GeneralizedKICfilter.cc

Public Member Functions

Static Public Member Functions

Private Member Functions

Private Attributes

Constructor & Destructor Documentation

◆ GeneralizedKICfilter() [1/2]

◆ GeneralizedKICfilter() [2/2]

◆ ~GeneralizedKICfilter()

Member Function Documentation

◆ add_filter_param() [1/4]

◆ add_filter_param() [2/4]

◆ add_filter_param() [3/4]

◆ add_filter_param() [4/4]

◆ apply()

◆ apply_alpha_aa_rama_check()

◆ apply_atom_pair_distance()

◆ apply_backbone_bin()

◆ apply_loop_bump_check()

◆ apply_rama_prepro_check()

◆ attach_boinc_ghost_observer()

◆ binname()

◆ clone()

◆ define_valid_filter_name_enumeration()

◆ get_filter_param() [1/4]

◆ get_filter_param() [2/4]

◆ get_filter_param() [3/4]

◆ get_filter_param() [4/4]

◆ get_filter_type_by_name()

◆ get_filter_type_name()

◆ get_loop_index()

◆ get_name()

◆ get_this_filter_type_name()

◆ load_bin_params()

◆ rama_cutoff_energy()

◆ resnum()

◆ set_attach_boinc_ghost_observer()

◆ set_binname()

◆ set_filter_type() [1/2]

◆ set_filter_type() [2/2]

◆ set_rama_cutoff_energy()

◆ set_resnum()

Member Data Documentation

◆ attach_boinc_ghost_observer_

◆ bin_

◆ bin_transition_calculator_

◆ filter_params_bool_

◆ filter_params_real_

◆ filter_params_size_

◆ filter_params_string_

◆ filtertype_

◆ rama_threshold_

◆ resnum_