#include <MakeRotLibMover.hh>

Inheritance diagram for protocols::make_rot_lib::MakeRotLibMover:

[legend]

Public Member Functions
	MakeRotLibMover (bool const write_log_file=true)
	Default constructor. More...

	~MakeRotLibMover () override=default

void	apply (core::pose::Pose &pose) override
	Main Method. More...

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

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

void	init_rotamers (TorsionRangeVec const &chi_ranges, core::Size num_clusters, core::Real omg, utility::vector1< core::Real > bbs, utility::vector1< core::Size > bbids, core::Real eps, bool semirotameric)
	Initializes rotamer arrays based on data from the MRLOptionsData. More...

void	minimize_rotamer (RotData &rd, core::pose::Pose &pose, utility::vector1< core::Real > bbs, utility::vector1< core::Size > bb_ids, MakeRotLibPolymerType polymer_type)

void	minimize_all_rotamers (core::pose::Pose &pose, utility::vector1< core::Real > bbs, utility::vector1< core::Size > bb_ids, MakeRotLibPolymerType polymer_type)

void	seed_centroids (bool semirotameric)
	For k-medoids, seed centroids to nearest element of rotamers_. More...

void	calc_all_dist ()

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

bool	calc_medoids ()

bool	calc_centroids ()

bool	bbs_appropriate_for_definitions (utility::vector1< core::Real > bbs)
	returns if you should print definitions from this file More...

void	calc_final_rotamers ()

void	calc_final_rotamer_probs ()

void	calc_standard_deviations (core::pose::Pose &pose, utility::vector1< core::Real > bbs, utility::vector1< core::Size > bb_ids, MakeRotLibPolymerType polymer_type)

void	make_two_fold_symmetry_135_315 (RotDataVec &rdv, core::Size chi_num)
	brief Use to symmetrize if the 2 rotamers are falling near 0 (360) and 90 (270) like the symmetric chi2 of phenylalanine More...

void	make_two_fold_symmetry_0_180 (RotDataVec &rdv, core::Size chi_num)
	brief Use to symmetrize if the 1 rotamer is falling near 90 (270) like the symmetric chi1 of a n-aryl peptoid More...

void	make_three_fold_symmetry_90_210_330 (RotDataVec &rdv, core::Size chi_num)
	brief Use to symmetrize if the 2 rotamers are falling near 0 and 60 like with a tert-butyl group More...

void	print_rot_data (RotData &rd, utility::vector1< core::Size > bb_ids, std::ostream &os)

void	print_rot_data_vec (RotDataVec &rdv, utility::vector1< core::Size > bb_ids, std::ostream &os)

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

void	print_dunbrack02_rotlib (core::Real omg, utility::vector1< core::Real > bbs, utility::vector1< core::Size > bbids, core::Real eps, MakeRotLibPolymerType polymer_type, std::ostream &os)

void	print_definitions (std::ostream &os)

void	print_dunbrack10_rotlib (core::Real omg, utility::vector1< core::Real > bbs, utility::vector1< core::Size > bbids, 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 MoverOP	create ()

MoverCOP	get_self_ptr () const

MoverOP	get_self_ptr ()

MoverCAP	get_self_weak_ptr () const

MoverAP	get_self_weak_ptr ()

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

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...

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

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...

void	set_type (std::string const &setting)
	Set the 'type' string. More...

std::string	get_type () const

void	type (const std::string &type_in)
	Set the 'type' string. More...

std::string const &	type () const
	Get the set 'type' string. More...

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	parse_my_tag (TagCOP tag, basic::datacache::DataMap &data)
	Called by MoverFactory when constructing new Movers. Takes care of the specific mover's parsing. More...

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

jobdist::BasicJobCOP	get_current_job () const

virtual void	set_current_tag (std::string const &new_tag)

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...

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

virtual core::Real	last_proposal_density_ratio ()

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 void	provide_citation_info (basic::citation_manager::CitationCollectionList &) const
	Provide citations to the passed CitationCollectionList Subclasses should add the info for themselves and any other classes they use. More...

Private Attributes
core::scoring::ScoreFunctionOP	scrfxn_

core::Real	KbT_

RotDataVec	centroids_

RotDataVec	rotamers_

RotDataVec	final_rotamers_

bool	write_log_file_
	Are we writing a logfile for each application of the mover? Defaults to true, but can be disabled. 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 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

◆ MakeRotLibMover()

protocols::make_rot_lib::MakeRotLibMover::MakeRotLibMover ( bool const write_log_file = true )

Default constructor.

References core::scoring::get_score_function(), scrfxn_, protocols::make_rot_lib::TR(), and write_log_file_.

◆ ~MakeRotLibMover()

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

overridedefault

Member Function Documentation

◆ angle_diff()

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

Referenced by calc_dist().

◆ apply()

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

overridevirtual

◆ bbs_appropriate_for_definitions()

bool protocols::make_rot_lib::MakeRotLibMover::bbs_appropriate_for_definitions ( utility::vector1< core::Real > bbs )

returns if you should print definitions from this file

Referenced by apply().

◆ calc_all_dist()

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

References calc_dist(), centroids_, and rotamers_.

Referenced by apply().

◆ calc_centroids()

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

References calc_running_avg(), centroids_, and rotamers_.

Referenced by apply().

◆ calc_dist()

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(), calc_medoids(), and seed_centroids().

◆ calc_final_rotamer_probs()

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

References final_rotamers_, KbT_, and protocols::make_rot_lib::TR().

Referenced by apply().

◆ calc_final_rotamers()

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

References centroids_, final_rotamers_, protocols::jd2::JobDistributor::get_instance(), and rotamers_.

Referenced by apply().

◆ calc_medoids()

bool protocols::make_rot_lib::MakeRotLibMover::calc_medoids ( )

References calc_dist(), centroids_, and rotamers_.

Referenced by apply().

◆ calc_rotamer_clusters()

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

Determins closest cluster centroid for all rotamers.

References rotamers_.

Referenced by apply().

◆ calc_running_avg()

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 )

Referenced by calc_centroids().

◆ calc_standard_deviations()

void protocols::make_rot_lib::MakeRotLibMover::calc_standard_deviations	(	core::pose::Pose &	pose,
		utility::vector1< core::Real >	bbs,
		utility::vector1< core::Size >	bb_ids,
		MakeRotLibPolymerType	polymer_type
	)

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

Referenced by apply().

◆ get_name()

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

inlineoverridevirtual

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

Implements protocols::moves::Mover.

◆ init_centroids()

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

Initializes centroid arrays based on data from the MRLOptionsData.

References centroids_.

Referenced by apply().

◆ init_rotamers()

void protocols::make_rot_lib::MakeRotLibMover::init_rotamers	(	TorsionRangeVec const &	chi_ranges,
		core::Size	num_clusters,
		core::Real	omg,
		utility::vector1< core::Real >	bbs,
		utility::vector1< core::Size >	bbids,
		core::Real	eps,
		bool	semirotameric
	)

Initializes rotamer arrays based on data from the MRLOptionsData.

References rotamers_.

Referenced by apply().

◆ make_three_fold_symmetry_90_210_330()

void protocols::make_rot_lib::MakeRotLibMover::make_three_fold_symmetry_90_210_330	(	RotDataVec &	rdv,
		core::Size	chi_num
	)

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

Referenced by apply().

◆ make_two_fold_symmetry_0_180()

void protocols::make_rot_lib::MakeRotLibMover::make_two_fold_symmetry_0_180	(	RotDataVec &	rdv,
		core::Size	chi_num
	)

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

Referenced by apply().

◆ make_two_fold_symmetry_135_315()

void protocols::make_rot_lib::MakeRotLibMover::make_two_fold_symmetry_135_315	(	RotDataVec &	rdv,
		core::Size	chi_num
	)

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

Referenced by apply().

◆ minimize_all_rotamers()

void protocols::make_rot_lib::MakeRotLibMover::minimize_all_rotamers	(	core::pose::Pose &	pose,
		utility::vector1< core::Real >	bbs,
		utility::vector1< core::Size >	bb_ids,
		MakeRotLibPolymerType	polymer_type
	)

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

Referenced by apply().

◆ minimize_rotamer()

void protocols::make_rot_lib::MakeRotLibMover::minimize_rotamer	(	RotData &	rd,
		core::pose::Pose &	pose,
		utility::vector1< core::Real >	bbs,
		utility::vector1< core::Size >	bb_ids,
		MakeRotLibPolymerType	polymer_type
	)

Referenced by calc_standard_deviations(), and minimize_all_rotamers().

◆ print_avg_cluster_centroid_dist()

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

References centroids_, and rotamers_.

Referenced by apply().

◆ print_definitions()

void protocols::make_rot_lib::MakeRotLibMover::print_definitions ( std::ostream & os )

References centroids_, final_rotamers_, and core::sequence::left.

Referenced by apply().

◆ print_dunbrack02_rotlib()

void protocols::make_rot_lib::MakeRotLibMover::print_dunbrack02_rotlib	(	core::Real	omg,
		utility::vector1< core::Real >	bbs,
		utility::vector1< core::Size >	bbids,
		core::Real	eps,
		MakeRotLibPolymerType	polymer_type,
		std::ostream &	os
	)

References centroids_, final_rotamers_, protocols::mean_field::max(), and protocols::make_rot_lib::PEPTOID.

Referenced by apply().

◆ print_dunbrack10_rotlib()

void protocols::make_rot_lib::MakeRotLibMover::print_dunbrack10_rotlib	(	core::Real	omg,
		utility::vector1< core::Real >	bbs,
		utility::vector1< core::Size >	bbids,
		core::Real	eps,
		MakeRotLibPolymerType	polymer_type,
		std::ostream &	os
	)

References centroids_, final_rotamers_, protocols::mean_field::max(), and protocols::make_rot_lib::PEPTOID.

Referenced by apply().

◆ print_rot_data()

void protocols::make_rot_lib::MakeRotLibMover::print_rot_data	(	RotData &	rd,
		utility::vector1< core::Size >	bb_ids,
		std::ostream &	os
	)

Referenced by print_rot_data_vec().

◆ print_rot_data_vec()

void protocols::make_rot_lib::MakeRotLibMover::print_rot_data_vec	(	RotDataVec &	rdv,
		utility::vector1< core::Size >	bb_ids,
		std::ostream &	os
	)

References print_rot_data().

Referenced by apply().

◆ seed_centroids()

void protocols::make_rot_lib::MakeRotLibMover::seed_centroids ( bool semirotameric )

For k-medoids, seed centroids to nearest element of rotamers_.

References calc_dist(), centroids_, core::kinematics::distance(), and rotamers_.

Referenced by apply().

Member Data Documentation

◆ centroids_

RotDataVec protocols::make_rot_lib::MakeRotLibMover::centroids_

private

Referenced by apply(), calc_all_dist(), calc_centroids(), calc_final_rotamers(), calc_medoids(), init_centroids(), print_avg_cluster_centroid_dist(), print_definitions(), print_dunbrack02_rotlib(), print_dunbrack10_rotlib(), and seed_centroids().

◆ final_rotamers_

RotDataVec protocols::make_rot_lib::MakeRotLibMover::final_rotamers_

private

Referenced by apply(), calc_final_rotamer_probs(), calc_final_rotamers(), calc_standard_deviations(), print_definitions(), print_dunbrack02_rotlib(), and print_dunbrack10_rotlib().

◆ KbT_

core::Real protocols::make_rot_lib::MakeRotLibMover::KbT_

private

Referenced by apply(), calc_final_rotamer_probs(), and minimize_rotamer().

◆ rotamers_

RotDataVec protocols::make_rot_lib::MakeRotLibMover::rotamers_

private

Referenced by apply(), calc_all_dist(), calc_centroids(), calc_final_rotamers(), calc_medoids(), calc_rotamer_clusters(), init_rotamers(), minimize_all_rotamers(), print_avg_cluster_centroid_dist(), and seed_centroids().

◆ scrfxn_

core::scoring::ScoreFunctionOP protocols::make_rot_lib::MakeRotLibMover::scrfxn_

private

Referenced by calc_standard_deviations(), MakeRotLibMover(), and minimize_rotamer().

◆ write_log_file_

bool protocols::make_rot_lib::MakeRotLibMover::write_log_file_

private

Are we writing a logfile for each application of the mover? Defaults to true, but can be disabled.

Author: Vikram K. Mulligan (vmull.nosp@m.igan.nosp@m.@flat.nosp@m.iron.nosp@m.insti.nosp@m.tute.nosp@m..org)

Referenced by apply(), and MakeRotLibMover().

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

src/protocols/make_rot_lib/MakeRotLibMover.hh
src/protocols/make_rot_lib/MakeRotLibMover.cc

Public Member Functions

Private Attributes

Additional Inherited Members

Constructor & Destructor Documentation

◆ MakeRotLibMover()

◆ ~MakeRotLibMover()

Member Function Documentation

◆ angle_diff()

◆ apply()

◆ bbs_appropriate_for_definitions()

◆ calc_all_dist()

◆ calc_centroids()

◆ calc_dist()

◆ calc_final_rotamer_probs()

◆ calc_final_rotamers()

◆ calc_medoids()

◆ calc_rotamer_clusters()

◆ calc_running_avg()

◆ calc_standard_deviations()

◆ get_name()

◆ init_centroids()

◆ init_rotamers()

◆ make_three_fold_symmetry_90_210_330()

◆ make_two_fold_symmetry_0_180()

◆ make_two_fold_symmetry_135_315()

◆ minimize_all_rotamers()

◆ minimize_rotamer()

◆ print_avg_cluster_centroid_dist()

◆ print_definitions()

◆ print_dunbrack02_rotlib()

◆ print_dunbrack10_rotlib()

◆ print_rot_data()

◆ print_rot_data_vec()

◆ seed_centroids()

Member Data Documentation

◆ centroids_

◆ final_rotamers_

◆ KbT_

◆ rotamers_

◆ scrfxn_

◆ write_log_file_