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protocols::helical_bundle::PerturbBundle Class Reference

#include <PerturbBundle.hh>

Inheritance diagram for protocols::helical_bundle::PerturbBundle:
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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

 PerturbBundle ()
 Creator for PerturbBundle mover. More...
 
 PerturbBundle (PerturbBundle const &src)
 Copy constructor for PerturbBundle mover. More...
 
 ~PerturbBundle () override
 Destructor for PerturbBundle mover. More...
 
protocols::moves::MoverOP clone () const override
 Clone operator to create a pointer to a fresh PerturbBundle object that copies this one. More...
 
protocols::moves::MoverOP fresh_instance () const override
 Fresh_instance operator to create a pointer to a fresh PerturbBundle object that does NOT copy this one. More...
 
void apply (core::pose::Pose &pose) override
 Actually apply the mover to the pose. More...
 
void parse_my_tag (utility::tag::TagCOP tag, basic::datacache::DataMap &data) override
 parse XML (specifically in the context of the parser/Rosetta_scripting scheme) More...
 
void set_bundleparametersset_index (core::Size const val)
 Set which bundle parameters set will be used, if more than one is defined in the pose's Conformation object. More...
 
core::Size bundleparametersset_index () const
 Returns a value indicating which bundle parameters set will be used, if more than one is defined in the pose's Conformation object. More...
 
void reset_helices ()
 Clear the list of helices. More...
 
BundleParametrizationCalculatorOP add_helix (core::Size const helix_index)
 Add options for a new helix. More...
 
BundleParametrizationCalculatorCOP default_calculator_cop () const
 Access the default calculator (const access). More...
 
BundleParametrizationCalculatorOP default_calculator ()
 Access the default calculator (nonconst access). More...
 
BundleParametrizationCalculatorCOP individual_helix_calculator_cop (core::Size const helix_calculator_index) const
 Access the calculator for a given helix (const access). More...
 
BundleParametrizationCalculatorOP individual_helix_calculator (core::Size const helix_calculator_index)
 Access the calculator for a given helix (nonconst access). More...
 
core::Size n_helices () const
 Get the number of individual helices that have been configured (which is not necessarily the number of helices in the pose, since we might only be perturbing a subset). More...
 
std::string get_name () const override
 Each derived class must specify its name. The class name. More...
 
bool mover_is_unpublished () const override
 Indicate that this mover is unpublished. More...
 
utility::vector1
< basic::citation_manager::UnpublishedModuleInfoCOP > 
provide_authorship_info_for_unpublished () const override
 Provide authorship information for an unpublished Rosetta module. 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...
 

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

bool helix_not_defined (core::Size const helix_index) const
 Confirms that a helix has not yet been defined. Returns "true" if the helix has NOT been defined, false otherwise. More...
 
BundleParametrizationCalculatorCOP get_calculator_for_helix (core::Size const helix_index) const
 Get a calculator for a particular helix. More...
 
bool perturb_values (BundleParametersSetOP params_set) const
 Perturb the helical bundle parameter values in the pose, subject to the options already set. More...
 
void rebuild_conformation (core::pose::Pose &pose, BundleParametersSetOP params_set, core::Size const params_set_index, bool &failed) const
 Rebuild the helical bundle conformation using the bundle parameter values in the pose. More...
 
void write_report (BundleParametersSetOP params_set, bool const before) const
 Write out the perturbed Crick parameters. More...
 

Private Attributes

BundleParametrizationCalculatorOP default_calculator_
 The BundleParametrizationCalculator object that will be used for setting up default parameters. More...
 
utility::vector1< std::pair
< core::Size,
BundleParametrizationCalculatorOP > > 
individual_helix_calculators_
 The BundleParametrizationCalculator objects for individual helices. Cloned from the default calculator. More...
 
core::Size bundleparametersset_index_
 Which set of bundle parameters (if there exists more than one) should the mover alter? 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::PerturbBundle::PerturbBundle ( )

Creator for PerturbBundle mover.

protocols::helical_bundle::PerturbBundle::PerturbBundle ( PerturbBundle const &  src)

Copy constructor for PerturbBundle mover.

References individual_helix_calculators_.

protocols::helical_bundle::PerturbBundle::~PerturbBundle ( )
overridedefault

Destructor for PerturbBundle mover.

Member Function Documentation

BundleParametrizationCalculatorOP protocols::helical_bundle::PerturbBundle::add_helix ( core::Size const  helix_index)

Add options for a new helix.

Return value is a smart pointer to the BundleParametrizationCalculator for the new helix, cloned from the default_calculator_.

References default_calculator_, helix_not_defined(), and individual_helix_calculators_.

Referenced by parse_my_tag().

void protocols::helical_bundle::PerturbBundle::apply ( core::pose::Pose pose)
overridevirtual
core::Size protocols::helical_bundle::PerturbBundle::bundleparametersset_index ( ) const
inline

Returns a value indicating which bundle parameters set will be used, if more than one is defined in the pose's Conformation object.

A value of n indicates that the nth bundle paramets set encountered will be perturbed.

References bundleparametersset_index_.

Referenced by apply().

protocols::moves::MoverOP protocols::helical_bundle::PerturbBundle::clone ( ) const
overridevirtual

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

Reimplemented from protocols::moves::Mover.

BundleParametrizationCalculatorOP protocols::helical_bundle::PerturbBundle::default_calculator ( )
inline

Access the default calculator (nonconst access).

References default_calculator_.

Referenced by provide_xml_schema().

BundleParametrizationCalculatorCOP protocols::helical_bundle::PerturbBundle::default_calculator_cop ( ) const
inline

Access the default calculator (const access).

References default_calculator_.

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

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

Reimplemented from protocols::moves::Mover.

BundleParametrizationCalculatorCOP protocols::helical_bundle::PerturbBundle::get_calculator_for_helix ( core::Size const  helix_index) const
private

Get a calculator for a particular helix.

Returns nullptr if no calculator for this helix has been defined.

References individual_helix_calculators_.

Referenced by perturb_values().

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

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

Implements protocols::moves::Mover.

References mover_name().

bool protocols::helical_bundle::PerturbBundle::helix_not_defined ( core::Size const  helix_index) const
private

Confirms that a helix has not yet been defined. Returns "true" if the helix has NOT been defined, false otherwise.

References individual_helix_calculators_.

Referenced by add_helix().

BundleParametrizationCalculatorOP protocols::helical_bundle::PerturbBundle::individual_helix_calculator ( core::Size const  helix_calculator_index)

Access the calculator for a given helix (nonconst access).

References individual_helix_calculators_.

BundleParametrizationCalculatorCOP protocols::helical_bundle::PerturbBundle::individual_helix_calculator_cop ( core::Size const  helix_calculator_index) const

Access the calculator for a given helix (const access).

References individual_helix_calculators_.

bool protocols::helical_bundle::PerturbBundle::mover_is_unpublished ( ) const
overridevirtual

Indicate that this mover is unpublished.

Reimplemented from protocols::moves::Mover.

std::string protocols::helical_bundle::PerturbBundle::mover_name ( )
static
core::Size protocols::helical_bundle::PerturbBundle::n_helices ( ) const
inline

Get the number of individual helices that have been configured (which is not necessarily the number of helices in the pose, since we might only be perturbing a subset).

References individual_helix_calculators_.

Referenced by perturb_values().

void protocols::helical_bundle::PerturbBundle::parse_my_tag ( utility::tag::TagCOP  tag,
basic::datacache::DataMap &  data 
)
overridevirtual

parse XML (specifically in the context of the parser/Rosetta_scripting scheme)

Reimplemented from protocols::moves::Mover.

References add_helix(), protocols::helical_bundle::BPC_last_parameter_to_be_sampled, default_calculator_, reset_helices(), and protocols::helical_bundle::TR().

bool protocols::helical_bundle::PerturbBundle::perturb_values ( BundleParametersSetOP  params_set) const
private
utility::vector1< basic::citation_manager::UnpublishedModuleInfoCOP > protocols::helical_bundle::PerturbBundle::provide_authorship_info_for_unpublished ( ) const
overridevirtual

Provide authorship information for an unpublished Rosetta module.

Reimplemented from protocols::moves::Mover.

void protocols::helical_bundle::PerturbBundle::provide_xml_schema ( utility::tag::XMLSchemaDefinition &  xsd)
static
void protocols::helical_bundle::PerturbBundle::rebuild_conformation ( core::pose::Pose pose,
BundleParametersSetOP  params_set,
core::Size const  params_set_index,
bool failed 
) const
private
void protocols::helical_bundle::PerturbBundle::reset_helices ( )

Clear the list of helices.

Clears the individual_helix_calculators_ list.

References individual_helix_calculators_.

Referenced by parse_my_tag().

void protocols::helical_bundle::PerturbBundle::set_bundleparametersset_index ( core::Size const  val)
inline

Set which bundle parameters set will be used, if more than one is defined in the pose's Conformation object.

A value of n indicates that the nth bundle paramets set encountered will be perturbed.

References bundleparametersset_index_, and protocols::hybridization::val.

void protocols::helical_bundle::PerturbBundle::write_report ( BundleParametersSetOP  params_set,
bool const  before 
) const
private

Write out the perturbed Crick parameters.

The "before" parameter determines whether this is a pre-perturbation report or a post-perturbation report.

References protocols::helical_bundle::TR().

Referenced by apply().

Member Data Documentation

core::Size protocols::helical_bundle::PerturbBundle::bundleparametersset_index_
private

Which set of bundle parameters (if there exists more than one) should the mover alter?

Defaults to 1. Higher values indicate the nth set encountered in the ParametersSet list.

Referenced by bundleparametersset_index(), and set_bundleparametersset_index().

BundleParametrizationCalculatorOP protocols::helical_bundle::PerturbBundle::default_calculator_
private

The BundleParametrizationCalculator object that will be used for setting up default parameters.

Referenced by add_helix(), default_calculator(), default_calculator_cop(), parse_my_tag(), and perturb_values().

utility::vector1< std::pair< core::Size, BundleParametrizationCalculatorOP > > protocols::helical_bundle::PerturbBundle::individual_helix_calculators_
private

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