#include <GeneralizedKIC.hh>

Public Member Functions
	GeneralizedKIC ()
	Creator for GeneralizedKIC mover. More...

virtual	~GeneralizedKIC ()
	Destructor for GeneralizedKIC mover. More...

virtual protocols::moves::MoverOP	clone () const
	Clone operator to create a pointer to a fresh GeneralizedKIC object that copies this one. More...

virtual protocols::moves::MoverOP	fresh_instance () const
	Fresh_instance operator to create a pointer to a fresh GeneralizedKIC object that does NOT copy this one. More...

virtual void	apply (core::pose::Pose &pose)
	Actually apply the mover to the pose. More...

virtual std::string	get_name () const
	Returns the name of this mover ("GeneralizedKIC"). More...

virtual void	parse_my_tag (utility::tag::TagCOP tag, basic::datacache::DataMap &data, protocols::filters::Filters_map const &filters, protocols::moves::Movers_map const &movers, core::pose::Pose const &)
	parse XML (specifically in the context of the parser/Rosetta_scripting scheme) More...

void	add_loop_residue (core::Size const residue_index)
	Add a residue (by index in the pose) to the list of residues making up the loop to be closed. This function checks that the index is within the range of indices in the pose, and that there is a geometric connection between this residue and the previous one in the list. More...

void	set_mover_effect_on_bonded_geometry (core::Size const effect)
	Function to set the effect of this mover on parts of the pose that are covalently attached to the loop to be closed, but which aren't part of it. Settings are: 0 – Moves the loop only; can pull apart covalent bonds to anything outside of the loop that isn't an anchor point. 1 – Moves the loop and anything downstream of the loop in the foldtree. Can still pull apart connections to non-child geometry. More...

core::Size	get_mover_effect_on_bonded_geometry ()
	Function to get the effect of this mover on parts of the pose that are covalently attached to the loop to be closed, but which aren't part of it. Return values are: 0 – Moves the loop only; can pull apart covalent bonds to anything outside of the loop that isn't an anchor point. 1 – Moves the loop and anything downstream of the loop in the foldtree. Can still pull apart connections to non-child geometry. More...

void	set_build_ideal_geometry (bool const buildideal)
	Set whether or not this mover builds ideal geometry for the loop, or uses the existing geometry, imperfect bond lengths/angles and all. More...

void	set_pivot_atoms (core::Size const rsd1, std::string const &at1, core::Size const rsd2, std::string const &at2, core::Size const rsd3, std::string const &at3)
	Function to set the pivot atoms for kinematic closure: More...

bool	get_build_ideal_geometry ()
	Get whether or not this mover builds ideal geometry for the loop, or uses the existing geometry, imperfect bond lengths/angles and all. More...

bool	last_run_successful ()
	Returns whether or not the last call to apply() sucessfully closed the loop. Defaults to false if apply() hasn't yet been called. More...

void	close_bond (core::Size const rsd1, std::string const &at1, core::Size const rsd2, std::string const &at2, core::Size const rsd1_before, std::string const &at1_before, core::Size const rsd2_after, std::string const &at2_after, core::Real const &bondlength, core::Real const &bondangle1, core::Real const &bondangle2, core::Real const &torsion, bool const randomize_this_torsion, bool const randomize_flanking_torsions)
	Tells GeneralizedKIC to close a bond, setting bond length, bond angle, and bond torsion values. This actually just adds appropriate set_dihedral, set_bondangle, and set_bondlength perturbers to the perturber list. Note that subsequent perturbers OR the closure itself can overwrite the bond length, bond angle, or torsion angles set here. More...

void	set_selector_type (selector::selector_type const &stype)
	Set the selector (the algorithm controlling how a solution will be chosen from among the solutions passing filters). More...

void	set_selector_type (std::string const &stypename)
	Set the selector (the algorithm controlling how a solution will be chosen from among the solutions passing filters). This sets the selector by name. More...

void	set_selector_scorefunction (core::scoring::ScoreFunctionOP sfxn)
	Set the selector's scorefunction. More...

void	set_selector_kbt (core::Real const &kbt)
	Set the selector's Boltzmann temperature value. More...

selector::selector_type	get_selector_type () const
	Get the selector (the algorithm controlling how a solution will be chosen from among the solutions passing filters). More...

std::string	get_selector_type_name () const
	Get the name of the selector (the algorithm controlling how a solution will be chosen from among the solutions passing filters). More...

void	add_perturber ()
	Add a new perturber to the list of perturbers. More...

void	add_perturber (perturber::perturber_effect const &effect)
	Add a new perturber to the list of perturbers, setting the effect. More...

void	add_perturber (std::string const &effectname)
	Add a new perturber to the list of perturbers, setting the effect by effect name string. More...

void	set_perturber_effect (core::Size const perturber_index, perturber::perturber_effect const &effect)
	Set a perturber's effect. More...

void	add_value_to_perturber_value_list (core::Size const perturber_index, core::Real const &val)
	Add a value to the list of values that a perturber takes. More...

void	add_value_to_perturber_value_list (core::Real const &val)
	Add a value to the list of values that a perturber takes. This operates on the last perturber in the perturber list. More...

void	add_residue_to_perturber_residue_list (core::Size const perturber_index, core::Size const residue_index)
	Add a residue to the list of residues that a perturber takes. Note that residue_index is based on indices of the ORIGINAL POSE, not the loop in isolation. More...

void	add_residue_to_perturber_residue_list (core::Size const residue_index)
	Add a residue to the list of residues that a perturber takes. Note that residue_index is based on indices of the ORIGINAL POSE, not the loop in isolation. This version acts on the last perturber added. More...

void	add_atomset_to_perturber_atomset_list (core::Size const perturber_index, utility::vector1< core::id::NamedAtomID > const &atomset)
	Add a set of AtomIDs to the list of sets of AtomIDs that a perturber takes. More...

void	add_atomset_to_perturber_atomset_list (utility::vector1< core::id::NamedAtomID > const &atomset)
	Add a set of AtomIDs to the list of sets of AtomIDs that a perturber takes. This operates on the last perturber in the perturber list. More...

void	add_filter ()
	Add a new filter to the list of filters. More...

void	add_filter (filter::filter_type const &filtertype)
	Add a new filter to the list of filters, setting the filter type. More...

void	add_filter (std::string const &filtertypename)
	Add a new filter to the list of filters, setting the filter type by name. More...

void	add_filter_parameter (core::Size const filter_index, std::string const &param_name, core::Real const &value)
	Add a real-valued parameter to a filter's parameter list. More...

void	add_filter_parameter (core::Size const filter_index, std::string const &param_name, core::Size const value)
	Add an integer-valued parameter to a filter's parameter list. More...

void	add_filter_parameter (core::Size const filter_index, std::string const &param_name, bool const value)
	Add a Boolean-valued parameter to a filter's parameter list. More...

void	add_filter_parameter (core::Size const filter_index, std::string const &param_name, std::string const &value)
	Add a string-valued parameter to a filter's parameter list. More...

void	add_filter_parameter (std::string const &param_name, core::Real const &value)
	Add a real-valued parameter to the last filter's parameter list. More...

void	add_filter_parameter (std::string const &param_name, core::Size const value)
	Add an integer-valued parameter to the last filter's parameter list. More...

void	add_filter_parameter (std::string const &param_name, bool const value)
	Add a Boolean-valued parameter to the last filter's parameter list. More...

void	add_filter_parameter (std::string const &param_name, std::string const &value)
	Add a string-valued parameter to the last filter's parameter list. More...

void	set_closure_attempts (core::Size const attempts)
	Set the number of closure attempts. More...

core::Size	get_closure_attempts () const
	Returns the number of closure attempts. More...

void	set_ntries_before_giving_up (core::Size const ntries)
	Sets number of tries before giving up. More...

core::Size	get_ntries_before_giving_up () const
	Gets number of tries before giving up. More...

bool	n_closure_attempts_is_a_maximum () const
	Returns whether the number of closure attempts is a maximum number of attempts. More...

void	set_n_closure_attempts_is_a_maximum (bool const is_max)
	Sets whether the number of closure attempts is a maximum number of attempts. More...

Public Member Functions inherited from protocols::moves::Mover
	Mover ()

virtual	~Mover ()

virtual MoverSP	create ()

virtual void	apply (core::io::serialization::PipeMap &pmap)

virtual void	parse_state (SerializableState const &state)

virtual void	parse_def (utility::lua::LuaObject const &def, utility::lua::LuaObject const &score_fxns, utility::lua::LuaObject const &tasks, MoverCacheSP cache)

virtual void	save_state (SerializableState &state)

	Mover (std::string const &type_name)
	sets the type for a mover; name_ has been removed (2010/05/14) More...

	Mover (Mover const &other)

Mover &	operator= (Mover const &other)
	assignment operator More...

virtual core::Real	last_proposal_density_ratio ()

std::string const &	type () const

void	set_type (std::string const &setting)

std::string	get_current_tag () const
	A tag is a unique identifier used to identify structures produced by this Mover. get_current_tag() returns the tag, and set_current_tag( std::string tag ) sets the tag. This functionality is not intended for use with the 2008 job distributor. More...

void	set_current_tag (std::string const &new_tag)

virtual void	set_input_pose (PoseCOP pose)
	setter for poses contained for rms More...

virtual void	set_native_pose (PoseCOP pose)
	setter for native poses contained for rms -— we should get rid of this method? it is widely used, but a bit unsafe More...

PoseCOP	get_input_pose () const

PoseCOP	get_native_pose () const

virtual void	test_move (Pose &pose)
	: Unit test support function. Apply one move to a given pose. Allows extra test specific functions to be called before applying More...

void	type (const std::string &type_in)

std::string	get_type () const

MoverStatus	get_last_move_status () const
	end parser interface, start Job Distributor interface///////////// More...

void	reset_status ()
	resets status to SUCCESS, meant to be used before an apply(). The job distributor (august 08 vintage) uses this to ensure non-accumulation of status across apply()s. More...

virtual core::pose::PoseOP	get_additional_output ()
	Mechanism by which a mover may return multiple output poses from a single input pose. More...

virtual void	clear_info ()
	Strings container can be used to return miscellaneous info (as std::string) from a mover, such as notes about the results of apply(). The job distributor (Apr 09 vintage) will check this function to see if your protocol wants to add string info to the Job that ran this mover. One way this can be useful is that later, a JobOutputter may include/append this info to an output file. More...

virtual Strings &	info ()
	non-const accessor More...

virtual Strings const &	info () const
	const accessor More...

virtual bool	reinitialize_for_each_job () const
	Inform the Job Distributor (August '08 vintage) whether this object needs to be freshly regenerated on each use. More...

virtual bool	reinitialize_for_new_input () const
	Inform the Job Distributor (August '08 vintage) whether this object needs to be regenerated when the input pose is about to change, (for example, if the Mover has special code on the first apply() that is only valid for that one input pose). More...

void	set_current_job (protocols::jobdist::BasicJobCOP job)

jobdist::BasicJobCOP	get_current_job () const

virtual void	show (std::ostream &output=std::cout) const
	Outputs details about the Mover, including current settings. More...

Private Member Functions
void	get_path (core::Size const first_atom, core::Size const second_atom, core::conformation::Residue const &rsd, utility::vector1< core::Size > &path_indices)
	Gets a path through atoms in the residue from one connection atom to another within a residue. More...

core::Size	get_connection (core::Size const res_with_connection, core::Size const other_res, core::pose::Pose const &pose)
	Function to get the FIRST connection in res_with_connection that connects it to other_res: More...

bool	has_geometric_connection (core::Size const residue1, core::Size const residue2, core::pose::Pose const &pose)
	Function that returns true if two residues in a pose have a direct geometric connection, and false otherwise. More...

void	infer_anchor_connIDs (core::pose::Pose const &pose)
	As the list of residues in the loop to be closed is updated, we need to figure out how that loop is connected to the geometry outside of the loop (i.e. what's considred the connection to stationary geometry). This function loops through all connIDs on the terminal residues of the loop to be closed and picks the first one that links to geometry not in the loop as the anchor connnection. TODO: Add a manual override to specifiy that a different connection is the anchor. More...

void	addloweranchor (core::pose::Pose &perturbedloop_pose, core::pose::Pose const &pose)
	Find the residue that is the anchor of the lower end of the loop that we're about to close and add it to the loop pose by a jump. More...

void	addloopgeometry (core::pose::Pose &perturbedloop_pose, core::pose::Pose const &pose, bool const build_ideal, core::Size const effect_on_bonded_geom, utility::vector1< std::pair< core::Size, core::Size > > &residue_map)
	Add the loop geometry from the starting pose to the temporary pose used for kinematic closure. This will also add the downstream geometry if effect_on_bonded_geom==1. Finally, this will build ideal geometry if build_ideal==true. More...

void	addupperanchor (core::pose::Pose &perturbedloop_pose, core::pose::Pose const &pose)
	Find the residue that is the anchor of the upper end of the loop that we're about to close and add it to the loop pose by a bond. More...

bool	doKIC (core::pose::Pose &pose, core::pose::Pose const &original_pose, utility::vector1< std::pair< core::Size, core::Size > > const &residue_map)
	Do the actual kinematic closure. More...

void	generate_atomlist (core::pose::Pose const &pose, utility::vector1< std::pair< core::Size, core::Size > > const &residue_map)
	Generate the list of atomIDs for the chain that will be closed by kinematic closure. More...

void	generate_bridgeobjects_data_from_atomlist (utility::vector1< utility::vector1< core::Real > > &atoms, utility::vector1< core::Real > &dt, utility::vector1< core::Real > &da, utility::vector1< core::Real > &db, utility::vector1< core::Size > &order)
	Generate the numeric::kinematic_closure::bridgeObjects data from the atomlist_ object. More...

core::Size	get_perturbedloop_rsd (core::Size const original_pose_rsd, utility::vector1< std::pair< core::Size, core::Size > > const &residue_map)
	Given a residue_map vector of pairs, where each pair is < residue_index_in_perturbedloop_pose, residue_index_in_original_pose >, and a residue index in the original pose, return the corresponding residue index in the perturbed loop pose. More...

void	pick_pivots (core::pose::Pose const &original_pose, utility::vector1< std::pair< core::Size, core::Size > > const &residue_map, utility::vector1< core::Size > &pivots)
	Pick the pivots for kinematic closure. More...

void	apply_perturbations (core::pose::Pose const &loop_pose, core::pose::Pose const &original_pose, utility::vector1< std::pair< core::Size, core::Size > > const &residue_map, utility::vector1< core::Real > &torsions, utility::vector1< core::Real > &bondangles, utility::vector1< core::Real > &bondlengths) const
	Apply the list of perturbers (everything in perturberlist_) to alter the desired torsion, desired angle, and desired bond length lists prior to calling bridgeObjects. More...

void	filter_solutions (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< utility::vector1< core::Real > > &torsions, utility::vector1< utility::vector1< core::Real > > &bondangles, utility::vector1< utility::vector1< core::Real > > &bondlengths, int &nsol) const
	Apply filters to the list of solutions, and proceed to eliminate any and all that fail to pass filters. More...

void	select_solution (core::pose::Pose &pose, core::pose::Pose const &original_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< utility::vector1< utility::vector1< core::Real > > > const &torsions, utility::vector1< utility::vector1< utility::vector1< core::Real > > > const &bondangles, utility::vector1< utility::vector1< utility::vector1< core::Real > > > const &bondlengths, utility::vector1< core::Size > const &nsol_for_attempt, core::Size const total_solutions) const
	Applies the selector to choose a solution and set a loop pose. More...

void	prune_extra_atoms (utility::vector1< core::Size > &pivots)
	Trims extra atoms from the start and end of the atom list, if the first and last pivots are not the fifth and fifth-last atoms, respectively. More...

Private Attributes
utility::vector1< core::Size >	loopresidues_
	The list of residues (as inidices of the original pose) making up the loop to be closed. More...

core::Size	effect_on_bonded_geometry_
	The effect of the GeneralizedKIC mover on geometry that is covalently bound to the loop to be closed, but which is not part of that loop segment. 0 means that the mover will only move the loop, possibly tearing apart covalent bonds to other parts of the pose. 1 means that the mover will move the loop along with anything that is downstream in the FoldTree. More...

core::Size	lower_anchor_connID_
	The lower end of the loop to be closed is presumably connected to geometry that is not moved by this mover. However, the connection could be through backbone or sidechain. The mover needs to know the connection ID on the lower end of the loop to the anchor geometry. Note: This will be set to 0 if the only connection that this residue can form is to the loop. More...

core::Size	upper_anchor_connID_
	The upper end of the loop to be closed is presumably connected to geometry that is not moved by this mover. However, the connection could be through backbone or sidechain. The mover needs to know the connection ID on the upper end of the loop to the anchor geometry. Note: This will be set to 0 if the only connection that this residue can form is to the loop. More...

bool	build_ideal_geometry_
	Should the mover build ideal geometry for the loop to be closed? Default true. More...

bool	last_run_successful_
	Was the last apply() successful in generating a new kinematically-closed structure? More...

utility::vector1< std::pair < core::id::AtomID, numeric::xyzVector< core::Real > > >	atomlist_
	List of the atoms in the segment to be closed, and their x,y,z coordinates. Note that the atomIDs refer to residue indices that correspond to the temporary pose created by the apply() function, not to the indices in the original pose. More...

core::Size	pivot_1_rsd_
	Pivot residue 1 (index based on original pose). More...

std::string	pivot_1_atmname_
	Pivot atom 1 name. More...

core::Size	pivot_2_rsd_
	Pivot residue 2 (index based on original pose). More...

std::string	pivot_2_atmname_
	Pivot atom 2 name. More...

core::Size	pivot_3_rsd_
	Pivot residue 3 (index based on original pose). More...

std::string	pivot_3_atmname_
	Pivot atom 3 name. More...

perturber::GeneralizedKICperturberOPs	perturberlist_
	List of GeneralizedKICperturbers to apply prior to kinematic closure. More...

filter::GeneralizedKICfilterOPs	filterlist_
	List of GeneralizedKICfilters to apply to eliminate bad solutions. More...

selector::GeneralizedKICselectorOP	selector_
	The selection algorithm to use to pick a solution from the set of solutions passing the filters. More...

core::Size	n_closure_attempts_
	The number of closure attempts to carry out. More...

bool	n_closure_attempts_is_a_maximum_
	Should n_closure_attempts_ be the number attempted, or a maximum number of attempts? If false, n_closure_attempts_ attempts are made, and then a solution is chosen. If true, attempts are made until a solution is found OR n_closure_attempts_ is reached. More...

protocols::filters::ContingentFilterOP	rosettascripts_filter_
	Owning pointer for the RosettaScripts ContingentFilter associated with this mover, if there is one. More...

bool	rosettascripts_filter_exists_
	Bool determining whether there exists a RosettaScripts ContingentFilter associated with this mover. More...

core::Size	ntries_before_giving_up_
	The number of tries to make before giving up if no solution has been found yet. More...

Additional Inherited Members
Public Types inherited from protocols::moves::Mover
typedef utility::tag::TagCOP	TagCOP

typedef core::pose::Pose	Pose

typedef core::pose::PoseCOP	PoseCOP

typedef protocols::filters::Filters_map	Filters_map

typedef std::list< std::string >	Strings

Static Public Member Functions inherited from protocols::moves::Mover
static std::string	name ()

static void	register_options ()
	Overload this static method if you access options within the mover. More...

Protected Member Functions inherited from protocols::moves::Mover
void	set_last_move_status (MoverStatus status)
	nonvirtual setter for MoverStatus last_status_. Protected means that only the mover itself will be able to change its own status. The job distributor (august 08 vintage) is aware of status set with this function and will do what the MoverStatus says. More...

Constructor & Destructor Documentation

protocols::generalized_kinematic_closure::GeneralizedKIC::GeneralizedKIC ( )

Creator for GeneralizedKIC mover.

Referenced by clone(), and fresh_instance().

protocols::generalized_kinematic_closure::GeneralizedKIC::~GeneralizedKIC ( )

virtual

Destructor for GeneralizedKIC mover.

Member Function Documentation

void protocols::generalized_kinematic_closure::GeneralizedKIC::add_atomset_to_perturber_atomset_list	(	core::Size const	perturber_index,
		utility::vector1< core::id::NamedAtomID > const &	atomset
	)

Add a set of AtomIDs to the list of sets of AtomIDs that a perturber takes.

References perturberlist_, and runtime_assert_string_msg.

Referenced by add_atomset_to_perturber_atomset_list(), close_bond(), and parse_my_tag().

void protocols::generalized_kinematic_closure::GeneralizedKIC::add_atomset_to_perturber_atomset_list ( utility::vector1< core::id::NamedAtomID > const & atomset )

Add a set of AtomIDs to the list of sets of AtomIDs that a perturber takes. This operates on the last perturber in the perturber list.

References add_atomset_to_perturber_atomset_list(), perturberlist_, and runtime_assert_string_msg.

void protocols::generalized_kinematic_closure::GeneralizedKIC::add_filter ( )

Add a new filter to the list of filters.

References filterlist_.

Referenced by add_filter(), and parse_my_tag().

void protocols::generalized_kinematic_closure::GeneralizedKIC::add_filter ( filter::filter_type const & filtertype )

Add a new filter to the list of filters, setting the filter type.

References add_filter(), and filterlist_.

void protocols::generalized_kinematic_closure::GeneralizedKIC::add_filter ( std::string const & filtertypename )

Add a new filter to the list of filters, setting the filter type by name.

See src/protocols/generalized_kinematic_closure/filter/GeneralizedKICfilter.cc for the list of filter type names.

References add_filter(), and filterlist_.

void protocols::generalized_kinematic_closure::GeneralizedKIC::add_filter_parameter	(	core::Size const	filter_index,
		std::string const &	param_name,
		core::Real const &	value
	)

Add a real-valued parameter to a filter's parameter list.

References filterlist_.

Referenced by add_filter_parameter(), and parse_my_tag().

void protocols::generalized_kinematic_closure::GeneralizedKIC::add_filter_parameter	(	core::Size const	filter_index,
		std::string const &	param_name,
		core::Size const	value
	)

Add an integer-valued parameter to a filter's parameter list.

References filterlist_.

void protocols::generalized_kinematic_closure::GeneralizedKIC::add_filter_parameter	(	core::Size const	filter_index,
		std::string const &	param_name,
		bool const	value
	)

Add a Boolean-valued parameter to a filter's parameter list.

References filterlist_.

void protocols::generalized_kinematic_closure::GeneralizedKIC::add_filter_parameter	(	core::Size const	filter_index,
		std::string const &	param_name,
		std::string const &	value
	)

Add a string-valued parameter to a filter's parameter list.

References filterlist_.

void protocols::generalized_kinematic_closure::GeneralizedKIC::add_filter_parameter	(	std::string const &	param_name,
		core::Real const &	value
	)

Add a real-valued parameter to the last filter's parameter list.

References add_filter_parameter(), and filterlist_.

void protocols::generalized_kinematic_closure::GeneralizedKIC::add_filter_parameter	(	std::string const &	param_name,
		core::Size const	value
	)

Add an integer-valued parameter to the last filter's parameter list.

References add_filter_parameter(), and filterlist_.

void protocols::generalized_kinematic_closure::GeneralizedKIC::add_filter_parameter	(	std::string const &	param_name,
		bool const	value
	)

Add a Boolean-valued parameter to the last filter's parameter list.

References add_filter_parameter(), and filterlist_.

void protocols::generalized_kinematic_closure::GeneralizedKIC::add_filter_parameter	(	std::string const &	param_name,
		std::string const &	value
	)

Add a string-valued parameter to the last filter's parameter list.

References add_filter_parameter(), and filterlist_.

void protocols::generalized_kinematic_closure::GeneralizedKIC::add_loop_residue ( core::Size const residue_index )

Add a residue (by index in the pose) to the list of residues making up the loop to be closed. This function checks that the index is within the range of indices in the pose, and that there is a geometric connection between this residue and the previous one in the list.

References loopresidues_, and protocols::generalized_kinematic_closure::TR.

Referenced by parse_my_tag().

void protocols::generalized_kinematic_closure::GeneralizedKIC::add_perturber ( )

Add a new perturber to the list of perturbers.

References perturberlist_.

Referenced by add_perturber(), close_bond(), and parse_my_tag().

void protocols::generalized_kinematic_closure::GeneralizedKIC::add_perturber ( perturber::perturber_effect const & effect )

Add a new perturber to the list of perturbers, setting the effect.

References add_perturber(), and perturberlist_.

void protocols::generalized_kinematic_closure::GeneralizedKIC::add_perturber ( std::string const & effectname )

Add a new perturber to the list of perturbers, setting the effect by effect name string.

References add_perturber(), and perturberlist_.

void protocols::generalized_kinematic_closure::GeneralizedKIC::add_residue_to_perturber_residue_list	(	core::Size const	perturber_index,
		core::Size const	residue_index
	)

Add a residue to the list of residues that a perturber takes. Note that residue_index is based on indices of the ORIGINAL POSE, not the loop in isolation.

References perturberlist_, and runtime_assert_string_msg.

Referenced by add_residue_to_perturber_residue_list(), and parse_my_tag().

void protocols::generalized_kinematic_closure::GeneralizedKIC::add_residue_to_perturber_residue_list ( core::Size const residue_index )

Add a residue to the list of residues that a perturber takes. Note that residue_index is based on indices of the ORIGINAL POSE, not the loop in isolation. This version acts on the last perturber added.

References add_residue_to_perturber_residue_list(), perturberlist_, and runtime_assert_string_msg.

void protocols::generalized_kinematic_closure::GeneralizedKIC::add_value_to_perturber_value_list	(	core::Size const	perturber_index,
		core::Real const &	val
	)

Add a value to the list of values that a perturber takes.

References perturberlist_, and runtime_assert_string_msg.

Referenced by add_value_to_perturber_value_list(), close_bond(), and parse_my_tag().

void protocols::generalized_kinematic_closure::GeneralizedKIC::add_value_to_perturber_value_list ( core::Real const & val )

Add a value to the list of values that a perturber takes. This operates on the last perturber in the perturber list.

References add_value_to_perturber_value_list(), perturberlist_, and runtime_assert_string_msg.

void protocols::generalized_kinematic_closure::GeneralizedKIC::addloopgeometry	(	core::pose::Pose &	perturbedloop_pose,
		core::pose::Pose const &	pose,
		bool const	build_ideal,
		core::Size const	effect_on_bonded_geom,
		utility::vector1< std::pair< core::Size, core::Size > > &	residue_map
	)

private

Add the loop geometry from the starting pose to the temporary pose used for kinematic closure. This will also add the downstream geometry if effect_on_bonded_geom==1. Finally, this will build ideal geometry if build_ideal==true.

References core::pose::Pose::append_residue_by_bond(), core::conformation::Residue::clone(), loopresidues_, lower_anchor_connID_, core::pose::Pose::n_residue(), core::conformation::Residue::n_residue_connections(), core::pose::Pose::residue(), core::conformation::Residue::residue_connection_partner(), and utility_exit_with_message.

Referenced by apply().

void protocols::generalized_kinematic_closure::GeneralizedKIC::addloweranchor	(	core::pose::Pose &	perturbedloop_pose,
		core::pose::Pose const &	pose
	)

private

Find the residue that is the anchor of the lower end of the loop that we're about to close and add it to the loop pose by a jump.

References core::pose::Pose::append_residue_by_jump(), core::pose::Pose::clear(), core::conformation::Residue::clone(), loopresidues_, lower_anchor_connID_, core::pose::Pose::residue(), core::conformation::Residue::residue_connection_partner(), and utility_exit_with_message.

Referenced by apply().

void protocols::generalized_kinematic_closure::GeneralizedKIC::addupperanchor	(	core::pose::Pose &	perturbedloop_pose,
		core::pose::Pose const &	pose
	)

private

Find the residue that is the anchor of the upper end of the loop that we're about to close and add it to the loop pose by a bond.

References core::pose::Pose::append_residue_by_bond(), core::conformation::Residue::clone(), loopresidues_, core::pose::Pose::n_residue(), core::conformation::Residue::n_residue_connections(), core::pose::Pose::residue(), core::conformation::Residue::residue_connection_partner(), upper_anchor_connID_, and utility_exit_with_message.

Referenced by apply().

void protocols::generalized_kinematic_closure::GeneralizedKIC::apply ( core::pose::Pose & pose )

virtual

Actually apply the mover to the pose.

Implements protocols::moves::Mover.

References addloopgeometry(), addloweranchor(), addupperanchor(), build_ideal_geometry_, protocols::generalized_kinematic_closure::copy_loop_pose_to_original(), doKIC(), effect_on_bonded_geometry_, infer_anchor_connIDs(), last_run_successful_, loopresidues_, rosettascripts_filter_, rosettascripts_filter_exists_, protocols::generalized_kinematic_closure::TR, and utility_exit_with_message.

Referenced by filter_solutions().

void protocols::generalized_kinematic_closure::GeneralizedKIC::apply_perturbations	(	core::pose::Pose const &	loop_pose,
		core::pose::Pose const &	original_pose,
		utility::vector1< std::pair< core::Size, core::Size > > const &	residue_map,
		utility::vector1< core::Real > &	torsions,
		utility::vector1< core::Real > &	bondangles,
		utility::vector1< core::Real > &	bondlengths
	)		const

private

Apply the list of perturbers (everything in perturberlist_) to alter the desired torsion, desired angle, and desired bond length lists prior to calling bridgeObjects.

Apply the list of perturbers (everything in perturberlist_) to alter the desired torsion, desired angle, and desired bond length lists prior to calling bridgeObjects. Note that later perturbers might overwrite earlier perturbers' effects.

Detailed:

Parameters

[in]	loop_pose	– A pose consisting of just the loop to be closed.
[in]	original_pose	– A pose consisting of the full, original structure.
[in]	residue_map	– The mapping of (residue in loop_pose, residue in original_pose).
[in,out]	torsions	– The desired torsion angles, potentially altered or overwritten by the perturbers.
[in,out]	bondangles	– The desired bond angles, potentially altered or overwritten by the perturbers.
[in,out]	bondlenghts	– The desired bond lengths, potentially altered or overwritten by the perturbers.

References atomlist_, perturberlist_, and protocols::generalized_kinematic_closure::TR.

Referenced by doKIC().

protocols::moves::MoverOP protocols::generalized_kinematic_closure::GeneralizedKIC::clone ( ) const

virtual

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

Reimplemented from protocols::moves::Mover.

References GeneralizedKIC().

Referenced by parse_my_tag().

void protocols::generalized_kinematic_closure::GeneralizedKIC::close_bond	(	core::Size const	rsd1,
		std::string const &	at1,
		core::Size const	rsd2,
		std::string const &	at2,
		core::Size const	rsd1_before,
		std::string const &	at1_before,
		core::Size const	rsd2_after,
		std::string const &	at2_after,
		core::Real const &	bondlength,
		core::Real const &	bondangle1,
		core::Real const &	bondangle2,
		core::Real const &	torsion,
		bool const	randomize_this_torsion,
		bool const	randomize_flanking_torsions
	)

Tells GeneralizedKIC to close a bond, setting bond length, bond angle, and bond torsion values. This actually just adds appropriate set_dihedral, set_bondangle, and set_bondlength perturbers to the perturber list. Note that subsequent perturbers OR the closure itself can overwrite the bond length, bond angle, or torsion angles set here.

Detailed:

Parameters

[in]	rsd1	– The index of the first atom's residue (indexed based on residue indices in the original pose).
[in]	at1	– The name of the first atom defining the bond to be closed.
[in]	rsd2	– The index of the second atom's residue (indexed based on residue indices in the original pose).
[in]	at1	– The name of the second atom defining the bond to be closed.
[in]	bondlength	– The length of the bond between the two atoms.
[in]	bondangle1	– The bond angle defined by (atom preceding at1 in the chain to be closed), (atm1), (atm2).
[in]	bondangle1	– The bond angle defined by (atm1), (atm2), (atom following at2 in the chain to be closed).
[in]	torsion	– The torsion angle defined by (atom preceding at1 in the chain to be closed), (atm1), (atm2), (atom following at2 in the chain to be closed).

References add_atomset_to_perturber_atomset_list(), add_perturber(), add_value_to_perturber_value_list(), protocols::RG, and numeric::random::RandomGenerator::uniform().

Referenced by parse_my_tag().

bool protocols::generalized_kinematic_closure::GeneralizedKIC::doKIC	(	core::pose::Pose &	pose,
		core::pose::Pose const &	original_pose,
		utility::vector1< std::pair< core::Size, core::Size > > const &	residue_map
	)

private

Do the actual kinematic closure.

Inputs are pose (the loop to be closed), original_pose (the reference pose, unchanged by operation), and residue_map (the mapping of residues from pose to original_pose). Output is pose (the loop to be closed, in a new, closed conformation if successful) and a boolean value indicating success or failure.

References apply_perturbations(), atomlist_, bridgeObjects(), filter_solutions(), generate_atomlist(), generate_bridgeobjects_data_from_atomlist(), get_ntries_before_giving_up(), n_closure_attempts_, n_closure_attempts_is_a_maximum(), protocols::forge::methods::order(), pick_pivots(), select_solution(), and protocols::generalized_kinematic_closure::TR.

Referenced by apply().

void protocols::generalized_kinematic_closure::GeneralizedKIC::filter_solutions	(	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< utility::vector1< core::Real > > &	torsions,
		utility::vector1< utility::vector1< core::Real > > &	bondangles,
		utility::vector1< utility::vector1< core::Real > > &	bondlengths,
		int &	nsol
	)		const

private

Apply filters to the list of solutions, and proceed to eliminate any and all that fail to pass filters.

This removes entries from the torsions, bondangles, and bondlengths lists, and decrements nsol (the number of solutions) appropriately.

Parameters

[in]	original_pose	– A pose consisting of the full, original structure.
[in]	loop_pose	– A pose consisting of just the loop to be closed.
[in]	residue_map	– The mapping of (residue in loop_pose, residue in original_pose).
[in]	atomlist	– The list of atomIDs in the chain that was closed, plus their xyz coordinates from the original pose.
[in,out]	torsions	– The torsion angles returned by bridgeObjects, as a matrix of [solution #][torsion index]. Columns can be deleted by filters.
[in,out]	bondangles	– The bond angles returned by bridgeObjects, as a matrix of [solution #][bondangle index]. Columns can be deleted by filters.
[in,out]	bondlenghts	– The bond lengths returned by bridgeObjects, as a matrix of [solution #][bondlength index]. Columns can be deleted by filters.
[in,out]	nsol	– The number of solutions, which can be decremented as filters delete solutions. Note that this must be an int, not a core::Size.

This removes entries from the torsions, bondangles, and bondlengths lists, and decrements nsol (the number of solutions) appropriately.

Parameters

[in,out]	torsions	– The torsion angles returned by bridgeObjects, as a matrix of [solution #][torsion index]. Columns can be deleted by filters.
[in,out]	bondangles	– The bond angles returned by bridgeObjects, as a matrix of [solution #][bondangle index]. Columns can be deleted by filters.
[in,out]	bondlenghts	– The bond lengths returned by bridgeObjects, as a matrix of [solution #][bondlength index]. Columns can be deleted by filters.
[in,out]	nsol	– The number of solutions, which can be decremented as filters delete solutions. Note that this must be an int, not a core::Size.

References apply(), filterlist_, and protocols::generalized_kinematic_closure::TR.

Referenced by doKIC().

protocols::moves::MoverOP protocols::generalized_kinematic_closure::GeneralizedKIC::fresh_instance ( ) const

virtual

Fresh_instance operator to create a pointer to a fresh GeneralizedKIC object that does NOT copy this one.

Reimplemented from protocols::moves::Mover.

References GeneralizedKIC().

void protocols::generalized_kinematic_closure::GeneralizedKIC::generate_atomlist	(	core::pose::Pose const &	pose,
		utility::vector1< std::pair< core::Size, core::Size > > const &	residue_map
	)

private

Generate the list of atomIDs for the chain that will be closed by kinematic closure.

References core::conformation::Residue::atom_base(), atomlist_, get_connection(), get_path(), core::pose::Pose::n_residue(), nres, core::pose::Pose::residue(), core::conformation::Residue::residue_connect_atom_index(), runtime_assert_string_msg, and core::conformation::Residue::xyz().

Referenced by doKIC().

void protocols::generalized_kinematic_closure::GeneralizedKIC::generate_bridgeobjects_data_from_atomlist	(	utility::vector1< utility::vector1< core::Real > > &	atoms,
		utility::vector1< core::Real > &	dt,
		utility::vector1< core::Real > &	da,
		utility::vector1< core::Real > &	db,
		utility::vector1< core::Size > &	order
	)

private

Generate the numeric::kinematic_closure::bridgeObjects data from the atomlist_ object.

References atomlist_, chainTORS(), and protocols::kinmatch::xyz().

Referenced by doKIC().

bool protocols::generalized_kinematic_closure::GeneralizedKIC::get_build_ideal_geometry ( )

inline

Get whether or not this mover builds ideal geometry for the loop, or uses the existing geometry, imperfect bond lengths/angles and all.

References build_ideal_geometry_.

core::Size protocols::generalized_kinematic_closure::GeneralizedKIC::get_closure_attempts ( ) const

inline

Returns the number of closure attempts.

Perturbation, closure, and filtering is carried out for every closure attempt. Successful closures from ALL attempts are then selected from by selectors.

References n_closure_attempts_.

core::Size protocols::generalized_kinematic_closure::GeneralizedKIC::get_connection	(	core::Size const	res_with_connection,
		core::Size const	other_res,
		core::pose::Pose const &	pose
	)

private

Function to get the FIRST connection in res_with_connection that connects it to other_res:

References core::conformation::Residue::connections_to_residue(), core::pose::Pose::n_residue(), nres, core::pose::Pose::residue(), and runtime_assert_string_msg.

Referenced by generate_atomlist().

core::Size protocols::generalized_kinematic_closure::GeneralizedKIC::get_mover_effect_on_bonded_geometry ( )

inline

Function to get the effect of this mover on parts of the pose that are covalently attached to the loop to be closed, but which aren't part of it. Return values are: 0 – Moves the loop only; can pull apart covalent bonds to anything outside of the loop that isn't an anchor point. 1 – Moves the loop and anything downstream of the loop in the foldtree. Can still pull apart connections to non-child geometry.

References effect_on_bonded_geometry_.

std::string protocols::generalized_kinematic_closure::GeneralizedKIC::get_name ( ) const

virtual

Returns the name of this mover ("GeneralizedKIC").

Implements protocols::moves::Mover.

core::Size protocols::generalized_kinematic_closure::GeneralizedKIC::get_ntries_before_giving_up ( ) const

inline

Gets number of tries before giving up.

The algorithm tries n_closure_attempts_ times if and only if at least one solution is found in the first ntries_before_giving_up_ attempts.

References ntries_before_giving_up_.

Referenced by doKIC().

void protocols::generalized_kinematic_closure::GeneralizedKIC::get_path	(	core::Size const	first_atom,
		core::Size const	second_atom,
		core::conformation::Residue const &	rsd,
		utility::vector1< core::Size > &	path_indices
	)

private

Gets a path through atoms in the residue from one connection atom to another within a residue.

get_path

This is not necessarily the shortest path, geometrically, but hopefully it will do for our purposes. (I didn't want to reimplement Dijkstra's algorithm, since that would tax my programming abilities and would result in unnecessarily slow performance.) This algorithm works by stepping back (child->parent) from the higher-index atom until (a) it finds the lower-index atom, or (b) it reaches the root. If it reaches the root, it then starts at the lower-index atom and traces back until it reaches an atom already in the path. The chosen path is therefore the path from one atom, to the nearest common ancestor, to the other atom.

Parameters

[in]	first_atom	– The index of the first atom in the path.
[in]	second_atom	– The index of the first atom in the path.
[in]	rsd	– The residue object (const instance).
[out]	path_indices	– The list of indices of the atoms found in the path.

Author: Vikram K. Mulligan

References core::chemical::ResidueType::atom_base(), core::conformation::Residue::natoms(), runtime_assert_string_msg, and core::conformation::Residue::type().

Referenced by generate_atomlist().

core::Size protocols::generalized_kinematic_closure::GeneralizedKIC::get_perturbedloop_rsd	(	core::Size const	original_pose_rsd,
		utility::vector1< std::pair< core::Size, core::Size > > const &	residue_map
	)

private

Given a residue_map vector of pairs, where each pair is < residue_index_in_perturbedloop_pose, residue_index_in_original_pose >, and a residue index in the original pose, return the corresponding residue index in the perturbed loop pose.

References utility_exit_with_message.

selector::selector_type protocols::generalized_kinematic_closure::GeneralizedKIC::get_selector_type ( ) const

inline

Get the selector (the algorithm controlling how a solution will be chosen from among the solutions passing filters).

References selector_.

std::string protocols::generalized_kinematic_closure::GeneralizedKIC::get_selector_type_name ( ) const

inline

Get the name of the selector (the algorithm controlling how a solution will be chosen from among the solutions passing filters).

References selector_.

bool protocols::generalized_kinematic_closure::GeneralizedKIC::has_geometric_connection	(	core::Size const	residue1,
		core::Size const	residue2,
		core::pose::Pose const &	pose
	)

private

Function that returns true if two residues in a pose have a direct geometric connection, and false otherwise.

References core::conformation::Residue::is_bonded(), and core::pose::Pose::residue().

void protocols::generalized_kinematic_closure::GeneralizedKIC::infer_anchor_connIDs ( core::pose::Pose const & pose )

private

As the list of residues in the loop to be closed is updated, we need to figure out how that loop is connected to the geometry outside of the loop (i.e. what's considred the connection to stationary geometry). This function loops through all connIDs on the terminal residues of the loop to be closed and picks the first one that links to geometry not in the loop as the anchor connnection. TODO: Add a manual override to specifiy that a different connection is the anchor.

References core::conformation::Residue::connection_incomplete(), protocols::generalized_kinematic_closure::is_in_list(), loopresidues_, lower_anchor_connID_, core::conformation::Residue::n_residue_connections(), core::pose::Pose::residue(), core::conformation::Residue::residue_connection_partner(), and upper_anchor_connID_.

Referenced by apply().

bool protocols::generalized_kinematic_closure::GeneralizedKIC::last_run_successful ( )

inline

Returns whether or not the last call to apply() sucessfully closed the loop. Defaults to false if apply() hasn't yet been called.

References last_run_successful_.

bool protocols::generalized_kinematic_closure::GeneralizedKIC::n_closure_attempts_is_a_maximum ( ) const

inline

Returns whether the number of closure attempts is a maximum number of attempts.

If true, attempts are made until a solution is found OR n_closure_attempts_ is reached. If false, n_closure_attempts_ attempts are made, and then a solution is chosen from among the successful solutions (if any).

References n_closure_attempts_is_a_maximum_.

Referenced by doKIC().

void protocols::generalized_kinematic_closure::GeneralizedKIC::parse_my_tag	(	utility::tag::TagCOP	tag,
		basic::datacache::DataMap &	data,
		protocols::filters::Filters_map const &	filters,
		protocols::moves::Movers_map const &	movers,
		core::pose::Pose const &
	)

virtual

parse XML (specifically in the context of the parser/Rosetta_scripting scheme)

Reimplemented from protocols::moves::Mover.

References add_atomset_to_perturber_atomset_list(), add_filter(), add_filter_parameter(), add_loop_residue(), add_perturber(), add_residue_to_perturber_residue_list(), add_value_to_perturber_value_list(), clone(), close_bond(), utility::pointer::owning_ptr< T >::get(), protocols::rosetta_scripts::parse_filter(), protocols::rosetta_scripts::parse_score_function(), rosettascripts_filter_, rosettascripts_filter_exists_, runtime_assert_string_msg, set_closure_attempts(), set_n_closure_attempts_is_a_maximum(), set_ntries_before_giving_up(), set_pivot_atoms(), set_selector_kbt(), set_selector_scorefunction(), set_selector_type(), and protocols::generalized_kinematic_closure::TR.

void protocols::generalized_kinematic_closure::GeneralizedKIC::pick_pivots	(	core::pose::Pose const &	original_pose,
		utility::vector1< std::pair< core::Size, core::Size > > const &	residue_map,
		utility::vector1< core::Size > &	pivots
	)

private

Pick the pivots for kinematic closure.

References core::conformation::Residue::atom_index(), atomlist_, protocols::generalized_kinematic_closure::get_original_pose_rsd(), core::conformation::Residue::has(), pivot_1_atmname_, pivot_1_rsd_, pivot_2_atmname_, pivot_2_rsd_, pivot_3_atmname_, pivot_3_rsd_, prune_extra_atoms(), core::pose::Pose::residue(), and runtime_assert_string_msg.

Referenced by doKIC().

void protocols::generalized_kinematic_closure::GeneralizedKIC::prune_extra_atoms ( utility::vector1< core::Size > & pivots )

private

Trims extra atoms from the start and end of the atom list, if the first and last pivots are not the fifth and fifth-last atoms, respectively.

References atomlist_, and runtime_assert_string_msg.

Referenced by pick_pivots().

void protocols::generalized_kinematic_closure::GeneralizedKIC::select_solution	(	core::pose::Pose &	pose,
		core::pose::Pose const &	original_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< utility::vector1< utility::vector1< core::Real > > > const &	torsions,
		utility::vector1< utility::vector1< utility::vector1< core::Real > > > const &	bondangles,
		utility::vector1< utility::vector1< utility::vector1< core::Real > > > const &	bondlengths,
		utility::vector1< core::Size > const &	nsol_for_attempt,
		core::Size const	total_solutions
	)		const

private

Applies the selector to choose a solution and set a loop pose.

Parameters

[in,out]	pose	– The loop to be closed. This function puts it into its new, closed conformation.
[in]	original_pose	– The original pose. Can be used for reference by selectors.
[in]	residue_map	– Mapping of (loop residue, original pose residue).
[in]	atomlist	– The list of (AtomID, original XYZ coordinates of atoms) representing the chain that was closed.
[in]	torsions	– Matrix of [closure attempt #][solution #][torsion #] with torsion values for each torsion angle in the chain. A selector will pick one solution.
[in]	bondangles	– Matrix of [closure attempt #][solution #][angle #] with bond angle values for each bond angle in the chain. A selector will pick one solution.
[in]	bondlengths	– Matrix of [closure attempt #][solution #][bondlength #] with bond length for each bond in the chain. A selector will pick one solution.
[in]	nsol_for_attempt	– List of the number of solutions for each attempt.
[in]	total_solutions	– Total number of solutions found.

References selector_.

Referenced by doKIC().

void protocols::generalized_kinematic_closure::GeneralizedKIC::set_build_ideal_geometry ( bool const buildideal )

inline

Set whether or not this mover builds ideal geometry for the loop, or uses the existing geometry, imperfect bond lengths/angles and all.

References build_ideal_geometry_.

void protocols::generalized_kinematic_closure::GeneralizedKIC::set_closure_attempts ( core::Size const attempts )

Set the number of closure attempts.

Perturbation, closure, and filtering is carried out for every closure attempt. Successful closures from ALL attempts are then selected from by selectors.

References n_closure_attempts_, and protocols::generalized_kinematic_closure::TR.

Referenced by parse_my_tag().

void protocols::generalized_kinematic_closure::GeneralizedKIC::set_mover_effect_on_bonded_geometry ( core::Size const effect )

Function to set the effect of this mover on parts of the pose that are covalently attached to the loop to be closed, but which aren't part of it. Settings are: 0 – Moves the loop only; can pull apart covalent bonds to anything outside of the loop that isn't an anchor point. 1 – Moves the loop and anything downstream of the loop in the foldtree. Can still pull apart connections to non-child geometry.

References effect_on_bonded_geometry_, and utility_exit_with_message.

void protocols::generalized_kinematic_closure::GeneralizedKIC::set_n_closure_attempts_is_a_maximum ( bool const is_max )

inline

Sets whether the number of closure attempts is a maximum number of attempts.

If true, attempts are made until a solution is found OR n_closure_attempts_ is reached. If false, n_closure_attempts_ attempts are made, and then a solution is chosen from among the successful solutions (if any).

References n_closure_attempts_is_a_maximum_.

Referenced by parse_my_tag().

void protocols::generalized_kinematic_closure::GeneralizedKIC::set_ntries_before_giving_up ( core::Size const ntries )

Sets number of tries before giving up.

If this is set to 0, then no such check is made. The algorithm tries n_closure_attempts_ times if and only if at least one solution is found in the first ntries_before_giving_up_ attempts.

References ntries_before_giving_up_, and protocols::generalized_kinematic_closure::TR.

Referenced by parse_my_tag().

void protocols::generalized_kinematic_closure::GeneralizedKIC::set_perturber_effect	(	core::Size const	perturber_index,
		perturber::perturber_effect const &	effect
	)

Set a perturber's effect.

Detailed:

Parameters

[in]	perturber_index	– The index in the list of perturbers already added.
[in]	effect	– The perturber effect type, based on the perturber::perturber_effect enum (e.g. set_dihedral, randomize_backbone, etc.).

References perturberlist_, and runtime_assert_string_msg.

void protocols::generalized_kinematic_closure::GeneralizedKIC::set_pivot_atoms	(	core::Size const	rsd1,
		std::string const &	at1,
		core::Size const	rsd2,
		std::string const &	at2,
		core::Size const	rsd3,
		std::string const &	at3
	)

Function to set the pivot atoms for kinematic closure:

References pivot_1_atmname_, pivot_1_rsd_, pivot_2_atmname_, pivot_2_rsd_, pivot_3_atmname_, and pivot_3_rsd_.

Referenced by parse_my_tag().

void protocols::generalized_kinematic_closure::GeneralizedKIC::set_selector_kbt ( core::Real const & kbt )

Set the selector's Boltzmann temperature value.

References selector_.

Referenced by parse_my_tag().

void protocols::generalized_kinematic_closure::GeneralizedKIC::set_selector_scorefunction ( core::scoring::ScoreFunctionOP sfxn )

Set the selector's scorefunction.

References selector_.

Referenced by parse_my_tag().

void protocols::generalized_kinematic_closure::GeneralizedKIC::set_selector_type ( selector::selector_type const & stype )

Set the selector (the algorithm controlling how a solution will be chosen from among the solutions passing filters).

References selector_.

Referenced by parse_my_tag().

void protocols::generalized_kinematic_closure::GeneralizedKIC::set_selector_type ( std::string const & stypename )

Set the selector (the algorithm controlling how a solution will be chosen from among the solutions passing filters). This sets the selector by name.

References selector_.

Member Data Documentation

utility::vector1< std::pair < core::id::AtomID, numeric::xyzVector<core::Real> > > protocols::generalized_kinematic_closure::GeneralizedKIC::atomlist_

private

List of the atoms in the segment to be closed, and their x,y,z coordinates. Note that the atomIDs refer to residue indices that correspond to the temporary pose created by the apply() function, not to the indices in the original pose.

Referenced by apply_perturbations(), doKIC(), generate_atomlist(), generate_bridgeobjects_data_from_atomlist(), pick_pivots(), and prune_extra_atoms().

bool protocols::generalized_kinematic_closure::GeneralizedKIC::build_ideal_geometry_

private

Should the mover build ideal geometry for the loop to be closed? Default true.

Referenced by apply(), get_build_ideal_geometry(), and set_build_ideal_geometry().

core::Size protocols::generalized_kinematic_closure::GeneralizedKIC::effect_on_bonded_geometry_

private

The effect of the GeneralizedKIC mover on geometry that is covalently bound to the loop to be closed, but which is not part of that loop segment. 0 means that the mover will only move the loop, possibly tearing apart covalent bonds to other parts of the pose. 1 means that the mover will move the loop along with anything that is downstream in the FoldTree.

Referenced by apply(), get_mover_effect_on_bonded_geometry(), and set_mover_effect_on_bonded_geometry().

filter::GeneralizedKICfilterOPs protocols::generalized_kinematic_closure::GeneralizedKIC::filterlist_

private

List of GeneralizedKICfilters to apply to eliminate bad solutions.

Referenced by add_filter(), add_filter_parameter(), and filter_solutions().

bool protocols::generalized_kinematic_closure::GeneralizedKIC::last_run_successful_

private

Was the last apply() successful in generating a new kinematically-closed structure?

Referenced by apply(), and last_run_successful().

utility::vector1< core::Size > protocols::generalized_kinematic_closure::GeneralizedKIC::loopresidues_

private

The list of residues (as inidices of the original pose) making up the loop to be closed.

Referenced by add_loop_residue(), addloopgeometry(), addloweranchor(), addupperanchor(), apply(), and infer_anchor_connIDs().

core::Size protocols::generalized_kinematic_closure::GeneralizedKIC::lower_anchor_connID_

private

The lower end of the loop to be closed is presumably connected to geometry that is not moved by this mover. However, the connection could be through backbone or sidechain. The mover needs to know the connection ID on the lower end of the loop to the anchor geometry. Note: This will be set to 0 if the only connection that this residue can form is to the loop.

Referenced by addloopgeometry(), addloweranchor(), and infer_anchor_connIDs().

core::Size protocols::generalized_kinematic_closure::GeneralizedKIC::n_closure_attempts_

private

The number of closure attempts to carry out.

Perturbation, closure, and filtering is carried out for every closure attempt. Successful closures from ALL attempts are then selected from by selectors. Zero means no limit.

Referenced by doKIC(), get_closure_attempts(), and set_closure_attempts().

bool protocols::generalized_kinematic_closure::GeneralizedKIC::n_closure_attempts_is_a_maximum_

private

Should n_closure_attempts_ be the number attempted, or a maximum number of attempts? If false, n_closure_attempts_ attempts are made, and then a solution is chosen. If true, attempts are made until a solution is found OR n_closure_attempts_ is reached.

Referenced by n_closure_attempts_is_a_maximum(), and set_n_closure_attempts_is_a_maximum().

core::Size protocols::generalized_kinematic_closure::GeneralizedKIC::ntries_before_giving_up_

private

The number of tries to make before giving up if no solution has been found yet.

If this is set to 0, then no such check is made. The algorithm tries n_closure_attempts_ times if and only if at least one solution is found in the first ntries_before_giving_up_ attempts.

Referenced by get_ntries_before_giving_up(), and set_ntries_before_giving_up().

perturber::GeneralizedKICperturberOPs protocols::generalized_kinematic_closure::GeneralizedKIC::perturberlist_

private

List of GeneralizedKICperturbers to apply prior to kinematic closure.

Referenced by add_atomset_to_perturber_atomset_list(), add_perturber(), add_residue_to_perturber_residue_list(), add_value_to_perturber_value_list(), apply_perturbations(), and set_perturber_effect().

std::string protocols::generalized_kinematic_closure::GeneralizedKIC::pivot_1_atmname_

private

Pivot atom 1 name.

Referenced by pick_pivots(), and set_pivot_atoms().

core::Size protocols::generalized_kinematic_closure::GeneralizedKIC::pivot_1_rsd_

private

Pivot residue 1 (index based on original pose).

Referenced by pick_pivots(), and set_pivot_atoms().

std::string protocols::generalized_kinematic_closure::GeneralizedKIC::pivot_2_atmname_

private

Pivot atom 2 name.

Referenced by pick_pivots(), and set_pivot_atoms().

core::Size protocols::generalized_kinematic_closure::GeneralizedKIC::pivot_2_rsd_

private

Pivot residue 2 (index based on original pose).

Referenced by pick_pivots(), and set_pivot_atoms().

std::string protocols::generalized_kinematic_closure::GeneralizedKIC::pivot_3_atmname_

private

Pivot atom 3 name.

Referenced by pick_pivots(), and set_pivot_atoms().

core::Size protocols::generalized_kinematic_closure::GeneralizedKIC::pivot_3_rsd_

private

Pivot residue 3 (index based on original pose).

Referenced by pick_pivots(), and set_pivot_atoms().

protocols::filters::ContingentFilterOP protocols::generalized_kinematic_closure::GeneralizedKIC::rosettascripts_filter_

private

Owning pointer for the RosettaScripts ContingentFilter associated with this mover, if there is one.

Referenced by apply(), and parse_my_tag().

bool protocols::generalized_kinematic_closure::GeneralizedKIC::rosettascripts_filter_exists_

private

Bool determining whether there exists a RosettaScripts ContingentFilter associated with this mover.

Referenced by apply(), and parse_my_tag().

selector::GeneralizedKICselectorOP protocols::generalized_kinematic_closure::GeneralizedKIC::selector_

private

The selection algorithm to use to pick a solution from the set of solutions passing the filters.

Referenced by get_selector_type(), get_selector_type_name(), select_solution(), set_selector_kbt(), set_selector_scorefunction(), and set_selector_type().

core::Size protocols::generalized_kinematic_closure::GeneralizedKIC::upper_anchor_connID_

private

The upper end of the loop to be closed is presumably connected to geometry that is not moved by this mover. However, the connection could be through backbone or sidechain. The mover needs to know the connection ID on the upper end of the loop to the anchor geometry. Note: This will be set to 0 if the only connection that this residue can form is to the loop.

Referenced by addupperanchor(), and infer_anchor_connIDs().

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

src/protocols/generalized_kinematic_closure/GeneralizedKIC.hh
src/protocols/generalized_kinematic_closure/GeneralizedKIC.cc

Public Member Functions

Private Member Functions

Private Attributes

Additional Inherited Members

Constructor & Destructor Documentation

Member Function Documentation

Member Data Documentation