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protocols::loops::loop_mover::refine::LoopMover_Refine_CCD Class Reference

#include <LoopMover_CCD.hh>

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Collaboration diagram for protocols::loops::loop_mover::refine::LoopMover_Refine_CCD:
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Public Member Functions

 LoopMover_Refine_CCD ()
 
 LoopMover_Refine_CCD (protocols::loops::LoopsOP loops_in)
 
 LoopMover_Refine_CCD (protocols::loops::LoopsOP loops_in, core::scoring::ScoreFunctionOP scorefxn)
 
 ~LoopMover_Refine_CCD ()
 
virtual protocols::moves::MoverOP clone () const
 Clone this object. More...
 
void set_default_settings ()
 
void set_redesign_loop (bool value=true)
 
bool get_redesign_loop ()
 
void set_task_factory (core::pack::task::TaskFactoryCOP task_factory_in)
 
core::pack::task::TaskFactoryCOP get_task_factory () const
 
void parse_my_tag (utility::tag::TagPtr const tag, protocols::moves::DataMap &, protocols::filters::Filters_map const &, protocols::moves::Movers_map const &, core::pose::Pose const &)
 Called by MoverFactory when constructing new Movers. Takes care of the specific mover's parsing. More...
 
void apply (core::pose::Pose &pose)
 Apply the loop-build protocol to the input pose. More...
 
virtual std::string get_name () const
 Each derived class must specify its name. The class name. More...
 
void outer_cycles (core::Size value)
 
void max_inner_cycles (core::Size value)
 
void repack_period (core::Size value)
 
void temp_initial (core::Real value)
 
void temp_final (core::Real value)
 
void set_fold_tree_from_loops (bool const s)
 
bool set_fold_tree_from_loops () const
 
core::kinematics::MoveMapOP move_map () const
 
void move_map (core::kinematics::MoveMapOP mm)
 
protocols::loops::LoopsCOP get_loops () const
 
void set_flank_residue_min (bool value)
 
bool flank_residue_min () const
 
core::Size inner_cycles () const
 
core::Size current_cycle_number () const
 
core::Size repack_period () const
 
void setup_movemap (core::pose::Pose const &pose, protocols::loops::Loops const &loops, utility::vector1< bool > const &allow_repack, core::kinematics::MoveMapOP &movemap)
 setup an appropriate movemap for the given loops More...
 
- Public Member Functions inherited from protocols::loops::loop_mover::LoopMover
 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...
 
virtual ~LoopMover ()
 
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 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::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
 
std::string torsion_features_string (core::pose::Pose const &pose) const
 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 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 ~Mover ()
 
virtual MoverSP create ()
 
virtual void apply (core::io::serialization::PipeMap &pmap)
 
virtual void parse_state (SerializableState const &state)
 
virtual void parse_def (utility::lua::LuaObject const &def, utility::lua::LuaObject const &score_fxns, utility::lua::LuaObject const &tasks, MoverCacheSP cache)
 
virtual void save_state (SerializableState &state)
 
 Mover (std::string const &type_name)
 sets the type for a mover; name_ has been removed (2010/05/14) More...
 
 Mover (Mover const &other)
 
Moveroperator= (Mover const &other)
 assignment operator More...
 
virtual core::Real last_proposal_density_ratio ()
 
std::string const & type () const
 
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...
 
void set_current_tag (std::string const &new_tag)
 
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 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...
 
void type (const std::string &type_in)
 
std::string get_type () const
 
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...
 
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 reinitialize_for_each_job () const
 this function informs 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
 this function informs 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
 this is like clone(), except it generates a new mover object freshly created with the default ctor. This function should be pure virtual but that would disrupt the code base; MAKE SURE YOU DEFINE IT if you want to have your mover be a protocol handed to the job distributor (august 08 vintage). More...
 
void set_current_job (protocols::jobdist::BasicJobCOP job)
 
jobdist::BasicJobCOP get_current_job () const
 

Protected Member Functions

void read_options ()
 
virtual basic::Tracer & tr () const
 
- Protected Member Functions inherited from protocols::loops::loop_mover::LoopMover
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)
 
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...
 

Protected Attributes

core::pack::task::TaskFactoryOP task_factory_
 
bool redesign_loop_
 

Private Member Functions

core::scoring::ScoreFunctionOP get_new_ramping_scorefxn ()
 
core::scoring::ScoreFunctionOP ramping_scorefxn ()
 
void setup_foldtree_and_add_cutpoint_variants (core::pose::Pose &pose)
 
core::pack::task::PackerTaskOP get_packer_task (core::pose::Pose const &pose)
 
void increase_chainbreak_weight_and_update_monte_carlo (Size iteration_number, core::scoring::ScoreFunctionOP local_scorefxn, protocols::moves::MonteCarlo &mc, core::pose::Pose &pose)
 
void debugging_output (core::pose::Pose &pose)
 

Private Attributes

bool packing_isolated_to_active_loops_
 
bool set_fold_tree_from_loops_
 
bool user_defined_move_map_
 
bool flank_residue_min_
 
bool debug_
 
bool repack_neighbors_
 
core::Size outer_cycles_
 
core::Size max_inner_cycles_
 
core::Size inner_cycles_
 
core::Size current_cycle_number_
 
core::Size repack_period_
 
core::Real temp_initial_
 
core::Real temp_final_
 
core::kinematics::FoldTreeOP original_fold_tree_
 
core::kinematics::MoveMapOP move_map_
 
core::scoring::ScoreFunctionOP ramping_scorefxn_
 

Friends

std::ostream & operator<< (std::ostream &os, LoopMover_Refine_CCD const &mover)
 

Additional Inherited Members

- Public Types inherited from protocols::loops::loop_mover::LoopMover
typedef core::kinematics::MoveMapOP MoveMapOP
 
- 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. these options will end up in -help of your application if users of this mover call register_options. do this recursively! if you use movers within your mover, call their register_options in your register_options() method. More...
 

Constructor & Destructor Documentation

protocols::loops::loop_mover::refine::LoopMover_Refine_CCD::LoopMover_Refine_CCD ( )
protocols::loops::loop_mover::refine::LoopMover_Refine_CCD::LoopMover_Refine_CCD ( protocols::loops::LoopsOP  loops_in)
protocols::loops::loop_mover::refine::LoopMover_Refine_CCD::LoopMover_Refine_CCD ( protocols::loops::LoopsOP  loops_in,
core::scoring::ScoreFunctionOP  scorefxn 
)
protocols::loops::loop_mover::refine::LoopMover_Refine_CCD::~LoopMover_Refine_CCD ( )

Member Function Documentation

void protocols::loops::loop_mover::refine::LoopMover_Refine_CCD::apply ( core::pose::Pose )
virtual

Apply the loop-build protocol to the input pose.

Implements protocols::loops::loop_mover::LoopMover.

References core::scoring::chainbreak, protocols::loops::loop_mover::refine::CHAINBREAK_SCORE_RAMP_FACTOR, protocols::loops::loop_mover::refine::LoopRefineInnerCycleFactory::create_inner_cycle(), current_cycle_number_, debugging_output(), core::pose::Pose::fold_tree(), protocols::loops::loop_mover::refine::LoopRefineInnerCycleFactory::get_instance(), protocols::moves::Mover::get_native_pose(), get_new_ramping_scorefxn(), get_packer_task(), protocols::loops::loop_mover::refine::IC_RefineCCDStandard, increase_chainbreak_weight_and_update_monte_carlo(), inner_cycles_, protocols::loops::loop_mover::LoopMover::loops(), max_inner_cycles_, move_map_, original_fold_tree_, outer_cycles_, core::pack::pack_rotamers(), ramping_scorefxn(), protocols::loops::remove_cutpoint_variants(), protocols::loops::loop_mover::LoopMover::resolve_loop_indices(), set_fold_tree_from_loops_, protocols::loops::loop_mover::LoopMover::set_loops_from_pose_observer_cache(), protocols::moves::Mover::set_native_pose(), setup_foldtree_and_add_cutpoint_variants(), setup_movemap(), task_factory_, temp_final_, temp_initial_, tr(), and protocols::loops::loop_mover::LoopMover::use_loops_from_observer_cache().

Referenced by protocols::protein_interface_design::movers::LoopMoverFromCommandLine::apply(), protocols::protein_interface_design::movers::LoopRemodel::apply(), protocols::antibody2::RefineOneCDRLoop::apply(), protocols::comparative_modeling::LoopRelaxMover::apply(), protocols::protein_interface_design::movers::Splice::apply(), protocols::LoopRefine::apply(), protocols::dna::DesignProteinBackboneAroundDNA::ccd(), and protocols::forge::remodel::RemodelMover::confirm_sequence().

protocols::moves::MoverOP protocols::loops::loop_mover::refine::LoopMover_Refine_CCD::clone ( ) const
virtual

Clone this object.

Reimplemented from protocols::moves::Mover.

References LoopMover_Refine_CCD().

core::Size protocols::loops::loop_mover::refine::LoopMover_Refine_CCD::current_cycle_number ( ) const
inline

References current_cycle_number_.

void protocols::loops::loop_mover::refine::LoopMover_Refine_CCD::debugging_output ( core::pose::Pose pose)
private
bool protocols::loops::loop_mover::refine::LoopMover_Refine_CCD::flank_residue_min ( ) const
inline

References flank_residue_min_.

protocols::loops::LoopsCOP protocols::loops::loop_mover::refine::LoopMover_Refine_CCD::get_loops ( ) const
std::string protocols::loops::loop_mover::refine::LoopMover_Refine_CCD::get_name ( ) const
virtual

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

Reimplemented from protocols::loops::loop_mover::LoopMover.

core::scoring::ScoreFunctionOP protocols::loops::loop_mover::refine::LoopMover_Refine_CCD::get_new_ramping_scorefxn ( )
private
core::pack::task::PackerTaskOP protocols::loops::loop_mover::refine::LoopMover_Refine_CCD::get_packer_task ( core::pose::Pose const &  pose)
private
bool protocols::loops::loop_mover::refine::LoopMover_Refine_CCD::get_redesign_loop ( )
inline

References redesign_loop_.

core::pack::task::TaskFactoryCOP protocols::loops::loop_mover::refine::LoopMover_Refine_CCD::get_task_factory ( ) const

References task_factory_.

void protocols::loops::loop_mover::refine::LoopMover_Refine_CCD::increase_chainbreak_weight_and_update_monte_carlo ( Size  iteration_number,
core::scoring::ScoreFunctionOP  local_scorefxn,
protocols::moves::MonteCarlo mc,
core::pose::Pose pose 
)
private
core::Size protocols::loops::loop_mover::refine::LoopMover_Refine_CCD::inner_cycles ( ) const
inline

References inner_cycles_.

void protocols::loops::loop_mover::refine::LoopMover_Refine_CCD::max_inner_cycles ( core::Size  value)
inline
loop_mover::LoopMover::MoveMapOP protocols::loops::loop_mover::refine::LoopMover_Refine_CCD::move_map ( ) const
void protocols::loops::loop_mover::refine::LoopMover_Refine_CCD::move_map ( core::kinematics::MoveMapOP  mm)
void protocols::loops::loop_mover::refine::LoopMover_Refine_CCD::outer_cycles ( core::Size  value)
inline
void protocols::loops::loop_mover::refine::LoopMover_Refine_CCD::parse_my_tag ( utility::tag::TagPtr const  tag,
protocols::moves::DataMap data,
protocols::filters::Filters_map const &  filters,
protocols::moves::Movers_map const &  movers,
core::pose::Pose const &  pose 
)
virtual

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 stop executions. This, however, calls attention to the lack of this method, which could be due to something as silly as a wrong parameters definition.

Reimplemented from protocols::moves::Mover.

References protocols::moves::DataMap::get(), protocols::loops::loops_definers::load_loop_definitions(), protocols::loops::loop_mover::LoopMover::loops(), max_inner_cycles_, move_map(), move_map_, outer_cycles_, packing_isolated_to_active_loops_, protocols::rosetta_scripts::parse_movemap(), protocols::rosetta_scripts::parse_task_operations(), set_fold_tree_from_loops(), protocols::loops::loop_mover::LoopMover::set_scorefxn(), set_task_factory(), protocols::loops::loop_mover::LoopMover::set_use_loops_from_observer_cache(), task_factory_, temp_final(), and temp_initial().

core::scoring::ScoreFunctionOP protocols::loops::loop_mover::refine::LoopMover_Refine_CCD::ramping_scorefxn ( )
private
void protocols::loops::loop_mover::refine::LoopMover_Refine_CCD::read_options ( )
protected
void protocols::loops::loop_mover::refine::LoopMover_Refine_CCD::repack_period ( core::Size  value)
inline
core::Size protocols::loops::loop_mover::refine::LoopMover_Refine_CCD::repack_period ( ) const
inline

References repack_period_.

void protocols::loops::loop_mover::refine::LoopMover_Refine_CCD::set_default_settings ( )
void protocols::loops::loop_mover::refine::LoopMover_Refine_CCD::set_flank_residue_min ( bool  value)
inline
void protocols::loops::loop_mover::refine::LoopMover_Refine_CCD::set_fold_tree_from_loops ( bool const  s)
inline
bool protocols::loops::loop_mover::refine::LoopMover_Refine_CCD::set_fold_tree_from_loops ( ) const
inline

References set_fold_tree_from_loops_.

Referenced by parse_my_tag().

void protocols::loops::loop_mover::refine::LoopMover_Refine_CCD::set_redesign_loop ( bool  value = true)
inline
void protocols::loops::loop_mover::refine::LoopMover_Refine_CCD::set_task_factory ( core::pack::task::TaskFactoryCOP  task_factory_in)
void protocols::loops::loop_mover::refine::LoopMover_Refine_CCD::setup_foldtree_and_add_cutpoint_variants ( core::pose::Pose pose)
private
void protocols::loops::loop_mover::refine::LoopMover_Refine_CCD::setup_movemap ( core::pose::Pose const &  pose,
protocols::loops::Loops const &  loops,
utility::vector1< bool > const &  allow_repack,
core::kinematics::MoveMapOP movemap 
)

setup an appropriate movemap for the given loops

Parameters
[in]loopsThe loops to model.
[in]allow_repackIndicates whether or not to allow a position to repack.
[out]movemapOutput movemap, all settings added here.
Remarks
will enforce the false movemap

References protocols::loops::loop_mover::LoopMover::enforce_false_movemap(), core::pose::symmetry::is_symmetric(), protocols::loops::loops_set_move_map(), core::pose::symmetry::make_symmetric_movemap(), move_map_, and user_defined_move_map_.

Referenced by apply().

void protocols::loops::loop_mover::refine::LoopMover_Refine_CCD::temp_final ( core::Real  value)
inline
void protocols::loops::loop_mover::refine::LoopMover_Refine_CCD::temp_initial ( core::Real  value)
inline
basic::Tracer & protocols::loops::loop_mover::refine::LoopMover_Refine_CCD::tr ( ) const
protectedvirtual

Friends And Related Function Documentation

std::ostream& operator<< ( std::ostream &  os,
LoopMover_Refine_CCD const &  mover 
)
friend

Member Data Documentation

core::Size protocols::loops::loop_mover::refine::LoopMover_Refine_CCD::current_cycle_number_
private
bool protocols::loops::loop_mover::refine::LoopMover_Refine_CCD::debug_
private

Referenced by debugging_output(), and read_options().

bool protocols::loops::loop_mover::refine::LoopMover_Refine_CCD::flank_residue_min_
private
core::Size protocols::loops::loop_mover::refine::LoopMover_Refine_CCD::inner_cycles_
private
core::Size protocols::loops::loop_mover::refine::LoopMover_Refine_CCD::max_inner_cycles_
private
core::kinematics::MoveMapOP protocols::loops::loop_mover::refine::LoopMover_Refine_CCD::move_map_
private
core::kinematics::FoldTreeOP protocols::loops::loop_mover::refine::LoopMover_Refine_CCD::original_fold_tree_
private
core::Size protocols::loops::loop_mover::refine::LoopMover_Refine_CCD::outer_cycles_
private
bool protocols::loops::loop_mover::refine::LoopMover_Refine_CCD::packing_isolated_to_active_loops_
private
core::scoring::ScoreFunctionOP protocols::loops::loop_mover::refine::LoopMover_Refine_CCD::ramping_scorefxn_
private
bool protocols::loops::loop_mover::refine::LoopMover_Refine_CCD::redesign_loop_
protected
bool protocols::loops::loop_mover::refine::LoopMover_Refine_CCD::repack_neighbors_
private

Referenced by get_packer_task(), and read_options().

core::Size protocols::loops::loop_mover::refine::LoopMover_Refine_CCD::repack_period_
private
bool protocols::loops::loop_mover::refine::LoopMover_Refine_CCD::set_fold_tree_from_loops_
private
core::pack::task::TaskFactoryOP protocols::loops::loop_mover::refine::LoopMover_Refine_CCD::task_factory_
protected
core::Real protocols::loops::loop_mover::refine::LoopMover_Refine_CCD::temp_final_
private
core::Real protocols::loops::loop_mover::refine::LoopMover_Refine_CCD::temp_initial_
private
bool protocols::loops::loop_mover::refine::LoopMover_Refine_CCD::user_defined_move_map_
private

Referenced by move_map(), and setup_movemap().


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