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protocols::protein_interface_design::movers::LoopRemodel Class Reference

#include <LoopRemodel.hh>

Inheritance diagram for protocols::protein_interface_design::movers::LoopRemodel:
Inheritance graph

Public Member Functions

 LoopRemodel ()
 LoopRemodel (std::string const &protocol, std::string const &loop_start, std::string const &loop_end, core::Size const cycles, bool const perturb, bool const refine, bool const hurry, core::scoring::ScoreFunctionOP hires_score, core::scoring::ScoreFunctionOP lores_score, protocols::loops::LoopsCOP loops, core::fragment::FragSetOP frag1, core::fragment::FragSetOP frag3, core::fragment::FragSetOP frag9)
bool perturb ()
void perturb (bool const setting)
bool refine ()
void refine (bool const setting)
bool hurry ()
void hurry (bool const setting)
protocols::moves::MoverOP clone () const override
 Return a clone of the Mover object. More...
protocols::moves::MoverOP fresh_instance () const override
 Generates a new Mover object freshly created with the default ctor. More...
void apply (core::pose::Pose &pose) override
 a dummy apply so that instantiation of this baseclass would be possible. More...
void parse_my_tag (utility::tag::TagCOP tag, basic::datacache::DataMap &data) override
 Called by MoverFactory when constructing new Movers. Takes care of the specific mover's parsing. More...
 ~LoopRemodel () override
std::string get_name () const override
 Each derived class must specify its name. The class name. More...
- Public Member Functions inherited from protocols::calc_taskop_movers::DesignRepackMover
 DesignRepackMover ()
 DesignRepackMover (std::string const &name)
void setup_packer_and_movemap (core::pose::Pose const &pose)
void min_rb (utility::vector1< bool > const &min_rb)
void min_rb (bool const min_rb)
 in most cases, there would only be one rb dof making it useful to have a non-vector accessor to min_rb_. However, if the pose has multiple jumps, setting min_rb_ in this way might cause trouble in other parts of the code. More...
utility::vector1< bool > const & min_rb () const
bool min_rb_set () const
void min_sc (core::select::residue_selector::ResidueSelectorOP min_sc)
utility::vector1< boolmin_sc (core::pose::Pose const &pose) const
bool min_sc_set () const
void min_bb (core::select::residue_selector::ResidueSelectorOP min_bb)
utility::vector1< boolmin_bb (core::pose::Pose const &pose) const
bool min_bb_set () const
bool optimize_foldtree () const
void optimize_foldtree (bool const opt)
void prevent_repacking (utility::vector1< core::Size > const &p)
utility::vector1< core::Size >
const & 
prevent_repacking () const
void restrict_to_repacking (utility::vector1< core::Size > const &p)
utility::vector1< core::Size >
const & 
restrict_to_repacking () const
void design (bool const des)
bool design () const
void set_scorefxn_repack (core::scoring::ScoreFunctionCOP scorefxn)
void set_scorefxn_minimize (core::scoring::ScoreFunctionCOP scorefxn)
core::scoring::ScoreFunctionOP scorefxn_repack () const
core::scoring::ScoreFunctionOP scorefxn_minimize () const
core::pack::task::PackerTaskCOP task () const
core::pack::task::PackerTaskOPtask ()
void clear_task ()
 after fiddling with a task from outside this mover, clear it, or else, on the next iteration through the mover the changes will be remembered More...
void clear_task_factory ()
void use_preset_task (bool const bt)
bool use_preset_task () const
void task_factory (core::pack::task::TaskFactoryOP p)
core::pack::task::TaskFactoryOPtask_factory ()
core::pack::task::TaskFactoryOP task_factory () const
 ~DesignRepackMover () override
void target_residues (core::select::residue_selector::ResidueSelectorCOP setting)
 Replace the current target_residue setting with the passed residue selector. More...
core::select::residue_selector::ResidueSelectorCOP target_residues () const
utility::vector1< core::Sizetarget_residues (core::pose::Pose const &pose) const
- 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...
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
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::calc_taskop_movers::DesignRepackMover
get_xsd_complex_type ()
- 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 Member Functions

bool pick_loop_frags (protocols::loops::LoopsCOP loops, std::string const &full_seqeuence, std::string const &full_ss)

Private Attributes

std::string protocol_
core::scoring::ScoreFunctionOP hires_score_
core::scoring::ScoreFunctionOP lores_score_
std::string loop_start_
std::string loop_end_
core::Size cycles_
bool perturb_
bool refine_
bool hurry_
protocols::loops::LoopsOP loops_
core::fragment::FragSetOP frag1_
core::fragment::FragSetOP frag3_
core::fragment::FragSetOP frag9_

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...
- Protected Attributes inherited from protocols::calc_taskop_movers::DesignRepackMover
core::scoring::ScoreFunctionOP scorefxn_repack_
core::scoring::ScoreFunctionOP scorefxn_minimize_
bool repack_partner1_
bool repack_partner2_
bool design_partner1_
bool design_partner2_
utility::vector1< boolmin_rb_
utility::vector1< boolcurr_min_sc_
utility::vector1< boolcurr_min_bb_
utility::vector1< boolcurr_min_rb_
bool min_rb_set_
core::Real interface_distance_cutoff_
bool repack_non_ala_
bool optimize_foldtree_
bool automatic_repacking_definition_
core::pack::task::PackerTaskOP task_
bool use_preset_task_
utility::vector1< boolallowed_aas_
utility::vector1< core::Sizeprevent_repacking_
utility::vector1< core::Sizerestrict_to_repacking_
core::pack::task::TaskFactoryOP task_factory_
bool symmetry_

Constructor & Destructor Documentation

protocols::protein_interface_design::movers::LoopRemodel::LoopRemodel ( )
protocols::protein_interface_design::movers::LoopRemodel::LoopRemodel ( std::string const &  protocol,
std::string const &  loop_start,
std::string const &  loop_end,
core::Size const  cycles,
bool const  perturb,
bool const  refine,
bool const  hurry,
core::scoring::ScoreFunctionOP  hires_score,
core::scoring::ScoreFunctionOP  lores_score,
protocols::loops::LoopsCOP  loops,
core::fragment::FragSetOP  frag1,
core::fragment::FragSetOP  frag3,
core::fragment::FragSetOP  frag9 
protocols::protein_interface_design::movers::LoopRemodel::~LoopRemodel ( )

Member Function Documentation

void protocols::protein_interface_design::movers::LoopRemodel::apply ( core::pose::Pose )

a dummy apply so that instantiation of this baseclass would be possible.

Reimplemented from protocols::calc_taskop_movers::DesignRepackMover.

References protocols::forge::methods::add_cutpoint_variants(), protocols::loops::loop_mover::LoopMover::add_fragments(), protocols::forge::remodel::RemodelLoopMover::add_fragments(), protocols::protein_interface_design::movers::SaveAndRetrieveSidechains::allsc(), protocols::loops::loop_mover::IndependentLoopMover::apply(), protocols::protein_interface_design::movers::SaveAndRetrieveSidechains::apply(), protocols::loops::loop_closure::kinematic_closure::KinematicWrapper::apply(), protocols::loops::loop_mover::refine::LoopMover_Refine_KIC::apply(), protocols::loops::loop_mover::refine::LoopMover_Refine_CCD::apply(), protocols::minimization_packing::PackRotamersMover::apply(), protocols::forge::remodel::RemodelLoopMover::apply(), protocols::moves::MonteCarlo::boltzmann(), core::chemical::CENTROID_t, core::scoring::chainbreak, cycles_, protocols::calc_taskop_movers::DesignRepackMover::design(), protocols::simple_filters::dssp(), protocols::moves::FAIL_DO_NOT_RETRY, protocols::moves::FAIL_RETRY, core::pose::Pose::fold_tree(), protocols::forge::methods::fold_tree_from_loops(), frag1_, frag3_, frag9_, core::chemical::FULL_ATOM_t, protocols::moves::Mover::get_last_move_status(), hires_score_, hurry_, core::scoring::dssp::Dssp::insert_ss_into_pose(), protocols::moves::MonteCarlo::last_accepted_pose(), loop_end_, loop_start_, loops_, protocols::loops::loops_set_move_map(), lores_score_, protocols::moves::MS_SUCCESS, core::scoring::omega, core::pose::parse_resnum(), perturb(), perturb_, pick_loop_frags(), protocols::calc_taskop_movers::DesignRepackMover::prevent_repacking(), protocol_, protocols::moves::MonteCarlo::recover_low(), refine(), refine_, core::util::remove_cutpoint_variants(), protocols::forge::remodel::RemodelLoopMover::scorefunction(), core::pose::Pose::secstruct(), core::pose::Pose::sequence(), protocols::moves::MonteCarlo::set_autotemp(), protocols::moves::Mover::set_last_move_status(), protocols::moves::Mover::set_native_pose(), protocols::loops::loop_mover::refine::LoopMover_Refine_KIC::set_redesign_loop(), protocols::loops::loop_mover::refine::LoopMover_Refine_CCD::set_redesign_loop(), protocols::loops::loop_mover::IndependentLoopMover::set_strict_loops(), protocols::moves::MonteCarlo::show_counters(), core::pose::Pose::size(), protocols::loops::Loop::start(), protocols::loops::Loop::stop(), core::util::switch_to_residue_type_set(), protocols::calc_taskop_movers::DesignRepackMover::task(), protocols::calc_taskop_movers::DesignRepackMover::task_factory(), protocols::moves::MonteCarlo::temperature(), protocols::protein_interface_design::movers::TR(), and core::pose::Pose::update_residue_neighbors().

protocols::moves::MoverOP protocols::protein_interface_design::movers::LoopRemodel::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.

protocols::moves::MoverOP protocols::protein_interface_design::movers::LoopRemodel::fresh_instance ( ) const

Generates a new Mover object freshly created with the default ctor.

fresh_instance is meant to return a new object of this class, created with the default constructor. 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. This is used by the August 08 job distributor.

Reimplemented from protocols::moves::Mover.

std::string protocols::protein_interface_design::movers::LoopRemodel::get_name ( ) const

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

Reimplemented from protocols::calc_taskop_movers::DesignRepackMover.

References mover_name().

bool protocols::protein_interface_design::movers::LoopRemodel::hurry ( )

References hurry_.

void protocols::protein_interface_design::movers::LoopRemodel::hurry ( bool const  setting)

References hurry_.

std::string protocols::protein_interface_design::movers::LoopRemodel::mover_name ( )
void protocols::protein_interface_design::movers::LoopRemodel::parse_my_tag ( utility::tag::TagCOP  tag,
basic::datacache::DataMap &  data 

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 force people to reimplement this method. However, we should be chatty about the fact that someone is using a RosettaScripts interface to a mover which didn't define parse_my_tag()

Reimplemented from protocols::calc_taskop_movers::DesignRepackMover.

References cycles_, protocols::calc_taskop_movers::DesignRepackMover::design(), core::pose::get_resnum_string(), core::scoring::get_score_function_name(), hires_score_, hurry_, loop_end_, loop_start_, loops_, lores_score_, core::scoring::parse_score_function(), core::pack::task::parse_task_operations(), perturb_, protocol_, refine_, protocols::calc_taskop_movers::DesignRepackMover::task_factory(), and protocols::protein_interface_design::movers::TR().

bool protocols::protein_interface_design::movers::LoopRemodel::perturb ( )

References perturb_.

Referenced by apply().

void protocols::protein_interface_design::movers::LoopRemodel::perturb ( bool const  setting)

References perturb_.

bool protocols::protein_interface_design::movers::LoopRemodel::pick_loop_frags ( protocols::loops::LoopsCOP  loops,
std::string const &  full_seqeuence,
std::string const &  full_ss 
void protocols::protein_interface_design::movers::LoopRemodel::provide_xml_schema ( utility::tag::XMLSchemaDefinition &  xsd)
bool protocols::protein_interface_design::movers::LoopRemodel::refine ( )

References refine_.

Referenced by apply().

void protocols::protein_interface_design::movers::LoopRemodel::refine ( bool const  setting)

References refine_.

Member Data Documentation

core::Size protocols::protein_interface_design::movers::LoopRemodel::cycles_

Referenced by apply(), and parse_my_tag().

core::fragment::FragSetOP protocols::protein_interface_design::movers::LoopRemodel::frag1_

Referenced by apply(), LoopRemodel(), and pick_loop_frags().

core::fragment::FragSetOP protocols::protein_interface_design::movers::LoopRemodel::frag3_

Referenced by apply(), LoopRemodel(), and pick_loop_frags().

core::fragment::FragSetOP protocols::protein_interface_design::movers::LoopRemodel::frag9_

Referenced by apply(), LoopRemodel(), and pick_loop_frags().

core::scoring::ScoreFunctionOP protocols::protein_interface_design::movers::LoopRemodel::hires_score_

Referenced by apply(), LoopRemodel(), and parse_my_tag().

bool protocols::protein_interface_design::movers::LoopRemodel::hurry_

Referenced by apply(), hurry(), and parse_my_tag().

std::string protocols::protein_interface_design::movers::LoopRemodel::loop_end_

Referenced by apply(), and parse_my_tag().

std::string protocols::protein_interface_design::movers::LoopRemodel::loop_start_

Referenced by apply(), and parse_my_tag().

protocols::loops::LoopsOP protocols::protein_interface_design::movers::LoopRemodel::loops_

Referenced by apply(), LoopRemodel(), and parse_my_tag().

core::scoring::ScoreFunctionOP protocols::protein_interface_design::movers::LoopRemodel::lores_score_

Referenced by apply(), LoopRemodel(), and parse_my_tag().

bool protocols::protein_interface_design::movers::LoopRemodel::perturb_

Referenced by apply(), parse_my_tag(), and perturb().

std::string protocols::protein_interface_design::movers::LoopRemodel::protocol_

Referenced by apply(), and parse_my_tag().

bool protocols::protein_interface_design::movers::LoopRemodel::refine_

Referenced by apply(), parse_my_tag(), and refine().

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