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protocols::helical_bundle::MakeBundleHelix Class Reference

#include <MakeBundleHelix.hh>

Inheritance diagram for protocols::helical_bundle::MakeBundleHelix:
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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

 MakeBundleHelix ()
 Default constructor. More...
 
 MakeBundleHelix (MakeBundleHelix const &src)
 Copy constructor. More...
 
 MakeBundleHelix (BundleParametrizationCalculatorCOP input_calculator)
 Initialization constructor: initializes this MakeBundleHelix mover with a BundleParametrizationCalculator. More...
 
 ~MakeBundleHelix () override
 Destructor. More...
 
protocols::moves::MoverOP clone () const override
 Clone operator to create a pointer to a fresh MakeBundleHelix object that copies this one. More...
 
protocols::moves::MoverOP fresh_instance () const override
 Fresh_instance operator to create a pointer to a fresh MakeBundleHelix object that does NOT copy this one. More...
 
void copy_unset_params_from_globals (BundleParametrizationCalculatorCOP global_calculator)
 Copy the parameter values for parameters that have not been set from the global parameters. More...
 
bool copy_params_from_previous_helices (core::pose::Pose const &prev_helices_pose)
 Copy the parameter values for parameters that copy values from previous helices, from the previous helices. More...
 
void apply (core::pose::Pose &pose) override
 Actually apply the mover to the pose. More...
 
void set_reset_pose (bool const reset_in)
 Set whether the input pose should be reset prior to building a helix. More...
 
bool reset_pose () const
 Returns a bool indicating whether the input pose will be reset prior to building a helix. More...
 
void set_helix_length (core::Size const helix_length_in)
 Set the length of the helix, in residues. More...
 
core::Size helix_length () const
 Returns a bool indicating whether the input pose will be reset prior to building a helix. More...
 
void set_residue_name (utility::vector1< std::string > const &names)
 Set the residue type(s) (full name, not 3-letter code) that will make up the helix. More...
 
std::string const & residue_name (core::Size const repeat_index) const
 Get the name (full name, not 3-letter code) of one of the residue types in the repeating unit that will make up the helix. More...
 
void set_minor_helix_params_from_file (std::string const &filename)
 Set the minor helix parameters by reading them in from a file. More...
 
bool last_apply_failed () const
 Returns "true" if the last call to the apply function failed, false otherwise. More...
 
BundleParametrizationCalculatorOP calculator_op ()
 Non-const access to the calculator. More...
 
BundleParametrizationCalculatorCOP calculator_cop () const
 Const access to the calculator. 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
 
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 val)
 Set whether the last call to the apply() function failed or not. More...
 
void add_parameter_info_to_pose (core::pose::Pose &pose)
 Add Crick parameter information to the Conformation object within the pose. More...
 

Private Attributes

bool reset_pose_
 Should the input pose be reset? More...
 
core::Size helix_length_
 Length of the helix, in residues. Defaults to 10. More...
 
utility::vector1< std::string > residue_name_
 Name (full-length, not 3-letter code) of the residue type(s) that the helix will be made of. More...
 
bool last_apply_failed_
 Did the last apply fail? More...
 
BundleParametrizationCalculatorOP calculator_
 The BundleParametrizationCalculator object, which keeps track of parameter values and does the actual parametric math. 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::MakeBundleHelix::MakeBundleHelix ( )

Default constructor.

Constructor for MakeBundleHelix mover.

References residue_name_, and set_minor_helix_params_from_file().

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

Copy constructor.

Copy constructor for MakeBundleHelix mover.

protocols::helical_bundle::MakeBundleHelix::MakeBundleHelix ( BundleParametrizationCalculatorCOP  input_calculator)

Initialization constructor: initializes this MakeBundleHelix mover with a BundleParametrizationCalculator.

Input calculator is cloned.

protocols::helical_bundle::MakeBundleHelix::~MakeBundleHelix ( )
override

Destructor.

Destructor for MakeBundleHelix mover.

Member Function Documentation

void protocols::helical_bundle::MakeBundleHelix::add_parameter_info_to_pose ( core::pose::Pose pose)
private

Add Crick parameter information to the Conformation object within the pose.

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

This function updates the bundle_parameters_ object's links to residues within the pose, and then copies the owning pointer into the pose's Conformation object.

Add Crick parameter information to the Conformation object within the pose.

This function updates the calculator's Parameters object's links to residues within the pose, and then clones the Parameters object into the pose's Conformation object. The new Parameters object will be added to a new ParameterSet object in the Conformation object.

References core::conformation::Conformation::add_parameters_set(), calculator_, core::pose::Pose::conformation(), helix_length(), core::conformation::Conformation::residue_cop(), and core::pose::Pose::size().

Referenced by apply().

void protocols::helical_bundle::MakeBundleHelix::apply ( core::pose::Pose pose)
overridevirtual
BundleParametrizationCalculatorCOP protocols::helical_bundle::MakeBundleHelix::calculator_cop ( ) const
inline

Const access to the calculator.

References calculator_.

BundleParametrizationCalculatorOP protocols::helical_bundle::MakeBundleHelix::calculator_op ( )
inline

Non-const access to the calculator.

References calculator_.

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

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

Reimplemented from protocols::moves::Mover.

bool protocols::helical_bundle::MakeBundleHelix::copy_params_from_previous_helices ( core::pose::Pose const &  prev_helices_pose)

Copy the parameter values for parameters that copy values from previous helices, from the previous helices.

This function should be called before apply().

Returns
Returns true for failure, false for success.

References calculator_.

void protocols::helical_bundle::MakeBundleHelix::copy_unset_params_from_globals ( BundleParametrizationCalculatorCOP  global_calculator)

Copy the parameter values for parameters that have not been set from the global parameters.

This function should be called before apply().

References calculator_.

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

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

Reimplemented from protocols::moves::Mover.

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

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

Implements protocols::moves::Mover.

References mover_name().

core::Size protocols::helical_bundle::MakeBundleHelix::helix_length ( ) const
inline

Returns a bool indicating whether the input pose will be reset prior to building a helix.

References helix_length_.

Referenced by add_parameter_info_to_pose(), and apply().

bool protocols::helical_bundle::MakeBundleHelix::last_apply_failed ( ) const
inline

Returns "true" if the last call to the apply function failed, false otherwise.

References last_apply_failed_.

Referenced by apply().

std::string protocols::helical_bundle::MakeBundleHelix::mover_name ( )
static
void protocols::helical_bundle::MakeBundleHelix::provide_xml_schema ( utility::tag::XMLSchemaDefinition &  xsd)
static
bool protocols::helical_bundle::MakeBundleHelix::reset_pose ( ) const
inline

Returns a bool indicating whether the input pose will be reset prior to building a helix.

References reset_pose_.

Referenced by apply().

std::string const& protocols::helical_bundle::MakeBundleHelix::residue_name ( core::Size const  repeat_index) const
inline

Get the name (full name, not 3-letter code) of one of the residue types in the repeating unit that will make up the helix.

References residue_name_.

Referenced by apply().

void protocols::helical_bundle::MakeBundleHelix::set_helix_length ( core::Size const  helix_length_in)
inline

Set the length of the helix, in residues.

References helix_length_.

void protocols::helical_bundle::MakeBundleHelix::set_last_apply_failed ( bool const  val)
inlineprivate

Set whether the last call to the apply() function failed or not.

Should only be called by the apply() function.

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

Referenced by apply().

void protocols::helical_bundle::MakeBundleHelix::set_minor_helix_params_from_file ( std::string const &  filename)

Set the minor helix parameters by reading them in from a file.

References calculator_.

Referenced by MakeBundleHelix().

void protocols::helical_bundle::MakeBundleHelix::set_reset_pose ( bool const  reset_in)
inline

Set whether the input pose should be reset prior to building a helix.

References reset_pose_.

void protocols::helical_bundle::MakeBundleHelix::set_residue_name ( utility::vector1< std::string > const &  names)
inline

Set the residue type(s) (full name, not 3-letter code) that will make up the helix.

If there is more than one residue per repeating unit in the minor helix, one residue name must be provided for each residue in the repeating unit. Note that there is no check that the size of the residue_name_ vector matches the number of residues in the repeating unit until apply time.

References residue_name_.

Member Data Documentation

BundleParametrizationCalculatorOP protocols::helical_bundle::MakeBundleHelix::calculator_
private
core::Size protocols::helical_bundle::MakeBundleHelix::helix_length_
private

Length of the helix, in residues. Defaults to 10.

Referenced by helix_length(), and set_helix_length().

bool protocols::helical_bundle::MakeBundleHelix::last_apply_failed_
private

Did the last apply fail?

Initialized to "false"; "true" if the last apply failed.

Referenced by last_apply_failed(), and set_last_apply_failed().

bool protocols::helical_bundle::MakeBundleHelix::reset_pose_
private

Should the input pose be reset?

Default true.

Referenced by reset_pose(), and set_reset_pose().

utility::vector1< std::string > protocols::helical_bundle::MakeBundleHelix::residue_name_
private

Name (full-length, not 3-letter code) of the residue type(s) that the helix will be made of.

Defaults to "ALA". One residue must be specified for each in the repeating unit.

Referenced by apply(), MakeBundleHelix(), residue_name(), and set_residue_name().


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