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protocols::surface_docking::FullatomRelaxMover Class Reference

#include <FullatomRelaxMover.hh>

Inheritance diagram for protocols::surface_docking::FullatomRelaxMover:
Inheritance graph
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Public Member Functions

 FullatomRelaxMover ()
 
 FullatomRelaxMover (FullatomRelaxMover const &src)
 
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...
 
 ~FullatomRelaxMover () override
 
void apply (core::pose::Pose &pose) override
 Main Method. More...
 
std::string get_name () const override
 Each derived class must specify its name. The class name. More...
 
void set_nmoves (const core::Size)
 
std::string get_sol_secondary_struct ()
 
std::string get_ads_secondary_struct ()
 
void set_surface_contact_mover (protocols::docking::FaDockingSlideIntoContactOP surface_contact_mover)
 
void set_surface_orient_mover (SurfaceOrientMoverOP surface_orient)
 
void set_surface_parameters (protocols::surface_docking::SurfaceParametersOP surface_parameters)
 
- 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
 
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 copy_data (FullatomRelaxMover object_to_copy_to, FullatomRelaxMover object_to_copy_from)
 
void inner_loop_refinement (core::pose::Pose &pose)
 
void outer_loop_refinement_solution (core::pose::Pose &pose)
 
void outer_loop_refinement_adsorbed (core::pose::Pose &pose)
 
void reorient_and_slide_into_surface (core::pose::Pose &pose)
 
void dock_mcm_on_surface (core::pose::Pose &pose)
 
void output_solution_state (core::pose::Pose &pose)
 
void refinement_cycle (core::pose::Pose &pose)
 
void setup_defaults ()
 
void setup_movers (const core::pose::Pose &pose)
 
void set_smallmovesize (core::Size scale)
 
void set_ljrepulsion_weight (core::Real weight_scale)
 
void set_ecounter (core::Size ecount)
 
void calc_secondary_struct (core::pose::Pose &pose)
 
void set_secondary_struct (core::pose::Pose &pose)
 
void reposition_above_surface (core::pose::Pose &pose)
 

Private Attributes

core::Real kT_
 
core::Size nmoves_
 
core::Size encounter_
 
core::Size encounter_cycle_
 
std::map< char, core::Realangle_max_
 
core::scoring::ScoreFunctionOP score_high_res_
 
std::string small_min_type_
 
std::string shear_min_type_
 
core::kinematics::MoveMapOP move_map_
 
moves::MonteCarloOP monte_carlo_
 
simple_moves::SmallMoverOP small_mover_
 
minimization_packing::MinMoverOP small_min_mover_
 
moves::SequenceMoverOP small_sequence_mover_
 
moves::TrialMoverOP small_trial_min_mover_
 
simple_moves::ShearMoverOP shear_mover_
 
minimization_packing::MinMoverOP shear_min_mover_
 
moves::SequenceMoverOP shear_sequence_mover_
 
moves::TrialMoverOP shear_trial_min_mover_
 
std::string sol_sec_struct_
 
std::string ads_sec_struct_
 
std::string sec_struct_
 
protocols::docking::FaDockingSlideIntoContactOP surface_contact_mover_
 
protocols::surface_docking::SurfaceOrientMoverOP surface_orient_
 
protocols::surface_docking::SurfaceParametersOP surface_parameters_
 
docking::DockMCMProtocolOP dock_mcm_
 
core::Size outer_loop_cycles_
 
core::Size inner_loop_cycles_
 

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::surface_docking::FullatomRelaxMover::FullatomRelaxMover ( )

References setup_defaults().

protocols::surface_docking::FullatomRelaxMover::FullatomRelaxMover ( FullatomRelaxMover const &  src)

References copy_data().

protocols::surface_docking::FullatomRelaxMover::~FullatomRelaxMover ( )
overridedefault

Member Function Documentation

void protocols::surface_docking::FullatomRelaxMover::apply ( core::pose::Pose )
overridevirtual
void protocols::surface_docking::FullatomRelaxMover::calc_secondary_struct ( core::pose::Pose pose)
private
protocols::moves::MoverOP protocols::surface_docking::FullatomRelaxMover::clone ( ) const
overridevirtual

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.

void protocols::surface_docking::FullatomRelaxMover::copy_data ( FullatomRelaxMover  object_to_copy_to,
FullatomRelaxMover  object_to_copy_from 
)
private
void protocols::surface_docking::FullatomRelaxMover::dock_mcm_on_surface ( core::pose::Pose pose)
private

References dock_mcm_, and protocols::TR().

Referenced by refinement_cycle().

protocols::moves::MoverOP protocols::surface_docking::FullatomRelaxMover::fresh_instance ( ) const
overridevirtual

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::surface_docking::FullatomRelaxMover::get_ads_secondary_struct ( )

References ads_sec_struct_.

std::string protocols::surface_docking::FullatomRelaxMover::get_name ( ) const
overridevirtual

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

Implements protocols::moves::Mover.

std::string protocols::surface_docking::FullatomRelaxMover::get_sol_secondary_struct ( )

References sol_sec_struct_.

void protocols::surface_docking::FullatomRelaxMover::inner_loop_refinement ( core::pose::Pose pose)
private
void protocols::surface_docking::FullatomRelaxMover::outer_loop_refinement_adsorbed ( core::pose::Pose pose)
private
void protocols::surface_docking::FullatomRelaxMover::outer_loop_refinement_solution ( core::pose::Pose pose)
private
void protocols::surface_docking::FullatomRelaxMover::output_solution_state ( core::pose::Pose pose)
private
void protocols::surface_docking::FullatomRelaxMover::refinement_cycle ( core::pose::Pose pose)
private
void protocols::surface_docking::FullatomRelaxMover::reorient_and_slide_into_surface ( core::pose::Pose pose)
private
void protocols::surface_docking::FullatomRelaxMover::reposition_above_surface ( core::pose::Pose pose)
private
void protocols::surface_docking::FullatomRelaxMover::set_ecounter ( core::Size  ecount)
private

References encounter_.

Referenced by apply().

void protocols::surface_docking::FullatomRelaxMover::set_ljrepulsion_weight ( core::Real  weight_scale)
private

References core::scoring::fa_rep, and score_high_res_.

Referenced by apply().

void protocols::surface_docking::FullatomRelaxMover::set_nmoves ( const core::Size  nmoves_in)

References nmoves_.

void protocols::surface_docking::FullatomRelaxMover::set_secondary_struct ( core::pose::Pose pose)
private
void protocols::surface_docking::FullatomRelaxMover::set_smallmovesize ( core::Size  scale)
private

References small_mover_.

Referenced by apply().

void protocols::surface_docking::FullatomRelaxMover::set_surface_contact_mover ( protocols::docking::FaDockingSlideIntoContactOP  surface_contact_mover)
void protocols::surface_docking::FullatomRelaxMover::set_surface_orient_mover ( SurfaceOrientMoverOP  surface_orient)

References surface_orient_.

void protocols::surface_docking::FullatomRelaxMover::set_surface_parameters ( protocols::surface_docking::SurfaceParametersOP  surface_parameters)

References surface_parameters_.

void protocols::surface_docking::FullatomRelaxMover::setup_defaults ( )
private
void protocols::surface_docking::FullatomRelaxMover::setup_movers ( const core::pose::Pose pose)
private

Member Data Documentation

std::string protocols::surface_docking::FullatomRelaxMover::ads_sec_struct_
private
std::map< char, core::Real > protocols::surface_docking::FullatomRelaxMover::angle_max_
private

Referenced by copy_data().

docking::DockMCMProtocolOP protocols::surface_docking::FullatomRelaxMover::dock_mcm_
private
core::Size protocols::surface_docking::FullatomRelaxMover::encounter_
private
core::Size protocols::surface_docking::FullatomRelaxMover::encounter_cycle_
private
core::Size protocols::surface_docking::FullatomRelaxMover::inner_loop_cycles_
private
core::Real protocols::surface_docking::FullatomRelaxMover::kT_
private
moves::MonteCarloOP protocols::surface_docking::FullatomRelaxMover::monte_carlo_
private
core::kinematics::MoveMapOP protocols::surface_docking::FullatomRelaxMover::move_map_
private
core::Size protocols::surface_docking::FullatomRelaxMover::nmoves_
private
core::Size protocols::surface_docking::FullatomRelaxMover::outer_loop_cycles_
private
core::scoring::ScoreFunctionOP protocols::surface_docking::FullatomRelaxMover::score_high_res_
private
std::string protocols::surface_docking::FullatomRelaxMover::sec_struct_
private
minimization_packing::MinMoverOP protocols::surface_docking::FullatomRelaxMover::shear_min_mover_
private
std::string protocols::surface_docking::FullatomRelaxMover::shear_min_type_
private
simple_moves::ShearMoverOP protocols::surface_docking::FullatomRelaxMover::shear_mover_
private

Referenced by copy_data(), and setup_movers().

moves::SequenceMoverOP protocols::surface_docking::FullatomRelaxMover::shear_sequence_mover_
private

Referenced by copy_data(), and setup_movers().

moves::TrialMoverOP protocols::surface_docking::FullatomRelaxMover::shear_trial_min_mover_
private
minimization_packing::MinMoverOP protocols::surface_docking::FullatomRelaxMover::small_min_mover_
private
std::string protocols::surface_docking::FullatomRelaxMover::small_min_type_
private
simple_moves::SmallMoverOP protocols::surface_docking::FullatomRelaxMover::small_mover_
private
moves::SequenceMoverOP protocols::surface_docking::FullatomRelaxMover::small_sequence_mover_
private

Referenced by copy_data(), and setup_movers().

moves::TrialMoverOP protocols::surface_docking::FullatomRelaxMover::small_trial_min_mover_
private
std::string protocols::surface_docking::FullatomRelaxMover::sol_sec_struct_
private
protocols::docking::FaDockingSlideIntoContactOP protocols::surface_docking::FullatomRelaxMover::surface_contact_mover_
private
protocols::surface_docking::SurfaceOrientMoverOP protocols::surface_docking::FullatomRelaxMover::surface_orient_
private
protocols::surface_docking::SurfaceParametersOP protocols::surface_docking::FullatomRelaxMover::surface_parameters_
private

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