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protocols::simple_moves::bin_transitions::PerturbByBins Class Reference

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

#include <PerturbByBins.hh>

Inheritance diagram for protocols::simple_moves::bin_transitions::PerturbByBins:
Inheritance graph
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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...
 
- 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 Stringsinfo ()
 non-const accessor More...
 
virtual Strings const & info () const
 const accessor More...
 
virtual bool mover_provides_citation_info () const
 Does this mover provide information about how to cite it? More...
 
virtual utility::vector1
< basic::citation_manager::CitationCollectionCOP > 
provide_citation_info () const
 Provide the citation. More...
 
virtual bool mover_is_unpublished () const
 Does this mover indicate that it is unpublished (and, by extension, that the author should be included in publications resulting from it)? More...
 
virtual utility::vector1
< basic::citation_manager::UnpublishedModuleInfoCOP > 
provide_authorship_info_for_unpublished () const
 Provide a list of authors and their e-mail addresses, as strings. 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_
 Start of residue range. More...
 
core::Size end_res_
 End of residue range. More...
 
std::string binfile_
 Bin transition probability data file. More...
 
bool binfile_loaded_
 Has the bin transition probability file been loaded already? More...
 
core::scoring::bin_transitions::BinTransitionCalculatorOP bin_transition_calculator_
 Owning pointer to the BinTransitionCalculator object used by this mover. More...
 
core::Size repeats_
 How many times will this be applied? More...
 
bool must_switch_bins_
 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

Constructor & Destructor Documentation

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

Default constructor.

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

Copy constructor.

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

Destructor.

Member Function Documentation

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

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.

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().

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

void protocols::simple_moves::bin_transitions::PerturbByBins::parse_my_tag ( utility::tag::TagCOP  tag,
basic::datacache::DataMap &   
)
overridevirtual
void protocols::simple_moves::bin_transitions::PerturbByBins::provide_xml_schema ( utility::tag::XMLSchemaDefinition &  xsd)
static
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().

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_, binfile_loaded_, protocols::moves::Mover::name(), and protocols::simple_moves::bin_transitions::TR().

Referenced by parse_my_tag().

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().

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().

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

core::scoring::bin_transitions::BinTransitionCalculatorOP protocols::simple_moves::bin_transitions::PerturbByBins::bin_transition_calculator_
private

Owning pointer to the BinTransitionCalculator object used by this mover.

Object created when the PerturbByBins mover is created.

Referenced by apply(), and set_binfile_and_load().

std::string protocols::simple_moves::bin_transitions::PerturbByBins::binfile_
private

Bin transition probability data file.

Referenced by set_binfile_and_load().

bool protocols::simple_moves::bin_transitions::PerturbByBins::binfile_loaded_
private

Has the bin transition probability file been loaded already?

This mover is not made to be re-used. Probability file should only be loaded once.

Referenced by set_binfile_and_load().

core::Size protocols::simple_moves::bin_transitions::PerturbByBins::end_res_
private

End of residue range.

Referenced by apply(), and set_residue_range().

bool protocols::simple_moves::bin_transitions::PerturbByBins::must_switch_bins_
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().

core::Size protocols::simple_moves::bin_transitions::PerturbByBins::repeats_
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().

core::Size protocols::simple_moves::bin_transitions::PerturbByBins::start_res_
private

Start of residue range.

Referenced by apply(), and set_residue_range().


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