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protocols::helical_bundle::PerturbBundleHelix Class Reference

#include <PerturbBundleHelix.hh>

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Public Types

typedef
core::conformation::parametric::Parameters 
Parameters
 
typedef
core::conformation::parametric::ParametersOP 
ParametersOP
 
typedef
core::conformation::parametric::ParametersSet 
ParametersSet
 
typedef
core::conformation::parametric::ParametersSetOP 
ParametersSetOP
 
typedef
protocols::helical_bundle::parameters::BundleParameters 
BundleParameters
 
typedef
protocols::helical_bundle::parameters::BundleParametersOP 
BundleParametersOP
 
typedef
protocols::helical_bundle::parameters::BundleParametersCOP 
BundleParametersCOP
 
typedef
protocols::helical_bundle::parameters::BundleParametersSet 
BundleParametersSet
 
typedef
protocols::helical_bundle::parameters::BundleParametersSetOP 
BundleParametersSetOP
 
typedef
protocols::helical_bundle::parameters::BundleParametersSetCOP 
BundleParametersSetCOP
 
- 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
 

Public Member Functions

 PerturbBundleHelix ()
 Creator for PerturbBundleHelix mover. More...
 
 ~PerturbBundleHelix () override
 Destructor for PerturbBundleHelix mover. More...
 
protocols::moves::MoverOP clone () const override
 Clone operator to create a pointer to a fresh PerturbBundleHelix object that copies this one. More...
 
protocols::moves::MoverOP fresh_instance () const override
 Fresh_instance operator to create a pointer to a fresh PerturbBundleHelix object that does NOT copy this one. More...
 
void apply (core::pose::Pose &pose) override
 Actually apply the mover to the pose. More...
 
void set_parameters_set_index (core::Size const index)
 Sets the index of the ParametersSet object in the pose that's being perturbed. More...
 
void set_parameters_index (core::Size const index)
 Sets the index of the Parameters object in the ParametersSet object in the pose that's being perturbed. More...
 
core::Size parameters_set_index () const
 Returns the index of the ParametersSet object in the pose that's being perturbed. More...
 
core::Size parameters_index () const
 Returns the index of the Parameters object in the ParametersSet object in the pose that's being perturbed. More...
 
bool last_apply_failed () const
 
std::string get_name () const override
 Returns the name of this mover ("PerturbBundleHelix"). 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
 
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 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 Member Functions

void set_last_apply_failed (bool const status)
 

Private Attributes

core::Size parameters_set_index_
 The index of the ParametersSet object in the pose that's being perturbed. More...
 
core::Size parameters_index_
 The index of the Parameters object in the ParametersSet object in the pose that's being perturbed. More...
 
bool last_apply_failed_
 Stores whether the last apply attempt failed. More...
 

Additional Inherited Members

- 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...
 

Member Typedef Documentation

Constructor & Destructor Documentation

protocols::helical_bundle::PerturbBundleHelix::PerturbBundleHelix ( )

Creator for PerturbBundleHelix mover.

protocols::helical_bundle::PerturbBundleHelix::~PerturbBundleHelix ( )
overridedefault

Destructor for PerturbBundleHelix mover.

Member Function Documentation

void protocols::helical_bundle::PerturbBundleHelix::apply ( core::pose::Pose pose)
overridevirtual
protocols::moves::MoverOP protocols::helical_bundle::PerturbBundleHelix::clone ( ) const
overridevirtual

Clone operator to create a pointer to a fresh PerturbBundleHelix object that copies this one.

Reimplemented from protocols::moves::Mover.

protocols::moves::MoverOP protocols::helical_bundle::PerturbBundleHelix::fresh_instance ( ) const
overridevirtual

Fresh_instance operator to create a pointer to a fresh PerturbBundleHelix object that does NOT copy this one.

Reimplemented from protocols::moves::Mover.

std::string protocols::helical_bundle::PerturbBundleHelix::get_name ( ) const
overridevirtual

Returns the name of this mover ("PerturbBundleHelix").

Implements protocols::moves::Mover.

References mover_name().

bool protocols::helical_bundle::PerturbBundleHelix::last_apply_failed ( ) const
inline
std::string protocols::helical_bundle::PerturbBundleHelix::mover_name ( )
static
core::Size protocols::helical_bundle::PerturbBundleHelix::parameters_index ( ) const
inline

Returns the index of the Parameters object in the ParametersSet object in the pose that's being perturbed.

This Parameters object contains the Crick parameters that define the helix that's being perturbed.

References parameters_index_.

Referenced by apply().

core::Size protocols::helical_bundle::PerturbBundleHelix::parameters_set_index ( ) const
inline

Returns the index of the ParametersSet object in the pose that's being perturbed.

This ParametersSet contains the Parameters object that defines the helix that's being perturbed.

References parameters_set_index_.

Referenced by apply().

void protocols::helical_bundle::PerturbBundleHelix::provide_xml_schema ( utility::tag::XMLSchemaDefinition &  xsd)
static
void protocols::helical_bundle::PerturbBundleHelix::set_last_apply_failed ( bool const  status)
inlineprivate

References last_apply_failed_.

Referenced by apply().

void protocols::helical_bundle::PerturbBundleHelix::set_parameters_index ( core::Size const  index)
inline

Sets the index of the Parameters object in the ParametersSet object in the pose that's being perturbed.

This Parameters object contains the Crick parameters that define the helix that's being perturbed.

References parameters_index_.

Referenced by protocols::helical_bundle::PerturbBundle::rebuild_conformation().

void protocols::helical_bundle::PerturbBundleHelix::set_parameters_set_index ( core::Size const  index)
inline

Sets the index of the ParametersSet object in the pose that's being perturbed.

This ParametersSet contains the Parameters object that defines the helix that's being perturbed.

References parameters_set_index_.

Referenced by protocols::helical_bundle::PerturbBundle::rebuild_conformation().

Member Data Documentation

bool protocols::helical_bundle::PerturbBundleHelix::last_apply_failed_
private

Stores whether the last apply attempt failed.

Referenced by last_apply_failed(), and set_last_apply_failed().

core::Size protocols::helical_bundle::PerturbBundleHelix::parameters_index_
private

The index of the Parameters object in the ParametersSet object in the pose that's being perturbed.

This Parameters object contains the Crick parameters that define the helix that's being perturbed.

Referenced by parameters_index(), and set_parameters_index().

core::Size protocols::helical_bundle::PerturbBundleHelix::parameters_set_index_
private

The index of the ParametersSet object in the pose that's being perturbed.

This ParametersSet contains the Parameters object that defines the helix that's being perturbed.

Referenced by parameters_set_index(), and set_parameters_set_index().


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