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protocols::rbsegment_relax::RBSegmentRelax Class Reference

#include <RBSegmentRelax.hh>

Inheritance diagram for protocols::rbsegment_relax::RBSegmentRelax:
Inheritance graph
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Public Member Functions

 RBSegmentRelax ()
 
 RBSegmentRelax (core::scoring::ScoreFunctionOP scorefxn, utility::vector1< RBSegment > const &RBSegment_input, protocols::loops::Loops const &Loops_input)
 
 ~RBSegmentRelax () override
 
void initialize (utility::vector1< core::fragment::FragSetOP > const &frag_libs, core::Real rnd=0.0)
 setup_RBSegmentRelax; initialize movesets to defaults More...
 
void apply (core::pose::Pose &pose) override
 apply method More...
 
std::string get_name () const override
 Each derived class must specify its name. The class name. More...
 
void add_helixMover (RBSegmentMoverOP newMover)
 
void add_strandMover (RBSegmentMoverOP newMover)
 
void add_genericRBMover (RBSegmentMoverOP newMover)
 
void add_compositeSegmentMover (RBSegmentMoverOP newMover)
 
void add_wholeStructureMover (protocols::moves::MoverOP newMover)
 
void clear_movesets ()
 
void set_temperature (core::Real start, core::Real final)
 
void set_helicalMoveStepsize (core::Real onAxisTrans, core::Real onAxisRot, core::Real offAxisTrans, core::Real offAxisRot)
 
void set_genericRBMoveStepsize (core::Real trans, core::Real rot)
 
void set_ncycles (int ncycles)
 
void set_cst_weight (core::Real wt)
 
void set_cst_width (core::Real width)
 
void set_randomize (core::Size rand)
 
void set_bootstrap (bool boot)
 
void set_skip_lr (bool skip)
 
void set_fix_ligands (bool fix)
 
- 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...
 

Private Member Functions

void set_default_movemap ()
 

Private Attributes

core::Real cst_weight_
 
core::Real cst_width_
 
core::Real cst_stdev_
 
core::Size cst_seqwidth_
 
core::scoring::ScoreFunctionOP scorefxn_
 
protocols::moves::MonteCarloOP mc_
 
core::Size cycles_
 
core::Real init_temp
 
core::Real final_temp
 
core::Real helical_sigT
 
core::Real helical_sigR
 
core::Real helical_sigOffAxisT
 
core::Real helical_sigOffAxisR
 
core::Real strand_sigT
 
core::Real strand_sigR
 
core::Real strand_sigOffAxisT
 
core::Real strand_sigOffAxisR
 
core::Real genericRB_sigT
 
core::Real genericRB_sigR
 
core::Real randomness_
 
core::Size rand_
 
bool no_lr_
 
bool bootstrap_
 
bool fix_ligands_
 
utility::vector1< RBSegmentrbsegs_input_
 
utility::vector1< RBSegmentrbsegs_remap_
 
protocols::loops::Loops loops_input_
 
utility::vector1
< core::fragment::FragSetOP
frag_libs_
 
std::vector
< protocols::moves::MoverOP
WholeStructureMoveSet_
 
std::vector< RBSegmentMoverOPHelixMoveSet_
 
std::vector< RBSegmentMoverOPStrandMoveSet_
 
std::vector< RBSegmentMoverOPGenericRBMoveSet_
 
std::vector< RBSegmentMoverOPCompositeSegmentMoveSet_
 

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
 
- 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 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

protocols::rbsegment_relax::RBSegmentRelax::RBSegmentRelax ( )
default
protocols::rbsegment_relax::RBSegmentRelax::RBSegmentRelax ( core::scoring::ScoreFunctionOP  scorefxn,
utility::vector1< RBSegment > const &  RBSegment_input,
protocols::loops::Loops const &  Loops_input 
)
protocols::rbsegment_relax::RBSegmentRelax::~RBSegmentRelax ( )
overridedefault

Member Function Documentation

void protocols::rbsegment_relax::RBSegmentRelax::add_compositeSegmentMover ( RBSegmentMoverOP  newMover)
void protocols::rbsegment_relax::RBSegmentRelax::add_genericRBMover ( RBSegmentMoverOP  newMover)

References GenericRBMoveSet_.

void protocols::rbsegment_relax::RBSegmentRelax::add_helixMover ( RBSegmentMoverOP  newMover)

References HelixMoveSet_.

void protocols::rbsegment_relax::RBSegmentRelax::add_strandMover ( RBSegmentMoverOP  newMover)

References StrandMoveSet_.

void protocols::rbsegment_relax::RBSegmentRelax::add_wholeStructureMover ( protocols::moves::MoverOP  newMover)
void protocols::rbsegment_relax::RBSegmentRelax::apply ( core::pose::Pose pose)
overridevirtual

apply method

Implements protocols::moves::Mover.

References protocols::viewer::add_conformation_viewer(), core::scoring::electron_density::add_dens_scores_from_cmdline_to_scorefxn(), protocols::comparative_modeling::LoopRelaxMover::apply(), protocols::minimization_packing::PackRotamersMover::apply(), bootstrap_, protocols::comparative_modeling::LoopRelaxMover::cmd_line_csts(), CompositeSegmentMoveSet_, core::scoring::coordinate_constraint, core::pack::task::TaskFactory::create_packer_task(), cst_seqwidth_, cst_stdev_, cst_weight_, cst_width_, cycles_, protocols::comparative_modeling::LoopRelaxMover::fa_scorefxn(), final_temp, fix_ligands_, core::pose::Pose::fold_tree(), protocols::loops::fold_tree_from_loops(), protocols::comparative_modeling::LoopRelaxMover::frag_libs(), frag_libs_, genericRB_sigR, genericRB_sigT, GenericRBMoveSet_, core::scoring::get_score_function(), HelixMoveSet_, protocols::loops::idealize_loop(), init_temp, protocols::comparative_modeling::LoopRelaxMover::intermedrelax(), core::kinematics::FoldTree::is_cutpoint(), core::pose::Pose::is_fullatom(), core::conformation::Residue::is_ligand(), protocols::comparative_modeling::LoopRelaxMover::loops(), loops_input_, mc_, no_lr_, rand_, randomness_, rbsegs_input_, rbsegs_remap_, protocols::comparative_modeling::LoopRelaxMover::refine(), protocols::antibody::design::relax, protocols::comparative_modeling::LoopRelaxMover::relax(), protocols::rbsegment_relax::remap_rb_segments(), protocols::comparative_modeling::LoopRelaxMover::remodel(), core::pose::Pose::residue(), protocols::rbsegment_relax::restore_pose_from_rbsegs(), scorefxn_, protocols::rbsegment_relax::set_constraints(), protocols::rbsegment_relax::RBSegmentMover::set_movement(), core::pose::Pose::set_omega(), core::pose::Pose::set_phi(), core::pose::Pose::set_psi(), protocols::rbsegment_relax::set_rb_constraints(), protocols::rbsegment_relax::RBSegmentMover::setResidueRange(), protocols::rbsegment_relax::setup_pose_from_rbsegs(), protocols::loops::Loops::size(), core::pose::Pose::size(), StrandMoveSet_, protocols::rbsegment_relax::TS(), and WholeStructureMoveSet_.

Referenced by protocols::RBSegmentRelaxImpl::apply().

void protocols::rbsegment_relax::RBSegmentRelax::clear_movesets ( )
std::string protocols::rbsegment_relax::RBSegmentRelax::get_name ( ) const
overridevirtual

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

Implements protocols::moves::Mover.

void protocols::rbsegment_relax::RBSegmentRelax::initialize ( utility::vector1< core::fragment::FragSetOP > const &  frag_libs,
core::Real  rnd = 0.0 
)
void protocols::rbsegment_relax::RBSegmentRelax::set_bootstrap ( bool  boot)
inline

References bootstrap_.

void protocols::rbsegment_relax::RBSegmentRelax::set_cst_weight ( core::Real  wt)

References cst_weight_.

void protocols::rbsegment_relax::RBSegmentRelax::set_cst_width ( core::Real  width)

References cst_width_.

void protocols::rbsegment_relax::RBSegmentRelax::set_default_movemap ( )
private
void protocols::rbsegment_relax::RBSegmentRelax::set_fix_ligands ( bool  fix)
inline

References fix_ligands_.

void protocols::rbsegment_relax::RBSegmentRelax::set_genericRBMoveStepsize ( core::Real  trans,
core::Real  rot 
)
void protocols::rbsegment_relax::RBSegmentRelax::set_helicalMoveStepsize ( core::Real  onAxisTrans,
core::Real  onAxisRot,
core::Real  offAxisTrans,
core::Real  offAxisRot 
)
void protocols::rbsegment_relax::RBSegmentRelax::set_ncycles ( int  ncycles)

References cycles_.

void protocols::rbsegment_relax::RBSegmentRelax::set_randomize ( core::Size  rand)
inline

References rand_.

Referenced by protocols::RBSegmentRelaxImpl::apply().

void protocols::rbsegment_relax::RBSegmentRelax::set_skip_lr ( bool  skip)
inline

References no_lr_.

void protocols::rbsegment_relax::RBSegmentRelax::set_temperature ( core::Real  start,
core::Real  final 
)

Member Data Documentation

bool protocols::rbsegment_relax::RBSegmentRelax::bootstrap_
private
std::vector< RBSegmentMoverOP > protocols::rbsegment_relax::RBSegmentRelax::CompositeSegmentMoveSet_
private
core::Size protocols::rbsegment_relax::RBSegmentRelax::cst_seqwidth_
private

Referenced by apply(), and RBSegmentRelax().

core::Real protocols::rbsegment_relax::RBSegmentRelax::cst_stdev_
private

Referenced by apply(), and RBSegmentRelax().

core::Real protocols::rbsegment_relax::RBSegmentRelax::cst_weight_
private
core::Real protocols::rbsegment_relax::RBSegmentRelax::cst_width_
private
core::Size protocols::rbsegment_relax::RBSegmentRelax::cycles_
private

Referenced by apply(), RBSegmentRelax(), and set_ncycles().

core::Real protocols::rbsegment_relax::RBSegmentRelax::final_temp
private
bool protocols::rbsegment_relax::RBSegmentRelax::fix_ligands_
private

Referenced by apply(), and set_fix_ligands().

utility::vector1< core::fragment::FragSetOP > protocols::rbsegment_relax::RBSegmentRelax::frag_libs_
private

Referenced by apply(), and initialize().

core::Real protocols::rbsegment_relax::RBSegmentRelax::genericRB_sigR
private
core::Real protocols::rbsegment_relax::RBSegmentRelax::genericRB_sigT
private
std::vector< RBSegmentMoverOP > protocols::rbsegment_relax::RBSegmentRelax::GenericRBMoveSet_
private
core::Real protocols::rbsegment_relax::RBSegmentRelax::helical_sigOffAxisR
private
core::Real protocols::rbsegment_relax::RBSegmentRelax::helical_sigOffAxisT
private
core::Real protocols::rbsegment_relax::RBSegmentRelax::helical_sigR
private
core::Real protocols::rbsegment_relax::RBSegmentRelax::helical_sigT
private
std::vector< RBSegmentMoverOP > protocols::rbsegment_relax::RBSegmentRelax::HelixMoveSet_
private
core::Real protocols::rbsegment_relax::RBSegmentRelax::init_temp
private
protocols::loops::Loops protocols::rbsegment_relax::RBSegmentRelax::loops_input_
private

Referenced by apply().

protocols::moves::MonteCarloOP protocols::rbsegment_relax::RBSegmentRelax::mc_
private

Referenced by apply().

bool protocols::rbsegment_relax::RBSegmentRelax::no_lr_
private

Referenced by apply(), RBSegmentRelax(), and set_skip_lr().

core::Size protocols::rbsegment_relax::RBSegmentRelax::rand_
private
core::Real protocols::rbsegment_relax::RBSegmentRelax::randomness_
private

Referenced by apply(), and initialize().

utility::vector1< RBSegment > protocols::rbsegment_relax::RBSegmentRelax::rbsegs_input_
private

Referenced by apply().

utility::vector1< RBSegment > protocols::rbsegment_relax::RBSegmentRelax::rbsegs_remap_
private

Referenced by apply().

core::scoring::ScoreFunctionOP protocols::rbsegment_relax::RBSegmentRelax::scorefxn_
private

Referenced by apply().

core::Real protocols::rbsegment_relax::RBSegmentRelax::strand_sigOffAxisR
private

Referenced by initialize(), and RBSegmentRelax().

core::Real protocols::rbsegment_relax::RBSegmentRelax::strand_sigOffAxisT
private

Referenced by initialize(), and RBSegmentRelax().

core::Real protocols::rbsegment_relax::RBSegmentRelax::strand_sigR
private

Referenced by initialize(), and RBSegmentRelax().

core::Real protocols::rbsegment_relax::RBSegmentRelax::strand_sigT
private

Referenced by initialize(), and RBSegmentRelax().

std::vector< RBSegmentMoverOP > protocols::rbsegment_relax::RBSegmentRelax::StrandMoveSet_
private
std::vector< protocols::moves::MoverOP > protocols::rbsegment_relax::RBSegmentRelax::WholeStructureMoveSet_
private

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