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protocols::helical_bundle::MakeBundle Class Reference

#include <MakeBundle.hh>

Inheritance diagram for protocols::helical_bundle::MakeBundle:
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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

 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...
 
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

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

Constructor & Destructor Documentation

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

Copy constructor for MakeBundle mover.

Creator for MakeBundle mover.

References make_bundle_helix_movers_.

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

Destructor for MakeBundle mover.

Member Function Documentation

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().

void protocols::helical_bundle::MakeBundle::apply ( core::pose::Pose pose)
overridevirtual
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().

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

Access the default calculator directly.

Const access.

References default_calculator_.

Referenced by provide_xml_schema().

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_.

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().

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().

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_.

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().

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.

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().

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

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().

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_.

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

Indicate that this mover is unpublished.

Reimplemented from protocols::moves::Mover.

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

void protocols::helical_bundle::MakeBundle::parse_my_tag ( utility::tag::TagCOP  tag,
basic::datacache::DataMap &  data 
)
overridevirtual
utility::vector1< basic::citation_manager::UnpublishedModuleInfoCOP > protocols::helical_bundle::MakeBundle::provide_authorship_info_for_unpublished ( ) const
overridevirtual

Provide authorship information for an unpublished Rosetta module.

Reimplemented from protocols::moves::Mover.

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

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 helix(), and n_helices().

Referenced by parse_my_tag().

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().

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().

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().

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().

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().

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().

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().

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().

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().

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().

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().

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().

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().

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

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().

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().

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().

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().

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().

bool protocols::helical_bundle::MakeBundle::default_helix_length_set_
private

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

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().

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().

bool protocols::helical_bundle::MakeBundle::last_apply_failed_
private

Did the last apply fail?

Referenced by last_apply_failed(), and set_last_apply_failed().

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().

bool protocols::helical_bundle::MakeBundle::reset_pose_
private

Should the input pose be reset?

Default true.

Referenced by reset_pose(), and set_reset_pose().

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: