#include <SecStructFinder.hh>

Inheritance diagram for protocols::ncbb::SecStructFinder:

[legend]

Public Member Functions
	SecStructFinder ()

	SecStructFinder (std::string const &residue, core::Size min_length=5, core::Size max_length=5, core::Real bin_size=10, core::Real dissimilarity=10, core::Real dihedral_min=-180, core::Real dihedral_max=180, core::Real dump_threshold=-10000, std::string dihedral_pattern="A", std::string alpha_beta_pattern="A", bool min_everything=false, bool cart=false, bool constrain=false)

	~SecStructFinder () 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...

protocols::moves::MoverOP	fresh_instance () const override
	Generates a new Mover object freshly created with the default ctor. More...

protocols::moves::MoverOP	clone () const override
	Return a clone of the Mover object. More...

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

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

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 Member Functions
std::string	alpha_to_beta (std::string alpha)

std::string	expand_pattern_to_fit (std::string pattern, core::Size length)

bool	uniq_refers_to_beta (char uniq)

void	initialize_pose (core::pose::Pose &pose)

std::string	make_filename (core::Size number_dihedrals, utility::vector1< core::Real > dihedrals)

bool	too_similar (core::Size i, core::Size j, utility::vector1< core::Real > dihedrals)

void	show_current_dihedrals (core::Size number_dihedral_sets, utility::vector1< char > uniqs, utility::vector1< core::Real > dihedrals)

Private Attributes
core::scoring::ScoreFunctionOP	score_fxn_

std::string	residue_

core::Size	min_length_

core::Size	max_length_

core::Real	bin_size_

core::Real	dump_threshold_

core::Real	dihedral_min_

core::Real	dihedral_max_

std::string	dihedral_pattern_

std::string	alpha_beta_pattern_

bool	min_everything_

bool	cart_

bool	constrain_

core::Real	dissimilarity_

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

◆ SecStructFinder() [1/2]

protocols::ncbb::SecStructFinder::SecStructFinder ( )

References core::scoring::constraints::add_fa_constraints_from_cmdline_to_scorefxn(), core::scoring::get_score_function(), and score_fxn_.

◆ SecStructFinder() [2/2]

protocols::ncbb::SecStructFinder::SecStructFinder	(	std::string const &	residue,
		core::Size	min_length = `5`,
		core::Size	max_length = `5`,
		core::Real	bin_size = `10`,
		core::Real	dissimilarity = `10`,
		core::Real	dihedral_min = `-180`,
		core::Real	dihedral_max = `180`,
		core::Real	dump_threshold = `-10000`,
		std::string	dihedral_pattern = `"A"`,
		std::string	alpha_beta_pattern = `"A"`,
		bool	min_everything = `false`,
		bool	cart = `false`,
		bool	constrain = `false`
	)

References core::scoring::constraints::add_fa_constraints_from_cmdline_to_scorefxn(), alpha_beta_pattern_, dihedral_max_, dihedral_min_, dihedral_pattern_, expand_pattern_to_fit(), core::scoring::get_score_function(), max_length_, min_length_, and score_fxn_.

◆ ~SecStructFinder()

protocols::ncbb::SecStructFinder::~SecStructFinder ( )

overridedefault

Member Function Documentation

◆ alpha_to_beta()

std::string protocols::ncbb::SecStructFinder::alpha_to_beta ( std::string alpha )

private

Referenced by initialize_pose().

◆ apply()

void protocols::ncbb::SecStructFinder::apply ( core::pose::Pose & )

overridevirtual

Main Method.

Implements protocols::moves::Mover.

◆ clone()

protocols::moves::MoverOP protocols::ncbb::SecStructFinder::clone ( ) const

overridevirtual

Return a clone of the Mover object.

clone is meant to return an OP'ed deep copy of this object. This really should be a pure virtual in the base class, but adding pure virtuals to Mover would massively disrupt the code. This default implementation crashes at runtime instead of compiletime if you try to call it. If this code is causing you problems, your Mover needs to override this function.

Reimplemented from protocols::moves::Mover.

References alpha_beta_pattern_, bin_size_, cart_, dihedral_max_, dihedral_min_, dihedral_pattern_, dissimilarity_, dump_threshold_, max_length_, min_everything_, min_length_, and residue_.

◆ expand_pattern_to_fit()

std::string protocols::ncbb::SecStructFinder::expand_pattern_to_fit	(	std::string	pattern,
		core::Size	length
	)

private

Referenced by parse_my_tag(), and SecStructFinder().

◆ fresh_instance()

protocols::moves::MoverOP protocols::ncbb::SecStructFinder::fresh_instance ( ) const

inlineoverridevirtual

Generates a new Mover object freshly created with the default ctor.

fresh_instance is meant to return a new object of this class, created with the default constructor. This really should be a pure virtual in the base class, but adding pure virtuals to Mover would massively disrupt the code. This default implementation crashes at runtime instead of compiletime if you try to call it. If this code is causing you problems, your Mover needs to override this function. This is used by the August 08 job distributor.

Reimplemented from protocols::moves::Mover.

◆ get_name()

std::string protocols::ncbb::SecStructFinder::get_name ( ) const

inlineoverridevirtual

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

Implements protocols::moves::Mover.

◆ initialize_pose()

void protocols::ncbb::SecStructFinder::initialize_pose ( core::pose::Pose & pose )

private

References alpha_beta_pattern_, alpha_to_beta(), core::pose::Pose::append_residue_by_bond(), core::pose::Pose::append_residue_by_jump(), core::chemical::FA_STANDARD, min_length_, protocols::moves::Mover::name(), and residue_.

Referenced by apply().

◆ make_filename()

std::string protocols::ncbb::SecStructFinder::make_filename	(	core::Size	number_dihedrals,
		utility::vector1< core::Real >	dihedrals
	)

private

References dihedral_pattern_, protocols::abinitio::filename(), min_length_, and residue_.

Referenced by apply().

◆ parse_my_tag()

void protocols::ncbb::SecStructFinder::parse_my_tag	(	utility::tag::TagCOP	tag,
		basic::datacache::DataMap &	data
	)

overridevirtual

Called by MoverFactory when constructing new Movers. Takes care of the specific mover's parsing.

Some movers need not be parsed, so we shouldn't force people to reimplement this method. However, we should be chatty about the fact that someone is using a RosettaScripts interface to a mover which didn't define parse_my_tag()

Reimplemented from protocols::moves::Mover.

References alpha_beta_pattern_, bin_size_, cart_, dihedral_pattern_, dissimilarity_, dump_threshold_, expand_pattern_to_fit(), max_length_, min_everything_, min_length_, residue_, and protocols::TR().

◆ show_current_dihedrals()

void protocols::ncbb::SecStructFinder::show_current_dihedrals	(	core::Size	number_dihedral_sets,
		utility::vector1< char >	uniqs,
		utility::vector1< core::Real >	dihedrals
	)