Rosetta Protocols  2014.35
Public Member Functions | Protected Member Functions | Private Attributes | List of all members
protocols::docking::DockingLowResEnsemble Class Reference

#include <DockingLowResEnsemble.hh>

Public Member Functions

 DockingLowResEnsemble ()
 Default constructor. More...
 ~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. More...
virtual protocols::moves::MoverOP clone () const
 Return a clone of the Mover object. More...
virtual void show (std::ostream &out=std::cout) const
void set_ensemble1 (DockingEnsembleOP ensemble1)
void set_ensemble2 (DockingEnsembleOP ensemble2)
- Public Member Functions inherited from protocols::docking::DockingLowRes
 DockingLowRes ()
 Default constructor. More...
 ~DockingLowRes ()
 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_objects_with_flags ()
 Instantiates non-primitive members based on the value of the primitive members. More...
moves::MonteCarloOP get_mc ()
virtual void apply (core::pose::Pose &pose)
 Perform several cycles of rigid-body Monte Carlo moves and adapt the step size. More...
virtual std::string get_name () const
 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...
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)
- Public Member Functions inherited from protocols::moves::Mover
 Mover ()
virtual ~Mover ()
virtual MoverSP create ()
virtual void apply (core::io::serialization::PipeMap &pmap)
virtual void parse_state (SerializableState const &state)
virtual void parse_def (utility::lua::LuaObject const &def, utility::lua::LuaObject const &score_fxns, utility::lua::LuaObject const &tasks, MoverCacheSP cache)
virtual void save_state (SerializableState &state)
 Mover (std::string const &type_name)
 sets the type for a mover; name_ has been removed (2010/05/14) More...
 Mover (Mover const &other)
Moveroperator= (Mover const &other)
 assignment operator More...
virtual core::Real last_proposal_density_ratio ()
std::string const & type () const
void set_type (std::string const &setting)
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...
void set_current_tag (std::string const &new_tag)
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 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...
void type (const std::string &type_in)
virtual void parse_my_tag (TagCOP tag, basic::datacache::DataMap &data, Filters_map const &filters, Movers_map const &movers, Pose const &pose)
 Called by MoverFactory when constructing new Movers. Takes care of the specific mover's parsing. More...
std::string get_type () const
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...
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 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...
void set_current_job (protocols::jobdist::BasicJobCOP job)
jobdist::BasicJobCOP get_current_job () const

Protected Member Functions

virtual void finalize_setup (core::pose::Pose &pose)
 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 Attributes

protocols::docking::ConformerSwitchMoverOP ensemble1_mover_
protocols::docking::ConformerSwitchMoverOP ensemble2_mover_

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::stringStrings
- 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_
DockJumps movable_jumps_
protocols::moves::SequenceMoverOP docking_lowres_protocol_
core::scoring::ScoreFunctionCOP scorefxn_

Constructor & Destructor Documentation

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

Default constructor.

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

Referenced by clone().

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

protocols::moves::MoverOP protocols::docking::DockingLowResEnsemble::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::docking::DockingLowRes.

References DockingLowResEnsemble().

void protocols::docking::DockingLowResEnsemble::finalize_setup ( core::pose::Pose pose)
void protocols::docking::DockingLowResEnsemble::set_ensemble1 ( DockingEnsembleOP  ensemble1)
void protocols::docking::DockingLowResEnsemble::set_ensemble2 ( DockingEnsembleOP  ensemble2)
void protocols::docking::DockingLowResEnsemble::show ( std::ostream &  out = std::cout) const

Show the complete setup of the docking protocol

Reimplemented from protocols::docking::DockingLowRes.

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

Member Data Documentation

protocols::docking::ConformerSwitchMoverOP protocols::docking::DockingLowResEnsemble::ensemble1_mover_

Referenced by finalize_setup(), set_ensemble1(), and show().

protocols::docking::ConformerSwitchMoverOP protocols::docking::DockingLowResEnsemble::ensemble2_mover_

Referenced by finalize_setup(), set_ensemble2(), and show().

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