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protocols::loops::loop_mover::refine::LoopMover_Refine_KIC Class Reference

#include <LoopMover_KIC.hh>

Inheritance diagram for protocols::loops::loop_mover::refine::LoopMover_Refine_KIC:
Inheritance graph
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Public Member Functions

 LoopMover_Refine_KIC ()
 
 LoopMover_Refine_KIC (protocols::loops::LoopsOP loops_in)
 
 LoopMover_Refine_KIC (protocols::loops::LoopsOP const loops_in, core::scoring::ScoreFunctionCOP scorefxn)
 
 ~LoopMover_Refine_KIC () override
 
void init (core::scoring::ScoreFunctionCOP scorefxn)
 
void set_default_settings ()
 
void set_redesign_loop (bool value=true)
 
bool get_redesign_loop ()
 
void set_flank_residue_min (bool value)
 
void set_task_factory (core::pack::task::TaskFactoryOP value)
 
bool get_task_factory ()
 
protocols::moves::MoverOP clone () const override
 Clone this object. More...
 
void apply (core::pose::Pose &pose) override
 
void show (std::ostream &output=std::cout) const override
 Outputs details about the Mover, including current settings. More...
 
void update_movemap_vectors (core::pose::Pose &pose, utility::vector1< core::kinematics::MoveMap > &move_maps)
 update the vector of movemaps, one for each loop in loops_ More...
 
void update_allow_sc_vectors (core::pose::Pose &pose, utility::vector1< utility::vector1< bool > > &allow_sc_vectors)
 update the vector of vectors of moveable side-chain positions, one for each loop in loops_ More...
 
void set_rottrials_from_kic_segment (core::pose::Pose &pose, core::pack::task::PackerTaskOP &rottrials_packer_task, core::Size kic_start, core::Size kic_end)
 
void set_movemap_from_kic_segment (core::pose::Pose &pose, core::kinematics::MoveMap &cur_mm, core::Size kic_start, core::Size kic_end)
 
std::string get_name () const override
 Each derived class must specify its name. The class name. 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...
 
 ~LoopMover () override
 
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::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 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 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...
 

Protected Member Functions

basic::Tracer & tr () const override
 
- Protected Member Functions inherited from protocols::loops::loop_mover::LoopMover
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)
 
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 Attributes

core::Real neighbor_dist_
 
core::Size max_seglen_
 
bool recover_low_
 
bool min_after_repack_
 
bool fix_natsc_
 
bool optimize_only_kic_region_sidechains_after_move_
 
bool flank_residue_min_
 

Additional Inherited Members

- Public Types inherited from protocols::loops::loop_mover::LoopMover
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
 

Constructor & Destructor Documentation

protocols::loops::loop_mover::refine::LoopMover_Refine_KIC::LoopMover_Refine_KIC ( )
protocols::loops::loop_mover::refine::LoopMover_Refine_KIC::LoopMover_Refine_KIC ( protocols::loops::LoopsOP  loops_in)
protocols::loops::loop_mover::refine::LoopMover_Refine_KIC::LoopMover_Refine_KIC ( protocols::loops::LoopsOP const  loops_in,
core::scoring::ScoreFunctionCOP  scorefxn 
)
protocols::loops::loop_mover::refine::LoopMover_Refine_KIC::~LoopMover_Refine_KIC ( )
overridedefault

Member Function Documentation

void protocols::loops::loop_mover::refine::LoopMover_Refine_KIC::apply ( core::pose::Pose pose)
overridevirtual

detailed Refines the polypeptide segments in the LoopMover_Refine_KIC::loops_ class variable from their current conformations. Uses Rosetta's all-atom respresentation and high-resolution scoring function (with an upweighted chain break term). At the beginning of this stage, unless the flag -loops:fix_natsc has been set, all residues within the neighbor distance of a loop (defined by -loops:neighbor_dist) are repacked and then subject to rotamer trials. The backbones of all loop residues, and the side-chains of all loop residues and neighbors are then subject to DFPmin. If -loops:fix_natsc is set, only the loop residues (and not the neighbors) will be subject to repacking, rotamer trials, and minimization. Consequently, if this stage has been preceeded by LoopMover_Perturb_KIC:model_loop, and the -loops:fix_natsc flag is omitted, the side-chains surrounding the loop will be optimized for the perturbed loop conformation, rather than the starting conformation that preceded the call to model_loop.

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

References core::pose::Pose::aa(), protocols::loops::Loops::add_loop(), protocols::loops::add_loop_flank_residues_bb_to_movemap(), core::pose::add_variant_type_to_pose_residue(), core::conformation::Residue::atom_name(), protocols::loops::Loops::begin(), protocols::moves::MonteCarlo::boltzmann(), core::scoring::cart_bonded, core::pose::Pose::conformation(), core::chemical::CUTPOINT_LOWER, core::chemical::CUTPOINT_UPPER, core::pack::interaction_graph::debug, core::conformation::Conformation::declare_chemical_bond(), core::pose::Pose::dump_pdb(), core::scoring::fa_rep, core::scoring::fa_sol, fix_natsc_, flank_residue_min_, protocols::loops::get_fa_scorefxn(), protocols::moves::Mover::get_native_pose(), core::conformation::Residue::has_variant_type(), core::pose::symmetry::is_symmetric(), protocols::moves::MonteCarlo::last_accepted_pose(), protocols::loops::loop_rmsd(), protocols::loops::loop_mover::LoopMover::loops(), protocols::loops::loop_mover::loops_set_chainbreak_weight(), protocols::loops::loops_set_move_map(), core::conformation::Residue::lower_connect_atom(), protocols::moves::MonteCarlo::lowest_score_pose(), core::pose::symmetry::make_residue_mask_symmetric(), core::conformation::map_string_to_torsion_bin_string(), protocols::mean_field::max(), max_seglen_, protocols::mean_field::min(), min_after_repack_, protocols::moves::Mover::name(), neighbor_dist_, core::scoring::occ_sol_exact, optimize_only_kic_region_sidechains_after_move_, core::conformation::membrane::out, core::pack::pack_rotamers(), core::scoring::rama, core::scoring::rama2b, protocols::moves::MonteCarlo::recover_low(), recover_low_, redesign_loop_, core::pose::Pose::residue(), protocols::loops::loop_mover::LoopMover::resolve_loop_indices(), core::scoring::rg, core::pack::rotamer_trials(), protocols::moves::MonteCarlo::score_function(), protocols::loops::loop_mover::LoopMover::scorefxn(), protocols::loops::select_loop_residues(), core::pose::Pose::sequence(), set_movemap_from_kic_segment(), set_rottrials_from_kic_segment(), protocols::moves::MonteCarlo::set_temperature(), protocols::moves::MonteCarlo::show_counters(), protocols::moves::MonteCarlo::show_scores(), core::pose::Pose::size(), task_factory, protocols::loops::loop_mover::LoopMover::torsion_features_string(), tr(), update_allow_sc_vectors(), update_movemap_vectors(), core::pose::Pose::update_residue_neighbors(), and core::conformation::Residue::upper_connect_atom().

Referenced by protocols::protein_interface_design::movers::LoopMoverFromCommandLine::apply(), protocols::protein_interface_design::movers::LoopRemodel::apply(), protocols::abinitio::AbrelaxMover::close_with_idealization(), protocols::forge::remodel::RemodelMover::confirm_sequence(), protocols::abinitio::AbrelaxApplication::fold(), protocols::protein_interface_design::movers::PlaceOnLoop::minimize_toward_stub(), protocols::tcr::refine_tcr_cdr_loops(), and protocols::tcr::remodel_tcr_cdr_loops().

protocols::moves::MoverOP protocols::loops::loop_mover::refine::LoopMover_Refine_KIC::clone ( ) const
overridevirtual

Clone this object.

Reimplemented from protocols::moves::Mover.

std::string protocols::loops::loop_mover::refine::LoopMover_Refine_KIC::get_name ( ) const
overridevirtual

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

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

References mover_name().

bool protocols::loops::loop_mover::refine::LoopMover_Refine_KIC::get_redesign_loop ( )
inline

References redesign_loop_.

bool protocols::loops::loop_mover::refine::LoopMover_Refine_KIC::get_task_factory ( )

References task_factory.

void protocols::loops::loop_mover::refine::LoopMover_Refine_KIC::init ( core::scoring::ScoreFunctionCOP  scorefxn)
std::string protocols::loops::loop_mover::refine::LoopMover_Refine_KIC::mover_name ( )
static
void protocols::loops::loop_mover::refine::LoopMover_Refine_KIC::provide_xml_schema ( utility::tag::XMLSchemaDefinition &  xsd)
static
void protocols::loops::loop_mover::refine::LoopMover_Refine_KIC::set_default_settings ( )
void protocols::loops::loop_mover::refine::LoopMover_Refine_KIC::set_flank_residue_min ( bool  value)
inline

References flank_residue_min_.

void protocols::loops::loop_mover::refine::LoopMover_Refine_KIC::set_movemap_from_kic_segment ( core::pose::Pose pose,
core::kinematics::MoveMap cur_mm,
core::Size  kic_start,
core::Size  kic_end 
)

detailed Sets the MoveMap for minimization used in LoopMover_Refine_KIC::apply() to only minimize the neighborhood around KIC segment that moved. May slightly hurt performance in de novo loop reconstruction, but may yield a speedup of 2X or more in cases of modeling very large or multiple segments (loop definitions), in conjunction with set_movemap_from_kic_segment(), which are both used when optimize_only_kic_region_sidechains_after_move_ is set to true.

References protocols::loops::Loops::add_loop(), fix_natsc_, protocols::loops::loops_set_move_map(), and neighbor_dist_.

Referenced by apply().

void protocols::loops::loop_mover::refine::LoopMover_Refine_KIC::set_redesign_loop ( bool  value = true)
inline
void protocols::loops::loop_mover::refine::LoopMover_Refine_KIC::set_rottrials_from_kic_segment ( core::pose::Pose pose,
core::pack::task::PackerTaskOP rottrials_packer_task,
core::Size  kic_start,
core::Size  kic_end 
)

detailed Sets the rotamer trials packer task used in LoopMover_Refine_KIC::apply() to only rotamer trial the neighborhood around KIC segment that moved. May slightly hurt performance in de novo loop reconstruction, but may yield a speedup of 2X or more in cases of modeling very large or multiple segments (loop definitions), in conjunction with set_movemap_from_kic_segment(), which are both used when optimize_only_kic_region_sidechains_after_move_ is set to true.

References neighbor_dist_, protocols::loops::select_loop_residues(), and core::pose::Pose::size().

Referenced by apply().

void protocols::loops::loop_mover::refine::LoopMover_Refine_KIC::set_task_factory ( core::pack::task::TaskFactoryOP  value)
void protocols::loops::loop_mover::refine::LoopMover_Refine_KIC::show ( std::ostream &  output = std::cout) const
overridevirtual

Outputs details about the Mover, including current settings.

Ideally, a child Mover should call Mover.show() and add additional information particular to that Mover.

Reimplemented from protocols::moves::Mover.

References fix_natsc_, max_seglen_, min_after_repack_, neighbor_dist_, optimize_only_kic_region_sidechains_after_move_, and recover_low_.

Referenced by protocols::loops::loop_mover::refine::operator<<().

basic::Tracer & protocols::loops::loop_mover::refine::LoopMover_Refine_KIC::tr ( ) const
overrideprotectedvirtual
void protocols::loops::loop_mover::refine::LoopMover_Refine_KIC::update_allow_sc_vectors ( core::pose::Pose pose,
utility::vector1< utility::vector1< bool > > &  allow_sc_vectors 
)

update the vector of vectors of moveable side-chain positions, one for each loop in loops_

detailed Update the allow_sc_vectors that define, for each loop in loops_, which residue side-chains may be subject to rotamer trials. Allows for rotamer trials to apply only to the neighborhood around the segment that KIC moved, in cases where multiple segments (loops) are defined.

References protocols::loops::Loops::add_loop(), fix_natsc_, protocols::loops::loop_mover::LoopMover::loops(), neighbor_dist_, protocols::loops::select_loop_residues(), and core::pose::Pose::size().

Referenced by apply().

void protocols::loops::loop_mover::refine::LoopMover_Refine_KIC::update_movemap_vectors ( core::pose::Pose pose,
utility::vector1< core::kinematics::MoveMap > &  move_maps 
)

update the vector of movemaps, one for each loop in loops_

detailed Update the MoveMaps that define, for each loop in loops_, which residues may be minimized. Allows for minimization to apply only to the neighborhood around the segment that KIC moved, in cases where multiple segments (loops) are defined.

References protocols::loops::Loops::add_loop(), fix_natsc_, protocols::loops::loop_mover::LoopMover::loops(), protocols::loops::loops_set_move_map(), and neighbor_dist_.

Referenced by apply().

Member Data Documentation

bool protocols::loops::loop_mover::refine::LoopMover_Refine_KIC::fix_natsc_
private
bool protocols::loops::loop_mover::refine::LoopMover_Refine_KIC::flank_residue_min_
private
core::Size protocols::loops::loop_mover::refine::LoopMover_Refine_KIC::max_seglen_
private

Referenced by apply(), set_default_settings(), and show().

bool protocols::loops::loop_mover::refine::LoopMover_Refine_KIC::min_after_repack_
private

Referenced by apply(), set_default_settings(), and show().

core::Real protocols::loops::loop_mover::refine::LoopMover_Refine_KIC::neighbor_dist_
private
bool protocols::loops::loop_mover::refine::LoopMover_Refine_KIC::optimize_only_kic_region_sidechains_after_move_
private

Referenced by apply(), set_default_settings(), and show().

bool protocols::loops::loop_mover::refine::LoopMover_Refine_KIC::recover_low_
private

Referenced by apply(), set_default_settings(), and show().

bool protocols::loops::loop_mover::refine::LoopMover_Refine_KIC::redesign_loop_
protected
core::pack::task::TaskFactoryOP protocols::loops::loop_mover::refine::LoopMover_Refine_KIC::task_factory
protected

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