#include <MakeRotLibMover.hh>

Public Member Functions
	MakeRotLibMover ()
	Default constructor. More...

virtual	~MakeRotLibMover ()

virtual void	apply (core::pose::Pose &pose)

virtual std::string	get_name () const
	Each derived class must specify its name. The class name. More...

void	init_centroids (CentroidRotNumVecVec const &centroid_data, core::Size num_chi)
	Initializes centroid arrays based on data from the MRLOptionsData. More...

void	init_rotamers (TorsionRangeVec const &chi_ranges, core::Size num_clusters, core::Real omg, core::Real phi, core::Real psi, core::Real eps)
	Initializes rotamer arrays based on data from the MRLOptionsData. More...

void	minimize_rotamer (RotData &rd, core::pose::Pose &pose, MakeRotLibPolymerType polymer_type)

void	minimize_all_rotamers (core::pose::Pose &pose, MakeRotLibPolymerType polymer_type)

void	calc_all_dist ()

bool	calc_rotamer_clusters ()
	Determins closest cluster centroid for all rotamers. More...

bool	calc_centroids ()

void	calc_final_rotamers ()

void	calc_final_rotamer_probs ()

void	calc_standard_deviations (core::pose::Pose &pose, MakeRotLibPolymerType polymer_type)

void	make_two_fold_symetry_135_315 (RotDataVec &rdv, core::Size chi_num)
	brief Use to symetrize if the 2 rotamers are falling near 0 (360) and 90 (270) like the symetric chi2 of phenylalanine More...

void	make_two_fold_symetry_0_180 (RotDataVec &rdv, core::Size chi_num)
	brief Use to symetrize if the 1 rotamer is falling near 90 (270) like the symetric chi1 of a n-aryl peptoid More...

void	make_three_fold_symetry_90_210_330 (RotDataVec &rdv, core::Size chi_num)
	brief Use to symetrize if the 2 rotamers are falling near 0 and 60 like with a tert-butyl group More...

void	print_rot_data (RotData &rd, std::ostream &os)

void	print_rot_data_vec (RotDataVec &rdv, std::ostream &os)

core::Real	print_avg_cluster_centroid_dist (std::ostream &os)

void	print_dunbrack02_rotlib (core::Real omg, core::Real phi, core::Real psi, core::Real eps, MakeRotLibPolymerType polymer_type, std::ostream &os)

core::Real	calc_dist (RotData &rd1, RotData &rd2)

core::Real	angle_diff (core::Real a1, core::Real a2)

void	calc_running_avg (core::Real angle_new, core::Real &angle_old, core::Size &count)
	calculates a runnig average. Tries to use the closest anglular value ( ie. the average of 350 degrees and 10 degrees should be 0 and not 180 )( ie. the average of 170 degrees and -170 degrees should be 180 and not 0 ) 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)

virtual MoverOP	clone () const
	Return a clone of the Mover object. More...

virtual void	parse_my_tag (TagCOP tag, basic::datacache::DataMap &data, Filters_map const &filters, Movers_map const &movers, Pose const &pose)
	Called by MoverFactory when constructing new Movers. Takes care of the specific mover's parsing. More...

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...

virtual MoverOP	fresh_instance () const
	Generates a new Mover object freshly created with the default ctor. 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 Attributes
core::scoring::ScoreFunctionOP	scrfxn_

RotDataVec	centroids_

RotDataVec	rotamers_

RotDataVec	final_rotamers_

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::make_rot_lib::MakeRotLibMover::MakeRotLibMover ( )

Default constructor.

References fa_atr, fa_dun, fa_intra_atr, fa_intra_rep, fa_rep, mm_lj_inter_atr, mm_lj_inter_rep, mm_lj_intra_atr, mm_lj_intra_rep, mm_twist, p_aa_pp, PRE_TALARIS_2013_STANDARD_WTS, rama, scrfxn_, and protocols::make_rot_lib::TR.

virtual protocols::make_rot_lib::MakeRotLibMover::~MakeRotLibMover ( )

inlinevirtual

Member Function Documentation

core::Real protocols::make_rot_lib::MakeRotLibMover::angle_diff	(	core::Real	a1,
		core::Real	a2
	)

Referenced by calc_dist().

void protocols::make_rot_lib::MakeRotLibMover::apply ( core::pose::Pose & pose )

virtual

void protocols::make_rot_lib::MakeRotLibMover::calc_all_dist ( )

References calc_dist(), centroids_, and rotamers_.

Referenced by apply().

bool protocols::make_rot_lib::MakeRotLibMover::calc_centroids ( )

References calc_running_avg(), centroids_, and rotamers_.

Referenced by apply().

core::Real protocols::make_rot_lib::MakeRotLibMover::calc_dist	(	RotData &	rd1,
		RotData &	rd2
	)

References angle_diff(), protocols::make_rot_lib::RotData::get_min_chi(), and protocols::make_rot_lib::RotData::get_num_chi().

Referenced by calc_all_dist().

void protocols::make_rot_lib::MakeRotLibMover::calc_final_rotamer_probs ( )

References final_rotamers_, and protocols::make_rot_lib::TR.

Referenced by apply().

void protocols::make_rot_lib::MakeRotLibMover::calc_final_rotamers ( )

References centroids_, final_rotamers_, num_clusters, and rotamers_.

Referenced by apply().

bool protocols::make_rot_lib::MakeRotLibMover::calc_rotamer_clusters ( )

Determins closest cluster centroid for all rotamers.

References rotamers_.

Referenced by apply().

void protocols::make_rot_lib::MakeRotLibMover::calc_running_avg	(	core::Real	angle_new,
		core::Real &	angle_old,
		core::Size &	count
	)

calculates a runnig average. Tries to use the closest anglular value ( ie. the average of 350 degrees and 10 degrees should be 0 and not 180 )( ie. the average of 170 degrees and -170 degrees should be 180 and not 0 )

References numeric::nonnegative_principal_angle_degrees(), and numeric::principal_angle_degrees().

Referenced by calc_centroids().

void protocols::make_rot_lib::MakeRotLibMover::calc_standard_deviations	(	core::pose::Pose &	pose,
		MakeRotLibPolymerType	polymer_type
	)

References final_rotamers_, minimize_rotamer(), numeric::nonnegative_principal_angle_degrees(), scrfxn_, core::pose::Pose::set_chi(), and protocols::make_rot_lib::TR.

Referenced by apply().

virtual std::string protocols::make_rot_lib::MakeRotLibMover::get_name ( ) const

inlinevirtual

Each derived class must specify its name. The class name.

Implements protocols::moves::Mover.

void protocols::make_rot_lib::MakeRotLibMover::init_centroids	(	CentroidRotNumVecVec const &	centroid_data,
		core::Size	num_chi
	)

Initializes centroid arrays based on data from the MRLOptionsData.

References angle, and centroids_.

Referenced by apply().

void protocols::make_rot_lib::MakeRotLibMover::init_rotamers	(	TorsionRangeVec const &	chi_ranges,
		core::Size	num_clusters,
		core::Real	omg,
		core::Real	phi,
		core::Real	psi,
		core::Real	eps
	)

Initializes rotamer arrays based on data from the MRLOptionsData.

References l, and rotamers_.

Referenced by apply().

void protocols::make_rot_lib::MakeRotLibMover::make_three_fold_symetry_90_210_330	(	RotDataVec &	rdv,
		core::Size	chi_num
	)

brief Use to symetrize if the 2 rotamers are falling near 0 and 60 like with a tert-butyl group

References numeric::nonnegative_principal_angle_degrees().

Referenced by apply().

void protocols::make_rot_lib::MakeRotLibMover::make_two_fold_symetry_0_180	(	RotDataVec &	rdv,
		core::Size	chi_num
	)

brief Use to symetrize if the 1 rotamer is falling near 90 (270) like the symetric chi1 of a n-aryl peptoid

References numeric::nonnegative_principal_angle_degrees().

Referenced by apply().

void protocols::make_rot_lib::MakeRotLibMover::make_two_fold_symetry_135_315	(	RotDataVec &	rdv,
		core::Size	chi_num
	)

brief Use to symetrize if the 2 rotamers are falling near 0 (360) and 90 (270) like the symetric chi2 of phenylalanine

References numeric::nonnegative_principal_angle_degrees().

Referenced by apply().

void protocols::make_rot_lib::MakeRotLibMover::minimize_all_rotamers	(	core::pose::Pose &	pose,
		MakeRotLibPolymerType	polymer_type
	)

References minimize_rotamer(), rotamers_, and protocols::make_rot_lib::TR.

Referenced by apply().

void protocols::make_rot_lib::MakeRotLibMover::minimize_rotamer	(	RotData &	rd,
		core::pose::Pose &	pose,
		MakeRotLibPolymerType	polymer_type
	)

Referenced by calc_standard_deviations(), and minimize_all_rotamers().

core::Real protocols::make_rot_lib::MakeRotLibMover::print_avg_cluster_centroid_dist ( std::ostream & os )

References centroids_, and rotamers_.

Referenced by apply().

void protocols::make_rot_lib::MakeRotLibMover::print_dunbrack02_rotlib	(	core::Real	omg,
		core::Real	phi,
		core::Real	psi,
		core::Real	eps,
		MakeRotLibPolymerType	polymer_type,
		std::ostream &	os
	)