A mover to set mainchain torsions by bin transition probabilities. More...

#include <PerturbByBins.hh>

Inheritance diagram for protocols::simple_moves::bin_transitions::PerturbByBins:

[legend]

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

	PerturbByBins (PerturbByBins const &src)
	Copy constructor. More...

	~PerturbByBins () override
	Destructor. More...

protocols::moves::MoverOP	clone () const override
	Clone – i.e. create a new object copying this one and return an owning pointer to the copy. More...

protocols::moves::MoverOP	fresh_instance () const override
	Get a new instance of this mover (NOT copying). More...

void	apply (core::pose::Pose &pose) override
	Apply the mover to a pose. More...

void	parse_my_tag (utility::tag::TagCOP tag, basic::datacache::DataMap &) override
	Parse XML for RosettaScripts. More...

void	set_binfile_and_load (std::string const &name)
	Set the bin transition probability file. More...

void	set_residue_range (core::Size const start, core::Size const end)
	Set the residue ranges. If set to (0,0), the start and end of the pose are used as the range bounds. More...

void	set_repeats (core::Size const repeats_in)
	Set the number of repeats. More...

void	set_must_switch_bins (bool const val)
	Sets whether the residue that is being perturbed can stay within its own bin (in which case new mainchain torsions are drawn from within the bin), or whether it must jump to a different bin. True means it must jump. More...

core::Size	repeats () const
	Return the number of iterations at apply time. More...

bool	must_switch_bins () const
	Can the residue that is being perturbed stay within its own bin (in which case new mainchain torsions are drawn from within the bin), or must it jump to a different bin? More...

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

void	provide_citation_info (basic::citation_manager::CitationCollectionList &citations) const override
	Provide citations to the passed CitationCollectionList. 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...

Static Public Member Functions
static std::string	mover_name ()

static void	provide_xml_schema (utility::tag::XMLSchemaDefinition &xsd)

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...

Private Types
typedef protocols::moves::Mover	moverclass

Private Attributes
core::Size	start_res_ = 0
	Start of residue range. More...

core::Size	end_res_ = 0
	End of residue range. More...

std::string	binfile_ = "ABBA"
	Bin transition probability data file. More...

core::scoring::bin_transitions::BinTransitionCalculatorCOP	bin_transition_calculator_
	Owning pointer to the BinTransitionCalculator object used by this mover. More...

core::Size	repeats_ = 1
	How many times will this be applied? More...

bool	must_switch_bins_ = false
	Can the residue that is being perturbed stay within its own bin (in which case new mainchain torsions are drawn from within the bin), or must it jump to a different bin? Default false (i.e. need not switch bins). 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

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...

Detailed Description

A mover to set mainchain torsions by bin transition probabilities.

Member Typedef Documentation

◆ moverclass

typedef protocols::moves::Mover protocols::simple_moves::bin_transitions::PerturbByBins::moverclass

private

Constructor & Destructor Documentation

◆ PerturbByBins() [1/2]

protocols::simple_moves::bin_transitions::PerturbByBins::PerturbByBins ( )

Default constructor.

◆ PerturbByBins() [2/2]

protocols::simple_moves::bin_transitions::PerturbByBins::PerturbByBins ( PerturbByBins const & src )

Copy constructor.

◆ ~PerturbByBins()

protocols::simple_moves::bin_transitions::PerturbByBins::~PerturbByBins ( )

overridedefault

Destructor.

Member Function Documentation

◆ apply()

void protocols::simple_moves::bin_transitions::PerturbByBins::apply ( core::pose::Pose & pose )

overridevirtual

Apply the mover to a pose.

Implements protocols::moves::Mover.

References core::id::BB, bin_transition_calculator_, core::pose::Pose::conformation(), end_res_, core::conformation::Residue::mainchain_torsions(), must_switch_bins(), repeats(), core::pose::Pose::residue(), core::scoring::rg, core::pose::Pose::set_torsion(), core::pose::Pose::size(), start_res_, protocols::simple_moves::bin_transitions::TR(), and core::pose::Pose::update_residue_neighbors().

◆ clone()

protocols::moves::MoverOP protocols::simple_moves::bin_transitions::PerturbByBins::clone ( ) const

inlineoverridevirtual

Clone – i.e. create a new object copying this one and return an owning pointer to the copy.

Reimplemented from protocols::moves::Mover.

◆ fresh_instance()

protocols::moves::MoverOP protocols::simple_moves::bin_transitions::PerturbByBins::fresh_instance ( ) const

inlineoverridevirtual

Get a new instance of this mover (NOT copying).

Reimplemented from protocols::moves::Mover.

◆ get_name()

std::string protocols::simple_moves::bin_transitions::PerturbByBins::get_name ( ) const

overridevirtual

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

Implements protocols::moves::Mover.

References mover_name().

◆ mover_name()

std::string protocols::simple_moves::bin_transitions::PerturbByBins::mover_name ( )

static

Referenced by get_name(), protocols::simple_moves::bin_transitions::PerturbByBinsCreator::keyname(), provide_citation_info(), and provide_xml_schema().

◆ must_switch_bins()

bool protocols::simple_moves::bin_transitions::PerturbByBins::must_switch_bins ( ) const

inline

Can the residue that is being perturbed stay within its own bin (in which case new mainchain torsions are drawn from within the bin), or must it jump to a different bin?

References must_switch_bins_.

Referenced by apply().

◆ parse_my_tag()

void protocols::simple_moves::bin_transitions::PerturbByBins::parse_my_tag	(	utility::tag::TagCOP	tag,
		basic::datacache::DataMap &
	)

overridevirtual

Parse XML for RosettaScripts.

Reimplemented from protocols::moves::Mover.

References set_binfile_and_load(), set_must_switch_bins(), set_repeats(), set_residue_range(), and protocols::simple_moves::bin_transitions::TR().

◆ provide_citation_info()

void protocols::simple_moves::bin_transitions::PerturbByBins::provide_citation_info ( basic::citation_manager::CitationCollectionList & citations ) const

overridevirtual

Provide citations to the passed CitationCollectionList.

Reimplemented from protocols::moves::Mover.

References mover_name().

◆ provide_xml_schema()

void protocols::simple_moves::bin_transitions::PerturbByBins::provide_xml_schema ( utility::tag::XMLSchemaDefinition & xsd )

static

References mover_name(), and protocols::moves::xsd_type_definition_w_attributes().

Referenced by protocols::simple_moves::bin_transitions::PerturbByBinsCreator::provide_xml_schema().

◆ repeats()

core::Size protocols::simple_moves::bin_transitions::PerturbByBins::repeats ( ) const

inline

Return the number of iterations at apply time.

A value of 1 means that a single residue in the range will randomly be selected and flipped to another bin (with probabilities based on its neighbours and the bin transition probabilities. Higher values mean that this operation will be repeated. If set to 0, defaults to 1.

References repeats_.

Referenced by apply().

◆ set_binfile_and_load()

void protocols::simple_moves::bin_transitions::PerturbByBins::set_binfile_and_load ( std::string const & name )

Set the bin transition probability file.

Also, loads the object.

References bin_transition_calculator_, binfile_, protocols::moves::Mover::name(), and protocols::simple_moves::bin_transitions::TR().

Referenced by parse_my_tag().

◆ set_must_switch_bins()

void protocols::simple_moves::bin_transitions::PerturbByBins::set_must_switch_bins ( bool const val )

Sets whether the residue that is being perturbed can stay within its own bin (in which case new mainchain torsions are drawn from within the bin), or whether it must jump to a different bin. True means it must jump.

References must_switch_bins_, protocols::simple_moves::bin_transitions::TR(), and protocols::hybridization::val.

Referenced by parse_my_tag().

◆ set_repeats()

void protocols::simple_moves::bin_transitions::PerturbByBins::set_repeats ( core::Size const repeats_in )

Set the number of repeats.

A value of 1 means that a single residue in the range will randomly be selected and flipped to another bin (with probabilities based on its neighbours and the bin transition probabilities. Higher values mean that this operation will be repeated. If set to 0, defaults to 1.

References repeats_, and protocols::simple_moves::bin_transitions::TR().

Referenced by parse_my_tag().

◆ set_residue_range()

void protocols::simple_moves::bin_transitions::PerturbByBins::set_residue_range	(	core::Size const	start,
		core::Size const	end
	)

Set the residue ranges. If set to (0,0), the start and end of the pose are used as the range bounds.

References core::sequence::end, end_res_, protocols::loops::start, start_res_, and protocols::simple_moves::bin_transitions::TR().

Referenced by parse_my_tag().

Member Data Documentation

◆ bin_transition_calculator_

core::scoring::bin_transitions::BinTransitionCalculatorCOP protocols::simple_moves::bin_transitions::PerturbByBins::bin_transition_calculator_

private

Owning pointer to the BinTransitionCalculator object used by this mover.

Referenced by apply(), and set_binfile_and_load().

◆ binfile_

std::string protocols::simple_moves::bin_transitions::PerturbByBins::binfile_ = "ABBA"

private

Bin transition probability data file.

Defaults to "ABBA".

Referenced by set_binfile_and_load().

◆ end_res_

core::Size protocols::simple_moves::bin_transitions::PerturbByBins::end_res_ = 0

private

End of residue range.

Referenced by apply(), and set_residue_range().

◆ must_switch_bins_

bool protocols::simple_moves::bin_transitions::PerturbByBins::must_switch_bins_ = false

private

Can the residue that is being perturbed stay within its own bin (in which case new mainchain torsions are drawn from within the bin), or must it jump to a different bin? Default false (i.e. need not switch bins).

Referenced by must_switch_bins(), and set_must_switch_bins().

◆ repeats_

core::Size protocols::simple_moves::bin_transitions::PerturbByBins::repeats_ = 1

private

How many times will this be applied?

A value of 1 means that a single residue in the range will randomly be selected and flipped to another bin (with probabilities based on its neighbours and the bin transition probabilities. Higher values mean that this operation will be repeated. Defaults to 1.

Referenced by repeats(), and set_repeats().

◆ start_res_

core::Size protocols::simple_moves::bin_transitions::PerturbByBins::start_res_ = 0

private

Start of residue range.

Referenced by apply(), and set_residue_range().

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

src/protocols/simple_moves/bin_transitions/PerturbByBins.hh
src/protocols/simple_moves/bin_transitions/PerturbByBins.cc

Public Member Functions

Static Public Member Functions

Private Types

Private Attributes

Additional Inherited Members

Detailed Description

Member Typedef Documentation

◆ moverclass

Constructor & Destructor Documentation

◆ PerturbByBins() [1/2]

◆ PerturbByBins() [2/2]

◆ ~PerturbByBins()

Member Function Documentation

◆ apply()

◆ clone()

◆ fresh_instance()

◆ get_name()

◆ mover_name()

◆ must_switch_bins()

◆ parse_my_tag()

◆ provide_citation_info()

◆ provide_xml_schema()

◆ repeats()

◆ set_binfile_and_load()

◆ set_must_switch_bins()

◆ set_repeats()

◆ set_residue_range()

Member Data Documentation

◆ bin_transition_calculator_

◆ binfile_

◆ end_res_

◆ must_switch_bins_

◆ repeats_

◆ start_res_