#include <MakeBundleHelix.hh>

Inheritance diagram for protocols::helical_bundle::MakeBundleHelix:

[legend]

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 Strings &	info ()
	non-const accessor More...

virtual Strings const &	info () const
	const accessor More...

virtual void	provide_citation_info (basic::citation_manager::CitationCollectionList &) const
	Provide citations to the passed CitationCollectionList Subclasses should add the info for themselves and any other classes they use. 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

◆ BundleParameters

typedef protocols::helical_bundle::parameters::BundleParameters protocols::helical_bundle::MakeBundleHelix::BundleParameters

◆ BundleParametersCOP

typedef protocols::helical_bundle::parameters::BundleParametersCOP protocols::helical_bundle::MakeBundleHelix::BundleParametersCOP

◆ BundleParametersOP

typedef protocols::helical_bundle::parameters::BundleParametersOP protocols::helical_bundle::MakeBundleHelix::BundleParametersOP

◆ BundleParametersSet

typedef protocols::helical_bundle::parameters::BundleParametersSet protocols::helical_bundle::MakeBundleHelix::BundleParametersSet

◆ BundleParametersSetCOP

typedef protocols::helical_bundle::parameters::BundleParametersSetCOP protocols::helical_bundle::MakeBundleHelix::BundleParametersSetCOP

◆ BundleParametersSetOP

typedef protocols::helical_bundle::parameters::BundleParametersSetOP protocols::helical_bundle::MakeBundleHelix::BundleParametersSetOP

◆ Parameters

typedef core::conformation::parametric::Parameters protocols::helical_bundle::MakeBundleHelix::Parameters

◆ ParametersOP

typedef core::conformation::parametric::ParametersOP protocols::helical_bundle::MakeBundleHelix::ParametersOP

◆ ParametersSet

typedef core::conformation::parametric::ParametersSet protocols::helical_bundle::MakeBundleHelix::ParametersSet

◆ ParametersSetOP

typedef core::conformation::parametric::ParametersSetOP protocols::helical_bundle::MakeBundleHelix::ParametersSetOP

Constructor & Destructor Documentation

◆ MakeBundleHelix() [1/3]

protocols::helical_bundle::MakeBundleHelix::MakeBundleHelix ( )

Default constructor.

Constructor for MakeBundleHelix mover.

References residue_name_, and set_minor_helix_params_from_file().

◆ MakeBundleHelix() [2/3]

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

Copy constructor.

Copy constructor for MakeBundleHelix mover.

◆ MakeBundleHelix() [3/3]

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

Initialization constructor: initializes this MakeBundleHelix mover with a BundleParametrizationCalculator.

Input calculator is cloned.

◆ ~MakeBundleHelix()

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

override

Destructor.

Destructor for MakeBundleHelix mover.

Member Function Documentation

◆ add_parameter_info_to_pose()

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().

◆ apply()

void protocols::helical_bundle::MakeBundleHelix::apply ( core::pose::Pose & pose )

overridevirtual

Actually apply the mover to the pose.

Implements protocols::moves::Mover.

References add_parameter_info_to_pose(), protocols::cyclic_peptide::PeptideStubMover::add_residue(), core::pose::Pose::append_pose_by_jump(), protocols::cyclic_peptide::PeptideStubMover::apply(), protocols::helical_bundle::BPC_repeating_unit_offset, protocols::helical_bundle::BPC_residues_per_repeat, calculator_, core::pose::Pose::clear(), helix_length(), last_apply_failed(), protocols::cyclic_peptide::PeptideStubMover::reset_mover_data(), reset_pose(), residue_name(), residue_name_, set_last_apply_failed(), protocols::cyclic_peptide::PeptideStubMover::set_reset_mode(), and protocols::helical_bundle::TR().

◆ calculator_cop()

BundleParametrizationCalculatorCOP protocols::helical_bundle::MakeBundleHelix::calculator_cop ( ) const

inline

Const access to the calculator.

References calculator_.

◆ calculator_op()

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

inline

Non-const access to the calculator.

References calculator_.

◆ clone()

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.

◆ copy_params_from_previous_helices()

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_.

◆ copy_unset_params_from_globals()

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_.

◆ fresh_instance()

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.

◆ get_name()

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().

◆ helix_length()

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().

◆ last_apply_failed()

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().

◆ mover_name()

std::string protocols::helical_bundle::MakeBundleHelix::mover_name ( )

static

Referenced by get_name(), protocols::helical_bundle::MakeBundleHelixCreator::keyname(), and provide_xml_schema().

◆ provide_xml_schema()

void protocols::helical_bundle::MakeBundleHelix::provide_xml_schema ( utility::tag::XMLSchemaDefinition & xsd )

static

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

Referenced by protocols::helical_bundle::MakeBundleHelixCreator::provide_xml_schema().

◆ reset_pose()

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().

◆ residue_name()

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().

◆ set_helix_length()

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_.

◆ set_last_apply_failed()

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().

◆ set_minor_helix_params_from_file()

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_, and protocols::abinitio::filename().

Referenced by MakeBundleHelix().

◆ set_reset_pose()

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_.

◆ set_residue_name()

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

◆ calculator_

BundleParametrizationCalculatorOP protocols::helical_bundle::MakeBundleHelix::calculator_

private

The BundleParametrizationCalculator object, which keeps track of parameter values and does the actual parametric math.

Referenced by add_parameter_info_to_pose(), apply(), calculator_cop(), calculator_op(), copy_params_from_previous_helices(), copy_unset_params_from_globals(), and set_minor_helix_params_from_file().

◆ helix_length_

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().

◆ last_apply_failed_

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().

◆ reset_pose_

bool protocols::helical_bundle::MakeBundleHelix::reset_pose_

private

Should the input pose be reset?

Default true.

Referenced by reset_pose(), and set_reset_pose().

◆ residue_name_

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:

src/protocols/helical_bundle/MakeBundleHelix.hh
src/protocols/helical_bundle/MakeBundleHelix.cc

Public Types

Public Member Functions

Static Public Member Functions

Private Member Functions

Private Attributes

Additional Inherited Members

Member Typedef Documentation

◆ BundleParameters

◆ BundleParametersCOP

◆ BundleParametersOP

◆ BundleParametersSet

◆ BundleParametersSetCOP

◆ BundleParametersSetOP

◆ Parameters

◆ ParametersOP

◆ ParametersSet

◆ ParametersSetOP

Constructor & Destructor Documentation

◆ MakeBundleHelix() [1/3]

◆ MakeBundleHelix() [2/3]

◆ MakeBundleHelix() [3/3]

◆ ~MakeBundleHelix()

Member Function Documentation

◆ add_parameter_info_to_pose()

◆ apply()

◆ calculator_cop()

◆ calculator_op()

◆ clone()

◆ copy_params_from_previous_helices()

◆ copy_unset_params_from_globals()

◆ fresh_instance()

◆ get_name()

◆ helix_length()

◆ last_apply_failed()

◆ mover_name()

◆ provide_xml_schema()

◆ reset_pose()

◆ residue_name()

◆ set_helix_length()

◆ set_last_apply_failed()

◆ set_minor_helix_params_from_file()

◆ set_reset_pose()

◆ set_residue_name()

Member Data Documentation

◆ calculator_

◆ helix_length_

◆ last_apply_failed_

◆ reset_pose_

◆ residue_name_