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protocols::docking::DockingLowRes Class Reference

#include <DockingLowRes.hh>

Inheritance diagram for protocols::docking::DockingLowRes:
Inheritance graph

Public Member Functions

 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...
protocols::moves::MoverOP clone () const override
 Return a clone of the Mover object. 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 ()
virtual core::Size get_current_conformer_ensemble1 ()
virtual core::Size get_current_conformer_ensemble2 ()
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 show (std::ostream &out=std::cout) const override
virtual void lowres_inner_cycle (core::pose::Pose &pose)
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...

Public Attributes

bool flags_and_objects_are_in_sync_
bool first_apply_with_current_setup_

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::SequenceMoverOP rb_seq_
protocols::moves::TrialMoverOP rb_trial_
protocols::moves::MonteCarloOP mc_
core::Real trans_magnitude_
core::Real rot_magnitude_
core::Real accept_rate_
core::Real num_rb_trials_
core::Real num_rb_accepted_
core::Size inner_cycles_
core::Size outer_cycles_
bool chi_
bool bb_
bool nb_list_
core::Real temperature_
DockJumps movable_jumps_
core::scoring::ScoreFunctionCOP scorefxn_
protocols::moves::PyMOLMoverOP pymol_mover_
bool view_in_pymol_


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

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...

Constructor & Destructor Documentation

◆ DockingLowRes() [1/3]

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

Default constructor.

References init().

◆ ~DockingLowRes()

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

◆ DockingLowRes() [2/3]

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().

◆ DockingLowRes() [3/3]

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

◆ apply()

void protocols::docking::DockingLowRes::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_, finalize_setup(), first_apply_with_current_setup_, flags_and_objects_are_in_sync_, lowres_inner_cycle(), mc_, outer_cycles_, rot_magnitude_, show(), sync_magnitudes_with_flags(), sync_objects_with_flags(), protocols::docking::TR(), and trans_magnitude_.

◆ calc_accept_rate()

void protocols::docking::DockingLowRes::calc_accept_rate ( )

◆ clone()

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

Reimplemented in protocols::docking::DockingLowResEnsemble.

◆ finalize_setup()

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

◆ get_accept_rate()

core::Real protocols::docking::DockingLowRes::get_accept_rate ( )

◆ get_current_conformer_ensemble1()

core::Size protocols::docking::DockingLowRes::get_current_conformer_ensemble1 ( )

◆ get_current_conformer_ensemble2()

core::Size protocols::docking::DockingLowRes::get_current_conformer_ensemble2 ( )

◆ get_inner_cycles()

core::Size protocols::docking::DockingLowRes::get_inner_cycles ( )

◆ get_mc()

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

◆ get_movable_jumps()

DockJumps protocols::docking::DockingLowRes::get_movable_jumps ( )

References movable_jumps_.

◆ get_name()

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

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

Implements protocols::moves::Mover.

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

◆ get_outer_cycles()

core::Size protocols::docking::DockingLowRes::get_outer_cycles ( )

References outer_cycles_.

◆ get_pymol_mover()

protocols::moves::PyMOLMoverOP protocols::docking::DockingLowRes::get_pymol_mover ( )

◆ get_rb_mover()

protocols::rigid::RigidBodyPerturbNoCenterMoverOP protocols::docking::DockingLowRes::get_rb_mover ( )

◆ get_rb_seq()

protocols::moves::SequenceMoverOP protocols::docking::DockingLowRes::get_rb_seq ( )

◆ get_rb_trial()

protocols::moves::TrialMoverOP protocols::docking::DockingLowRes::get_rb_trial ( )

References rb_trial_.

◆ get_rot_magnitude()

core::Real protocols::docking::DockingLowRes::get_rot_magnitude ( )

◆ get_scorefxn()

core::scoring::ScoreFunctionCOP protocols::docking::DockingLowRes::get_scorefxn ( )

References scorefxn_.

◆ get_temperature()

core::Real protocols::docking::DockingLowRes::get_temperature ( )

References temperature_.

◆ get_trans_magnitude()

core::Real protocols::docking::DockingLowRes::get_trans_magnitude ( )

Option getters - added by SSRB.

References trans_magnitude_.

Referenced by protocols::docking::DockingLowResEnsemble::initialize_movers().

◆ get_view_in_pymol()

bool protocols::docking::DockingLowRes::get_view_in_pymol ( )

◆ init()

void protocols::docking::DockingLowRes::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.

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

Referenced by DockingLowRes().

◆ lowres_inner_cycle()

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

◆ pymol_color_change()

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

◆ reset_rb_trial_counters()

void protocols::docking::DockingLowRes::reset_rb_trial_counters ( )

◆ rigid_body_trial()

void protocols::docking::DockingLowRes::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 num_rb_accepted_, num_rb_trials_, pymol_color_change(), rb_trial_, protocols::docking::TR(), and view_in_pymol_.

Referenced by protocols::docking::DockingLowResEnsemble::adaptive_inner_cycle(), and lowres_inner_cycle().

◆ set_default()

void protocols::docking::DockingLowRes::set_default ( )

Assigns default values to primitive members.

References accept_rate_, bb_, chi_, inner_cycles_, nb_list_, num_rb_accepted_, num_rb_trials_, outer_cycles_, sync_magnitudes_with_flags(), temperature_, and view_in_pymol_.

Referenced by init().

◆ set_inner_cycles()

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

◆ set_outer_cycles()

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

◆ set_rb_trial()

void protocols::docking::DockingLowRes::set_rb_trial ( protocols::moves::TrialMoverOP  rb_trial_in)

◆ set_rot_magnitude()

void protocols::docking::DockingLowRes::set_rot_magnitude ( core::Real  rot_magnitude)

References rot_magnitude_.

Referenced by sync_magnitudes_with_flags().

◆ set_scorefxn()

void protocols::docking::DockingLowRes::set_scorefxn ( core::scoring::ScoreFunctionCOP  scorefxn)

◆ set_trans_magnitude()

void protocols::docking::DockingLowRes::set_trans_magnitude ( core::Real  trans_magnitude)

References trans_magnitude_.

Referenced by sync_magnitudes_with_flags().

◆ show()

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

◆ sync_magnitudes_with_flags()

void protocols::docking::DockingLowRes::sync_magnitudes_with_flags ( )

References set_rot_magnitude(), and set_trans_magnitude().

Referenced by apply(), and set_default().

◆ sync_objects_with_flags()

void protocols::docking::DockingLowRes::sync_objects_with_flags ( )

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

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

Referenced by apply(), and init().

Friends And Related Function Documentation

◆ operator<<

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

Member Data Documentation

◆ accept_rate_

core::Real protocols::docking::DockingLowRes::accept_rate_

◆ bb_

bool protocols::docking::DockingLowRes::bb_

◆ chi_

bool protocols::docking::DockingLowRes::chi_

◆ first_apply_with_current_setup_

bool protocols::docking::DockingLowRes::first_apply_with_current_setup_

Referenced by apply(), and sync_objects_with_flags().

◆ flags_and_objects_are_in_sync_

bool protocols::docking::DockingLowRes::flags_and_objects_are_in_sync_

◆ inner_cycles_

core::Size protocols::docking::DockingLowRes::inner_cycles_

◆ mc_

protocols::moves::MonteCarloOP protocols::docking::DockingLowRes::mc_

◆ movable_jumps_

DockJumps protocols::docking::DockingLowRes::movable_jumps_

◆ movemap_

core::kinematics::MoveMapOP protocols::docking::DockingLowRes::movemap_

◆ nb_list_

bool protocols::docking::DockingLowRes::nb_list_

Referenced by set_default().

◆ num_rb_accepted_

core::Real protocols::docking::DockingLowRes::num_rb_accepted_

◆ num_rb_trials_

core::Real protocols::docking::DockingLowRes::num_rb_trials_

◆ outer_cycles_

core::Size protocols::docking::DockingLowRes::outer_cycles_

◆ pymol_mover_

protocols::moves::PyMOLMoverOP protocols::docking::DockingLowRes::pymol_mover_

◆ rb_mover_

protocols::rigid::RigidBodyPerturbNoCenterMoverOP protocols::docking::DockingLowRes::rb_mover_

◆ rb_seq_

protocols::moves::SequenceMoverOP protocols::docking::DockingLowRes::rb_seq_

◆ rb_trial_

protocols::moves::TrialMoverOP protocols::docking::DockingLowRes::rb_trial_

◆ rot_magnitude_

core::Real protocols::docking::DockingLowRes::rot_magnitude_

◆ scorefxn_

core::scoring::ScoreFunctionCOP protocols::docking::DockingLowRes::scorefxn_

◆ temperature_

core::Real protocols::docking::DockingLowRes::temperature_

◆ trans_magnitude_

core::Real protocols::docking::DockingLowRes::trans_magnitude_

◆ view_in_pymol_

bool protocols::docking::DockingLowRes::view_in_pymol_

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