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protocols::grafting::simple_movers::DeleteRegionMover Class Reference

Delete a region of a pose. Mover Wrapper to grafting utility function. More...

#include <DeleteRegionMover.hh>

Inheritance diagram for protocols::grafting::simple_movers::DeleteRegionMover:
Inheritance graph
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Public Member Functions

 DeleteRegionMover ()
 
 DeleteRegionMover (core::Size const res_start, core::Size const res_end)
 
 DeleteRegionMover (DeleteRegionMover const &src)
 
 ~DeleteRegionMover () override
 
void apply (core::pose::Pose &pose) override
 Main Method. More...
 
void region (std::string const &res_start, std::string const &res_end)
 Set the region of the pose where deletion will occur. More...
 
void set_residue_selector (core::select::residue_selector::ResidueSelectorCOP selector)
 Sets the residue selector. More...
 
void set_rechain (bool rechain)
 
void set_add_terminal_types_on_rechain (bool add)
 
void set_add_jump_on_rechain (bool add)
 
protocols::moves::MoverOP clone () const override
 Return a clone of the Mover object. More...
 
protocols::moves::MoverOP fresh_instance () const override
 Generates a new Mover object freshly created with the default ctor. More...
 
void parse_my_tag (TagCOP tag, basic::datacache::DataMap &data) override
 Called by MoverFactory when constructing new Movers. Takes care of the specific mover's parsing. More...
 
std::string get_name () const override
 Each derived class must specify its name. The class name. More...
 
bool mover_provides_citation_info () const override
 Does this mover provide information about how to cite it? More...
 
utility::vector1
< basic::citation_manager::CitationCollectionCOP > 
provide_citation_info () const override
 Provide the citation. More...
 
utility::vector1
< basic::citation_manager::UnpublishedModuleInfoCOP > 
provide_authorship_info_for_unpublished () const override
 This mover is published, and provides citation info. It can also provide unpublished info for the residue selector that it uses. 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_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...
 

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 add_terminus_variants (core::pose::Pose &pose, core::Size const resid) const
 Adds terminal variants to residues resid and resid-1. More...
 
void add_cutpoint_variants (core::pose::Pose &pose, core::Size const resid) const
 Adds cutpoint variants to residues resid and resid-1. More...
 

Private Attributes

core::select::residue_selector::ResidueSelectorCOP selector_
 
core::Size nter_overhang_
 
core::Size cter_overhang_
 
bool rechain_
 
bool add_terminal_types_on_rechain_
 
bool add_jump_on_rechain_
 

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

Delete a region of a pose. Mover Wrapper to grafting utility function.

Constructor & Destructor Documentation

protocols::grafting::simple_movers::DeleteRegionMover::DeleteRegionMover ( )
protocols::grafting::simple_movers::DeleteRegionMover::DeleteRegionMover ( core::Size const  res_start,
core::Size const  res_end 
)
protocols::grafting::simple_movers::DeleteRegionMover::DeleteRegionMover ( DeleteRegionMover const &  src)

References selector_.

protocols::grafting::simple_movers::DeleteRegionMover::~DeleteRegionMover ( )
overridedefault

Member Function Documentation

void protocols::grafting::simple_movers::DeleteRegionMover::add_cutpoint_variants ( core::pose::Pose pose,
core::Size const  resid 
) const
private

Adds cutpoint variants to residues resid and resid-1.

Adds terminal variants to residues resid and resid-1.

Parameters
[in,out]posePose to be modified
[in]residResidue number for the residue that would have the lower cutpoint variant

Residue resid-1 will have upper_cutpoint variant, and residue resid will have lower_cutpoit variant

Parameters
[in,out]posePose to be modified
[in]residResidue number for the residue that would have the lower terminus variant

Residue resid-1 will have upper_terminus variant, and residue resid will have lower_terminus variant

References core::pose::add_variant_type_to_pose_residue(), core::chemical::CUTPOINT_LOWER, core::chemical::CUTPOINT_UPPER, and core::pose::Pose::size().

Referenced by apply().

void protocols::grafting::simple_movers::DeleteRegionMover::add_terminus_variants ( core::pose::Pose pose,
core::Size const  resid 
) const
private

Adds terminal variants to residues resid and resid-1.

Parameters
[in,out]posePose to be modified
[in]residResidue number for the residue that would have the lower terminus variant

Residue resid-1 will have upper_terminus variant, and residue resid will have lower_terminus variant

References core::pose::add_lower_terminus_type_to_pose_residue(), core::pose::add_upper_terminus_type_to_pose_residue(), and core::pose::Pose::size().

Referenced by apply().

void protocols::grafting::simple_movers::DeleteRegionMover::apply ( core::pose::Pose )
overridevirtual
protocols::moves::MoverOP protocols::grafting::simple_movers::DeleteRegionMover::clone ( ) const
overridevirtual

Return a clone of the Mover object.

clone is meant to return an OP'ed deep copy of this object. This really should be a pure virtual in the base class, but adding pure virtuals to Mover would massively disrupt the code. This default implementation crashes at runtime instead of compiletime if you try to call it. If this code is causing you problems, your Mover needs to override this function.

Reimplemented from protocols::moves::Mover.

protocols::moves::MoverOP protocols::grafting::simple_movers::DeleteRegionMover::fresh_instance ( ) const
overridevirtual

Generates a new Mover object freshly created with the default ctor.

fresh_instance is meant to return a new object of this class, created with the default constructor. This really should be a pure virtual in the base class, but adding pure virtuals to Mover would massively disrupt the code. This default implementation crashes at runtime instead of compiletime if you try to call it. If this code is causing you problems, your Mover needs to override this function. This is used by the August 08 job distributor.

Reimplemented from protocols::moves::Mover.

std::string protocols::grafting::simple_movers::DeleteRegionMover::get_name ( ) const
overridevirtual

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

Implements protocols::moves::Mover.

References mover_name().

std::string protocols::grafting::simple_movers::DeleteRegionMover::mover_name ( )
static
bool protocols::grafting::simple_movers::DeleteRegionMover::mover_provides_citation_info ( ) const
overridevirtual

Does this mover provide information about how to cite it?

Returns true.

Reimplemented from protocols::moves::Mover.

void protocols::grafting::simple_movers::DeleteRegionMover::parse_my_tag ( TagCOP  tag,
basic::datacache::DataMap &  data 
)
overridevirtual

Called by MoverFactory when constructing new Movers. Takes care of the specific mover's parsing.

Some movers need not be parsed, so we shouldn't force people to reimplement this method. However, we should be chatty about the fact that someone is using a RosettaScripts interface to a mover which didn't define parse_my_tag()

Reimplemented from protocols::moves::Mover.

References add_jump_on_rechain_, add_terminal_types_on_rechain_, cter_overhang_, core::sequence::end, nter_overhang_, core::select::residue_selector::parse_residue_selector(), rechain_, region(), selector_, and protocols::loops::start.

utility::vector1< basic::citation_manager::UnpublishedModuleInfoCOP > protocols::grafting::simple_movers::DeleteRegionMover::provide_authorship_info_for_unpublished ( ) const
overridevirtual

This mover is published, and provides citation info. It can also provide unpublished info for the residue selector that it uses.

Reimplemented from protocols::moves::Mover.

References selector_.

utility::vector1< basic::citation_manager::CitationCollectionCOP > protocols::grafting::simple_movers::DeleteRegionMover::provide_citation_info ( ) const
overridevirtual

Provide the citation.

Returns
A vector of citation collections. This allows the mover to provide citations for itself and for any modules that it invokes.

Reimplemented from protocols::moves::Mover.

References selector_.

void protocols::grafting::simple_movers::DeleteRegionMover::provide_xml_schema ( utility::tag::XMLSchemaDefinition &  xsd)
static
void protocols::grafting::simple_movers::DeleteRegionMover::region ( std::string const &  res_start,
std::string const &  res_end 
)

Set the region of the pose where deletion will occur.

References selector_.

Referenced by DeleteRegionMover(), and parse_my_tag().

void protocols::grafting::simple_movers::DeleteRegionMover::set_add_jump_on_rechain ( bool  add)
inline
void protocols::grafting::simple_movers::DeleteRegionMover::set_add_terminal_types_on_rechain ( bool  add)
inline
void protocols::grafting::simple_movers::DeleteRegionMover::set_rechain ( bool  rechain)
inline

References rechain_.

void protocols::grafting::simple_movers::DeleteRegionMover::set_residue_selector ( core::select::residue_selector::ResidueSelectorCOP  selector)

Member Data Documentation

bool protocols::grafting::simple_movers::DeleteRegionMover::add_jump_on_rechain_
private
bool protocols::grafting::simple_movers::DeleteRegionMover::add_terminal_types_on_rechain_
private
core::Size protocols::grafting::simple_movers::DeleteRegionMover::cter_overhang_
private

Referenced by apply(), and parse_my_tag().

core::Size protocols::grafting::simple_movers::DeleteRegionMover::nter_overhang_
private

Referenced by apply(), and parse_my_tag().

bool protocols::grafting::simple_movers::DeleteRegionMover::rechain_
private

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

core::select::residue_selector::ResidueSelectorCOP protocols::grafting::simple_movers::DeleteRegionMover::selector_
private

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