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protocols::pose_length_moves::NearNativeLoopCloser Class Reference

#include <NearNativeLoopCloser.hh>

Inheritance diagram for protocols::pose_length_moves::NearNativeLoopCloser:
Inheritance graph
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Public Member Functions

 NearNativeLoopCloser ()
 
 NearNativeLoopCloser (int resAdjustmentStartLow, int resAdjustmentStartHigh, int resAdjustmentStopLow, int resAdjustmentStopHigh, int resAdjustmentStartLow_sheet, int resAdjustmentStartHigh_sheet, int resAdjustmentStopLow_sheet, int resAdjustmentStopHigh_sheet, core::Size loopLengthRangeLow, core::Size loopLengthRangeHigh, core::Size resBeforeLoop, core::Size resAfterLoop, char chainBeforeLoop, char chainAfterLoop, core::Real rmsThreshold, core::Real max_vdw_change, bool idealExtension, bool ideal, bool output_closed, std::string closure_type="lookback", std::string allowed_loop_abegos="")
 
moves::MoverOP clone () const override
 Return a clone of the Mover object. More...
 
core::Real close_loop (Pose &pose)
 
void apply (Pose &pose) override
 Main Method. More...
 
void combine_chains (Pose &pose)
 
void extendRegion (bool towardCTerm, core::Size resStart, char neighborResType, core::Size numberAddRes, core::pose::PoseOP &poseOP)
 
core::pose::PoseOP create_maximum_length_pose (char resTypeBeforeLoop, char resTypeAfterLoop, core::pose::Pose pose)
 
utility::vector1< PossibleLoopOPcreate_potential_loops (core::pose::Pose pose)
 
void parse_my_tag (utility::tag::TagCOP tag, basic::datacache::DataMap &datamap) override
 Called by MoverFactory when constructing new Movers. Takes care of the specific mover's parsing. More...
 
core::pose::PoseOP get_additional_output () override
 Mechanism by which a mover may return multiple output poses from a single input pose. More...
 
core::pose::PoseOP get_additional_output_with_rmsd (core::Real &return_rmsd)
 
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...
 
virtual MoverOP fresh_instance () const
 Generates a new Mover object freshly created with the default ctor. 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...
 
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...
 
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

int resAdjustmentStartLow_
 
int resAdjustmentStartHigh_
 
int resAdjustmentStopLow_
 
int resAdjustmentStopHigh_
 
int resAdjustmentStartLow_sheet_
 
int resAdjustmentStartHigh_sheet_
 
int resAdjustmentStopLow_sheet_
 
int resAdjustmentStopHigh_sheet_
 
core::Size loopLengthRangeLow_
 
core::Size loopLengthRangeHigh_
 
core::Size resBeforeLoop_
 
core::Size resAfterLoop_
 
char chainBeforeLoop_
 
char chainAfterLoop_
 
core::Real rmsThreshold_
 
bool idealExtension_
 
bool output_closed_
 
bool output_all_
 
bool top_outputed_
 
core::Real max_vdw_change_
 
bool ideal_
 
std::string closure_type_
 
std::string pose_name_
 
protocols::indexed_structure_store::SSHashedFragmentStoreSSHashedFragmentStore_
 
utility::vector1< PossibleLoopOPpossibleLoops_
 
std::string allowed_loop_abegos_
 

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...
 

Constructor & Destructor Documentation

protocols::pose_length_moves::NearNativeLoopCloser::NearNativeLoopCloser ( )
protocols::pose_length_moves::NearNativeLoopCloser::NearNativeLoopCloser ( int  resAdjustmentStartLow,
int  resAdjustmentStartHigh,
int  resAdjustmentStopLow,
int  resAdjustmentStopHigh,
int  resAdjustmentStartLow_sheet,
int  resAdjustmentStartHigh_sheet,
int  resAdjustmentStopLow_sheet,
int  resAdjustmentStopHigh_sheet,
core::Size  loopLengthRangeLow,
core::Size  loopLengthRangeHigh,
core::Size  resBeforeLoop,
core::Size  resAfterLoop,
char  chainBeforeLoop,
char  chainAfterLoop,
core::Real  rmsThreshold,
core::Real  max_vdw_change,
bool  idealExtension,
bool  ideal,
bool  output_closed,
std::string  closure_type = "lookback",
std::string  allowed_loop_abegos = "" 
)

Member Function Documentation

void protocols::pose_length_moves::NearNativeLoopCloser::apply ( Pose )
overridevirtual

Main Method.

Implements protocols::moves::Mover.

References close_loop().

moves::MoverOP protocols::pose_length_moves::NearNativeLoopCloser::clone ( ) const
inlineoverridevirtual

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.

Real protocols::pose_length_moves::NearNativeLoopCloser::close_loop ( Pose pose)
void protocols::pose_length_moves::NearNativeLoopCloser::combine_chains ( Pose pose)
core::pose::PoseOP protocols::pose_length_moves::NearNativeLoopCloser::create_maximum_length_pose ( char  resTypeBeforeLoop,
char  resTypeAfterLoop,
core::pose::Pose  pose 
)
vector1< PossibleLoopOP > protocols::pose_length_moves::NearNativeLoopCloser::create_potential_loops ( core::pose::Pose  pose)
void protocols::pose_length_moves::NearNativeLoopCloser::extendRegion ( bool  towardCTerm,
core::Size  resStart,
char  neighborResType,
core::Size  numberAddRes,
core::pose::PoseOP poseOP 
)
core::pose::PoseOP protocols::pose_length_moves::NearNativeLoopCloser::get_additional_output ( )
overridevirtual

Mechanism by which a mover may return multiple output poses from a single input pose.

fpd

Supported in JD2. Will attempt to grab additional poses until a nullptr is returned.

Mechanism by which a mover may return multiple output poses from a single input pose. After apply is called, calling this function will return subsequent output poses. NULL is returned if the mover has no more output poses remaining. The base class implementation returns NULL always; multi-output movers must override this. RosettaScripts uses this interface to produce a 'branched' protocol.

Reimplemented from protocols::moves::Mover.

References get_additional_output_with_rmsd().

core::pose::PoseOP protocols::pose_length_moves::NearNativeLoopCloser::get_additional_output_with_rmsd ( core::Real return_rmsd)
std::string protocols::pose_length_moves::NearNativeLoopCloser::get_name ( ) const
overridevirtual

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

Implements protocols::moves::Mover.

References mover_name().

std::string protocols::pose_length_moves::NearNativeLoopCloser::mover_name ( )
static
void protocols::pose_length_moves::NearNativeLoopCloser::parse_my_tag ( utility::tag::TagCOP  tag,
basic::datacache::DataMap &  data 
)
overridevirtual
void protocols::pose_length_moves::NearNativeLoopCloser::provide_xml_schema ( utility::tag::XMLSchemaDefinition &  xsd)
static

Member Data Documentation

std::string protocols::pose_length_moves::NearNativeLoopCloser::allowed_loop_abegos_
private
char protocols::pose_length_moves::NearNativeLoopCloser::chainAfterLoop_
private
char protocols::pose_length_moves::NearNativeLoopCloser::chainBeforeLoop_
private
std::string protocols::pose_length_moves::NearNativeLoopCloser::closure_type_
private
bool protocols::pose_length_moves::NearNativeLoopCloser::ideal_
private
bool protocols::pose_length_moves::NearNativeLoopCloser::idealExtension_
private
core::Size protocols::pose_length_moves::NearNativeLoopCloser::loopLengthRangeHigh_
private
core::Size protocols::pose_length_moves::NearNativeLoopCloser::loopLengthRangeLow_
private
core::Real protocols::pose_length_moves::NearNativeLoopCloser::max_vdw_change_
private
bool protocols::pose_length_moves::NearNativeLoopCloser::output_all_
private
bool protocols::pose_length_moves::NearNativeLoopCloser::output_closed_
private
std::string protocols::pose_length_moves::NearNativeLoopCloser::pose_name_
private
utility::vector1<PossibleLoopOP> protocols::pose_length_moves::NearNativeLoopCloser::possibleLoops_
private
int protocols::pose_length_moves::NearNativeLoopCloser::resAdjustmentStartHigh_
private
int protocols::pose_length_moves::NearNativeLoopCloser::resAdjustmentStartHigh_sheet_
private
int protocols::pose_length_moves::NearNativeLoopCloser::resAdjustmentStartLow_
private
int protocols::pose_length_moves::NearNativeLoopCloser::resAdjustmentStartLow_sheet_
private
int protocols::pose_length_moves::NearNativeLoopCloser::resAdjustmentStopHigh_
private
int protocols::pose_length_moves::NearNativeLoopCloser::resAdjustmentStopHigh_sheet_
private
int protocols::pose_length_moves::NearNativeLoopCloser::resAdjustmentStopLow_
private
int protocols::pose_length_moves::NearNativeLoopCloser::resAdjustmentStopLow_sheet_
private
core::Size protocols::pose_length_moves::NearNativeLoopCloser::resAfterLoop_
private
core::Size protocols::pose_length_moves::NearNativeLoopCloser::resBeforeLoop_
private
core::Real protocols::pose_length_moves::NearNativeLoopCloser::rmsThreshold_
private
protocols::indexed_structure_store::SSHashedFragmentStore* protocols::pose_length_moves::NearNativeLoopCloser::SSHashedFragmentStore_
private
bool protocols::pose_length_moves::NearNativeLoopCloser::top_outputed_
private

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