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protocols::docking::DockingLowRes Class Reference

#include <DockingLowRes.hh>

Inheritance diagram for protocols::docking::DockingLowRes:
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Collaboration diagram for protocols::docking::DockingLowRes:
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Public Member Functions

 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...
 
protocols::moves::MoverOP clone () const
 clone has to be overridden only if clone invocation is expected. 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)
 
virtual void show (std::ostream &out=std::cout) const
 
- 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
 

Public Attributes

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_
 

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 Member Functions

void init (DockJumps const movable_jumps, core::scoring::ScoreFunctionCOP scorefxn)
 Sets up the instance of DockingLowRes and initializes all members based on values passed in at construction or via the command line. More...
 

Private Attributes

core::kinematics::MoveMapOP movemap_
 
protocols::rigid::RigidBodyPerturbNoCenterMoverOP rb_mover_
 
protocols::moves::MonteCarloOP mc_
 
core::Real trans_magnitude_
 
core::Real rot_magnitude_
 
core::Real accept_rate_
 
core::Size inner_cycles_
 
core::Size outer_cycles_
 
bool chi_
 
bool bb_
 
bool nb_list_
 
core::Real temperature_
 

Friends

std::ostream & operator<< (std::ostream &out, const DockingLowRes &dp)
 

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
protocols::filters::Filters_map 
Filters_map
 
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...
 

Constructor & Destructor Documentation

protocols::docking::DockingLowRes::DockingLowRes ( )

Default constructor.

References init().

Referenced by clone().

protocols::docking::DockingLowRes::~DockingLowRes ( )
protocols::docking::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.

References init().

protocols::docking::DockingLowRes::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.

References init().

Member Function Documentation

void protocols::docking::DockingLowRes::apply ( core::pose::Pose pose)
virtual

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

DockingLowRes.apply

Detailed:
Remarks
currently used only in the low-resolution step (centroid mode)
References: pose_docking_centroid_rigid_body_adaptive from pose_docking.cc and
rigid_body_MC_cycle_adaptive from dock_structure.cc
Authors
Monica Berrondo October 22 2007
Last Modified: October 22 2007

Implements protocols::moves::Mover.

References accept_rate_, finalize_setup(), first_apply_with_current_setup_, flags_and_objects_are_in_sync_, mc_, outer_cycles_, rigid_body_trial(), rot_magnitude_, show(), sync_objects_with_flags(), protocols::TR(), and trans_magnitude_.

protocols::moves::MoverOP protocols::docking::DockingLowRes::clone ( ) const
virtual

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.

Reimplemented in protocols::docking::DockingLowResEnsemble.

References DockingLowRes().

void protocols::docking::DockingLowRes::finalize_setup ( core::pose::Pose pose)
protectedvirtual

Performs the portion of setup of non-primitive members that requires a pose - called on apply.

Reimplemented in protocols::docking::DockingLowResEnsemble.

References docking_lowres_protocol_, movemap_, protocols::rigid::n2c, rb_mover_, rot_magnitude_, and trans_magnitude_.

Referenced by apply(), and protocols::docking::DockingLowResEnsemble::finalize_setup().

moves::MonteCarloOP protocols::docking::DockingLowRes::get_mc ( )

References mc_.

std::string protocols::docking::DockingLowRes::get_name ( ) const
virtual

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

Implements protocols::moves::Mover.

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

void protocols::docking::DockingLowRes::init ( DockJumps const  movable_jumps,
core::scoring::ScoreFunctionCOP  scorefxn 
)
private

Sets up the instance of DockingLowRes and initializes all members based on values passed in at construction or via the command line.

References core::scoring::ScoreFunctionFactory::create_score_function(), movable_jumps_, scorefxn_, set_default(), sync_objects_with_flags(), and protocols::moves::Mover::type().

Referenced by DockingLowRes().

void protocols::docking::DockingLowRes::rigid_body_trial ( core::pose::Pose pose)

Perform a cycle of rigid-body Monte Carlo moves.

rigid_body_trial

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.
Remarks
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 pose_docking.cc and
rigid_body_MC_cycle from dock_structure.cc
Authors
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::docking::DockingLowRes::set_default ( )

Assigns default values to primitive members.

References accept_rate_, bb_, chi_, inner_cycles_, nb_list_, outer_cycles_, rot_magnitude_, temperature_, and trans_magnitude_.

Referenced by init().

void protocols::docking::DockingLowRes::set_inner_cycles ( core::Size  inner_cycles)
inline

References inner_cycles_.

void protocols::docking::DockingLowRes::set_outer_cycles ( core::Size  outer_cycles)
inline

References outer_cycles_.

void protocols::docking::DockingLowRes::set_scorefxn ( core::scoring::ScoreFunctionCOP  scorefxn)
void protocols::docking::DockingLowRes::show ( std::ostream &  out = std::cout) const
virtual
void protocols::docking::DockingLowRes::sync_objects_with_flags ( )

Instantiates non-primitive members based on the value of the primitive members.

References bb_, chi_, docking_lowres_protocol_, first_apply_with_current_setup_, flags_and_objects_are_in_sync_, mc_, movable_jumps_, movemap_, rb_mover_, scorefxn_, and temperature_.

Referenced by apply(), and init().

Friends And Related Function Documentation

std::ostream& operator<< ( std::ostream &  out,
const DockingLowRes dp 
)
friend

Member Data Documentation

core::Real protocols::docking::DockingLowRes::accept_rate_
private
bool protocols::docking::DockingLowRes::bb_
private
bool protocols::docking::DockingLowRes::chi_
private
protocols::moves::SequenceMoverOP protocols::docking::DockingLowRes::docking_lowres_protocol_
bool protocols::docking::DockingLowRes::first_apply_with_current_setup_

Referenced by apply(), and sync_objects_with_flags().

bool protocols::docking::DockingLowRes::flags_and_objects_are_in_sync_
core::Size protocols::docking::DockingLowRes::inner_cycles_
private
protocols::moves::MonteCarloOP protocols::docking::DockingLowRes::mc_
private
DockJumps protocols::docking::DockingLowRes::movable_jumps_

Referenced by init(), and sync_objects_with_flags().

core::kinematics::MoveMapOP protocols::docking::DockingLowRes::movemap_
private
bool protocols::docking::DockingLowRes::nb_list_
private

Referenced by set_default().

core::Size protocols::docking::DockingLowRes::outer_cycles_
private
protocols::rigid::RigidBodyPerturbNoCenterMoverOP protocols::docking::DockingLowRes::rb_mover_
private
core::Real protocols::docking::DockingLowRes::rot_magnitude_
private
core::scoring::ScoreFunctionCOP protocols::docking::DockingLowRes::scorefxn_
core::Real protocols::docking::DockingLowRes::temperature_
private
core::Real protocols::docking::DockingLowRes::trans_magnitude_
private

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