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protocols::docking::DockingLowResEnsemble Class Reference

#include <DockingLowResEnsemble.hh>

Inheritance diagram for protocols::docking::DockingLowResEnsemble:
Inheritance graph
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Public Member Functions

 DockingLowResEnsemble ()
 Default constructor. More...
 
 ~DockingLowResEnsemble () override
 
 DockingLowResEnsemble (core::scoring::ScoreFunctionCOP scorefxn, DockJumps const movable_jumps)
 Constructor with two arguments. The first is scorefunction to be used for docking, the second is the DockJumps. More...
 
void ensemble_defaults ()
 
protocols::moves::MoverOP clone () const override
 Return a clone of the Mover object. More...
 
core::Size get_current_conformer_ensemble1 () override
 
core::Size get_current_conformer_ensemble2 () override
 
void show (std::ostream &out=std::cout) const override
 
void set_ensemble1 (DockingEnsembleOP ensemble1)
 
void set_ensemble2 (DockingEnsembleOP ensemble2)
 
void lowres_inner_cycle (core::pose::Pose &pose) override
 
void adaptive_inner_cycle (core::pose::Pose &pose)
 
void try_all_conformers (core::pose::Pose &pose)
 
void initialize_movers ()
 
void calc_ensemble_accept_rate_ ()
 
void reset_ensemble_trial_counters ()
 
- Public Member Functions inherited from protocols::docking::DockingLowRes
 DockingLowRes ()
 Default constructor. More...
 
 ~DockingLowRes () override
 
 DockingLowRes (core::scoring::ScoreFunctionCOP scorefxn, core::Size const rb_jump=1)
 Constructor with two arguments. The first is scorefunction to be used for docking, the second is the jump to dock over. More...
 
 DockingLowRes (core::scoring::ScoreFunctionCOP scorefxn, DockJumps const movable_jumps)
 Constructor with two arguments. The first is scorefunction to be used for docking, the second is the DockJumps. More...
 
void set_default ()
 Assigns default values to primitive members. More...
 
void set_scorefxn (core::scoring::ScoreFunctionCOP scorefxn)
 
void sync_magnitudes_with_flags ()
 
void sync_objects_with_flags ()
 Instantiates non-primitive members based on the value of the primitive members. More...
 
moves::MonteCarloOP get_mc ()
 
void apply (core::pose::Pose &pose) override
 Perform several cycles of rigid-body Monte Carlo moves and adapt the step size. More...
 
std::string get_name () const override
 Each derived class must specify its name. The class name. More...
 
void rigid_body_trial (core::pose::Pose &pose)
 Perform a cycle of rigid-body Monte Carlo moves. More...
 
core::Real get_trans_magnitude ()
 Option getters - added by SSRB. More...
 
core::Real get_rot_magnitude ()
 
core::Real get_accept_rate ()
 
core::Size get_inner_cycles ()
 
core::Size get_outer_cycles ()
 
core::Real get_temperature ()
 
protocols::moves::TrialMoverOP get_rb_trial ()
 
protocols::moves::SequenceMoverOP get_rb_seq ()
 
protocols::rigid::RigidBodyPerturbNoCenterMoverOP get_rb_mover ()
 
DockJumps get_movable_jumps ()
 
core::scoring::ScoreFunctionCOP get_scorefxn ()
 
protocols::moves::PyMOLMoverOP get_pymol_mover ()
 
bool get_view_in_pymol ()
 
void set_inner_cycles (core::Size inner_cycles)
 
void set_outer_cycles (core::Size outer_cycles)
 
void set_trans_magnitude (core::Real trans_magnitude)
 
void set_rot_magnitude (core::Real rot_magnitude)
 
void set_rb_trial (protocols::moves::TrialMoverOP rb_trial_in)
 
void reset_rb_trial_counters ()
 
void calc_accept_rate ()
 
void pymol_color_change (core::pose::Pose &pose)
 
- 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 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...
 

Protected Member Functions

void finalize_setup (core::pose::Pose &pose) override
 Performs the portion of setup of non-primitive members that requires a pose - called on 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...
 

Private Member Functions

void ensemble1_trial (core::pose::Pose &pose)
 
void ensemble2_trial (core::pose::Pose &pose)
 

Private Attributes

protocols::docking::ConformerSwitchMoverOP ensemble1_mover_
 
protocols::docking::ConformerSwitchMoverOP ensemble2_mover_
 
core::Size current_outer_cycle_
 
core::Real accept_rate_ens1_
 
core::Real num_trials_ens1_
 
core::Real num_accepted_ens1_
 
core::Real accept_rate_ens2_
 
core::Real num_trials_ens2_
 
core::Real num_accepted_ens2_
 
core::Real rb_trial_wt_
 
core::Real ens1_trial_wt_
 
core::Real ens2_trial_wt_
 
protocols::moves::SequenceMoverOP ensemble1_seq_
 
protocols::moves::SequenceMoverOP ensemble2_seq_
 
protocols::moves::TrialMoverOP ensemble1_trial_
 
protocols::moves::TrialMoverOP ensemble2_trial_
 
core::Size current_conformer_ensemble1_
 
core::Size current_conformer_ensemble2_
 

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...
 
- Public Attributes inherited from protocols::docking::DockingLowRes
bool flags_and_objects_are_in_sync_
 
bool first_apply_with_current_setup_
 

Constructor & Destructor Documentation

protocols::docking::DockingLowResEnsemble::DockingLowResEnsemble ( )

Default constructor.

References protocols::moves::Mover::type().

protocols::docking::DockingLowResEnsemble::~DockingLowResEnsemble ( )
overridedefault
protocols::docking::DockingLowResEnsemble::DockingLowResEnsemble ( core::scoring::ScoreFunctionCOP  scorefxn,
DockJumps const  movable_jumps 
)

Constructor with two arguments. The first is scorefunction to be used for docking, the second is the DockJumps.

References protocols::moves::Mover::type().

Member Function Documentation

void protocols::docking::DockingLowResEnsemble::adaptive_inner_cycle ( core::pose::Pose pose)
void protocols::docking::DockingLowResEnsemble::calc_ensemble_accept_rate_ ( )
protocols::moves::MoverOP protocols::docking::DockingLowResEnsemble::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::docking::DockingLowRes.

void protocols::docking::DockingLowResEnsemble::ensemble1_trial ( core::pose::Pose pose)
private
void protocols::docking::DockingLowResEnsemble::ensemble2_trial ( core::pose::Pose pose)
private
void protocols::docking::DockingLowResEnsemble::ensemble_defaults ( )
void protocols::docking::DockingLowResEnsemble::finalize_setup ( core::pose::Pose pose)
overrideprotectedvirtual
core::Size protocols::docking::DockingLowResEnsemble::get_current_conformer_ensemble1 ( )
overridevirtual
core::Size protocols::docking::DockingLowResEnsemble::get_current_conformer_ensemble2 ( )
overridevirtual
void protocols::docking::DockingLowResEnsemble::initialize_movers ( )
void protocols::docking::DockingLowResEnsemble::lowres_inner_cycle ( core::pose::Pose pose)
overridevirtual
void protocols::docking::DockingLowResEnsemble::reset_ensemble_trial_counters ( )
void protocols::docking::DockingLowResEnsemble::set_ensemble1 ( DockingEnsembleOP  ensemble1)
void protocols::docking::DockingLowResEnsemble::set_ensemble2 ( DockingEnsembleOP  ensemble2)

References ensemble2_mover_.

void protocols::docking::DockingLowResEnsemble::show ( std::ostream &  out = std::cout) const
overridevirtual

Show the complete setup of the docking protocol

Reimplemented from protocols::docking::DockingLowRes.

References ensemble1_mover_, ensemble2_mover_, and protocols::docking::DockingLowRes::show().

void protocols::docking::DockingLowResEnsemble::try_all_conformers ( core::pose::Pose pose)

Member Data Documentation

core::Real protocols::docking::DockingLowResEnsemble::accept_rate_ens1_
private
core::Real protocols::docking::DockingLowResEnsemble::accept_rate_ens2_
private
core::Size protocols::docking::DockingLowResEnsemble::current_conformer_ensemble1_
private
core::Size protocols::docking::DockingLowResEnsemble::current_conformer_ensemble2_
private
core::Size protocols::docking::DockingLowResEnsemble::current_outer_cycle_
private
core::Real protocols::docking::DockingLowResEnsemble::ens1_trial_wt_
private
core::Real protocols::docking::DockingLowResEnsemble::ens2_trial_wt_
private
protocols::docking::ConformerSwitchMoverOP protocols::docking::DockingLowResEnsemble::ensemble1_mover_
private
protocols::moves::SequenceMoverOP protocols::docking::DockingLowResEnsemble::ensemble1_seq_
private
protocols::moves::TrialMoverOP protocols::docking::DockingLowResEnsemble::ensemble1_trial_
private
protocols::docking::ConformerSwitchMoverOP protocols::docking::DockingLowResEnsemble::ensemble2_mover_
private
protocols::moves::SequenceMoverOP protocols::docking::DockingLowResEnsemble::ensemble2_seq_
private
protocols::moves::TrialMoverOP protocols::docking::DockingLowResEnsemble::ensemble2_trial_
private
core::Real protocols::docking::DockingLowResEnsemble::num_accepted_ens1_
private
core::Real protocols::docking::DockingLowResEnsemble::num_accepted_ens2_
private
core::Real protocols::docking::DockingLowResEnsemble::num_trials_ens1_
private
core::Real protocols::docking::DockingLowResEnsemble::num_trials_ens2_
private
core::Real protocols::docking::DockingLowResEnsemble::rb_trial_wt_
private

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