Rosetta 3.5
 All Classes Namespaces Files Functions Variables Typedefs Enumerations Enumerator Friends Macros Pages
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
Collaboration diagram for protocols::symmetric_docking::SymDockingLowRes:
Collaboration graph

Public Member Functions

 SymDockingLowRes (core::scoring::ScoreFunctionCOP scorefxn_in)
moves::MoverOP clone () const
 clone has to be overridden only if clone invocation is expected. More...
 ~SymDockingLowRes ()
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 ()
virtual void apply (core::pose::Pose &pose)
 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...
virtual std::string get_name () const
 Each derived class must specify its name. The class name. More...
- 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
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 (TagPtr const tag, 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
 this function informs 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
 this function informs 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
 this is like clone(), except it generates a new mover object freshly created with the default ctor. This function should be pure virtual but that would disrupt the code base; MAKE SURE YOU DEFINE IT if you want to have your mover be a protocol handed to the job distributor (august 08 vintage). More...
void set_current_job (protocols::jobdist::BasicJobCOP job)
jobdist::BasicJobCOP get_current_job () const

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_
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::TagPtr TagPtr
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. these options will end up in -help of your application if users of this mover call register_options. do this recursively! if you use movers within your mover, call their register_options in your register_options() method. 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

Constructor & Destructor Documentation

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

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

Referenced by clone().

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

Member Function Documentation

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
Last Modified: 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_.

moves::MoverOP protocols::symmetric_docking::SymDockingLowRes::clone ( ) const

clone has to be overridden only if clone invocation is expected.

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.

References SymDockingLowRes().

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

References mc_.

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

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

Implements protocols::moves::Mover.

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

Perform a cycle of rigid-body Monte Carlo moves.


Detailed: 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
Last Modified: 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().

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

References mc_, scorefxn_, and temperature_.

Referenced by set_default().

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

Member Data Documentation

Real protocols::symmetric_docking::SymDockingLowRes::accept_rate_
bool protocols::symmetric_docking::SymDockingLowRes::bb_
bool protocols::symmetric_docking::SymDockingLowRes::chi_
moves::SequenceMoverOP protocols::symmetric_docking::SymDockingLowRes::docking_lowres_protocol_
int protocols::symmetric_docking::SymDockingLowRes::inner_cycles_

Referenced by rigid_body_trial(), and set_default().

moves::MonteCarloOP protocols::symmetric_docking::SymDockingLowRes::mc_
core::kinematics::MoveMapOP protocols::symmetric_docking::SymDockingLowRes::movemap_

Referenced by set_default_move_map().

bool protocols::symmetric_docking::SymDockingLowRes::nb_list_

Referenced by set_default().

int protocols::symmetric_docking::SymDockingLowRes::outer_cycles_

Referenced by apply(), and set_default().

rigid::RigidBodyDofSeqPerturbMoverOP protocols::symmetric_docking::SymDockingLowRes::rb_mover_
Real protocols::symmetric_docking::SymDockingLowRes::rot_magnitude_
core::scoring::ScoreFunctionCOP protocols::symmetric_docking::SymDockingLowRes::scorefxn_

Referenced by set_default_mc().

Real protocols::symmetric_docking::SymDockingLowRes::temperature_

Referenced by set_default(), and set_default_mc().

Real protocols::symmetric_docking::SymDockingLowRes::trans_magnitude_

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