Public Member Functions | Static Public Member Functions | Private Attributes | List of all members
protocols::pose_length_moves::NearNativeLoopCloser Class Reference

#include <NearNativeLoopCloser.hh>

Inheritance diagram for protocols::pose_length_moves::NearNativeLoopCloser:
Inheritance graph

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="", std::string label_loop="", std::string fragment_store_path="", std::string fragment_store_format="", std::string fragment_store_compression="", core::Size numb_stubs_to_consider=1)
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 switch_chain_order (Pose &pose, utility::vector1< core::Size > new_chain_order)
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 void provide_citation_info (basic::citation_manager::CitationCollectionList &) const
 Provide citations to the passed CitationCollectionList Subclasses should add the info for themselves and any other classes they use. 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_
core::Size numb_outputed_
core::Size max_number_of_results_
bool top_outputed_
core::Real max_vdw_change_
bool ideal_
std::string closure_type_
std::string pose_name_
std::string label_loop_
protocols::indexed_structure_store::SSHashedFragmentStoreOP SSHashedFragmentStoreOP_
utility::vector1< PossibleLoopOPpossibleLoops_
std::string allowed_loop_abegos_
std::string fragment_store_path_
std::string fragment_store_format_
std::string fragment_store_compression_
core::Size numb_stubs_to_consider_

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

◆ NearNativeLoopCloser() [1/2]

protocols::pose_length_moves::NearNativeLoopCloser::NearNativeLoopCloser ( )

◆ NearNativeLoopCloser() [2/2]

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 = "",
std::string  label_loop = "",
std::string  fragment_store_path = "",
std::string  fragment_store_format = "",
std::string  fragment_store_compression = "",
core::Size  numb_stubs_to_consider = 1 

Member Function Documentation

◆ apply()

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

◆ clone()

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

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.

◆ close_loop()

Real protocols::pose_length_moves::NearNativeLoopCloser::close_loop ( Pose pose)

◆ combine_chains()

void protocols::pose_length_moves::NearNativeLoopCloser::combine_chains ( Pose pose)

◆ create_maximum_length_pose()

core::pose::PoseOP protocols::pose_length_moves::NearNativeLoopCloser::create_maximum_length_pose ( char  resTypeBeforeLoop,
char  resTypeAfterLoop,
core::pose::Pose  pose 

◆ create_potential_loops()

vector1< PossibleLoopOP > protocols::pose_length_moves::NearNativeLoopCloser::create_potential_loops ( core::pose::Pose  pose)

◆ extendRegion()

void protocols::pose_length_moves::NearNativeLoopCloser::extendRegion ( bool  towardCTerm,
core::Size  resStart,
char  neighborResType,
core::Size  numberAddRes,
core::pose::PoseOP poseOP 

◆ get_additional_output()

core::pose::PoseOP protocols::pose_length_moves::NearNativeLoopCloser::get_additional_output ( )

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


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().

◆ get_additional_output_with_rmsd()

core::pose::PoseOP protocols::pose_length_moves::NearNativeLoopCloser::get_additional_output_with_rmsd ( core::Real return_rmsd)

◆ get_name()

std::string protocols::pose_length_moves::NearNativeLoopCloser::get_name ( ) const

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

Implements protocols::moves::Mover.

References mover_name().

◆ mover_name()

std::string protocols::pose_length_moves::NearNativeLoopCloser::mover_name ( )

◆ parse_my_tag()

void protocols::pose_length_moves::NearNativeLoopCloser::parse_my_tag ( utility::tag::TagCOP  tag,
basic::datacache::DataMap data 

◆ provide_xml_schema()

void protocols::pose_length_moves::NearNativeLoopCloser::provide_xml_schema ( utility::tag::XMLSchemaDefinition &  xsd)

◆ switch_chain_order()

void protocols::pose_length_moves::NearNativeLoopCloser::switch_chain_order ( Pose pose,
utility::vector1< core::Size new_chain_order 

Member Data Documentation

◆ allowed_loop_abegos_

std::string protocols::pose_length_moves::NearNativeLoopCloser::allowed_loop_abegos_

◆ chainAfterLoop_

char protocols::pose_length_moves::NearNativeLoopCloser::chainAfterLoop_

◆ chainBeforeLoop_

char protocols::pose_length_moves::NearNativeLoopCloser::chainBeforeLoop_

◆ closure_type_

std::string protocols::pose_length_moves::NearNativeLoopCloser::closure_type_

◆ fragment_store_compression_

std::string protocols::pose_length_moves::NearNativeLoopCloser::fragment_store_compression_

◆ fragment_store_format_

std::string protocols::pose_length_moves::NearNativeLoopCloser::fragment_store_format_

◆ fragment_store_path_

std::string protocols::pose_length_moves::NearNativeLoopCloser::fragment_store_path_

◆ ideal_

bool protocols::pose_length_moves::NearNativeLoopCloser::ideal_

◆ idealExtension_

bool protocols::pose_length_moves::NearNativeLoopCloser::idealExtension_

◆ label_loop_

std::string protocols::pose_length_moves::NearNativeLoopCloser::label_loop_

◆ loopLengthRangeHigh_

core::Size protocols::pose_length_moves::NearNativeLoopCloser::loopLengthRangeHigh_

◆ loopLengthRangeLow_

core::Size protocols::pose_length_moves::NearNativeLoopCloser::loopLengthRangeLow_

◆ max_number_of_results_

core::Size protocols::pose_length_moves::NearNativeLoopCloser::max_number_of_results_

◆ max_vdw_change_

core::Real protocols::pose_length_moves::NearNativeLoopCloser::max_vdw_change_

◆ numb_outputed_

core::Size protocols::pose_length_moves::NearNativeLoopCloser::numb_outputed_

◆ numb_stubs_to_consider_

core::Size protocols::pose_length_moves::NearNativeLoopCloser::numb_stubs_to_consider_

◆ output_all_

bool protocols::pose_length_moves::NearNativeLoopCloser::output_all_

◆ output_closed_

bool protocols::pose_length_moves::NearNativeLoopCloser::output_closed_

◆ pose_name_

std::string protocols::pose_length_moves::NearNativeLoopCloser::pose_name_

◆ possibleLoops_

utility::vector1<PossibleLoopOP> protocols::pose_length_moves::NearNativeLoopCloser::possibleLoops_

◆ resAdjustmentStartHigh_

int protocols::pose_length_moves::NearNativeLoopCloser::resAdjustmentStartHigh_

◆ resAdjustmentStartHigh_sheet_

int protocols::pose_length_moves::NearNativeLoopCloser::resAdjustmentStartHigh_sheet_

◆ resAdjustmentStartLow_

int protocols::pose_length_moves::NearNativeLoopCloser::resAdjustmentStartLow_

◆ resAdjustmentStartLow_sheet_

int protocols::pose_length_moves::NearNativeLoopCloser::resAdjustmentStartLow_sheet_

◆ resAdjustmentStopHigh_

int protocols::pose_length_moves::NearNativeLoopCloser::resAdjustmentStopHigh_

◆ resAdjustmentStopHigh_sheet_

int protocols::pose_length_moves::NearNativeLoopCloser::resAdjustmentStopHigh_sheet_

◆ resAdjustmentStopLow_

int protocols::pose_length_moves::NearNativeLoopCloser::resAdjustmentStopLow_

◆ resAdjustmentStopLow_sheet_

int protocols::pose_length_moves::NearNativeLoopCloser::resAdjustmentStopLow_sheet_

◆ resAfterLoop_

core::Size protocols::pose_length_moves::NearNativeLoopCloser::resAfterLoop_

◆ resBeforeLoop_

core::Size protocols::pose_length_moves::NearNativeLoopCloser::resBeforeLoop_

◆ rmsThreshold_

core::Real protocols::pose_length_moves::NearNativeLoopCloser::rmsThreshold_

◆ SSHashedFragmentStoreOP_

protocols::indexed_structure_store::SSHashedFragmentStoreOP protocols::pose_length_moves::NearNativeLoopCloser::SSHashedFragmentStoreOP_

◆ top_outputed_

bool protocols::pose_length_moves::NearNativeLoopCloser::top_outputed_

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