Public Member Functions | Private Types | Private Attributes | List of all members
protocols::symmetric_docking::SymDockingLowRes Class Reference

#include <SymDockingLowRes.hh>

Inheritance diagram for protocols::symmetric_docking::SymDockingLowRes:
Inheritance graph

Public Member Functions

 SymDockingLowRes (core::scoring::ScoreFunctionCOP scorefxn_in)
moves::MoverOP clone () const override
 Return a clone of the Mover object. More...
 ~SymDockingLowRes () override
void set_default (core::pose::Pose &pose)
void set_default_mc (core::pose::Pose &pose)
void set_default_protocol (core::pose::Pose &pose)
void set_default_move_map (core::pose::Pose &pose)
moves::MonteCarloOP get_mc ()
moves::PyMOLMoverOP get_pymol_mover ()
void apply (core::pose::Pose &pose) override
 Perform several cycles of rigid-body Monte Carlo moves and adapt the step size. More...
void rigid_body_trial (core::pose::Pose &pose)
 Perform a cycle of rigid-body Monte Carlo moves. More...
std::string get_name () const override
 Each derived class must specify its name. The class name. More...
- 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 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...

Private Types

typedef core::Real Real

Private Attributes

core::scoring::ScoreFunctionCOP scorefxn_
core::kinematics::MoveMapOP movemap_
moves::MonteCarloOP mc_
moves::SequenceMoverOP docking_lowres_protocol_
rigid::RigidBodyDofSeqPerturbMoverOP rb_mover_
protocols::moves::PyMOLMoverOP pymol_mover_
int inner_cycles_
int outer_cycles_
Real trans_magnitude_
Real rot_magnitude_
Real accept_rate_
bool chi_
bool bb_
bool nb_list_
Real temperature_

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...

Member Typedef Documentation

◆ Real

Constructor & Destructor Documentation

◆ SymDockingLowRes()

protocols::symmetric_docking::SymDockingLowRes::SymDockingLowRes ( core::scoring::ScoreFunctionCOP  scorefxn_in)

◆ ~SymDockingLowRes()

protocols::symmetric_docking::SymDockingLowRes::~SymDockingLowRes ( )

Member Function Documentation

◆ apply()

void protocols::symmetric_docking::SymDockingLowRes::apply ( core::pose::Pose pose)

Perform several cycles of rigid-body Monte Carlo moves and adapt the step size.

currently used only in the low-resolution step (centroid mode)
References: pose_docking_centroid_rigid_body_adaptive from and
rigid_body_MC_cycle_adaptive from
Monica Berrondo October 22 2007

Implements protocols::moves::Mover.

References accept_rate_, mc_, outer_cycles_, rigid_body_trial(), rot_magnitude_, set_default(), protocols::symmetric_docking::TR(), and trans_magnitude_.

◆ clone()

moves::MoverOP protocols::symmetric_docking::SymDockingLowRes::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.

◆ get_mc()

moves::MonteCarloOP protocols::symmetric_docking::SymDockingLowRes::get_mc ( )

References mc_.

◆ get_name()

std::string protocols::symmetric_docking::SymDockingLowRes::get_name ( ) const

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

Implements protocols::moves::Mover.

◆ get_pymol_mover()

moves::PyMOLMoverOP protocols::symmetric_docking::SymDockingLowRes::get_pymol_mover ( )

References pymol_mover_.

◆ rigid_body_trial()

void protocols::symmetric_docking::SymDockingLowRes::rigid_body_trial ( core::pose::Pose pose)

Perform a cycle of rigid-body Monte Carlo moves.

Performs a number (nattempts) of MC rigid-body moves (of size trans_magnitude, rot_magnitude). The number of successful attempts is stored in accept_rate_ and used in adaptive trials.

the success_rate defines whether the translation/rotation size is increased or decreased for the next cycle. currently used only in the low-resolution step (centroid mode)
References: pose_docking_rigid_body_trial from and
rigid_body_MC_cycle from
Monica Berrondo October 22 2007

References accept_rate_, protocols::moves::accept_reject, docking_lowres_protocol_, inner_cycles_, mc_, rb_mover_, rot_magnitude_, and trans_magnitude_.

Referenced by apply().

◆ set_default()

void protocols::symmetric_docking::SymDockingLowRes::set_default ( core::pose::Pose pose)

◆ set_default_mc()

void protocols::symmetric_docking::SymDockingLowRes::set_default_mc ( core::pose::Pose pose)

References mc_, scorefxn_, and temperature_.

Referenced by set_default().

◆ set_default_move_map()

void protocols::symmetric_docking::SymDockingLowRes::set_default_move_map ( core::pose::Pose pose)

◆ set_default_protocol()

void protocols::symmetric_docking::SymDockingLowRes::set_default_protocol ( core::pose::Pose pose)

Member Data Documentation

◆ accept_rate_

Real protocols::symmetric_docking::SymDockingLowRes::accept_rate_

◆ bb_

bool protocols::symmetric_docking::SymDockingLowRes::bb_

◆ chi_

bool protocols::symmetric_docking::SymDockingLowRes::chi_

◆ docking_lowres_protocol_

moves::SequenceMoverOP protocols::symmetric_docking::SymDockingLowRes::docking_lowres_protocol_

◆ inner_cycles_

int protocols::symmetric_docking::SymDockingLowRes::inner_cycles_

Referenced by rigid_body_trial(), and set_default().

◆ mc_

moves::MonteCarloOP protocols::symmetric_docking::SymDockingLowRes::mc_

◆ movemap_

core::kinematics::MoveMapOP protocols::symmetric_docking::SymDockingLowRes::movemap_

Referenced by set_default_move_map().

◆ nb_list_

bool protocols::symmetric_docking::SymDockingLowRes::nb_list_

Referenced by set_default().

◆ outer_cycles_

int protocols::symmetric_docking::SymDockingLowRes::outer_cycles_

Referenced by apply(), and set_default().

◆ pymol_mover_

protocols::moves::PyMOLMoverOP protocols::symmetric_docking::SymDockingLowRes::pymol_mover_

◆ rb_mover_

rigid::RigidBodyDofSeqPerturbMoverOP protocols::symmetric_docking::SymDockingLowRes::rb_mover_

◆ rot_magnitude_

Real protocols::symmetric_docking::SymDockingLowRes::rot_magnitude_

◆ scorefxn_

core::scoring::ScoreFunctionCOP protocols::symmetric_docking::SymDockingLowRes::scorefxn_

Referenced by set_default_mc().

◆ temperature_

Real protocols::symmetric_docking::SymDockingLowRes::temperature_

Referenced by set_default(), and set_default_mc().

◆ trans_magnitude_

Real protocols::symmetric_docking::SymDockingLowRes::trans_magnitude_

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