protocols::generalized_kinematic_closure::filter::GeneralizedKICfilter Class Reference

#include <GeneralizedKICfilter.hh>

Public Member Functions
	GeneralizedKICfilter ()
	Creator for GeneralizedKICfilter. More...
	~GeneralizedKICfilter ()
	Destructor for GeneralizedKICfilter mover. 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...
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::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...

Private Member Functions
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::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::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 threshhold (or greater than a given threshhold if the user so specifies with the "greater_than" option). 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...

Constructor & Destructor Documentation

protocols::generalized_kinematic_closure::filter::GeneralizedKICfilter::GeneralizedKICfilter

(

)

Creator for GeneralizedKICfilter.

protocols::generalized_kinematic_closure::filter::GeneralizedKICfilter::~GeneralizedKICfilter

(

)

Destructor for GeneralizedKICfilter mover.

Member Function Documentation

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_.

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_.

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_.

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_.

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::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]	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.

Detailed:

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]	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 apply_atom_pair_distance(), apply_loop_bump_check(), protocols::generalized_kinematic_closure::filter::atom_pair_distance, filtertype_, and protocols::generalized_kinematic_closure::filter::loop_bump_check.

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::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 threshhold (or greater than a given threshhold 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]	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::copy_loop_pose_to_original(), dist_cutoff, numeric::xyzVector< class >::distance_squared(), get_filter_param(), core::conformation::Residue::has(), protocols::generalized_kinematic_closure::original_pose_residue_is_in_residue_map(), core::pose::Pose::residue(), runtime_assert_string_msg, protocols::generalized_kinematic_closure::set_loop_pose(), and core::conformation::Residue::xyz().

Referenced by apply().

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::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.

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]	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.

Returns "true" for pass and "false" for fail. This does NOT check for clashes within a residue – only between residues. However, if we're doing alpha- or beta- amino acids and the backbone carbonyl carbon is in the chain to be closed, then the carbonyl oxygen will also be checked for clashes.

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]	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(), core::conformation::Residue::connected_residue_at_resconn(), numeric::xyzVector< class >::distance_squared(), 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::AtomType::lj_radius(), core::conformation::Residue::mainchain_atoms(), core::pose::Pose::n_residue(), core::conformation::Residue::n_residue_connections(), nres, protocols::generalized_kinematic_closure::original_pose_residue_is_in_residue_map(), core::pose::Pose::residue(), protocols::generalized_kinematic_closure::set_loop_pose(), core::conformation::Residue::type(), and core::conformation::Residue::xyz().

Referenced by apply().

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().

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_.

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_.

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_.

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().

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::atom_pair_distance, protocols::generalized_kinematic_closure::filter::loop_bump_check, and protocols::generalized_kinematic_closure::filter::no_filter.

Referenced by get_filter_type_by_name(), and get_this_filter_type_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").

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().

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_, filtertype_, and runtime_assert_string_msg.

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_, get_filter_type_by_name(), and runtime_assert_string_msg.

Member Data Documentation

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().

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().

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().

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().

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().

---

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