#include <UnfoldedStateEnergyCalculatorMover.hh>

Inheritance diagram for protocols::unfolded_state_energy_calculator::UnfoldedStateEnergyCalculatorMover:

[legend]

Public Member Functions
	UnfoldedStateEnergyCalculatorMover (UnfoldedStateEnergyCalculatorJobDistributor &job_dist, core::scoring::ScoreFunctionCOP pack_scrfxn, core::scoring::ScoreFunctionCOP score_scrfxn, core::Size frag_length, std::string const &mut_aa, bool repack_fragments, bool native_sequence, std::string const &seq_match_seq, core::Size seq_match_pos, bool seq_match_frags)
	ctor More...

	~UnfoldedStateEnergyCalculatorMover () override
	dtor More...

	UnfoldedStateEnergyCalculatorMover (UnfoldedStateEnergyCalculatorMover const &usecm)
	cctor More...

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

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

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

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

bool	reinitialize_for_new_input () const override
	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...

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...

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 Member Functions
bool	fragment_check (Pose &pose, core::Size frag_start_pos)
	Check fragment residues should be polymeric and on same chain. More...

void	create_random_fragments (Pose &pose, utility::vector1< Pose > &fragments)

void	create_sequence_match_fragments (Pose &pose, utility::vector1< Pose > &fragments)

Private Attributes
UnfoldedStateEnergyCalculatorJobDistributor &	job_dist_

core::scoring::ScoreFunctionCOP	pack_scrfxn_

core::scoring::ScoreFunctionCOP	score_scrfxn_

core::Size	frag_length_

std::string	mut_aa_

bool	repack_fragments_

bool	native_sequence_

std::string	sequence_match_sequence_

core::Size	sequence_match_position_

bool	sequence_matched_fragments_

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

◆ UnfoldedStateEnergyCalculatorMover() [1/2]

protocols::unfolded_state_energy_calculator::UnfoldedStateEnergyCalculatorMover::UnfoldedStateEnergyCalculatorMover	(	UnfoldedStateEnergyCalculatorJobDistributor &	job_dist,
		core::scoring::ScoreFunctionCOP	pack_scrfxn,
		core::scoring::ScoreFunctionCOP	score_scrfxn,
		core::Size	frag_length,
		std::string const &	mut_aa,
		bool	repack_fragments,
		bool	native_sequence,
		std::string const &	seq_match_seq,
		core::Size	seq_match_pos,
		bool	seq_match_frags
	)

ctor

alternate ctor

◆ ~UnfoldedStateEnergyCalculatorMover()

protocols::unfolded_state_energy_calculator::UnfoldedStateEnergyCalculatorMover::~UnfoldedStateEnergyCalculatorMover ( )

overridedefault

dtor

◆ UnfoldedStateEnergyCalculatorMover() [2/2]

protocols::unfolded_state_energy_calculator::UnfoldedStateEnergyCalculatorMover::UnfoldedStateEnergyCalculatorMover ( UnfoldedStateEnergyCalculatorMover const & usecm )

cctor

Member Function Documentation

◆ apply()

void protocols::unfolded_state_energy_calculator::UnfoldedStateEnergyCalculatorMover::apply ( Pose & )

overridevirtual

Main Method.

Implements protocols::moves::Mover.

References protocols::unfolded_state_energy_calculator::UnfoldedStateEnergyCalculatorJobDistributor::add_unfolded_energy_data(), create_random_fragments(), create_sequence_match_fragments(), frag_length_, job_dist_, mut_aa_, native_sequence_, core::pack::pack_rotamers(), pack_scrfxn_, repack_fragments_, sequence_matched_fragments_, and protocols::unfolded_state_energy_calculator::UnfoldedStateEnergyCalculatorJobDistributor::set_energy_terms().

◆ create_random_fragments()

void protocols::unfolded_state_energy_calculator::UnfoldedStateEnergyCalculatorMover::create_random_fragments	(	Pose &	pose,
		utility::vector1< Pose > &	fragments
	)

private

References core::pose::Pose::append_residue_by_bond(), core::pose::Pose::append_residue_by_jump(), frag_length_, fragment_check(), core::chemical::ResidueTypeBase::is_protein(), core::pose::Pose::residue(), core::pose::Pose::size(), and core::conformation::Residue::type().

Referenced by apply().

◆ create_sequence_match_fragments()

void protocols::unfolded_state_energy_calculator::UnfoldedStateEnergyCalculatorMover::create_sequence_match_fragments	(	Pose &	pose,
		utility::vector1< Pose > &	fragments
	)

private

References core::pose::Pose::append_residue_by_bond(), core::pose::Pose::append_residue_by_jump(), frag_length_, fragment_check(), core::pose::Pose::residue(), core::pose::Pose::sequence(), sequence_match_position_, and sequence_match_sequence_.

Referenced by apply().

◆ fragment_check()

bool protocols::unfolded_state_energy_calculator::UnfoldedStateEnergyCalculatorMover::fragment_check	(	Pose &	pose,
		core::Size	frag_start_pos
	)

private

Check fragment residues should be polymeric and on same chain.

References core::pose::Pose::chain(), frag_length_, core::chemical::ResidueType::is_NA(), core::chemical::ResidueTypeBase::is_polymer(), core::pose::Pose::residue(), core::pose::Pose::size(), and core::conformation::Residue::type().

Referenced by create_random_fragments(), and create_sequence_match_fragments().

◆ fresh_instance()

protocols::moves::MoverOP protocols::unfolded_state_energy_calculator::UnfoldedStateEnergyCalculatorMover::fresh_instance ( ) const

overridevirtual

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::unfolded_state_energy_calculator::UnfoldedStateEnergyCalculatorMover::get_name ( ) const

overridevirtual

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

Implements protocols::moves::Mover.

◆ reinitialize_for_each_job()

bool protocols::unfolded_state_energy_calculator::UnfoldedStateEnergyCalculatorMover::reinitialize_for_each_job ( ) const

overridevirtual

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

Movers default to not regenerating

Reimplemented from protocols::moves::Mover.

◆ reinitialize_for_new_input()

bool protocols::unfolded_state_energy_calculator::UnfoldedStateEnergyCalculatorMover::reinitialize_for_new_input ( ) const

overridevirtual

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).

Movers default to not regenerating

Reimplemented from protocols::moves::Mover.

Member Data Documentation

◆ frag_length_

core::Size protocols::unfolded_state_energy_calculator::UnfoldedStateEnergyCalculatorMover::frag_length_

private

Referenced by apply(), create_random_fragments(), create_sequence_match_fragments(), and fragment_check().

◆ job_dist_

UnfoldedStateEnergyCalculatorJobDistributor& protocols::unfolded_state_energy_calculator::UnfoldedStateEnergyCalculatorMover::job_dist_

private

Referenced by apply().

◆ mut_aa_

std::string protocols::unfolded_state_energy_calculator::UnfoldedStateEnergyCalculatorMover::mut_aa_

private

Referenced by apply().

◆ native_sequence_

bool protocols::unfolded_state_energy_calculator::UnfoldedStateEnergyCalculatorMover::native_sequence_

private

Referenced by apply().

◆ pack_scrfxn_

core::scoring::ScoreFunctionCOP protocols::unfolded_state_energy_calculator::UnfoldedStateEnergyCalculatorMover::pack_scrfxn_

private

Referenced by apply().

◆ repack_fragments_

bool protocols::unfolded_state_energy_calculator::UnfoldedStateEnergyCalculatorMover::repack_fragments_

private

Referenced by apply().

◆ score_scrfxn_

core::scoring::ScoreFunctionCOP protocols::unfolded_state_energy_calculator::UnfoldedStateEnergyCalculatorMover::score_scrfxn_

private

◆ sequence_match_position_

core::Size protocols::unfolded_state_energy_calculator::UnfoldedStateEnergyCalculatorMover::sequence_match_position_

private

Referenced by create_sequence_match_fragments().

◆ sequence_match_sequence_

std::string protocols::unfolded_state_energy_calculator::UnfoldedStateEnergyCalculatorMover::sequence_match_sequence_

private

Referenced by create_sequence_match_fragments().

◆ sequence_matched_fragments_

bool protocols::unfolded_state_energy_calculator::UnfoldedStateEnergyCalculatorMover::sequence_matched_fragments_

private

Referenced by apply().

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

src/protocols/unfolded_state_energy_calculator/UnfoldedStateEnergyCalculatorMover.hh
src/protocols/unfolded_state_energy_calculator/UnfoldedStateEnergyCalculatorMover.cc

Public Member Functions

Private Member Functions

Private Attributes

Additional Inherited Members

Constructor & Destructor Documentation

◆ UnfoldedStateEnergyCalculatorMover() [1/2]

◆ ~UnfoldedStateEnergyCalculatorMover()

◆ UnfoldedStateEnergyCalculatorMover() [2/2]

Member Function Documentation

◆ apply()

◆ create_random_fragments()

◆ create_sequence_match_fragments()

◆ fragment_check()

◆ fresh_instance()

◆ get_name()

◆ reinitialize_for_each_job()

◆ reinitialize_for_new_input()

Member Data Documentation

◆ frag_length_

◆ job_dist_

◆ mut_aa_

◆ native_sequence_

◆ pack_scrfxn_

◆ repack_fragments_

◆ score_scrfxn_

◆ sequence_match_position_

◆ sequence_match_sequence_

◆ sequence_matched_fragments_