#include <MakeBundle.hh>

Inheritance diagram for protocols::helical_bundle::MakeBundle:

[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
	MakeBundle ()
	Creator for MakeBundle mover. More...

	MakeBundle (MakeBundle const &src)
	Copy constructor for MakeBundle mover. More...

	~MakeBundle () override
	Destructor for MakeBundle mover. More...

protocols::moves::MoverOP	clone () const override
	Clone operator to create a pointer to a fresh MakeBundle object that copies this one. More...

protocols::moves::MoverOP	fresh_instance () const override
	Fresh_instance operator to create a pointer to a fresh MakeBundle 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...

BundleParametrizationCalculatorOP	default_calculator_nonconst ()
	Access the default calculator directly. More...

BundleParametrizationCalculatorCOP	default_calculator () const
	Access the default calculator directly. More...

void	set_symmetry_options_from_tag (utility::tag::TagCOP tag)
	Set symmetry and symmetry_copies options based on an input tag. 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	add_helix ()
	Function to add a helix. More...

protocols::helical_bundle::MakeBundleHelixOP	helix (core::Size const &index)
	Non-const access to helix in the bundle. More...

protocols::helical_bundle::MakeBundleHelixCOP	helix_cop (core::Size const &index) const
	Const access to helix in the bundle. More...

core::Size	n_helices () const
	Returns the number of helices. More...

void	set_symmetry (core::Size const symmetry_in)
	Set the symmetry of the bundle. More...

core::Size	symmetry () const
	Get the symmetry of the bundle. More...

void	set_symmetry_copies (core::Size const symmetry_copies_in)
	Set how many of the symmetry copies actually get generated. More...

core::Size	symmetry_copies () const
	Get how many of the symmetry copies actually get generated. More...

void	set_default_crick_params_file (std::string const &input_string)
	Set the default Crick params file name. More...

void	initialize_default_calculator_from_default_crick_params_file ()
	Initialize the default calculator from the deafult Crick params file. More...

void	set_crick_params_file_for_helix (std::string const &filename, core::Size const helix_index)
	Set the Crick params file for a particular helix. More...

std::string const &	default_crick_params_file () const
	Returns the default Crick params file name. More...

void	set_default_residue_name (utility::vector1< std::string > const &names)
	Set the default residue name. More...

std::string const &	default_residue_name (core::Size const index_in_repeating_unit) const
	Returns the default residue name for a particular position in the repeating unit. More...

utility::vector1< std::string > const &	default_residue_name () const
	Returns the default residue name vector. More...

void	set_residue_name_for_helix (utility::vector1< std::string > const &names, core::Size const helix_index)
	Set the residue names for a given helix. More...

void	set_default_helix_length (core::Size const &val)
	Set the default number of residues per helix. More...

core::Size	default_helix_length () const
	Returns the default number of residues per helix. More...

void	set_helix_length_for_helix (core::Size const helix_length, core::Size const helix_index)
	Set the helix length, in residues, for the Nth helix. More...

void	set_use_degrees (bool const val=true)
	Set whether we're using degrees (true) or radians (false). More...

bool	use_degrees () const
	Get whether we're using degrees (true) or radians (false). More...

bool	last_apply_failed () const
	Returns true or false based on whether the last call to the apply() function failed (true) or succeeded (false). More...

std::string	get_name () const override
	Each derived class must specify its name. The class name. More...

void	provide_citation_info (basic::citation_manager::CitationCollectionList &) const override
	Provide the citation. 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 Strings &	info ()
	non-const accessor More...

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

Private Attributes
bool	reset_pose_
	Should the input pose be reset? More...

BundleParametrizationCalculatorOP	default_calculator_
	The BundleParameterizationCalculator object that will be used for setting up default parameters. More...

utility::vector1< protocols::helical_bundle::MakeBundleHelixOP >	make_bundle_helix_movers_
	A vector of owning pointers to the individual MakeBundleHelix movers that will make each of the helices in the bundle. More...

core::Size	bundle_symmetry_
	The symmetry of the bundle. More...

core::Size	bundle_symmetry_copies_
	The symmetry copies to generate. More...

std::string	default_crick_params_file_
	DEFAULTS: Default values for helix parameters if no other values are set: More...

utility::vector1< std::string >	default_residue_name_
	Default residue name. More...

core::Size	default_helix_length_
	Default number of residues in the helix. More...

bool	default_helix_length_set_
	Has the default number of residues in the helix been specified? More...

bool	use_degrees_
	Are we using degrees (true) or radians (false)? Default radians (false). More...

bool	last_apply_failed_
	Did the last apply fail? More...

bool	defaults_set_
	Have the default parameter values been set? 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::MakeBundle::BundleParameters

◆ BundleParametersCOP

typedef protocols::helical_bundle::parameters::BundleParametersCOP protocols::helical_bundle::MakeBundle::BundleParametersCOP

◆ BundleParametersOP

typedef protocols::helical_bundle::parameters::BundleParametersOP protocols::helical_bundle::MakeBundle::BundleParametersOP

◆ BundleParametersSet

typedef protocols::helical_bundle::parameters::BundleParametersSet protocols::helical_bundle::MakeBundle::BundleParametersSet

◆ BundleParametersSetCOP

typedef protocols::helical_bundle::parameters::BundleParametersSetCOP protocols::helical_bundle::MakeBundle::BundleParametersSetCOP

◆ BundleParametersSetOP

typedef protocols::helical_bundle::parameters::BundleParametersSetOP protocols::helical_bundle::MakeBundle::BundleParametersSetOP

◆ Parameters

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

◆ ParametersOP

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

◆ ParametersSet

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

◆ ParametersSetOP

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

Constructor & Destructor Documentation

◆ MakeBundle() [1/2]

protocols::helical_bundle::MakeBundle::MakeBundle ( )

Creator for MakeBundle mover.

References default_residue_name_, and initialize_default_calculator_from_default_crick_params_file().

◆ MakeBundle() [2/2]

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

Copy constructor for MakeBundle mover.

Creator for MakeBundle mover.

References make_bundle_helix_movers_.

◆ ~MakeBundle()

protocols::helical_bundle::MakeBundle::~MakeBundle ( )

overridedefault

Destructor for MakeBundle mover.

Member Function Documentation

◆ add_helix()

void protocols::helical_bundle::MakeBundle::add_helix ( )

Function to add a helix.

This creates a MakeBundleHelix mover that will be called at apply time. Note that this function assumes that default parameter values have been set already. They cannot be set after calling this function.

This creates a MakeBundleHelix mover that will be called at apply time. Note that this function assumes that defaults have been set already. They cannot be set after calling this function.

References default_calculator_, default_helix_length(), default_residue_name(), defaults_set_, helix(), and make_bundle_helix_movers_.

Referenced by parse_my_tag().

◆ apply()

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

overridevirtual

◆ clone()

protocols::moves::MoverOP protocols::helical_bundle::MakeBundle::clone ( ) const

overridevirtual

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

Reimplemented from protocols::moves::Mover.

Referenced by apply().

◆ default_calculator()

BundleParametrizationCalculatorCOP protocols::helical_bundle::MakeBundle::default_calculator ( ) const

inline

Access the default calculator directly.

Const access.

References default_calculator_.

Referenced by provide_xml_schema().

◆ default_calculator_nonconst()

BundleParametrizationCalculatorOP protocols::helical_bundle::MakeBundle::default_calculator_nonconst ( )

inline

Access the default calculator directly.

Nonconst access is potentially dangerous! Use with caution!

Note: Used by BundleGridSampler to access the contained MakeBundle mover's calculator directly.

References default_calculator_.

◆ default_crick_params_file()

std::string const & protocols::helical_bundle::MakeBundle::default_crick_params_file ( ) const

Returns the default Crick params file name.

References default_crick_params_file_.

Referenced by parse_my_tag().

◆ default_helix_length()

core::Size protocols::helical_bundle::MakeBundle::default_helix_length ( ) const

Returns the default number of residues per helix.

Returns the default number of residues in each helix.

References default_helix_length_.

Referenced by add_helix(), and parse_my_tag().

◆ default_residue_name() [1/2]

utility::vector1< std::string > const & protocols::helical_bundle::MakeBundle::default_residue_name ( ) const

Returns the default residue name vector.

References default_residue_name_.

Referenced by add_helix(), and parse_my_tag().

◆ default_residue_name() [2/2]

std::string const & protocols::helical_bundle::MakeBundle::default_residue_name ( core::Size const index_in_repeating_unit ) const

Returns the default residue name for a particular position in the repeating unit.

Returns the default residue name for a particular index in the repeating unit.

References default_residue_name_.

◆ fresh_instance()

protocols::moves::MoverOP protocols::helical_bundle::MakeBundle::fresh_instance ( ) const

overridevirtual

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

Reimplemented from protocols::moves::Mover.

◆ get_name()

std::string protocols::helical_bundle::MakeBundle::get_name ( ) const

overridevirtual

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

Implements protocols::moves::Mover.

References mover_name().

◆ helix()

protocols::helical_bundle::MakeBundleHelixOP protocols::helical_bundle::MakeBundle::helix ( core::Size const & index )

inline

Non-const access to helix in the bundle.

References make_bundle_helix_movers_.

Referenced by add_helix(), apply(), parse_my_tag(), set_crick_params_file_for_helix(), set_helix_length_for_helix(), and set_residue_name_for_helix().

◆ helix_cop()

protocols::helical_bundle::MakeBundleHelixCOP protocols::helical_bundle::MakeBundle::helix_cop ( core::Size const & index ) const

inline

Const access to helix in the bundle.

References make_bundle_helix_movers_.

◆ initialize_default_calculator_from_default_crick_params_file()

void protocols::helical_bundle::MakeBundle::initialize_default_calculator_from_default_crick_params_file ( )

Initialize the default calculator from the deafult Crick params file.

Initialize the default calculator from the default Crick params file.

Triggers a read from disk!

References default_calculator_, and default_crick_params_file_.

Referenced by MakeBundle(), and set_default_crick_params_file().

◆ last_apply_failed()

bool protocols::helical_bundle::MakeBundle::last_apply_failed ( ) const

inline

Returns true or false based on whether the last call to the apply() function failed (true) or succeeded (false).

The apply() function calls the private function set_last_apply_failed() to set this.

References last_apply_failed_.

◆ mover_name()

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

static

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

◆ n_helices()

core::Size protocols::helical_bundle::MakeBundle::n_helices ( ) const

inline

Returns the number of helices.

Note that this is not multiplied by the number of symmetry repeats. That is, if the bundle has 3-fold symmetry and 2 helices are defined, there will be 6 helices in the final structure, but this function would still return 2.

References make_bundle_helix_movers_.

Referenced by apply(), parse_my_tag(), set_crick_params_file_for_helix(), set_helix_length_for_helix(), and set_residue_name_for_helix().

◆ parse_my_tag()

void protocols::helical_bundle::MakeBundle::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_end_of_list, default_calculator_, default_crick_params_file(), default_helix_length(), default_residue_name(), defaults_set_, helix(), n_helices(), protocols::helical_bundle::parse_resnames(), reset_pose(), set_crick_params_file_for_helix(), set_default_crick_params_file(), set_default_helix_length(), set_default_residue_name(), set_helix_length_for_helix(), set_reset_pose(), set_residue_name_for_helix(), set_symmetry_options_from_tag(), set_use_degrees(), protocols::helical_bundle::TR(), and use_degrees().

◆ provide_citation_info()

void protocols::helical_bundle::MakeBundle::provide_citation_info ( basic::citation_manager::CitationCollectionList & citations ) const

overridevirtual

Provide the citation.

Reimplemented from protocols::moves::Mover.

◆ provide_xml_schema()

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

static

References protocols::helical_bundle::add_attributes_for_helix_params(), protocols::helical_bundle::add_attributes_for_make_bundle_minorhelix_defaults(), protocols::helical_bundle::add_attributes_for_make_bundle_symmetry(), protocols::helical_bundle::add_attributes_for_minor_helix_params(), protocols::helical_bundle::add_attributes_for_other_helix_params(), protocols::helical_bundle::BPC_end_of_list, default_calculator(), mover_name(), and protocols::moves::xsd_type_definition_w_attributes_and_repeatable_subelements().

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

◆ reset_pose()

bool protocols::helical_bundle::MakeBundle::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(), and parse_my_tag().

◆ set_crick_params_file_for_helix()

void protocols::helical_bundle::MakeBundle::set_crick_params_file_for_helix	(	std::string const &	filename,
		core::Size const	helix_index
	)

Set the Crick params file for a particular helix.

Triggers a read from disk!

References protocols::abinitio::filename(), helix(), and n_helices().

Referenced by parse_my_tag().

◆ set_default_crick_params_file()

void protocols::helical_bundle::MakeBundle::set_default_crick_params_file ( std::string const & input_string )

Set the default Crick params file name.

Triggers a read from disk!

References default_crick_params_file_, defaults_set_, and initialize_default_calculator_from_default_crick_params_file().

Referenced by parse_my_tag().

◆ set_default_helix_length()

void protocols::helical_bundle::MakeBundle::set_default_helix_length ( core::Size const & val )

Set the default number of residues per helix.

References default_helix_length_, defaults_set_, and protocols::hybridization::val.

Referenced by parse_my_tag().

◆ set_default_residue_name()

void protocols::helical_bundle::MakeBundle::set_default_residue_name ( utility::vector1< std::string > const & names )

Set the default residue name.

References default_residue_name_, and defaults_set_.

Referenced by parse_my_tag().

◆ set_helix_length_for_helix()

void protocols::helical_bundle::MakeBundle::set_helix_length_for_helix	(	core::Size const	helix_length,
		core::Size const	helix_index
	)

Set the helix length, in residues, for the Nth helix.

References helix(), and n_helices().

Referenced by parse_my_tag().

◆ set_last_apply_failed()

void protocols::helical_bundle::MakeBundle::set_last_apply_failed ( bool const val )

inlineprivate

Set whether the last apply failed.

Called by the apply() function.

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

Referenced by apply().

◆ set_reset_pose()

void protocols::helical_bundle::MakeBundle::set_reset_pose ( bool const reset_in )

inline

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

References reset_pose_.

Referenced by parse_my_tag().

◆ set_residue_name_for_helix()

void protocols::helical_bundle::MakeBundle::set_residue_name_for_helix	(	utility::vector1< std::string > const &	names,
		core::Size const	helix_index
	)

Set the residue names for a given helix.

References helix(), and n_helices().

Referenced by parse_my_tag().

◆ set_symmetry()

void protocols::helical_bundle::MakeBundle::set_symmetry ( core::Size const symmetry_in )

inline

Set the symmetry of the bundle.

See bundle_symmetry_ member variable for details.

References bundle_symmetry_.

Referenced by set_symmetry_options_from_tag().

◆ set_symmetry_copies()

void protocols::helical_bundle::MakeBundle::set_symmetry_copies ( core::Size const symmetry_copies_in )

inline

Set how many of the symmetry copies actually get generated.

See bundle_symmetry_copies_ member variable for details.

References bundle_symmetry_copies_.

Referenced by set_symmetry_options_from_tag().

◆ set_symmetry_options_from_tag()

void protocols::helical_bundle::MakeBundle::set_symmetry_options_from_tag ( utility::tag::TagCOP tag )

Set symmetry and symmetry_copies options based on an input tag.

References set_symmetry(), set_symmetry_copies(), symmetry(), symmetry_copies(), and protocols::helical_bundle::TR().

Referenced by parse_my_tag().

◆ set_use_degrees()

void protocols::helical_bundle::MakeBundle::set_use_degrees ( bool const val = true )

Set whether we're using degrees (true) or radians (false).

References default_calculator_, use_degrees(), use_degrees_, and protocols::hybridization::val.

Referenced by parse_my_tag().

◆ symmetry()

core::Size protocols::helical_bundle::MakeBundle::symmetry ( ) const

inline

Get the symmetry of the bundle.

See bundle_symmetry_ member variable for details.

References bundle_symmetry_.

Referenced by apply(), and set_symmetry_options_from_tag().

◆ symmetry_copies()

core::Size protocols::helical_bundle::MakeBundle::symmetry_copies ( ) const

inline

Get how many of the symmetry copies actually get generated.

See bundle_symmetry_copies_ member variable for details.

References bundle_symmetry_copies_.

Referenced by apply(), and set_symmetry_options_from_tag().

◆ use_degrees()

bool protocols::helical_bundle::MakeBundle::use_degrees ( ) const

inline

Get whether we're using degrees (true) or radians (false).

References use_degrees_.

Referenced by apply(), parse_my_tag(), and set_use_degrees().

Member Data Documentation

◆ bundle_symmetry_

core::Size protocols::helical_bundle::MakeBundle::bundle_symmetry_

private

The symmetry of the bundle.

"0" or "1" are asymmetric. "2" indicates 2-fold rotational symmetry, "3" indicates 3-fold rotational symmetry, and so forth. Note that this need not correspond to the number of helices defined. If 2 helices are defined with 3-fold symmetry, you end up with 6 helices.

Referenced by set_symmetry(), and symmetry().

◆ bundle_symmetry_copies_

core::Size protocols::helical_bundle::MakeBundle::bundle_symmetry_copies_

private

The symmetry copies to generate.

A value of 0 means to generate all copies. Higher values mean to generate only the first N copies. For example, if the symmetry were 16 but bundle_symmetry_copies_ were set to 4, only the first 4 symmetry repeats would be generated.

Referenced by set_symmetry_copies(), and symmetry_copies().

◆ default_calculator_

BundleParametrizationCalculatorOP protocols::helical_bundle::MakeBundle::default_calculator_

private

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

This object gets cloned by each of the make_bundle_helix_movers_, and they use it as the intial (default) state before setting up their own parameters.

Referenced by add_helix(), apply(), default_calculator(), default_calculator_nonconst(), initialize_default_calculator_from_default_crick_params_file(), parse_my_tag(), and set_use_degrees().

◆ default_crick_params_file_

std::string protocols::helical_bundle::MakeBundle::default_crick_params_file_

private

DEFAULTS: Default values for helix parameters if no other values are set:

Default Crick params file name

Referenced by default_crick_params_file(), initialize_default_calculator_from_default_crick_params_file(), and set_default_crick_params_file().

◆ default_helix_length_

core::Size protocols::helical_bundle::MakeBundle::default_helix_length_

private

Default number of residues in the helix.

Referenced by default_helix_length(), and set_default_helix_length().

◆ default_helix_length_set_

bool protocols::helical_bundle::MakeBundle::default_helix_length_set_

private

Has the default number of residues in the helix been specified?

◆ default_residue_name_

utility::vector1< std::string > protocols::helical_bundle::MakeBundle::default_residue_name_

private

Default residue name.

Referenced by default_residue_name(), MakeBundle(), and set_default_residue_name().

◆ defaults_set_

bool protocols::helical_bundle::MakeBundle::defaults_set_

private

Have the default parameter values been set?

If true, they cannot be set again. Note that once a helix is added, defaults_set_ becomes true. This ensures a sensible order of operations when calling the MakeBundle mover from code, where configuration is not necessarily happening in the order specified in the parse_my_tag() function.

Referenced by add_helix(), parse_my_tag(), set_default_crick_params_file(), set_default_helix_length(), and set_default_residue_name().

◆ last_apply_failed_

bool protocols::helical_bundle::MakeBundle::last_apply_failed_

private

Did the last apply fail?

Referenced by last_apply_failed(), and set_last_apply_failed().

◆ make_bundle_helix_movers_

utility::vector1< protocols::helical_bundle::MakeBundleHelixOP > protocols::helical_bundle::MakeBundle::make_bundle_helix_movers_

private

A vector of owning pointers to the individual MakeBundleHelix movers that will make each of the helices in the bundle.

Referenced by add_helix(), helix(), helix_cop(), MakeBundle(), and n_helices().

◆ reset_pose_

bool protocols::helical_bundle::MakeBundle::reset_pose_

private

Should the input pose be reset?

Default true.

Referenced by reset_pose(), and set_reset_pose().

◆ use_degrees_

bool protocols::helical_bundle::MakeBundle::use_degrees_

private

Are we using degrees (true) or radians (false)? Default radians (false).

Referenced by set_use_degrees(), and use_degrees().

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

src/protocols/helical_bundle/MakeBundle.hh
src/protocols/helical_bundle/MakeBundle.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

◆ MakeBundle() [1/2]

◆ MakeBundle() [2/2]

◆ ~MakeBundle()

Member Function Documentation

◆ add_helix()

◆ apply()

◆ clone()

◆ default_calculator()

◆ default_calculator_nonconst()

◆ default_crick_params_file()

◆ default_helix_length()

◆ default_residue_name() [1/2]

◆ default_residue_name() [2/2]

◆ fresh_instance()

◆ get_name()

◆ helix()

◆ helix_cop()

◆ initialize_default_calculator_from_default_crick_params_file()

◆ last_apply_failed()

◆ mover_name()

◆ n_helices()

◆ parse_my_tag()

◆ provide_citation_info()

◆ provide_xml_schema()

◆ reset_pose()

◆ set_crick_params_file_for_helix()

◆ set_default_crick_params_file()

◆ set_default_helix_length()

◆ set_default_residue_name()

◆ set_helix_length_for_helix()

◆ set_last_apply_failed()

◆ set_reset_pose()

◆ set_residue_name_for_helix()

◆ set_symmetry()

◆ set_symmetry_copies()

◆ set_symmetry_options_from_tag()

◆ set_use_degrees()

◆ symmetry()

◆ symmetry_copies()

◆ use_degrees()

Member Data Documentation

◆ bundle_symmetry_

◆ bundle_symmetry_copies_

◆ default_calculator_

◆ default_crick_params_file_

◆ default_helix_length_

◆ default_helix_length_set_

◆ default_residue_name_

◆ defaults_set_

◆ last_apply_failed_

◆ make_bundle_helix_movers_

◆ reset_pose_

◆ use_degrees_