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protocols::loops::loop_mover::LoopMover Class Referenceabstract

The loop-rebuild protocol. More...

#include <LoopMover.hh>

Inheritance diagram for protocols::loops::loop_mover::LoopMover:
Inheritance graph
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Public Types

typedef core::kinematics::MoveMapOP MoveMapOP
 
- 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

 LoopMover ()
 
 LoopMover (protocols::loops::LoopsOP loops_in)
 
 LoopMover (protocols::loops::LoopsFileData const &loops_from_file)
 
 LoopMover (protocols::loops::GuardedLoopsFromFileOP guarded_loops)
 
 LoopMover (LoopMover const &rhs)
 copy ctor More...
 
LoopMoveroperator= (LoopMover const &rhs)
 assignment operator More...
 
 ~LoopMover () override
 
std::string get_name () const override
 Each derived class must specify its name. The class name. More...
 
void set_guarded_loops_not_in_charge ()
 Inform the GuardedLoopsFromFile object that it is not in charge of updating its Loops object at the beginning of apply() More...
 
void apply (core::pose::Pose &) override=0
 Apply the loop-build protocol to the input pose. More...
 
void set_scorefxn (const core::scoring::ScoreFunctionOP score_in)
 
const
core::scoring::ScoreFunctionOP
scorefxn () const
 
void loops (protocols::loops::LoopsOP lptr)
 Set the loops pointer by giving the LoopMover resolved loop indices; implicity sets the GuardedLoopsFromFile object into a "not in charge" state (since something else must be controlling the the Loops object). The GuardedLoopFromFile object copies the pointer, not the data. More...
 
void loops (LoopsFileData const &loop_file_data)
 Set the loops by giving the LoopMover unresolved loop indices (which cannot be resolved until apply() ). More...
 
void loops (protocols::loops::loops_definers::LoopsDefinerOP setting)
 
void loops (protocols::loops::GuardedLoopsFromFileOP guarded_loops)
 Set the guarded_loops pointer. More...
 
protocols::loops::LoopsCOP loops () const
 Accessor for the loops data. Requires that the loop indices have been resolved; do not call this before apply() has been called. More...
 
protocols::loops::LoopsOP loops ()
 non-const accessor for the loops data. Requires that the loop indices have been resolved; do not call this before apply() has been called. More...
 
const utility::vector1
< core::fragment::FragSetOP > & 
frag_libs () const
 
core::conformation::torsion_bin_string torsion_features_string (core::pose::Pose const &pose) const
 create a string representing the torsion bins (ABEGX) for the loops defined in the guarded_loops_ object. A sentinal value of ppo_torbin_U is used to mark the boundaries between the separate loops (unused as long as there's only one Loop object in the guarded_loops_ object). More...
 
virtual void set_extended_torsions (core::pose::Pose &pose, Loop const &loop)
 Extend a loop. More...
 
void add_fragments (core::fragment::FragSetOP fragset)
 add a fragment set More...
 
void clear_fragments ()
 clear the list of fragment sets More...
 
MoveMapOP const & false_movemap () const
 explicit False settings in this MoveMap will override any automatically generated MoveMap settings during the loop modeling protocol More...
 
void false_movemap (MoveMapOP const &mm)
 explicit False settings in this MoveMap will override any automatically generated MoveMap settings during the loop modeling protocol More...
 
checkpoint::CheckPointerOPget_checkpoints ()
 
- 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 MoverOP clone () const
 Return a clone of the Mover object. 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...
 
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
 
virtual void parse_my_tag (TagCOP tag, basic::datacache::DataMap &data)
 Called by MoverFactory when constructing new Movers. Takes care of the specific mover's parsing. More...
 
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...
 

Protected Member Functions

core::Size enforce_false_movemap (MoveMapOP &mm) const
 import the false_movemap's explicit False settings into the given MoveMap More...
 
void set_loops_from_pose_observer_cache (core::pose::Pose const &pose)
 allow the loops to be set from the segments stored in the poses observer cache. makes it possible to have LoopMovers be part of parser protocols where the loops were determined by some previous on the fly step More...
 
bool use_loops_from_observer_cache () const
 
void set_use_loops_from_observer_cache (bool const loops_from_observer_cache)
 
virtual basic::Tracer & tr () const =0
 
void resolve_loop_indices (core::pose::Pose const &p)
 Turn the unresolved loop indices read in from disk into pose-specific loop indices. Must be called by derived classes at the beginning of apply. More...
 
- 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...
 

Private Member Functions

void init ()
 
void initForEqualOperatorAndCopyConstructor (LoopMover &lhs, LoopMover const &rhs)
 

Private Attributes

GuardedLoopsFromFileOP guarded_loops_
 
core::scoring::ScoreFunctionOP scorefxn_
 
utility::vector1
< core::fragment::FragSetOP
frag_libs_
 
checkpoint::CheckPointerOP checkpoints_
 
bool loops_from_observer_cache_
 
MoveMapOP false_movemap_
 explicit False settings in this MoveMap will override any automatically generated MoveMap settings during the loop modeling protocol More...
 

Additional Inherited Members

- 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...
 

Detailed Description

The loop-rebuild protocol.

Member Typedef Documentation

Constructor & Destructor Documentation

protocols::loops::loop_mover::LoopMover::LoopMover ( )

References init().

protocols::loops::loop_mover::LoopMover::LoopMover ( protocols::loops::LoopsOP  loops_in)

GuardedLoops constructed with a pointer to a loops object: sets the GuardedLoops object into it's "not in charge" mode; i.e. the external source of the LoopsOP is responsible for resolving loop indices

References init().

protocols::loops::loop_mover::LoopMover::LoopMover ( protocols::loops::LoopsFileData const &  loops_from_file)

GuardedLoops constructed with an unresolve-loop-indices object: sets the GuardedLoops object into it's "in charge" mode; i.e. before the loops object may be used, the loop indices must be resolved.

References init().

protocols::loops::loop_mover::LoopMover::LoopMover ( protocols::loops::GuardedLoopsFromFileOP  guarded_loops)

References init().

protocols::loops::loop_mover::LoopMover::LoopMover ( LoopMover const &  rhs)
protocols::loops::loop_mover::LoopMover::~LoopMover ( )
overridedefault

Member Function Documentation

void protocols::loops::loop_mover::LoopMover::add_fragments ( core::fragment::FragSetOP  fragset)
void protocols::loops::loop_mover::LoopMover::apply ( core::pose::Pose )
overridepure virtual
void protocols::loops::loop_mover::LoopMover::clear_fragments ( )

clear the list of fragment sets

References frag_libs_.

Size protocols::loops::loop_mover::LoopMover::enforce_false_movemap ( MoveMapOP mm) const
protected

import the false_movemap's explicit False settings into the given MoveMap

Returns
The number of False settings imported.

References false_movemap().

Referenced by protocols::loops::loop_mover::refine::LoopMover_Refine_CCD::setup_movemap().

LoopMover::MoveMapOP const & protocols::loops::loop_mover::LoopMover::false_movemap ( ) const

explicit False settings in this MoveMap will override any automatically generated MoveMap settings during the loop modeling protocol

References false_movemap_.

Referenced by protocols::forge::remodel::RemodelMover::confirm_sequence(), and enforce_false_movemap().

void protocols::loops::loop_mover::LoopMover::false_movemap ( MoveMapOP const &  mm)

explicit False settings in this MoveMap will override any automatically generated MoveMap settings during the loop modeling protocol

References false_movemap_.

const utility::vector1< core::fragment::FragSetOP > & protocols::loops::loop_mover::LoopMover::frag_libs ( ) const
checkpoint::CheckPointerOP & protocols::loops::loop_mover::LoopMover::get_checkpoints ( )
std::string protocols::loops::loop_mover::LoopMover::get_name ( ) const
overridevirtual
void protocols::loops::loop_mover::LoopMover::init ( void  )
private
void protocols::loops::loop_mover::LoopMover::initForEqualOperatorAndCopyConstructor ( LoopMover lhs,
LoopMover const &  rhs 
)
private
void protocols::loops::loop_mover::LoopMover::loops ( protocols::loops::LoopsOP  lptr)

Set the loops pointer by giving the LoopMover resolved loop indices; implicity sets the GuardedLoopsFromFile object into a "not in charge" state (since something else must be controlling the the Loops object). The GuardedLoopFromFile object copies the pointer, not the data.

References guarded_loops_.

void protocols::loops::loop_mover::LoopMover::loops ( LoopsFileData const &  loop_file_data)

Set the loops by giving the LoopMover unresolved loop indices (which cannot be resolved until apply() ).

References guarded_loops_.

void protocols::loops::loop_mover::LoopMover::loops ( protocols::loops::loops_definers::LoopsDefinerOP  setting)

References guarded_loops_.

void protocols::loops::loop_mover::LoopMover::loops ( protocols::loops::GuardedLoopsFromFileOP  guarded_loops)

Set the guarded_loops pointer.

References guarded_loops_.

protocols::loops::LoopsCOP protocols::loops::loop_mover::LoopMover::loops ( ) const
protocols::loops::LoopsOP protocols::loops::loop_mover::LoopMover::loops ( )

non-const accessor for the loops data. Requires that the loop indices have been resolved; do not call this before apply() has been called.

References guarded_loops_.

LoopMover & protocols::loops::loop_mover::LoopMover::operator= ( LoopMover const &  rhs)

assignment operator

References initForEqualOperatorAndCopyConstructor().

void protocols::loops::loop_mover::LoopMover::resolve_loop_indices ( core::pose::Pose const &  p)
protected
const core::scoring::ScoreFunctionOP & protocols::loops::loop_mover::LoopMover::scorefxn ( ) const
void protocols::loops::loop_mover::LoopMover::set_extended_torsions ( core::pose::Pose pose,
Loop const &  loop 
)
virtual
void protocols::loops::loop_mover::LoopMover::set_guarded_loops_not_in_charge ( )

Inform the GuardedLoopsFromFile object that it is not in charge of updating its Loops object at the beginning of apply()

References guarded_loops_.

void protocols::loops::loop_mover::LoopMover::set_loops_from_pose_observer_cache ( core::pose::Pose const &  pose)
protected

allow the loops to be set from the segments stored in the poses observer cache. makes it possible to have LoopMovers be part of parser protocols where the loops were determined by some previous on the fly step

Author
flo, march 2011

References guarded_loops_, loops(), core::pose::Pose::observer_cache(), core::pose::datacache::SPECIAL_SEGMENTS_OBSERVER, and tr().

Referenced by protocols::loops::loop_mover::refine::LoopMover_Refine_CCD::apply().

void protocols::loops::loop_mover::LoopMover::set_scorefxn ( const core::scoring::ScoreFunctionOP  score_in)
void protocols::loops::loop_mover::LoopMover::set_use_loops_from_observer_cache ( bool const  loops_from_observer_cache)
protected
core::conformation::torsion_bin_string protocols::loops::loop_mover::LoopMover::torsion_features_string ( core::pose::Pose const &  pose) const

create a string representing the torsion bins (ABEGX) for the loops defined in the guarded_loops_ object. A sentinal value of ppo_torbin_U is used to mark the boundaries between the separate loops (unused as long as there's only one Loop object in the guarded_loops_ object).

bin torsion angles as described in http://www.ncbi.nlm.nih.gov/pubmed/19646450

generates a string with the torsion angle bins, using uppercase letters as in the publication above for omega ~ 180, and lowercase letters for omega ~ 0; to be used in loop sampling analysis

Author
Amelie Stein
Date
April 26, 2012

References core::conformation::get_torsion_bin(), loops(), core::pose::Pose::omega(), core::pose::Pose::phi(), core::conformation::ppo_torbin_U, and core::pose::Pose::psi().

Referenced by protocols::loops::loop_mover::refine::LoopMover_Refine_KIC::apply(), and protocols::loops::loop_mover::perturb::LoopMover_Perturb_KIC::model_loop().

virtual basic::Tracer& protocols::loops::loop_mover::LoopMover::tr ( ) const
protectedpure virtual
bool protocols::loops::loop_mover::LoopMover::use_loops_from_observer_cache ( ) const
protected

Member Data Documentation

checkpoint::CheckPointerOP protocols::loops::loop_mover::LoopMover::checkpoints_
private
MoveMapOP protocols::loops::loop_mover::LoopMover::false_movemap_
private

explicit False settings in this MoveMap will override any automatically generated MoveMap settings during the loop modeling protocol

Referenced by false_movemap(), init(), and initForEqualOperatorAndCopyConstructor().

utility::vector1< core::fragment::FragSetOP > protocols::loops::loop_mover::LoopMover::frag_libs_
private
GuardedLoopsFromFileOP protocols::loops::loop_mover::LoopMover::guarded_loops_
private
bool protocols::loops::loop_mover::LoopMover::loops_from_observer_cache_
private
core::scoring::ScoreFunctionOP protocols::loops::loop_mover::LoopMover::scorefxn_
private

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