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protocols::ncbb::ResidueReplacementRebuildMover Class Reference

A simple method to mutate a pose fairly destructively, and barely recover. More...

#include <ResidueReplacementRebuildMover.hh>

Inheritance diagram for protocols::ncbb::ResidueReplacementRebuildMover:
Inheritance graph

Public Member Functions

 ResidueReplacementRebuildMover ()
 Constructors ///. More...
 ResidueReplacementRebuildMover (ResidueReplacementRebuildMover const &src)
 Copy constructor (not needed unless you need deep copies) More...
 ~ResidueReplacementRebuildMover () override
 Destructor (important for properly forward-declaring smart-pointer members) More...
core::pose::Pose make_new_pose (core::pose::Pose const &pose) const
 Mover Methods ///. More...
void apply (core::pose::Pose &pose) override
 Apply the mover. More...
void show (std::ostream &output=std::cout) const override
 Show the contents of the Mover. More...
void parse_my_tag (utility::tag::TagCOP tag, basic::datacache::DataMap &data) override
 Rosetta Scripts Support ///. More...
protocols::moves::MoverOP fresh_instance () const override
 required in the context of the parser/scripting scheme More...
protocols::moves::MoverOP clone () const override
 required in the context of the parser/scripting scheme More...
std::string get_name () const override
 Each derived class must specify its name. The class name. More...
void set_resi_chosen (core::Size const setting)
void set_resi_len (core::Size const setting)
void set_resname (std::string const &setting)
void score_function (core::scoring::ScoreFunctionCOP sfxn)
core::Size set_resi_chosen () const
core::Size set_resi_len () const
std::string set_resname () const
core::scoring::ScoreFunctionCOP score_function () const
- 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 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 Attributes

core::Size resi_chosen_ = 0
core::Size resi_len_ = 0
std::string resname_ = "ALA"
core::scoring::ScoreFunctionCOP scorefxn_

Additional Inherited Members

- 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
- 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...

Detailed Description

A simple method to mutate a pose fairly destructively, and barely recover.

Constructor & Destructor Documentation

protocols::ncbb::ResidueReplacementRebuildMover::ResidueReplacementRebuildMover ( )

Constructors ///.

Default constructor

protocols::ncbb::ResidueReplacementRebuildMover::ResidueReplacementRebuildMover ( ResidueReplacementRebuildMover const &  src)

Copy constructor (not needed unless you need deep copies)

Copy constructor.

protocols::ncbb::ResidueReplacementRebuildMover::~ResidueReplacementRebuildMover ( )

Destructor (important for properly forward-declaring smart-pointer members)

Member Function Documentation

void protocols::ncbb::ResidueReplacementRebuildMover::apply ( core::pose::Pose pose)
protocols::moves::MoverOP protocols::ncbb::ResidueReplacementRebuildMover::clone ( ) const

required in the context of the parser/scripting scheme

Reimplemented from protocols::moves::Mover.

protocols::moves::MoverOP protocols::ncbb::ResidueReplacementRebuildMover::fresh_instance ( ) const

required in the context of the parser/scripting scheme

Reimplemented from protocols::moves::Mover.

std::string protocols::ncbb::ResidueReplacementRebuildMover::get_name ( ) const

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

Implements protocols::moves::Mover.

References mover_name().

Pose protocols::ncbb::ResidueReplacementRebuildMover::make_new_pose ( core::pose::Pose const &  pose) const
std::string protocols::ncbb::ResidueReplacementRebuildMover::mover_name ( )
void protocols::ncbb::ResidueReplacementRebuildMover::parse_my_tag ( utility::tag::TagCOP  tag,
basic::datacache::DataMap &  data 

Rosetta Scripts Support ///.

parse XML tag (to use this Mover in Rosetta Scripts)

Reimplemented from protocols::moves::Mover.

References core::scoring::parse_score_function(), score_function(), set_resi_chosen(), set_resi_len(), and set_resname().

void protocols::ncbb::ResidueReplacementRebuildMover::provide_xml_schema ( utility::tag::XMLSchemaDefinition &  xsd)
void protocols::ncbb::ResidueReplacementRebuildMover::score_function ( core::scoring::ScoreFunctionCOP  sfxn)

References scorefxn_.

core::scoring::ScoreFunctionCOP protocols::ncbb::ResidueReplacementRebuildMover::score_function ( ) const

References scorefxn_.

Referenced by parse_my_tag().

void protocols::ncbb::ResidueReplacementRebuildMover::set_resi_chosen ( core::Size const  setting)

References resi_chosen_.

core::Size protocols::ncbb::ResidueReplacementRebuildMover::set_resi_chosen ( ) const

References resi_chosen_.

Referenced by parse_my_tag().

void protocols::ncbb::ResidueReplacementRebuildMover::set_resi_len ( core::Size const  setting)

References resi_len_.

core::Size protocols::ncbb::ResidueReplacementRebuildMover::set_resi_len ( ) const

References resi_len_.

Referenced by parse_my_tag().

void protocols::ncbb::ResidueReplacementRebuildMover::set_resname ( std::string const &  setting)

References resname_.

std::string protocols::ncbb::ResidueReplacementRebuildMover::set_resname ( ) const

References resname_.

Referenced by parse_my_tag().

void protocols::ncbb::ResidueReplacementRebuildMover::show ( std::ostream &  output = std::cout) const

Show the contents of the Mover.

Reimplemented from protocols::moves::Mover.

References protocols::moves::Mover::show().

Referenced by protocols::ncbb::operator<<().

Member Data Documentation

core::Size protocols::ncbb::ResidueReplacementRebuildMover::resi_chosen_ = 0
core::Size protocols::ncbb::ResidueReplacementRebuildMover::resi_len_ = 0

Referenced by apply(), make_new_pose(), and set_resi_len().

std::string protocols::ncbb::ResidueReplacementRebuildMover::resname_ = "ALA"

Referenced by apply(), make_new_pose(), and set_resname().

core::scoring::ScoreFunctionCOP protocols::ncbb::ResidueReplacementRebuildMover::scorefxn_

Referenced by apply(), and score_function().

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